tvc →
5.0.3+git20151221.80e144e+dfsg-2 →
armhf → 2018-12-18 06:22:42
sbuild (Debian sbuild) 0.71.0 (24 Aug 2016) on testwandboard
+==============================================================================+
| tvc 5.0.3+git20151221.80e144e+dfsg-2 (armhf) Tue, 18 Dec 2018 05:24:55 +0000 |
+==============================================================================+
Package: tvc
Version: 5.0.3+git20151221.80e144e+dfsg-2
Source Version: 5.0.3+git20151221.80e144e+dfsg-2
Distribution: buster-staging
Machine Architecture: armhf
Host Architecture: armhf
Build Architecture: armhf
I: NOTICE: Log filtering will replace 'var/lib/schroot/mount/buster-staging-armhf-sbuild-50529a9a-3496-4a0a-8a40-eb837a401aa3' with '<<CHROOT>>'
+------------------------------------------------------------------------------+
| Update chroot |
+------------------------------------------------------------------------------+
Get:1 http://172.17.0.1/private buster-staging InRelease [11.3 kB]
Get:2 http://172.17.0.1/private buster-staging/main Sources [11.3 MB]
Get:3 http://172.17.0.1/private buster-staging/main armhf Packages [13.0 MB]
Fetched 24.3 MB in 32s (758 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 755 kB of source archives.
Get:1 http://172.17.0.1/private buster-staging/main tvc 5.0.3+git20151221.80e144e+dfsg-2 (dsc) [2195 B]
Get:2 http://172.17.0.1/private buster-staging/main tvc 5.0.3+git20151221.80e144e+dfsg-2 (tar) [745 kB]
Get:3 http://172.17.0.1/private buster-staging/main tvc 5.0.3+git20151221.80e144e+dfsg-2 (diff) [8384 B]
Fetched 755 kB in 0s (1750 kB/s)
Download complete and in download only mode
I: NOTICE: Log filtering will replace 'build/tvc-7V3wB5/tvc-5.0.3+git20151221.80e144e+dfsg' with '<<PKGBUILDDIR>>'
I: NOTICE: Log filtering will replace 'build/tvc-7V3wB5' 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-w6byed/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-w6byed/gpg/pubring.kbx' created
gpg: /<<BUILDDIR>>/resolver-w6byed/gpg/trustdb.gpg: trustdb created
gpg: key 35506D9A48F77B2E: 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 35506D9A48F77B2E: "Sbuild Signer (Sbuild Build Dependency Archive Key) <buildd-tools-devel@lists.alioth.debian.org>" not changed
gpg: key 35506D9A48F77B2E: 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-w6byed/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-w6byed/apt_archive ./ Release [957 B]
Get:3 copy:/<<BUILDDIR>>/resolver-w6byed/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-w6byed/apt_archive ./ Sources [349 B]
Get:5 copy:/<<BUILDDIR>>/resolver-w6byed/apt_archive ./ Packages [433 B]
Fetched 2109 B in 1s (3055 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:
ca-certificates dbus dbus-user-session e2fsprogs-l10n krb5-locales libexpat1
libgpg-error-l10n libnss-systemd libpam-systemd libssl1.1 openssl
systemd-sysv
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 17 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-w6byed/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 (53.6 kB/s)
Selecting previously unselected package sbuild-build-depends-core-dummy.
(Reading database ... 15795 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 (>= 11~), cmake, libbamtools-dev, libjsoncpp-dev, libarmadillo-dev, libboost-math-dev, libsmithwaterman-dev
Filtered Build-Depends: debhelper (>= 11~), cmake, libbamtools-dev, libjsoncpp-dev, libarmadillo-dev, libboost-math-dev, libsmithwaterman-dev
dpkg-deb: building package 'sbuild-build-depends-tvc-dummy' in '/<<BUILDDIR>>/resolver-w6byed/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-w6byed/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-w6byed/apt_archive ./ Release [963 B]
Get:3 copy:/<<BUILDDIR>>/resolver-w6byed/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-w6byed/apt_archive ./ Sources [535 B]
Get:5 copy:/<<BUILDDIR>>/resolver-w6byed/apt_archive ./ Packages [620 B]
Fetched 2488 B in 1s (3611 B/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:
ca-certificates dbus dbus-user-session e2fsprogs-l10n krb5-locales
libgpg-error-l10n libnss-systemd libpam-systemd openssl systemd-sysv
Use 'apt autoremove' to remove them.
The following additional packages will be installed:
autoconf automake autopoint autotools-dev bsdmainutils cmake cmake-data
cpp-8 debhelper dh-autoreconf dh-strip-nondeterminism dwz file g++-8
gcc-7-base gcc-8 gcc-8-base gettext gettext-base groff-base hdf5-helpers
intltool-debian libaec-dev libaec0 libarchive-zip-perl libarchive13
libarmadillo-dev libarmadillo9 libarpack2 libarpack2-dev libasan5 libatomic1
libbamtools-dev libbamtools2.5.1 libblas-dev libblas3 libboost-math-dev
libboost-math1.67-dev libboost-math1.67.0 libboost1.67-dev libbsd0 libcc1-0
libcroco3 libcurl4 libdisorder-dev libdisorder0 libelf1
libfile-stripnondeterminism-perl libgcc-8-dev libgcc1 libgfortran4
libgfortran5 libglib2.0-0 libgomp1 libhdf5-100 libhdf5-cpp-100 libhdf5-dev
libicu63 libjpeg-dev libjpeg62-turbo libjpeg62-turbo-dev libjsoncpp-dev
libjsoncpp1 liblapack-dev liblapack3 libmagic-mgc libmagic1 libnghttp2-14
libpipeline1 libpsl5 librhash0 librtmp1 libsigsegv2 libsmithwaterman-dev
libsmithwaterman0 libssh2-1 libstdc++-8-dev libstdc++6 libsuperlu-dev
libsuperlu5 libsz2 libtool libubsan1 libuv1 libxml2 m4 man-db po-debconf
zlib1g-dev
Suggested packages:
autoconf-archive gnu-standards autoconf-doc wamerican | wordlist whois
vacation cmake-doc ninja-build gcc-8-locales dh-make gcc-8-doc
libstdc++6-8-dbg libgcc1-dbg libgomp1-dbg libitm1-dbg libatomic1-dbg
libasan5-dbg liblsan0-dbg libtsan0-dbg libubsan1-dbg libmpx2-dbg
libquadmath0-dbg gettext-doc libasprintf-dev libgettextpo-dev groff lrzip
libitpp-dev libbamtools-doc liblapack-doc libboost1.67-doc
libboost-atomic1.67-dev libboost-chrono1.67-dev libboost-container1.67-dev
libboost-context1.67-dev libboost-coroutine1.67-dev
libboost-date-time1.67-dev libboost-exception1.67-dev libboost-fiber1.67-dev
libboost-filesystem1.67-dev libboost-graph1.67-dev
libboost-graph-parallel1.67-dev libboost-iostreams1.67-dev
libboost-locale1.67-dev libboost-log1.67-dev libboost-mpi1.67-dev
libboost-mpi-python1.67-dev libboost-numpy1.67-dev
libboost-program-options1.67-dev libboost-python1.67-dev
libboost-random1.67-dev libboost-regex1.67-dev
libboost-serialization1.67-dev libboost-signals1.67-dev
libboost-stacktrace1.67-dev libboost-system1.67-dev libboost-test1.67-dev
libboost-thread1.67-dev libboost-timer1.67-dev libboost-type-erasure1.67-dev
libboost-wave1.67-dev libboost1.67-tools-dev libmpfrc++-dev libntl-dev
libhdf5-doc libstdc++-8-doc libsuperlu-doc libtool-doc gfortran
| fortran95-compiler gcj-jdk m4-doc apparmor less www-browser
libmail-box-perl
Recommended packages:
curl | wget | lynx libarchive-cpio-perl libglib2.0-data shared-mime-info
xdg-user-dirs publicsuffix libltdl-dev libmail-sendmail-perl
The following NEW packages will be installed:
autoconf automake autopoint autotools-dev bsdmainutils cmake cmake-data
debhelper dh-autoreconf dh-strip-nondeterminism dwz file gcc-7-base gettext
gettext-base groff-base hdf5-helpers intltool-debian libaec-dev libaec0
libarchive-zip-perl libarchive13 libarmadillo-dev libarmadillo9 libarpack2
libarpack2-dev libbamtools-dev libbamtools2.5.1 libblas-dev libblas3
libboost-math-dev libboost-math1.67-dev libboost-math1.67.0 libboost1.67-dev
libbsd0 libcroco3 libcurl4 libdisorder-dev libdisorder0 libelf1
libfile-stripnondeterminism-perl libgfortran4 libgfortran5 libglib2.0-0
libhdf5-100 libhdf5-cpp-100 libhdf5-dev libicu63 libjpeg-dev libjpeg62-turbo
libjpeg62-turbo-dev libjsoncpp-dev libjsoncpp1 liblapack-dev liblapack3
libmagic-mgc libmagic1 libnghttp2-14 libpipeline1 libpsl5 librhash0 librtmp1
libsigsegv2 libsmithwaterman-dev libsmithwaterman0 libssh2-1 libsuperlu-dev
libsuperlu5 libsz2 libtool libuv1 libxml2 m4 man-db po-debconf
sbuild-build-depends-tvc-dummy zlib1g-dev
The following packages will be upgraded:
cpp-8 g++-8 gcc-8 gcc-8-base libasan5 libatomic1 libcc1-0 libgcc-8-dev
libgcc1 libgomp1 libstdc++-8-dev libstdc++6 libubsan1
13 upgraded, 77 newly installed, 0 to remove and 4 not upgraded.
Need to get 64.1 MB/65.0 MB of archives.
After this operation, 285 MB of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-w6byed/apt_archive ./ sbuild-build-depends-tvc-dummy 0.invalid.0 [904 B]
Get:2 http://172.17.0.1/private buster-staging/main armhf libbsd0 armhf 0.9.1-1 [104 kB]
Get:3 http://172.17.0.1/private buster-staging/main armhf bsdmainutils armhf 11.1.2 [182 kB]
Get:4 http://172.17.0.1/private buster-staging/main armhf libcc1-0 armhf 8.2.0-12+rpi1 [30.1 kB]
Get:5 http://172.17.0.1/private buster-staging/main armhf gcc-8-base armhf 8.2.0-12+rpi1 [188 kB]
Get:6 http://172.17.0.1/private buster-staging/main armhf libgcc1 armhf 1:8.2.0-12+rpi1 [36.6 kB]
Get:7 http://172.17.0.1/private buster-staging/main armhf libgomp1 armhf 8.2.0-12+rpi1 [63.9 kB]
Get:8 http://172.17.0.1/private buster-staging/main armhf libatomic1 armhf 8.2.0-12+rpi1 [8108 B]
Get:9 http://172.17.0.1/private buster-staging/main armhf libasan5 armhf 8.2.0-12+rpi1 [318 kB]
Get:10 http://172.17.0.1/private buster-staging/main armhf libubsan1 armhf 8.2.0-12+rpi1 [104 kB]
Get:11 http://172.17.0.1/private buster-staging/main armhf g++-8 armhf 8.2.0-12+rpi1 [5942 kB]
Get:12 http://172.17.0.1/private buster-staging/main armhf libstdc++-8-dev armhf 8.2.0-12+rpi1 [1565 kB]
Get:13 http://172.17.0.1/private buster-staging/main armhf libgcc-8-dev armhf 8.2.0-12+rpi1 [3743 kB]
Get:14 http://172.17.0.1/private buster-staging/main armhf gcc-8 armhf 8.2.0-12+rpi1 [5848 kB]
Get:15 http://172.17.0.1/private buster-staging/main armhf cpp-8 armhf 8.2.0-12+rpi1 [5475 kB]
Get:16 http://172.17.0.1/private buster-staging/main armhf libstdc++6 armhf 8.2.0-12+rpi1 [326 kB]
Get:17 http://172.17.0.1/private buster-staging/main armhf groff-base armhf 1.22.3-10 [1005 kB]
Get:18 http://172.17.0.1/private buster-staging/main armhf libpipeline1 armhf 1.5.0-2 [25.1 kB]
Get:19 http://172.17.0.1/private buster-staging/main armhf man-db armhf 2.8.4-3 [1160 kB]
Get:20 http://172.17.0.1/private buster-staging/main armhf libmagic-mgc armhf 1:5.34-2 [239 kB]
Get:21 http://172.17.0.1/private buster-staging/main armhf libmagic1 armhf 1:5.34-2 [107 kB]
Get:22 http://172.17.0.1/private buster-staging/main armhf file armhf 1:5.34-2 [65.0 kB]
Get:23 http://172.17.0.1/private buster-staging/main armhf gettext-base armhf 0.19.8.1-9 [117 kB]
Get:24 http://172.17.0.1/private buster-staging/main armhf libsigsegv2 armhf 2.12-2 [32.3 kB]
Get:25 http://172.17.0.1/private buster-staging/main armhf m4 armhf 1.4.18-2 [185 kB]
Get:26 http://172.17.0.1/private buster-staging/main armhf autoconf all 2.69-11 [341 kB]
Get:27 http://172.17.0.1/private buster-staging/main armhf autotools-dev all 20180224.1 [77.0 kB]
Get:28 http://172.17.0.1/private buster-staging/main armhf automake all 1:1.16.1-4 [771 kB]
Get:29 http://172.17.0.1/private buster-staging/main armhf autopoint all 0.19.8.1-9 [434 kB]
Get:30 http://172.17.0.1/private buster-staging/main armhf cmake-data all 3.13.2-1 [1476 kB]
Get:31 http://172.17.0.1/private buster-staging/main armhf libicu63 armhf 63.1-5 [7976 kB]
Get:32 http://172.17.0.1/private buster-staging/main armhf libxml2 armhf 2.9.4+dfsg1-7+b1 [570 kB]
Get:33 http://172.17.0.1/private buster-staging/main armhf libarchive13 armhf 3.3.3-1 [269 kB]
Get:34 http://172.17.0.1/private buster-staging/main armhf libnghttp2-14 armhf 1.35.1-1 [70.8 kB]
Get:35 http://172.17.0.1/private buster-staging/main armhf libpsl5 armhf 0.20.2-2 [52.6 kB]
Get:36 http://172.17.0.1/private buster-staging/main armhf librtmp1 armhf 2.4+20151223.gitfa8646d.1-2 [54.0 kB]
Get:37 http://172.17.0.1/private buster-staging/main armhf libssh2-1 armhf 1.8.0-2 [125 kB]
Get:38 http://172.17.0.1/private buster-staging/main armhf libcurl4 armhf 7.62.0-1 [286 kB]
Get:39 http://172.17.0.1/private buster-staging/main armhf librhash0 armhf 1.3.6-3 [97.1 kB]
Get:40 http://172.17.0.1/private buster-staging/main armhf libuv1 armhf 1.24.0-1 [96.3 kB]
Get:41 http://172.17.0.1/private buster-staging/main armhf cmake armhf 3.13.2-1 [2563 kB]
Get:42 http://172.17.0.1/private buster-staging/main armhf libtool all 2.4.6-6 [547 kB]
Get:43 http://172.17.0.1/private buster-staging/main armhf dh-autoreconf all 19 [16.9 kB]
Get:44 http://172.17.0.1/private buster-staging/main armhf libarchive-zip-perl all 1.64-1 [96.8 kB]
Get:45 http://172.17.0.1/private buster-staging/main armhf libfile-stripnondeterminism-perl all 1.0.0-1 [19.5 kB]
Get:46 http://172.17.0.1/private buster-staging/main armhf dh-strip-nondeterminism all 1.0.0-1 [12.5 kB]
Get:47 http://172.17.0.1/private buster-staging/main armhf libelf1 armhf 0.170-0.5 [160 kB]
Get:48 http://172.17.0.1/private buster-staging/main armhf dwz armhf 0.12-3 [66.0 kB]
Get:49 http://172.17.0.1/private buster-staging/main armhf libglib2.0-0 armhf 2.58.1-2 [1051 kB]
Get:50 http://172.17.0.1/private buster-staging/main armhf gettext armhf 0.19.8.1-9 [1219 kB]
Get:51 http://172.17.0.1/private buster-staging/main armhf intltool-debian all 0.35.0+20060710.4 [26.3 kB]
Get:52 http://172.17.0.1/private buster-staging/main armhf po-debconf all 1.0.21 [248 kB]
Get:53 http://172.17.0.1/private buster-staging/main armhf debhelper all 11.5.4 [1003 kB]
Get:54 http://172.17.0.1/private buster-staging/main armhf hdf5-helpers armhf 1.10.0-patch1+docs-4+b2 [36.4 kB]
Get:55 http://172.17.0.1/private buster-staging/main armhf libaec-dev armhf 1.0.2-1 [19.1 kB]
Get:56 http://172.17.0.1/private buster-staging/main armhf libgfortran5 armhf 8.2.0-12+rpi1 [205 kB]
Get:57 http://172.17.0.1/private buster-staging/main armhf libblas3 armhf 3.8.0-2 [103 kB]
Get:58 http://172.17.0.1/private buster-staging/main armhf liblapack3 armhf 3.8.0-2 [1493 kB]
Get:59 http://172.17.0.1/private buster-staging/main armhf libarpack2 armhf 3.6.3-1+rpi1 [81.2 kB]
Get:60 http://172.17.0.1/private buster-staging/main armhf libarmadillo9 armhf 1:9.200.6+dfsg-1 [86.8 kB]
Get:61 http://172.17.0.1/private buster-staging/main armhf libblas-dev armhf 3.8.0-2 [113 kB]
Get:62 http://172.17.0.1/private buster-staging/main armhf liblapack-dev armhf 3.8.0-2 [1551 kB]
Get:63 http://172.17.0.1/private buster-staging/main armhf libarpack2-dev armhf 3.6.3-1+rpi1 [89.3 kB]
Get:64 http://172.17.0.1/private buster-staging/main armhf libgfortran4 armhf 7.3.0-19 [191 kB]
Get:65 http://172.17.0.1/private buster-staging/main armhf libhdf5-100 armhf 1.10.0-patch1+docs-4+b2 [1216 kB]
Get:66 http://172.17.0.1/private buster-staging/main armhf zlib1g-dev armhf 1:1.2.11.dfsg-1 [206 kB]
Get:67 http://172.17.0.1/private buster-staging/main armhf libhdf5-cpp-100 armhf 1.10.0-patch1+docs-4+b2 [117 kB]
Get:68 http://172.17.0.1/private buster-staging/main armhf libhdf5-dev armhf 1.10.0-patch1+docs-4+b2 [2150 kB]
Get:69 http://172.17.0.1/private buster-staging/main armhf libsuperlu-dev armhf 5.2.1+dfsg1-3 [18.2 kB]
Get:70 http://172.17.0.1/private buster-staging/main armhf libarmadillo-dev armhf 1:9.200.6+dfsg-1 [360 kB]
Get:71 http://172.17.0.1/private buster-staging/main armhf libbamtools2.5.1 armhf 2.5.1+dfsg-3 [128 kB]
Get:72 http://172.17.0.1/private buster-staging/main armhf libbamtools-dev armhf 2.5.1+dfsg-3 [21.8 kB]
Get:73 http://172.17.0.1/private buster-staging/main armhf libboost1.67-dev armhf 1.67.0-11 [8386 kB]
Get:74 http://172.17.0.1/private buster-staging/main armhf libboost-math1.67.0 armhf 1.67.0-11 [315 kB]
Get:75 http://172.17.0.1/private buster-staging/main armhf libboost-math1.67-dev armhf 1.67.0-11 [446 kB]
Get:76 http://172.17.0.1/private buster-staging/main armhf libboost-math-dev armhf 1.67.0.1+b1 [4128 B]
Get:77 http://172.17.0.1/private buster-staging/main armhf libdisorder0 armhf 0.0.2+git20130809.8062ee1-1 [4568 B]
Get:78 http://172.17.0.1/private buster-staging/main armhf libdisorder-dev armhf 0.0.2+git20130809.8062ee1-1 [4156 B]
Get:79 http://172.17.0.1/private buster-staging/main armhf libsmithwaterman0 armhf 0.0+git20160702.2610e25-7 [30.5 kB]
Get:80 http://172.17.0.1/private buster-staging/main armhf libsmithwaterman-dev armhf 0.0+git20160702.2610e25-7 [34.3 kB]
Get:81 http://172.17.0.1/private buster-staging/main armhf libjsoncpp-dev armhf 1.7.4-3 [78.6 kB]
debconf: delaying package configuration, since apt-utils is not installed
Fetched 64.1 MB in 19s (3327 kB/s)
Selecting previously unselected package libbsd0:armhf.
(Reading database ... 15795 files and directories currently installed.)
Preparing to unpack .../libbsd0_0.9.1-1_armhf.deb ...
Unpacking libbsd0:armhf (0.9.1-1) ...
Selecting previously unselected package bsdmainutils.
Preparing to unpack .../bsdmainutils_11.1.2_armhf.deb ...
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update-alternatives: using /usr/lib/arm-linux-gnueabihf/blas/libblas.so to provide /usr/lib/arm-linux-gnueabihf/libblas.so (libblas.so-arm-linux-gnueabihf) in auto mode
Setting up liblapack3:armhf (3.8.0-2) ...
update-alternatives: using /usr/lib/arm-linux-gnueabihf/lapack/liblapack.so.3 to provide /usr/lib/arm-linux-gnueabihf/liblapack.so.3 (liblapack.so.3-arm-linux-gnueabihf) in auto mode
Setting up libsuperlu5:armhf (5.2.1+dfsg1-3) ...
Setting up gcc-8 (8.2.0-12+rpi1) ...
Setting up g++-8 (8.2.0-12+rpi1) ...
Setting up libsuperlu-dev:armhf (5.2.1+dfsg1-3) ...
Setting up libboost1.67-dev:armhf (1.67.0-11) ...
Setting up libarpack2:armhf (3.6.3-1+rpi1) ...
Setting up liblapack-dev:armhf (3.8.0-2) ...
update-alternatives: using /usr/lib/arm-linux-gnueabihf/lapack/liblapack.so to provide /usr/lib/arm-linux-gnueabihf/liblapack.so (liblapack.so-arm-linux-gnueabihf) in auto mode
Setting up libhdf5-cpp-100:armhf (1.10.0-patch1+docs-4+b2) ...
Setting up libboost-math1.67-dev:armhf (1.67.0-11) ...
Setting up libarmadillo9 (1:9.200.6+dfsg-1) ...
Setting up libhdf5-dev (1.10.0-patch1+docs-4+b2) ...
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 libarpack2-dev:armhf (3.6.3-1+rpi1) ...
Setting up libboost-math-dev:armhf (1.67.0.1+b1) ...
Setting up libarmadillo-dev (1:9.200.6+dfsg-1) ...
Setting up dh-strip-nondeterminism (1.0.0-1) ...
Setting up debhelper (11.5.4) ...
Setting up dh-autoreconf (19) ...
Setting up sbuild-build-depends-tvc-dummy (0.invalid.0) ...
Processing triggers for libc-bin (2.28-2) ...
W: No sandbox user '_apt' on the system, can not drop privileges
+------------------------------------------------------------------------------+
| Build environment |
+------------------------------------------------------------------------------+
Kernel: Linux 4.8.0-0.bpo.2-armmp armhf (armv7l)
Toolchain package versions: binutils_2.31.1-10+rpi1 dpkg-dev_1.19.2 g++-8_8.2.0-12+rpi1 gcc-8_8.2.0-12+rpi1 libc6-dev_2.28-2 libstdc++-8-dev_8.2.0-12+rpi1 libstdc++6_8.2.0-12+rpi1 linux-libc-dev_4.18.20-2+rpi1
Package versions: adduser_3.118 apt_1.8.0~alpha2 autoconf_2.69-11 automake_1:1.16.1-4 autopoint_0.19.8.1-9 autotools-dev_20180224.1 base-files_10.1+rpi1 base-passwd_3.5.45 bash_4.4.18-3.1 binutils_2.31.1-10+rpi1 binutils-arm-linux-gnueabihf_2.31.1-10+rpi1 binutils-common_2.31.1-10+rpi1 bsdmainutils_11.1.2 bsdutils_1:2.33-0.2 build-essential_12.5 bzip2_1.0.6-9 ca-certificates_20170717 cmake_3.13.2-1 cmake-data_3.13.2-1 coreutils_8.30-1 cpio_2.12+dfsg-6 cpp_4:8.2.0-2+rpi1 cpp-8_8.2.0-12+rpi1 dash_0.5.10.2-2 dbus_1.12.12-1 dbus-user-session_1.12.12-1 debconf_1.5.69 debhelper_11.5.4 debianutils_4.8.6 dh-autoreconf_19 dh-strip-nondeterminism_1.0.0-1 diffutils_1:3.6-1 dirmngr_2.2.11-1 dmsetup_2:1.02.145-4.1+b5 dpkg_1.19.2 dpkg-dev_1.19.2 dwz_0.12-3 e2fslibs_1.44.4-2 e2fsprogs_1.44.4-2 e2fsprogs-l10n_1.44.4-2 fakeroot_1.23-1 fdisk_2.33-0.2 file_1:5.34-2 findutils_4.6.0+git+20181018-1 g++_4:8.2.0-2+rpi1 g++-8_8.2.0-12+rpi1 gcc_4:8.2.0-2+rpi1 gcc-4.6-base_4.6.4-5+rpi1 gcc-4.7-base_4.7.3-11+rpi1 gcc-4.8-base_4.8.5-4 gcc-4.9-base_4.9.4-2+rpi1+b19 gcc-5-base_5.5.0-8 gcc-7-base_7.3.0-19 gcc-8_8.2.0-12+rpi1 gcc-8-base_8.2.0-12+rpi1 gettext_0.19.8.1-9 gettext-base_0.19.8.1-9 gnupg_2.2.11-1 gnupg-agent_2.2.11-1 gnupg-l10n_2.2.11-1 gnupg-utils_2.2.11-1 gpg_2.2.11-1 gpg-agent_2.2.11-1 gpg-wks-client_2.2.11-1 gpg-wks-server_2.2.11-1 gpgconf_2.2.11-1 gpgsm_2.2.11-1 gpgv_2.2.11-1 grep_3.1-2 groff-base_1.22.3-10 gzip_1.9-2.1 hdf5-helpers_1.10.0-patch1+docs-4+b2 hostname_3.21 inetutils-ping_2:1.9.4-5 init-system-helpers_1.56 initramfs-tools_0.132 initramfs-tools-core_0.132 intltool-debian_0.35.0+20060710.4 klibc-utils_2.0.4-14+rpi1 kmod_25-2 krb5-locales_1.16.1-1 libacl1_2.2.52-3 libaec-dev_1.0.2-1 libaec0_1.0.2-1 libapparmor1_2.13.1-3+b1 libapt-pkg5.0_1.8.0~alpha2 libarchive-zip-perl_1.64-1 libarchive13_3.3.3-1 libargon2-1_0~20171227-0.1 libarmadillo-dev_1:9.200.6+dfsg-1 libarmadillo9_1:9.200.6+dfsg-1 libarpack2_3.6.3-1+rpi1 libarpack2-dev_3.6.3-1+rpi1 libasan5_8.2.0-12+rpi1 libassuan0_2.5.1-2 libatomic1_8.2.0-12+rpi1 libattr1_1:2.4.47-2 libaudit-common_1:2.8.4-2 libaudit1_1:2.8.4-2 libbamtools-dev_2.5.1+dfsg-3 libbamtools2.5.1_2.5.1+dfsg-3 libbinutils_2.31.1-10+rpi1 libblas-dev_3.8.0-2 libblas3_3.8.0-2 libblkid1_2.33-0.2 libboost-math-dev_1.67.0.1+b1 libboost-math1.67-dev_1.67.0-11 libboost-math1.67.0_1.67.0-11 libboost1.67-dev_1.67.0-11 libbsd0_0.9.1-1 libbz2-1.0_1.0.6-9 libc-bin_2.28-2 libc-dev-bin_2.28-2 libc6_2.28-2 libc6-dev_2.28-2 libcap-ng0_0.7.9-1 libcap2_1:2.25-1.2 libcc1-0_8.2.0-12+rpi1 libcom-err2_1.44.4-2 libcroco3_0.6.12-2 libcryptsetup12_2:2.0.6-1 libcryptsetup4_2:1.7.5-1 libcurl4_7.62.0-1 libdb5.3_5.3.28+dfsg1-0.2 libdbus-1-3_1.12.12-1 libdebconfclient0_0.245 libdevmapper1.02.1_2:1.02.145-4.1+b5 libdisorder-dev_0.0.2+git20130809.8062ee1-1 libdisorder0_0.0.2+git20130809.8062ee1-1 libdpkg-perl_1.19.2 libdrm-common_2.4.95-1+rpi1 libdrm2_2.4.95-1+rpi1 libelf1_0.170-0.5 libexpat1_2.2.6-1 libext2fs2_1.44.4-2 libfakeroot_1.23-1 libfdisk1_2.33-0.2 libffi6_3.2.1-9 libfile-stripnondeterminism-perl_1.0.0-1 libgcc-8-dev_8.2.0-12+rpi1 libgcc1_1:8.2.0-12+rpi1 libgcrypt20_1.8.4-4 libgdbm-compat4_1.18.1-2 libgdbm3_1.8.3-14 libgdbm6_1.18.1-2 libgfortran4_7.3.0-19 libgfortran5_8.2.0-12+rpi1 libglib2.0-0_2.58.1-2 libgmp10_2:6.1.2+dfsg-4 libgnutls30_3.5.19-1+b1 libgomp1_8.2.0-12+rpi1 libgpg-error-l10n_1.32-3 libgpg-error0_1.32-3 libgssapi-krb5-2_1.16.1-1 libhdf5-100_1.10.0-patch1+docs-4+b2 libhdf5-cpp-100_1.10.0-patch1+docs-4+b2 libhdf5-dev_1.10.0-patch1+docs-4+b2 libhogweed4_3.4.1~rc1-1 libicu63_63.1-5 libidn11_1.33-2.2 libidn2-0_2.0.5-1 libip4tc0_1.8.2-2+b1 libisl19_0.20-2 libjpeg-dev_1:1.5.2-2 libjpeg62-turbo_1:1.5.2-2+b1 libjpeg62-turbo-dev_1:1.5.2-2+b1 libjson-c3_0.12.1-1.3 libjsoncpp-dev_1.7.4-3 libjsoncpp1_1.7.4-3 libk5crypto3_1.16.1-1 libkeyutils1_1.5.9-9.3 libklibc_2.0.4-14+rpi1 libkmod2_25-2 libkrb5-3_1.16.1-1 libkrb5support0_1.16.1-1 libksba8_1.3.5-2 liblapack-dev_3.8.0-2 liblapack3_3.8.0-2 libldap-2.4-2_2.4.46+dfsg-5+rpi1+b1 libldap-common_2.4.46+dfsg-5+rpi1 liblz4-1_1.8.2-1+rpi1 liblzma5_5.2.2-1.3 libmagic-mgc_1:5.34-2 libmagic1_1:5.34-2 libmount1_2.33-0.2 libmpc3_1.1.0-1 libmpfr6_4.0.1-2 libncurses5_6.1+20181013-1 libncurses6_6.1+20181013-1 libncursesw5_6.1+20181013-1 libncursesw6_6.1+20181013-1 libnettle6_3.4.1~rc1-1 libnghttp2-14_1.35.1-1 libnpth0_1.6-1 libnss-systemd_239-15+rpi1 libp11-kit0_0.23.14-2 libpam-modules_1.1.8-3.8 libpam-modules-bin_1.1.8-3.8 libpam-runtime_1.1.8-3.8 libpam-systemd_239-15+rpi1 libpam0g_1.1.8-3.8 libpcre3_2:8.39-11+rpi1 libperl5.24_5.24.1-4 libperl5.28_5.28.1-3 libpipeline1_1.5.0-2 libplymouth4_0.9.4-1 libpng16-16_1.6.34-2+rpi1 libprocps7_2:3.3.15-2 libpsl5_0.20.2-2 libreadline7_7.0-5 librhash0_1.3.6-3 librtmp1_2.4+20151223.gitfa8646d.1-2 libsasl2-2_2.1.27~rc8-1 libsasl2-modules-db_2.1.27~rc8-1 libseccomp2_2.3.3-3 libselinux1_2.8-1 libsemanage-common_2.8-1 libsemanage1_2.8-1 libsepol1_2.8-1 libsigsegv2_2.12-2 libsmartcols1_2.33-0.2 libsmithwaterman-dev_0.0+git20160702.2610e25-7 libsmithwaterman0_0.0+git20160702.2610e25-7 libsqlite3-0_3.26.0-3 libss2_1.44.4-2 libssh2-1_1.8.0-2 libssl1.1_1.1.1a-1 libstdc++-8-dev_8.2.0-12+rpi1 libstdc++6_8.2.0-12+rpi1 libsuperlu-dev_5.2.1+dfsg1-3 libsuperlu5_5.2.1+dfsg1-3 libsystemd0_239-15+rpi1 libsz2_1.0.2-1 libtasn1-6_4.13-3 libtinfo5_6.1+20181013-1 libtinfo6_6.1+20181013-1 libtool_2.4.6-6 libubsan1_8.2.0-12+rpi1 libudev1_239-15+rpi1 libunistring2_0.9.10-1 libustr-1.0-1_1.0.4-6 libuuid1_2.33-0.2 libuv1_1.24.0-1 libxml2_2.9.4+dfsg1-7+b1 libzstd1_1.3.5+dfsg-1+rpi1 linux-base_4.5 linux-libc-dev_4.18.20-2+rpi1 login_1:4.5-1.1 lsb-base_10.2018112800+rpi1 m4_1.4.18-2 make_4.2.1-1.2 makedev_2.3.1-94 man-db_2.8.4-3 mawk_1.3.3-17 mount_2.33-0.2 multiarch-support_2.28-2 nano_3.2-1 ncurses-base_6.1+20181013-1 ncurses-bin_6.1+20181013-1 netbase_5.5 openssl_1.1.1a-1 passwd_1:4.5-1.1 patch_2.7.6-3 perl_5.28.1-3 perl-base_5.28.1-3 perl-modules-5.24_5.24.1-7 perl-modules-5.28_5.28.1-3 pinentry-curses_1.1.0-1 plymouth_0.9.4-1 po-debconf_1.0.21 procps_2:3.3.15-2 raspbian-archive-keyring_20120528.2 readline-common_7.0-5 sbuild-build-depends-core-dummy_0.invalid.0 sbuild-build-depends-tvc-dummy_0.invalid.0 sed_4.5-2 sensible-utils_0.0.12 systemd_239-15+rpi1 systemd-sysv_239-15+rpi1 sysvinit-utils_2.93-1 tar_1.30+dfsg-3+rpi1 tzdata_2018g-1 udev_239-15+rpi1 util-linux_2.33-0.2 xz-utils_5.2.2-1.3 zlib1g_1:1.2.11.dfsg-1 zlib1g-dev_1:1.2.11.dfsg-1
+------------------------------------------------------------------------------+
| Build |
+------------------------------------------------------------------------------+
Unpack source
-------------
gpgv: unknown type of key resource 'trustedkeys.kbx'
gpgv: keyblock resource '/sbuild-nonexistent/.gnupg/trustedkeys.kbx': General error
gpgv: Signature made Thu Dec 13 07:20:19 2018 UTC
gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1
gpgv: issuer "tille@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-2.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-2.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
Check disc space
----------------
Sufficient free space for build
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=buster-staging-armhf-sbuild
SCHROOT_CHROOT_NAME=buster-staging-armhf-sbuild
SCHROOT_COMMAND=env
SCHROOT_GID=109
SCHROOT_GROUP=buildd
SCHROOT_SESSION_ID=buster-staging-armhf-sbuild-50529a9a-3496-4a0a-8a40-eb837a401aa3
SCHROOT_UID=104
SCHROOT_USER=buildd
SHELL=/bin/sh
TERM=linux
USER=buildd
dpkg-buildpackage
-----------------
dpkg-buildpackage: info: source package tvc
dpkg-buildpackage: info: source version 5.0.3+git20151221.80e144e+dfsg-2
dpkg-buildpackage: info: source distribution unstable
dpkg-source --before-build .
dpkg-buildpackage: info: host architecture armhf
fakeroot debian/rules clean
dh clean
dh_clean
debian/rules build-arch
dh build-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 8.2.0
-- The CXX compiler identification is GNU 8.2.0
-- Check for working C compiler: /usr/bin/cc
-- Check for working C compiler: /usr/bin/cc -- works
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Detecting C compile features
-- Detecting C compile features - done
-- Check for working CXX compiler: /usr/bin/c++
-- Check for working CXX compiler: /usr/bin/c++ -- works
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- 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/tvcassembly.dir/build.make CMakeFiles/tvcassembly.dir/depend
make -f CMakeFiles/tvc.dir/build.make CMakeFiles/tvc.dir/depend
make -f CMakeFiles/tvcutils.dir/build.make CMakeFiles/tvcutils.dir/depend
make[3]: Entering directory '/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/obj-arm-linux-gnueabihf'
cd /<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg /<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg /<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/obj-arm-linux-gnueabihf /<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/obj-arm-linux-gnueabihf /<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/tvcassembly.dir/DependInfo.cmake --color=
make[3]: Entering directory '/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/obj-arm-linux-gnueabihf'
cd /<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg /<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg /<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/obj-arm-linux-gnueabihf /<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/obj-arm-linux-gnueabihf /<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/tvcutils.dir/DependInfo.cmake --color=
make[3]: Entering directory '/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/obj-arm-linux-gnueabihf'
cd /<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg /<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg /<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/obj-arm-linux-gnueabihf /<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/obj-arm-linux-gnueabihf /<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/tvc.dir/DependInfo.cmake --color=
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'
[ 1%] Building CXX object CMakeFiles/tvcassembly.dir/VariantCaller/TargetsManager.cpp.o
[ 3%] Building CXX object CMakeFiles/tvcassembly.dir/VariantCaller/IndelAssembly/IndelAssembly.cpp.o
/usr/bin/c++ -DALIGNSTATS_IGNORE -I/<<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
/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
[ 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
make[3]: Entering directory '/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/obj-arm-linux-gnueabihf'
[ 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/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
/<<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]
arma::set_stream_err1(null_ostream);
^~~~~~~~~~~~~~~
In file included from /usr/include/armadillo:353,
from /<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/VariantCaller.cpp:12:
/usr/include/armadillo_bits/debug.hpp:90:1: note: declared here
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]
arma::set_stream_err1(null_ostream);
^
In file included from /usr/include/armadillo:353,
from /<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/VariantCaller.cpp:12:
/usr/include/armadillo_bits/debug.hpp:90:1: note: declared here
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]
arma::set_stream_err1(null_ostream);
^
In file included from /usr/include/armadillo:353,
from /<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/VariantCaller.cpp:12:
/usr/include/armadillo_bits/debug.hpp:90:1: note: declared here
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]
arma::set_stream_err2(null_ostream);
^~~~~~~~~~~~~~~
In file included from /usr/include/armadillo:353,
from /<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/VariantCaller.cpp:12:
/usr/include/armadillo_bits/debug.hpp:101:1: note: declared here
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]
arma::set_stream_err2(null_ostream);
^
In file included from /usr/include/armadillo:353,
from /<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/VariantCaller.cpp:12:
/usr/include/armadillo_bits/debug.hpp:101:1: note: declared here
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]
arma::set_stream_err2(null_ostream);
^
In file included from /usr/include/armadillo:353,
from /<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/VariantCaller.cpp:12:
/usr/include/armadillo_bits/debug.hpp:101:1: note: declared here
set_stream_err2(std::ostream& user_stream)
^~~~~~~~~~~~~~~
[ 12%] 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
[ 14%] 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
In file included from /usr/include/c++/8/vector:69,
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++/8/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++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector<double>::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc: In member function 'void OptArgs::StringToDoubleVector(std::vector<double>&, const string&, const string&, char)':
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
[ 15%] 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
[ 17%] 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
[ 18%] 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
[ 20%] 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
[ 21%] 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'
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[ 23%] 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
[ 25%] 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
[ 26%] 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
[ 28%] 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
[ 29%] Building CXX object CMakeFiles/tvc.dir/VariantCaller/HotspotReader.cpp.o
/usr/bin/c++ -DALIGNSTATS_IGNORE -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/external/vcflib -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/external/freebayes/src -I/usr/include/jsoncpp -I/usr/include/bamtools -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/FlowDistEval -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/EnsembleEval -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Bookkeeping -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Reads -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Splice -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Filter -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/realignment -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/file-io -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/BaseCaller -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/Calibration -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/Util -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg -g -O2 -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
[ 31%] 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++/8/vector:69,
from /<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/tvcutils/unify_vcf.cpp:13:
/usr/include/c++/8/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++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector<markov_state>::iterator' {aka '__gnu_cxx::__normal_iterator<markov_state*, std::vector<markov_state> >'} changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/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++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<markov_state*, std::vector<markov_state> >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:69,
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++/8/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++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector<double>::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc: In member function 'void OptArgs::StringToDoubleVector(std::vector<double>&, const string&, const string&, char)':
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
[ 32%] 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
[ 34%] 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
[ 35%] 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
[ 37%] 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
[ 39%] 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
[ 40%] 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]
fread(buf, 1, 28, fp->file);
^~~~~~~~~~~~~~~~~~~~~~~~~~~
[ 42%] 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
[ 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%] 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
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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/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++/8/vector:69,
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++/8/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++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector<DPTreephaser>::iterator' {aka '__gnu_cxx::__normal_iterator<DPTreephaser*, std::vector<DPTreephaser> >'} changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:64,
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++/8/bits/stl_vector.h: In constructor 'PersistingThreadObjects::PersistingThreadObjects(const InputStructures&)':
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<DPTreephaser*, std::vector<DPTreephaser> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
[ 51%] 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
[ 53%] 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'
[ 53%] Built target tvcutils
[ 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:191:22: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'std::vector<float>::size_type' {aka 'unsigned int'} [-Wformat=]
fprintf(stdout, "ref.size()=%lu; ", ref.size());
^~~~~~~~~~~~~~~~~~ ~~~~~~~~~~
/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Filter/VariantAssist.cpp:192:22: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'std::vector<float>::size_type' {aka 'unsigned int'} [-Wformat=]
fprintf(stdout, "var.size()=%lu; ", var.size());
^~~~~~~~~~~~~~~~~~ ~~~~~~~~~~
/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Filter/VariantAssist.cpp:193:22: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'std::vector<double>::size_type' {aka 'unsigned int'} [-Wformat=]
fprintf(stdout, "both.size()=%lu; ", both.size());
^~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~
[ 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
/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/SigmaGenerator.cpp.o -c /<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/EnsembleEval/SigmaGenerator.cpp
[ 68%] Building CXX object CMakeFiles/tvc.dir/VariantCaller/EnsembleEval/SkewGenerator.cpp.o
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[ 70%] Building CXX object CMakeFiles/tvc.dir/VariantCaller/EnsembleEval/PosteriorInference.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
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[ 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]
fread(buf, 1, 28, fp->file);
^~~~~~~~~~~~~~~~~~~~~~~~~~~
[ 84%] Building CXX object CMakeFiles/tvc.dir/external/freebayes/src/AlleleParser.cpp.o
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[ 85%] Building CXX object CMakeFiles/tvc.dir/BaseCaller/PIDloop.cpp.o
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[ 87%] Building CXX object CMakeFiles/tvc.dir/BaseCaller/DPTreephaser.cpp.o
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[ 89%] Building CXX object CMakeFiles/tvc.dir/Calibration/LinearCalibrationModel.cpp.o
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[ 90%] Building CXX object CMakeFiles/tvc.dir/Calibration/FlowAlignment.cpp.o
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[ 92%] Building CXX object CMakeFiles/tvc.dir/Util/OptArgs.cpp.o
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[ 93%] Building CXX object CMakeFiles/tvc.dir/realignment/Realigner.cpp.o
/usr/bin/c++ -DALIGNSTATS_IGNORE -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/external/vcflib -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/external/freebayes/src -I/usr/include/jsoncpp -I/usr/include/bamtools -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/FlowDistEval -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/EnsembleEval -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Bookkeeping -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Reads -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Splice -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Filter -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/realignment -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/file-io -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/BaseCaller -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/Calibration -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/Util -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg -g -O2 -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++/8/vector:69,
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++/8/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++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector<double>::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc: In member function 'void OptArgs::StringToDoubleVector(std::vector<double>&, const string&, const string&, char)':
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_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
make[3]: Leaving directory '/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/obj-arm-linux-gnueabihf'
[100%] Built target tvc
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/usr/bin/cmake -E cmake_progress_start /<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/obj-arm-linux-gnueabihf/CMakeFiles 0
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dh_auto_test -a
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
Start 4: tvcutils_call
1/8 Test #4: tvcutils_call .................................... Passed 0.07 sec
Start 5: tvcutils_prepare_hotspots_call
2/8 Test #5: tvcutils_prepare_hotspots_call ................... Passed 0.04 sec
Start 6: tvcutils_validate_bed_call
3/8 Test #1: tvc_call ......................................... Passed 0.16 sec
Start 7: tvcutils_unify_vcf_call
4/8 Test #6: tvcutils_validate_bed_call ....................... Passed 0.03 sec
Start 8: tvcassembly_call
5/8 Test #7: tvcutils_unify_vcf_call .......................... Passed 0.03 sec
6/8 Test #8: tvcassembly_call ................................. Passed 0.03 sec
7/8 Test #2: tvc_test_1_thread_sse_off ........................ Passed 6.01 sec
8/8 Test #3: tvc_test_4_threads_sse_off_with_parameter_file ... Passed 6.33 sec
100% tests passed, 0 tests failed out of 8
Total Test time (real) = 6.37 sec
make[1]: Leaving directory '/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/obj-arm-linux-gnueabihf'
create-stamp debian/debhelper-build-stamp
fakeroot debian/rules binary-arch
dh binary-arch
dh_testroot -a
dh_prep -a
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cd obj-arm-linux-gnueabihf && make -j4 install DESTDIR=/<<BUILDDIR>>/tvc-5.0.3\+git20151221.80e144e\+dfsg/debian/tvc AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true"
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make -f CMakeFiles/Makefile2 all
make[2]: Entering directory '/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/obj-arm-linux-gnueabihf'
make -f CMakeFiles/tvcassembly.dir/build.make CMakeFiles/tvcassembly.dir/depend
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make -f CMakeFiles/tvcutils.dir/build.make CMakeFiles/tvcutils.dir/depend
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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=
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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=
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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
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make[3]: Entering directory '/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/obj-arm-linux-gnueabihf'
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make -f CMakeFiles/tvc.dir/build.make CMakeFiles/tvc.dir/build
[ 10%] Built target tvcassembly
[ 31%] Built target tvcutils
make[3]: Entering directory '/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/obj-arm-linux-gnueabihf'
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[100%] Built target tvc
make[2]: Leaving directory '/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/obj-arm-linux-gnueabihf'
/usr/bin/cmake -E cmake_progress_start /<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/obj-arm-linux-gnueabihf/CMakeFiles 0
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make[2]: Entering directory '/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/obj-arm-linux-gnueabihf'
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make[2]: Leaving directory '/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/obj-arm-linux-gnueabihf'
Install the project...
/usr/bin/cmake -P cmake_install.cmake
-- Install configuration: "None"
-- Installing: /<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/bin/tvc
-- Installing: /<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/bin/tvcassembly
-- Installing: /<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/bin/tvcutils
-- Installing: /<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/bin/variant_caller_pipeline.py
-- Installing: /<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/share/TVC/pluginMedia
-- Installing: /<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/share/TVC/pluginMedia/parameter_sets
-- Installing: /<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/share/TVC/pluginMedia/parameter_sets/ampliseq_germline_lowstringency_pgm_parameters.json
-- Installing: /<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/share/TVC/pluginMedia/parameter_sets/ampliseq_somatic_lowstringency_pgm_parameters.json
-- Installing: /<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/share/TVC/pluginMedia/parameter_sets/ampliseqexome_germline_lowstringency_p1_parameters.json
-- Installing: /<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/share/TVC/pluginMedia/parameter_sets/ampliseqexome_somatic_lowstringency_p1_parameters.json
-- Installing: /<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/share/TVC/pluginMedia/parameter_sets/ocp_somatic_lowstringency_pgm_parameters.json
-- Installing: /<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/share/TVC/pluginMedia/parameter_sets/pgx4_germline_lowstringency_pgm_parameters.json
-- Installing: /<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/share/TVC/pluginMedia/parameter_sets/targetseq_germline_lowstringency_p1_parameters.json
-- Installing: /<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/share/TVC/sse
-- Installing: /<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/share/TVC/sse/ampliseqexome_germline_p1_hiq_motifset.txt
-- Installing: /<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/share/TVC/sse/motifset.txt
-- Installing: /<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/share/TVC/examples
-- Installing: /<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/share/TVC/examples/example1
-- Installing: /<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/share/TVC/examples/example1/expected
-- Installing: /<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/share/TVC/examples/example1/expected/TSVC_variants.vcf
-- Installing: /<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/share/TVC/examples/example1/expected/small_variants.vcf
-- Installing: /<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/share/TVC/examples/example1/reference.dict
-- Installing: /<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/share/TVC/examples/example1/reference.fasta
-- Installing: /<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/share/TVC/examples/example1/reference.fasta.fai
-- Installing: /<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/share/TVC/examples/example1/test.bam
-- Installing: /<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/share/TVC/examples/example1/test.bam.bai
-- Installing: /<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/share/TVC/examples/example1/test.bed
-- Installing: /<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/share/TVC/examples/example1/test_merged_plain.bed
-- Installing: /<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/share/TVC/examples/example1/test_original.bed
-- Installing: /<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/share/TVC/examples/example1/test_unmerged_detail.bed
make[1]: Leaving directory '/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/obj-arm-linux-gnueabihf'
dh_installdocs -a
dh_installchangelogs -a
dh_lintian -a
dh_perl -a
dh_link -a
dh_strip_nondeterminism -a
dh_compress -a
dh_fixperms -a
dh_missing -a
dh_strip -a
dh_makeshlibs -a
dh_shlibdeps -a
dpkg-shlibdeps: warning: debian/tvc/usr/bin/tvcassembly contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/tvc/usr/bin/tvc contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/tvc/usr/bin/tvcutils contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/tvc/usr/bin/tvcassembly debian/tvc/usr/bin/tvc debian/tvc/usr/bin/tvcutils were not linked against ld-linux-armhf.so.3 (they use none of the library's symbols)
dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/tvc/usr/bin/tvc was not linked against liblapack.so.3 (it uses none of the library's symbols)
dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/tvc/usr/bin/tvc debian/tvc/usr/bin/tvcutils were not linked against libdisorder.so.0 (they use none of the library's symbols)
dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/tvc/usr/bin/tvc was not linked against libblas.so.3 (it uses 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-2_armhf.deb'.
dpkg-deb: building package 'tvc' in '../tvc_5.0.3+git20151221.80e144e+dfsg-2_armhf.deb'.
dpkg-genbuildinfo --build=any
dpkg-genchanges --build=any -mRaspbian wandboard test autobuilder <root@raspbian.org> >../tvc_5.0.3+git20151221.80e144e+dfsg-2_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 2018-12-18T05:49:02Z
Finished
--------
I: Built successfully
+------------------------------------------------------------------------------+
| Post Build Chroot |
+------------------------------------------------------------------------------+
+------------------------------------------------------------------------------+
| Changes |
+------------------------------------------------------------------------------+
tvc_5.0.3+git20151221.80e144e+dfsg-2_armhf.changes:
---------------------------------------------------
Format: 1.8
Date: Thu, 13 Dec 2018 08:07:07 +0100
Source: tvc
Binary: tvc
Architecture: armhf
Version: 5.0.3+git20151221.80e144e+dfsg-2
Distribution: buster-staging
Urgency: medium
Maintainer: Raspbian wandboard test autobuilder <root@raspbian.org>
Changed-By: Andreas Tille <tille@debian.org>
Description:
tvc - genetic variant caller for Ion Torrent sequencing platforms
Closes: 916322
Changes:
tvc (5.0.3+git20151221.80e144e+dfsg-2) unstable; urgency=medium
.
[ Logan Rosen ]
* Enable build with ld --as-needed
Closes: #916322
.
[ Andreas Tille ]
* Remove trailing whitespace in debian/changelog
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Checksums-Sha256:
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Files:
a8a14c0edb635ee10579662d209d1d4b 12415480 debug optional tvc-dbgsym_5.0.3+git20151221.80e144e+dfsg-2_armhf.deb
534abba4aa3ee7517b1e9ba68f0a3e56 6735 science optional tvc_5.0.3+git20151221.80e144e+dfsg-2_armhf.buildinfo
1b60fba83616e1d5d2a7af159e618938 923492 science optional tvc_5.0.3+git20151221.80e144e+dfsg-2_armhf.deb
+------------------------------------------------------------------------------+
| Package contents |
+------------------------------------------------------------------------------+
tvc-dbgsym_5.0.3+git20151221.80e144e+dfsg-2_armhf.deb
-----------------------------------------------------
new Debian package, version 2.0.
size 12415480 bytes: control archive=660 bytes.
488 bytes, 12 lines control
318 bytes, 3 lines md5sums
Package: tvc-dbgsym
Source: tvc
Version: 5.0.3+git20151221.80e144e+dfsg-2
Auto-Built-Package: debug-symbols
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 12505
Depends: tvc (= 5.0.3+git20151221.80e144e+dfsg-2)
Section: debug
Priority: optional
Description: debug symbols for tvc
Build-Ids: 4f9cbeef6d0711b03466ac2c12ffdef25ab611b6 6642248e7402aa30b7ab458ea8191d2bf73e2524 e443e4991b71292c28b92e8361015b39476b43a4
drwxr-xr-x root/root 0 2018-12-13 07:07 ./
drwxr-xr-x root/root 0 2018-12-13 07:07 ./usr/
drwxr-xr-x root/root 0 2018-12-13 07:07 ./usr/lib/
drwxr-xr-x root/root 0 2018-12-13 07:07 ./usr/lib/debug/
drwxr-xr-x root/root 0 2018-12-13 07:07 ./usr/lib/debug/.build-id/
drwxr-xr-x root/root 0 2018-12-13 07:07 ./usr/lib/debug/.build-id/4f/
-rw-r--r-- root/root 2702688 2018-12-13 07:07 ./usr/lib/debug/.build-id/4f/9cbeef6d0711b03466ac2c12ffdef25ab611b6.debug
drwxr-xr-x root/root 0 2018-12-13 07:07 ./usr/lib/debug/.build-id/66/
-rw-r--r-- root/root 9059476 2018-12-13 07:07 ./usr/lib/debug/.build-id/66/42248e7402aa30b7ab458ea8191d2bf73e2524.debug
drwxr-xr-x root/root 0 2018-12-13 07:07 ./usr/lib/debug/.build-id/e4/
-rw-r--r-- root/root 1028732 2018-12-13 07:07 ./usr/lib/debug/.build-id/e4/43e4991b71292c28b92e8361015b39476b43a4.debug
drwxr-xr-x root/root 0 2018-12-13 07:07 ./usr/share/
drwxr-xr-x root/root 0 2018-12-13 07:07 ./usr/share/doc/
lrwxrwxrwx root/root 0 2018-12-13 07:07 ./usr/share/doc/tvc-dbgsym -> tvc
tvc_5.0.3+git20151221.80e144e+dfsg-2_armhf.deb
----------------------------------------------
new Debian package, version 2.0.
size 923492 bytes: control archive=1700 bytes.
1031 bytes, 16 lines control
2459 bytes, 28 lines md5sums
Package: tvc
Version: 5.0.3+git20151221.80e144e+dfsg-2
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 2892
Depends: libarmadillo9 (>= 1:9.200.6+dfsg), libbamtools2.5.1, libblas3 | libblas.so.3, libc6 (>= 2.27), libdisorder0 (>= 0.0.2), libgcc1 (>= 1:3.5), libjsoncpp1 (>= 1.7.4), liblapack3 | liblapack.so.3, libsmithwaterman0 (>= 0.0+git20160702.2610e25), libstdc++6 (>= 5.2), zlib1g (>= 1:1.1.4), python
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 2018-12-13 07:07 ./
drwxr-xr-x root/root 0 2018-12-13 07:07 ./usr/
drwxr-xr-x root/root 0 2018-12-13 07:07 ./usr/bin/
-rwxr-xr-x root/root 880548 2018-12-13 07:07 ./usr/bin/tvc
-rwxr-xr-x root/root 162004 2018-12-13 07:07 ./usr/bin/tvcassembly
-rwxr-xr-x root/root 469496 2018-12-13 07:07 ./usr/bin/tvcutils
-rwxr-xr-x root/root 12989 2015-12-21 20:38 ./usr/bin/variant_caller_pipeline.py
drwxr-xr-x root/root 0 2018-12-13 07:07 ./usr/share/
drwxr-xr-x root/root 0 2018-12-13 07:07 ./usr/share/TVC/
drwxr-xr-x root/root 0 2018-12-13 07:07 ./usr/share/TVC/examples/
drwxr-xr-x root/root 0 2018-12-13 07:07 ./usr/share/TVC/examples/example1/
drwxr-xr-x root/root 0 2018-12-13 07:07 ./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 2018-12-13 07:07 ./usr/share/TVC/pluginMedia/
drwxr-xr-x root/root 0 2018-12-13 07:07 ./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 2018-12-13 07:07 ./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 2018-12-13 07:07 ./usr/share/doc/
drwxr-xr-x root/root 0 2018-12-13 07:07 ./usr/share/doc/tvc/
-rw-r--r-- root/root 1078 2018-12-13 07:07 ./usr/share/doc/tvc/README.Debian
-rw-r--r-- root/root 1047 2018-12-13 07:07 ./usr/share/doc/tvc/changelog.Debian.gz
-rw-r--r-- root/root 2939 2018-12-13 07:07 ./usr/share/doc/tvc/copyright
drwxr-xr-x root/root 0 2018-12-13 07:07 ./usr/share/lintian/
drwxr-xr-x root/root 0 2018-12-13 07:07 ./usr/share/lintian/overrides/
-rw-r--r-- root/root 135 2018-12-13 07:07 ./usr/share/lintian/overrides/tvc
+------------------------------------------------------------------------------+
| Post Build |
+------------------------------------------------------------------------------+
+------------------------------------------------------------------------------+
| Cleanup |
+------------------------------------------------------------------------------+
Purging /<<BUILDDIR>>
Not cleaning session: cloned chroot in use
+------------------------------------------------------------------------------+
| Summary |
+------------------------------------------------------------------------------+
Build Architecture: armhf
Build-Space: 146700
Build-Time: 764
Distribution: buster-staging
Host Architecture: armhf
Install-Time: 626
Job: tvc_5.0.3+git20151221.80e144e+dfsg-2
Machine Architecture: armhf
Package: tvc
Package-Time: 1447
Source-Version: 5.0.3+git20151221.80e144e+dfsg-2
Space: 146700
Status: successful
Version: 5.0.3+git20151221.80e144e+dfsg-2
--------------------------------------------------------------------------------
Finished at 2018-12-18T05:49:02Z
Build needed 00:24:07, 146700k disc space