tvc →
5.0.3+git20151221.80e144e+dfsg-3 →
armhf → 2020-03-06 11:28:08
sbuild (Debian sbuild) 0.71.0 (24 Aug 2016) on bm-wb-04
+==============================================================================+
| tvc 5.0.3+git20151221.80e144e+dfsg-3 (armhf) Fri, 06 Mar 2020 11:01:21 +0000 |
+==============================================================================+
Package: tvc
Version: 5.0.3+git20151221.80e144e+dfsg-3
Source Version: 5.0.3+git20151221.80e144e+dfsg-3
Distribution: bullseye-staging
Machine Architecture: armhf
Host Architecture: armhf
Build Architecture: armhf
I: NOTICE: Log filtering will replace 'var/lib/schroot/mount/bullseye-staging-armhf-sbuild-4d977767-0071-4978-8e02-e23fab1dc4aa' with '<<CHROOT>>'
+------------------------------------------------------------------------------+
| Update chroot |
+------------------------------------------------------------------------------+
Get:1 http://172.17.0.1/private bullseye-staging InRelease [11.3 kB]
Get:2 http://172.17.0.1/private bullseye-staging/main Sources [11.6 MB]
Get:3 http://172.17.0.1/private bullseye-staging/main armhf Packages [12.8 MB]
Fetched 24.4 MB in 26s (942 kB/s)
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
+------------------------------------------------------------------------------+
| Fetch source files |
+------------------------------------------------------------------------------+
Check APT
---------
Checking available source versions...
Download source files with APT
------------------------------
Reading package lists...
NOTICE: 'tvc' packaging is maintained in the 'Git' version control system at:
https://salsa.debian.org/med-team/tvc.git
Please use:
git clone https://salsa.debian.org/med-team/tvc.git
to retrieve the latest (possibly unreleased) updates to the package.
Need to get 756 kB of source archives.
Get:1 http://172.17.0.1/private bullseye-staging/main tvc 5.0.3+git20151221.80e144e+dfsg-3 (dsc) [2200 B]
Get:2 http://172.17.0.1/private bullseye-staging/main tvc 5.0.3+git20151221.80e144e+dfsg-3 (tar) [745 kB]
Get:3 http://172.17.0.1/private bullseye-staging/main tvc 5.0.3+git20151221.80e144e+dfsg-3 (diff) [8968 B]
Fetched 756 kB in 0s (4837 kB/s)
Download complete and in download only mode
I: NOTICE: Log filtering will replace 'build/tvc-DDETIG/tvc-5.0.3+git20151221.80e144e+dfsg' with '<<PKGBUILDDIR>>'
I: NOTICE: Log filtering will replace 'build/tvc-DDETIG' 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-sxIOHP/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-sxIOHP/gpg/pubring.kbx' created
gpg: /<<BUILDDIR>>/resolver-sxIOHP/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-sxIOHP/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-sxIOHP/apt_archive ./ Release [957 B]
Get:3 copy:/<<BUILDDIR>>/resolver-sxIOHP/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-sxIOHP/apt_archive ./ Sources [349 B]
Get:5 copy:/<<BUILDDIR>>/resolver-sxIOHP/apt_archive ./ Packages [431 B]
Fetched 2107 B in 1s (2699 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:
libpam-cap netbase
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 27 not upgraded.
Need to get 852 B of archives.
After this operation, 0 B of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-sxIOHP/apt_archive ./ sbuild-build-depends-core-dummy 0.invalid.0 [852 B]
debconf: delaying package configuration, since apt-utils is not installed
Fetched 852 B in 0s (0 B/s)
Selecting previously unselected package sbuild-build-depends-core-dummy.
(Reading database ... 12215 files and directories currently installed.)
Preparing to unpack .../sbuild-build-depends-core-dummy_0.invalid.0_armhf.deb ...
Unpacking sbuild-build-depends-core-dummy (0.invalid.0) ...
Setting up sbuild-build-depends-core-dummy (0.invalid.0) ...
W: No sandbox user '_apt' on the system, can not drop privileges
+------------------------------------------------------------------------------+
| Check architectures |
+------------------------------------------------------------------------------+
Arch check ok (armhf included in any)
+------------------------------------------------------------------------------+
| Install package build dependencies |
+------------------------------------------------------------------------------+
Setup apt archive
-----------------
Merged Build-Depends: debhelper-compat (= 12), cmake, libbamtools-dev, libjsoncpp-dev, libarmadillo-dev, libboost-math-dev, libsmithwaterman-dev
Filtered Build-Depends: debhelper-compat (= 12), cmake, libbamtools-dev, libjsoncpp-dev, libarmadillo-dev, libboost-math-dev, libsmithwaterman-dev
dpkg-deb: building package 'sbuild-build-depends-tvc-dummy' in '/<<BUILDDIR>>/resolver-sxIOHP/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-sxIOHP/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-sxIOHP/apt_archive ./ Release [963 B]
Get:3 copy:/<<BUILDDIR>>/resolver-sxIOHP/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-sxIOHP/apt_archive ./ Sources [535 B]
Get:5 copy:/<<BUILDDIR>>/resolver-sxIOHP/apt_archive ./ Packages [619 B]
Fetched 2487 B in 1s (3324 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:
libpam-cap netbase
Use 'apt autoremove' to remove them.
The following additional packages will be installed:
autoconf automake autopoint autotools-dev bsdmainutils cmake cmake-data
debhelper dh-autoreconf dh-strip-nondeterminism dwz file gcc-10-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
libbrotli1 libbsd0 libcroco3 libcurl4 libdebhelper-perl libdisorder-dev
libdisorder0 libelf1 libexpat1 libfile-stripnondeterminism-perl libgcc-s1
libgfortran5 libglib2.0-0 libgssapi-krb5-2 libhdf5-103 libhdf5-cpp-103
libhdf5-dev libicu63 libjpeg-dev libjpeg62-turbo libjpeg62-turbo-dev
libjsoncpp-dev libjsoncpp1 libk5crypto3 libkeyutils1 libkrb5-3
libkrb5support0 liblapack-dev liblapack3 libmagic-mgc libmagic1 libncurses6
libncursesw6 libnghttp2-14 libpipeline1 libprocps7 libpsl5 librhash0
librtmp1 libsigsegv2 libsmithwaterman-dev libsmithwaterman0 libssh2-1
libssl1.1 libsub-override-perl libsuperlu-dev libsuperlu5 libsz2 libtinfo5
libtinfo6 libtool libuchardet0 libuv1 libxml2 m4 man-db ncurses-bin
po-debconf procps sensible-utils zlib1g-dev
Suggested packages:
autoconf-archive gnu-standards autoconf-doc wamerican | wordlist whois
vacation cmake-doc ninja-build dh-make 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-contract1.67-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
krb5-doc krb5-user libhdf5-doc libsuperlu-doc libtool-doc gfortran
| fortran95-compiler gcj-jdk m4-doc apparmor less www-browser
libmail-box-perl
Recommended packages:
curl | wget | lynx ca-certificates libarchive-cpio-perl libglib2.0-data
shared-mime-info xdg-user-dirs krb5-locales libgpm2 publicsuffix libltdl-dev
libmail-sendmail-perl psmisc
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-10-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
libbrotli1 libbsd0 libcroco3 libcurl4 libdebhelper-perl libdisorder-dev
libdisorder0 libelf1 libexpat1 libfile-stripnondeterminism-perl libgcc-s1
libgfortran5 libglib2.0-0 libgssapi-krb5-2 libhdf5-103 libhdf5-cpp-103
libhdf5-dev libicu63 libjpeg-dev libjpeg62-turbo libjpeg62-turbo-dev
libjsoncpp-dev libjsoncpp1 libk5crypto3 libkeyutils1 libkrb5-3
libkrb5support0 liblapack-dev liblapack3 libmagic-mgc libmagic1 libncurses6
libnghttp2-14 libpipeline1 libprocps7 libpsl5 librhash0 librtmp1 libsigsegv2
libsmithwaterman-dev libsmithwaterman0 libssh2-1 libssl1.1
libsub-override-perl libsuperlu-dev libsuperlu5 libsz2 libtinfo5 libtool
libuchardet0 libuv1 libxml2 m4 man-db po-debconf procps
sbuild-build-depends-tvc-dummy sensible-utils zlib1g-dev
The following packages will be upgraded:
libncursesw6 libtinfo6 ncurses-bin
3 upgraded, 93 newly installed, 0 to remove and 24 not upgraded.
Need to get 47.4 MB of archives.
After this operation, 288 MB of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-sxIOHP/apt_archive ./ sbuild-build-depends-tvc-dummy 0.invalid.0 [904 B]
Get:2 http://172.17.0.1/private bullseye-staging/main armhf libtinfo6 armhf 6.2-1 [321 kB]
Get:3 http://172.17.0.1/private bullseye-staging/main armhf ncurses-bin armhf 6.2-1 [414 kB]
Get:4 http://172.17.0.1/private bullseye-staging/main armhf libncursesw6 armhf 6.2-1 [104 kB]
Get:5 http://172.17.0.1/private bullseye-staging/main armhf libbsd0 armhf 0.10.0-1 [112 kB]
Get:6 http://172.17.0.1/private bullseye-staging/main armhf libtinfo5 armhf 6.2-1 [318 kB]
Get:7 http://172.17.0.1/private bullseye-staging/main armhf bsdmainutils armhf 11.1.2 [182 kB]
Get:8 http://172.17.0.1/private bullseye-staging/main armhf gcc-10-base armhf 10-20200222-1+rpi1 [196 kB]
Get:9 http://172.17.0.1/private bullseye-staging/main armhf libgcc-s1 armhf 10-20200222-1+rpi1 [36.1 kB]
Get:10 http://172.17.0.1/private bullseye-staging/main armhf libuchardet0 armhf 0.0.6-3 [62.2 kB]
Get:11 http://172.17.0.1/private bullseye-staging/main armhf groff-base armhf 1.22.4-4 [783 kB]
Get:12 http://172.17.0.1/private bullseye-staging/main armhf libpipeline1 armhf 1.5.2-2 [29.6 kB]
Get:13 http://172.17.0.1/private bullseye-staging/main armhf man-db armhf 2.9.1-1 [1262 kB]
Get:14 http://172.17.0.1/private bullseye-staging/main armhf libncurses6 armhf 6.2-1 [79.5 kB]
Get:15 http://172.17.0.1/private bullseye-staging/main armhf libprocps7 armhf 2:3.3.15-2 [58.9 kB]
Get:16 http://172.17.0.1/private bullseye-staging/main armhf procps armhf 2:3.3.15-2 [235 kB]
Get:17 http://172.17.0.1/private bullseye-staging/main armhf sensible-utils all 0.0.12+nmu1 [16.0 kB]
Get:18 http://172.17.0.1/private bullseye-staging/main armhf libmagic-mgc armhf 1:5.38-4 [262 kB]
Get:19 http://172.17.0.1/private bullseye-staging/main armhf libmagic1 armhf 1:5.38-4 [112 kB]
Get:20 http://172.17.0.1/private bullseye-staging/main armhf file armhf 1:5.38-4 [66.9 kB]
Get:21 http://172.17.0.1/private bullseye-staging/main armhf gettext-base armhf 0.19.8.1-10 [117 kB]
Get:22 http://172.17.0.1/private bullseye-staging/main armhf libsigsegv2 armhf 2.12-2 [32.3 kB]
Get:23 http://172.17.0.1/private bullseye-staging/main armhf m4 armhf 1.4.18-4 [185 kB]
Get:24 http://172.17.0.1/private bullseye-staging/main armhf autoconf all 2.69-11.1 [341 kB]
Get:25 http://172.17.0.1/private bullseye-staging/main armhf autotools-dev all 20180224.1 [77.0 kB]
Get:26 http://172.17.0.1/private bullseye-staging/main armhf automake all 1:1.16.1-4 [771 kB]
Get:27 http://172.17.0.1/private bullseye-staging/main armhf autopoint all 0.19.8.1-10 [435 kB]
Get:28 http://172.17.0.1/private bullseye-staging/main armhf cmake-data all 3.16.3-1 [1628 kB]
Get:29 http://172.17.0.1/private bullseye-staging/main armhf libicu63 armhf 63.2-2 [7974 kB]
Get:30 http://172.17.0.1/private bullseye-staging/main armhf libxml2 armhf 2.9.4+dfsg1-8 [593 kB]
Get:31 http://172.17.0.1/private bullseye-staging/main armhf libarchive13 armhf 3.4.0-1+b1 [292 kB]
Get:32 http://172.17.0.1/private bullseye-staging/main armhf libbrotli1 armhf 1.0.7-6 [261 kB]
Get:33 http://172.17.0.1/private bullseye-staging/main armhf libkeyutils1 armhf 1.6.1-2 [14.5 kB]
Get:34 http://172.17.0.1/private bullseye-staging/main armhf libkrb5support0 armhf 1.17-6+b1 [61.5 kB]
Get:35 http://172.17.0.1/private bullseye-staging/main armhf libk5crypto3 armhf 1.17-6+b1 [112 kB]
Get:36 http://172.17.0.1/private bullseye-staging/main armhf libssl1.1 armhf 1.1.1d-2 [1268 kB]
Get:37 http://172.17.0.1/private bullseye-staging/main armhf libkrb5-3 armhf 1.17-6+b1 [316 kB]
Get:38 http://172.17.0.1/private bullseye-staging/main armhf libgssapi-krb5-2 armhf 1.17-6+b1 [134 kB]
Get:39 http://172.17.0.1/private bullseye-staging/main armhf libnghttp2-14 armhf 1.40.0-1+b2 [74.2 kB]
Get:40 http://172.17.0.1/private bullseye-staging/main armhf libpsl5 armhf 0.20.2-2 [52.6 kB]
Get:41 http://172.17.0.1/private bullseye-staging/main armhf librtmp1 armhf 2.4+20151223.gitfa8646d.1-2+b1 [54.3 kB]
Get:42 http://172.17.0.1/private bullseye-staging/main armhf libssh2-1 armhf 1.8.0-2.1 [126 kB]
Get:43 http://172.17.0.1/private bullseye-staging/main armhf libcurl4 armhf 7.68.0-1 [286 kB]
Get:44 http://172.17.0.1/private bullseye-staging/main armhf libexpat1 armhf 2.2.9-1 [71.5 kB]
Get:45 http://172.17.0.1/private bullseye-staging/main armhf libjsoncpp1 armhf 1.7.4-3.1 [65.8 kB]
Get:46 http://172.17.0.1/private bullseye-staging/main armhf librhash0 armhf 1.3.9-1 [133 kB]
Get:47 http://172.17.0.1/private bullseye-staging/main armhf libuv1 armhf 1.34.2-1 [114 kB]
Get:48 http://172.17.0.1/private bullseye-staging/main armhf cmake armhf 3.16.3-1 [2648 kB]
Get:49 http://172.17.0.1/private bullseye-staging/main armhf libtool all 2.4.6-13 [513 kB]
Get:50 http://172.17.0.1/private bullseye-staging/main armhf dh-autoreconf all 19 [16.9 kB]
Get:51 http://172.17.0.1/private bullseye-staging/main armhf libdebhelper-perl all 12.9 [183 kB]
Get:52 http://172.17.0.1/private bullseye-staging/main armhf libarchive-zip-perl all 1.67-2 [104 kB]
Get:53 http://172.17.0.1/private bullseye-staging/main armhf libsub-override-perl all 0.09-2 [10.2 kB]
Get:54 http://172.17.0.1/private bullseye-staging/main armhf libfile-stripnondeterminism-perl all 1.6.3-2 [23.7 kB]
Get:55 http://172.17.0.1/private bullseye-staging/main armhf dh-strip-nondeterminism all 1.6.3-2 [14.7 kB]
Get:56 http://172.17.0.1/private bullseye-staging/main armhf libelf1 armhf 0.176-1.1 [158 kB]
Get:57 http://172.17.0.1/private bullseye-staging/main armhf dwz armhf 0.13-5 [142 kB]
Get:58 http://172.17.0.1/private bullseye-staging/main armhf libglib2.0-0 armhf 2.62.5-1 [1140 kB]
Get:59 http://172.17.0.1/private bullseye-staging/main armhf libcroco3 armhf 0.6.13-1 [133 kB]
Get:60 http://172.17.0.1/private bullseye-staging/main armhf gettext armhf 0.19.8.1-10 [1219 kB]
Get:61 http://172.17.0.1/private bullseye-staging/main armhf intltool-debian all 0.35.0+20060710.5 [26.8 kB]
Get:62 http://172.17.0.1/private bullseye-staging/main armhf po-debconf all 1.0.21 [248 kB]
Get:63 http://172.17.0.1/private bullseye-staging/main armhf debhelper all 12.9 [994 kB]
Get:64 http://172.17.0.1/private bullseye-staging/main armhf hdf5-helpers armhf 1.10.4+repack-11 [35.3 kB]
Get:65 http://172.17.0.1/private bullseye-staging/main armhf libaec0 armhf 1.0.4-1 [20.0 kB]
Get:66 http://172.17.0.1/private bullseye-staging/main armhf libsz2 armhf 1.0.4-1 [6664 B]
Get:67 http://172.17.0.1/private bullseye-staging/main armhf libaec-dev armhf 1.0.4-1 [17.8 kB]
Get:68 http://172.17.0.1/private bullseye-staging/main armhf libblas3 armhf 3.9.0-1 [108 kB]
Get:69 http://172.17.0.1/private bullseye-staging/main armhf libgfortran5 armhf 10-20200222-1+rpi1 [229 kB]
Get:70 http://172.17.0.1/private bullseye-staging/main armhf liblapack3 armhf 3.9.0-1 [1597 kB]
Get:71 http://172.17.0.1/private bullseye-staging/main armhf libarpack2 armhf 3.7.0-3 [85.7 kB]
Get:72 http://172.17.0.1/private bullseye-staging/main armhf libsuperlu5 armhf 5.2.1+dfsg1-4 [126 kB]
Get:73 http://172.17.0.1/private bullseye-staging/main armhf libarmadillo9 armhf 1:9.800.4+dfsg-1 [93.4 kB]
Get:74 http://172.17.0.1/private bullseye-staging/main armhf libblas-dev armhf 3.9.0-1 [113 kB]
Get:75 http://172.17.0.1/private bullseye-staging/main armhf liblapack-dev armhf 3.9.0-1 [2981 kB]
Get:76 http://172.17.0.1/private bullseye-staging/main armhf libarpack2-dev armhf 3.7.0-3 [96.2 kB]
Get:77 http://172.17.0.1/private bullseye-staging/main armhf libhdf5-103 armhf 1.10.4+repack-11 [1280 kB]
Get:78 http://172.17.0.1/private bullseye-staging/main armhf zlib1g-dev armhf 1:1.2.11.dfsg-1.2 [203 kB]
Get:79 http://172.17.0.1/private bullseye-staging/main armhf libjpeg62-turbo armhf 1:1.5.2-2+b1 [110 kB]
Get:80 http://172.17.0.1/private bullseye-staging/main armhf libjpeg62-turbo-dev armhf 1:1.5.2-2+b1 [179 kB]
Get:81 http://172.17.0.1/private bullseye-staging/main armhf libjpeg-dev all 1:1.5.2-2 [57.5 kB]
Get:82 http://172.17.0.1/private bullseye-staging/main armhf libhdf5-cpp-103 armhf 1.10.4+repack-11 [126 kB]
Get:83 http://172.17.0.1/private bullseye-staging/main armhf libhdf5-dev armhf 1.10.4+repack-11 [2235 kB]
Get:84 http://172.17.0.1/private bullseye-staging/main armhf libsuperlu-dev armhf 5.2.1+dfsg1-4 [18.4 kB]
Get:85 http://172.17.0.1/private bullseye-staging/main armhf libarmadillo-dev armhf 1:9.800.4+dfsg-1 [379 kB]
Get:86 http://172.17.0.1/private bullseye-staging/main armhf libbamtools2.5.1 armhf 2.5.1+dfsg-5 [132 kB]
Get:87 http://172.17.0.1/private bullseye-staging/main armhf libbamtools-dev armhf 2.5.1+dfsg-5 [22.1 kB]
Get:88 http://172.17.0.1/private bullseye-staging/main armhf libboost1.67-dev armhf 1.67.0-17 [8389 kB]
Get:89 http://172.17.0.1/private bullseye-staging/main armhf libboost-math1.67.0 armhf 1.67.0-17 [321 kB]
Get:90 http://172.17.0.1/private bullseye-staging/main armhf libboost-math1.67-dev armhf 1.67.0-17 [463 kB]
Get:91 http://172.17.0.1/private bullseye-staging/main armhf libboost-math-dev armhf 1.67.0.2+b11 [4452 B]
Get:92 http://172.17.0.1/private bullseye-staging/main armhf libdisorder0 armhf 0.0.2+git20130809.8062ee1-1 [4568 B]
Get:93 http://172.17.0.1/private bullseye-staging/main armhf libdisorder-dev armhf 0.0.2+git20130809.8062ee1-1 [4156 B]
Get:94 http://172.17.0.1/private bullseye-staging/main armhf libsmithwaterman0 armhf 0.0+git20160702.2610e25-7 [30.5 kB]
Get:95 http://172.17.0.1/private bullseye-staging/main armhf libsmithwaterman-dev armhf 0.0+git20160702.2610e25-7 [34.3 kB]
Get:96 http://172.17.0.1/private bullseye-staging/main armhf libjsoncpp-dev armhf 1.7.4-3.1 [81.0 kB]
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Setting up autopoint (0.19.8.1-10) ...
Setting up libk5crypto3:armhf (1.17-6+b1) ...
Setting up libdisorder-dev:armhf (0.0.2+git20130809.8062ee1-1) ...
Setting up zlib1g-dev:armhf (1:1.2.11.dfsg-1.2) ...
Setting up sensible-utils (0.0.12+nmu1) ...
Setting up librhash0:armhf (1.3.9-1) ...
Setting up libuchardet0:armhf (0.0.6-3) ...
Setting up procps (2:3.3.15-2) ...
update-alternatives: using /usr/bin/w.procps to provide /usr/bin/w (w) in auto mode
Setting up libsub-override-perl (0.09-2) ...
Setting up libssh2-1:armhf (1.8.0-2.1) ...
Setting up cmake-data (3.16.3-1) ...
Setting up libkrb5-3:armhf (1.17-6+b1) ...
Setting up libbsd0:armhf (0.10.0-1) ...
Setting up libtinfo5:armhf (6.2-1) ...
Setting up libelf1:armhf (0.176-1.1) ...
Setting up libxml2:armhf (2.9.4+dfsg1-8) ...
Setting up libblas-dev:armhf (3.9.0-1) ...
update-alternatives: using /usr/lib/arm-linux-gnueabihf/blas/libblas.so to provide /usr/lib/arm-linux-gnueabihf/libblas.so (libblas.so-arm-linux-gnueabihf) in auto mode
Setting up libsz2:armhf (1.0.4-1) ...
Setting up libjsoncpp1:armhf (1.7.4-3.1) ...
Setting up libfile-stripnondeterminism-perl (1.6.3-2) ...
Setting up libjsoncpp-dev:armhf (1.7.4-3.1) ...
Setting up libboost-math1.67-dev:armhf (1.67.0-17) ...
Setting up libtool (2.4.6-13) ...
Setting up libarchive13:armhf (3.4.0-1+b1) ...
Setting up libboost-math-dev:armhf (1.67.0.2+b11) ...
Setting up libaec-dev:armhf (1.0.4-1) ...
Setting up libjpeg-dev (1:1.5.2-2) ...
Setting up libsuperlu5:armhf (5.2.1+dfsg1-4) ...
Setting up m4 (1.4.18-4) ...
Setting up libgcc-s1:armhf (10-20200222-1+rpi1) ...
Setting up libbamtools-dev:armhf (2.5.1+dfsg-5) ...
Setting up bsdmainutils (11.1.2) ...
update-alternatives: using /usr/bin/bsd-write to provide /usr/bin/write (write) in auto mode
update-alternatives: using /usr/bin/bsd-from to provide /usr/bin/from (from) in auto mode
Setting up libgssapi-krb5-2:armhf (1.17-6+b1) ...
Setting up libcroco3:armhf (0.6.13-1) ...
Setting up libsmithwaterman-dev (0.0+git20160702.2610e25-7) ...
Setting up libgfortran5:armhf (10-20200222-1+rpi1) ...
Setting up autoconf (2.69-11.1) ...
Setting up dh-strip-nondeterminism (1.6.3-2) ...
Setting up dwz (0.13-5) ...
Setting up groff-base (1.22.4-4) ...
Setting up libcurl4:armhf (7.68.0-1) ...
Setting up libsuperlu-dev:armhf (5.2.1+dfsg1-4) ...
Setting up automake (1:1.16.1-4) ...
update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode
Setting up liblapack3:armhf (3.9.0-1) ...
update-alternatives: using /usr/lib/arm-linux-gnueabihf/lapack/liblapack.so.3 to provide /usr/lib/arm-linux-gnueabihf/liblapack.so.3 (liblapack.so.3-arm-linux-gnueabihf) in auto mode
Setting up gettext (0.19.8.1-10) ...
Setting up libarpack2:armhf (3.7.0-3) ...
Setting up man-db (2.9.1-1) ...
Not building database; man-db/auto-update is not 'true'.
Setting up intltool-debian (0.35.0+20060710.5) ...
Setting up libhdf5-103:armhf (1.10.4+repack-11) ...
Setting up liblapack-dev:armhf (3.9.0-1) ...
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 cmake (3.16.3-1) ...
Setting up libarmadillo9 (1:9.800.4+dfsg-1) ...
Setting up libarpack2-dev:armhf (3.7.0-3) ...
Setting up po-debconf (1.0.21) ...
Setting up libhdf5-cpp-103:armhf (1.10.4+repack-11) ...
Setting up libhdf5-dev (1.10.4+repack-11) ...
update-alternatives: using /usr/lib/arm-linux-gnueabihf/pkgconfig/hdf5-serial.pc to provide /usr/lib/arm-linux-gnueabihf/pkgconfig/hdf5.pc (hdf5.pc) in auto mode
Setting up libarmadillo-dev (1:9.800.4+dfsg-1) ...
Setting up dh-autoreconf (19) ...
Setting up debhelper (12.9) ...
Setting up sbuild-build-depends-tvc-dummy (0.invalid.0) ...
Processing triggers for libc-bin (2.29-10+rpi1) ...
W: No sandbox user '_apt' on the system, can not drop privileges
+------------------------------------------------------------------------------+
| Build environment |
+------------------------------------------------------------------------------+
Kernel: Linux 4.9.0-0.bpo.4-armmp armhf (armv7l)
Toolchain package versions: binutils_2.34-3+rpi1 dpkg-dev_1.19.7 g++-9_9.2.1-25+rpi1 gcc-9_9.2.1-25+rpi1 libc6-dev_2.29-10+rpi1 libstdc++-9-dev_9.2.1-25+rpi1 libstdc++6_9.2.1-25+rpi1 linux-libc-dev_5.2.17-1+rpi1+b2
Package versions: adduser_3.118 apt_1.8.4+b1 autoconf_2.69-11.1 automake_1:1.16.1-4 autopoint_0.19.8.1-10 autotools-dev_20180224.1 base-files_11+rpi1 base-passwd_3.5.47 bash_5.0-6 binutils_2.34-3+rpi1 binutils-arm-linux-gnueabihf_2.34-3+rpi1 binutils-common_2.34-3+rpi1 bsdmainutils_11.1.2 bsdutils_1:2.34-0.1 build-essential_12.8 bzip2_1.0.8-2 cmake_3.16.3-1 cmake-data_3.16.3-1 coreutils_8.30-3 cpp_4:9.2.1-3.1+rpi1 cpp-9_9.2.1-25+rpi1 dash_0.5.10.2-6 debconf_1.5.73 debhelper_12.9 debianutils_4.9.1 dh-autoreconf_19 dh-strip-nondeterminism_1.6.3-2 diffutils_1:3.7-3 dirmngr_2.2.19-2 dpkg_1.19.7 dpkg-dev_1.19.7 dwz_0.13-5 e2fsprogs_1.45.5-2 fakeroot_1.24-1 fdisk_2.34-0.1 file_1:5.38-4 findutils_4.7.0-1 g++_4:9.2.1-3.1+rpi1 g++-9_9.2.1-25+rpi1 gcc_4:9.2.1-3.1+rpi1 gcc-10-base_10-20200222-1+rpi1 gcc-9_9.2.1-25+rpi1 gcc-9-base_9.2.1-25+rpi1 gettext_0.19.8.1-10 gettext-base_0.19.8.1-10 gnupg_2.2.19-2 gnupg-l10n_2.2.19-2 gnupg-utils_2.2.19-2 gpg_2.2.19-2 gpg-agent_2.2.19-2 gpg-wks-client_2.2.19-2 gpg-wks-server_2.2.19-2 gpgconf_2.2.19-2 gpgsm_2.2.19-2 gpgv_2.2.19-2 grep_3.4-1 groff-base_1.22.4-4 gzip_1.10-1 hdf5-helpers_1.10.4+repack-11 hostname_3.23 init-system-helpers_1.57 intltool-debian_0.35.0+20060710.5 iputils-ping_3:20190709-3 libacl1_2.2.53-5 libaec-dev_1.0.4-1 libaec0_1.0.4-1 libapt-pkg5.0_1.8.4+b1 libarchive-zip-perl_1.67-2 libarchive13_3.4.0-1+b1 libarmadillo-dev_1:9.800.4+dfsg-1 libarmadillo9_1:9.800.4+dfsg-1 libarpack2_3.7.0-3 libarpack2-dev_3.7.0-3 libasan5_9.2.1-25+rpi1 libassuan0_2.5.3-7 libatomic1_9.2.1-25+rpi1 libattr1_1:2.4.48-5 libaudit-common_1:2.8.5-2 libaudit1_1:2.8.5-2+b1 libbamtools-dev_2.5.1+dfsg-5 libbamtools2.5.1_2.5.1+dfsg-5 libbinutils_2.34-3+rpi1 libblas-dev_3.9.0-1 libblas3_3.9.0-1 libblkid1_2.34-0.1 libboost-math-dev_1.67.0.2+b11 libboost-math1.67-dev_1.67.0-17 libboost-math1.67.0_1.67.0-17 libboost1.67-dev_1.67.0-17 libbrotli1_1.0.7-6 libbsd0_0.10.0-1 libbz2-1.0_1.0.8-2 libc-bin_2.29-10+rpi1 libc-dev-bin_2.29-10+rpi1 libc6_2.29-10+rpi1 libc6-dev_2.29-10+rpi1 libcap-ng0_0.7.9-2.1 libcap2_1:2.32-1 libcap2-bin_1:2.32-1 libcc1-0_9.2.1-25+rpi1 libcom-err2_1.45.5-2 libcroco3_0.6.13-1 libcrypt-dev_1:4.4.10-10+b5 libcrypt1_1:4.4.10-10+b5 libctf-nobfd0_2.34-3+rpi1 libctf0_2.34-3+rpi1 libcurl4_7.68.0-1 libdb5.3_5.3.28+dfsg1-0.6 libdebconfclient0_0.251 libdebhelper-perl_12.9 libdisorder-dev_0.0.2+git20130809.8062ee1-1 libdisorder0_0.0.2+git20130809.8062ee1-1 libdpkg-perl_1.19.7 libelf1_0.176-1.1 libexpat1_2.2.9-1 libext2fs2_1.45.5-2 libfakeroot_1.24-1 libfdisk1_2.34-0.1 libffi7_3.3-3 libfile-stripnondeterminism-perl_1.6.3-2 libgcc-9-dev_9.2.1-25+rpi1 libgcc-s1_10-20200222-1+rpi1 libgcc1_1:9.2.1-25+rpi1 libgcrypt20_1.8.5-3 libgdbm-compat4_1.18.1-5 libgdbm6_1.18.1-5 libgfortran5_10-20200222-1+rpi1 libglib2.0-0_2.62.5-1 libgmp10_2:6.2.0+dfsg-4 libgnutls30_3.6.12-2 libgomp1_9.2.1-25+rpi1 libgpg-error0_1.37-1 libgssapi-krb5-2_1.17-6+b1 libhdf5-103_1.10.4+repack-11 libhdf5-cpp-103_1.10.4+repack-11 libhdf5-dev_1.10.4+repack-11 libhogweed5_3.5.1+really3.5.1-2 libicu63_63.2-2 libidn2-0_2.2.0-2 libisl22_0.22.1-1 libjpeg-dev_1:1.5.2-2 libjpeg62-turbo_1:1.5.2-2+b1 libjpeg62-turbo-dev_1:1.5.2-2+b1 libjsoncpp-dev_1.7.4-3.1 libjsoncpp1_1.7.4-3.1 libk5crypto3_1.17-6+b1 libkeyutils1_1.6.1-2 libkrb5-3_1.17-6+b1 libkrb5support0_1.17-6+b1 libksba8_1.3.5-2 liblapack-dev_3.9.0-1 liblapack3_3.9.0-1 libldap-2.4-2_2.4.49+dfsg-1+rpi1 libldap-common_2.4.49+dfsg-1+rpi1 liblz4-1_1.9.2-2 liblzma5_5.2.4-1 libmagic-mgc_1:5.38-4 libmagic1_1:5.38-4 libmount1_2.34-0.1 libmpc3_1.1.0-1 libmpfr6_4.0.2-1 libncurses6_6.2-1 libncursesw6_6.2-1 libnettle7_3.5.1+really3.5.1-2 libnghttp2-14_1.40.0-1+b2 libnpth0_1.6-1 libp11-kit0_0.23.20-1 libpam-cap_1:2.32-1 libpam-modules_1.3.1-5 libpam-modules-bin_1.3.1-5 libpam-runtime_1.3.1-5 libpam0g_1.3.1-5 libpcre2-8-0_10.34-7 libpcre3_2:8.39-12 libperl5.30_5.30.0-9 libpipeline1_1.5.2-2 libprocps7_2:3.3.15-2 libpsl5_0.20.2-2 libreadline7_7.0-5 libreadline8_8.0-4 librhash0_1.3.9-1 librtmp1_2.4+20151223.gitfa8646d.1-2+b1 libsasl2-2_2.1.27+dfsg-2 libsasl2-modules-db_2.1.27+dfsg-2 libseccomp2_2.4.2-2+rpi1 libselinux1_3.0-1 libsemanage-common_3.0-1 libsemanage1_3.0-1 libsepol1_3.0-1 libsigsegv2_2.12-2 libsmartcols1_2.34-0.1 libsmithwaterman-dev_0.0+git20160702.2610e25-7 libsmithwaterman0_0.0+git20160702.2610e25-7 libsqlite3-0_3.31.1-3 libss2_1.45.5-2 libssh2-1_1.8.0-2.1 libssl1.1_1.1.1d-2 libstdc++-9-dev_9.2.1-25+rpi1 libstdc++6_9.2.1-25+rpi1 libsub-override-perl_0.09-2 libsuperlu-dev_5.2.1+dfsg1-4 libsuperlu5_5.2.1+dfsg1-4 libsystemd0_244.3-1+rpi1 libsz2_1.0.4-1 libtasn1-6_4.16.0-2 libtinfo5_6.2-1 libtinfo6_6.2-1 libtool_2.4.6-13 libubsan1_9.2.1-25+rpi1 libuchardet0_0.0.6-3 libudev1_244.3-1+rpi1 libunistring2_0.9.10-2 libuuid1_2.34-0.1 libuv1_1.34.2-1 libxml2_2.9.4+dfsg1-8 libzstd1_1.4.4+dfsg-3+rpi1 linux-libc-dev_5.2.17-1+rpi1+b2 login_1:4.8.1-1 logsave_1.45.5-2 lsb-base_11.1.0+rpi1 m4_1.4.18-4 make_4.2.1-1.2 man-db_2.9.1-1 mawk_1.3.4.20200120-2 mount_2.34-0.1 ncurses-base_6.1+20191019-1 ncurses-bin_6.2-1 netbase_6.1 passwd_1:4.8.1-1 patch_2.7.6-6 perl_5.30.0-9 perl-base_5.30.0-9 perl-modules-5.30_5.30.0-9 pinentry-curses_1.1.0-3 po-debconf_1.0.21 procps_2:3.3.15-2 raspbian-archive-keyring_20120528.2 readline-common_8.0-4 sbuild-build-depends-core-dummy_0.invalid.0 sbuild-build-depends-tvc-dummy_0.invalid.0 sed_4.7-1 sensible-utils_0.0.12+nmu1 sysvinit-utils_2.96-2.1 tar_1.30+dfsg-6 tzdata_2019c-3 util-linux_2.34-0.1 xz-utils_5.2.4-1 zlib1g_1:1.2.11.dfsg-1.2 zlib1g-dev_1:1.2.11.dfsg-1.2
+------------------------------------------------------------------------------+
| Build |
+------------------------------------------------------------------------------+
Unpack source
-------------
gpgv: unknown type of key resource 'trustedkeys.kbx'
gpgv: keyblock resource '/sbuild-nonexistent/.gnupg/trustedkeys.kbx': General error
gpgv: Signature made Sun Mar 1 05:51:37 2020 UTC
gpgv: using RSA key 90E2D2C1AD146A1B7EBB891DBBC17EBB1396F2F7
gpgv: issuer "stuart@debian.org"
gpgv: Can't check signature: No public key
dpkg-source: warning: failed to verify signature on ./tvc_5.0.3+git20151221.80e144e+dfsg-3.dsc
dpkg-source: info: extracting tvc in /<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg
dpkg-source: info: unpacking tvc_5.0.3+git20151221.80e144e+dfsg.orig.tar.xz
dpkg-source: info: unpacking tvc_5.0.3+git20151221.80e144e+dfsg-3.debian.tar.xz
dpkg-source: info: using patch list from debian/patches/series
dpkg-source: info: applying cmake.patch
dpkg-source: info: applying bamtools.patch
dpkg-source: info: applying help.patch
dpkg-source: info: applying hurd.patch
dpkg-source: info: applying sse.patch
dpkg-source: info: applying use_debian_packaged_smithwaterman.patch
dpkg-source: info: applying python3.patch
Check 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=bullseye-staging-armhf-sbuild
SCHROOT_CHROOT_NAME=bullseye-staging-armhf-sbuild
SCHROOT_COMMAND=env
SCHROOT_GID=109
SCHROOT_GROUP=buildd
SCHROOT_SESSION_ID=bullseye-staging-armhf-sbuild-4d977767-0071-4978-8e02-e23fab1dc4aa
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-3
dpkg-buildpackage: info: source distribution unstable
dpkg-source --before-build .
dpkg-buildpackage: info: host architecture armhf
debian/rules clean
dh clean
dh_clean
debian/rules binary-arch
dh binary-arch
dh_update_autotools_config -a
dh_autoreconf -a
dh_auto_configure -a
cd obj-arm-linux-gnueabihf && cmake -DCMAKE_INSTALL_PREFIX=/usr -DCMAKE_BUILD_TYPE=None -DCMAKE_INSTALL_SYSCONFDIR=/etc -DCMAKE_INSTALL_LOCALSTATEDIR=/var -DCMAKE_EXPORT_NO_PACKAGE_REGISTRY=ON -DCMAKE_FIND_PACKAGE_NO_PACKAGE_REGISTRY=ON -DCMAKE_INSTALL_RUNSTATEDIR=/run "-GUnix Makefiles" -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_INSTALL_LIBDIR=lib/arm-linux-gnueabihf ..
-- The C compiler identification is GNU 9.2.1
-- The CXX compiler identification is GNU 9.2.1
-- 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=
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[ 1%] Building CXX object CMakeFiles/tvcassembly.dir/VariantCaller/IndelAssembly/IndelAssembly.cpp.o
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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/tvcassembly.dir/VariantCaller/IndelAssembly/IndelAssembly.cpp.o -c /<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/IndelAssembly/IndelAssembly.cpp
/usr/bin/c++ -DALIGNSTATS_IGNORE -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/external/vcflib -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/external/freebayes/src -I/usr/include/jsoncpp -I/usr/include/bamtools -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/FlowDistEval -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/EnsembleEval -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Bookkeeping -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Reads -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Splice -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Filter -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/realignment -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/file-io -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/BaseCaller -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/Calibration -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/Util -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o CMakeFiles/tvcassembly.dir/VariantCaller/TargetsManager.cpp.o -c /<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/TargetsManager.cpp
[ 4%] Building CXX object CMakeFiles/tvcutils.dir/VariantCaller/tvcutils/tvcutils.cpp.o
/usr/bin/c++ -DALIGNSTATS_IGNORE -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/external/vcflib -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/external/freebayes/src -I/usr/include/jsoncpp -I/usr/include/bamtools -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/FlowDistEval -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/EnsembleEval -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Bookkeeping -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Reads -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Splice -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Filter -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/realignment -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/file-io -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/BaseCaller -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/Calibration -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/Util -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o CMakeFiles/tvcutils.dir/VariantCaller/tvcutils/tvcutils.cpp.o -c /<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/tvcutils/tvcutils.cpp
Scanning dependencies of target tvc
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[ 6%] Building CXX object CMakeFiles/tvc.dir/VariantCaller/VariantCaller.cpp.o
/usr/bin/c++ -DALIGNSTATS_IGNORE -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/external/vcflib -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/external/freebayes/src -I/usr/include/jsoncpp -I/usr/include/bamtools -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/FlowDistEval -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/EnsembleEval -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Bookkeeping -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Reads -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Splice -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Filter -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/realignment -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/file-io -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/BaseCaller -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/Calibration -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/Util -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o CMakeFiles/tvc.dir/VariantCaller/VariantCaller.cpp.o -c /<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/VariantCaller.cpp
[ 7%] Building CXX object CMakeFiles/tvcutils.dir/VariantCaller/tvcutils/prepare_hotspots.cpp.o
/usr/bin/c++ -DALIGNSTATS_IGNORE -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/external/vcflib -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/external/freebayes/src -I/usr/include/jsoncpp -I/usr/include/bamtools -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/FlowDistEval -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/EnsembleEval -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Bookkeeping -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Reads -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Splice -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Filter -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/realignment -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/file-io -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/BaseCaller -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/Calibration -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/Util -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o CMakeFiles/tvcutils.dir/VariantCaller/tvcutils/prepare_hotspots.cpp.o -c /<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/tvcutils/prepare_hotspots.cpp
[ 9%] Building CXX object CMakeFiles/tvcassembly.dir/VariantCaller/SampleManager.cpp.o
/usr/bin/c++ -DALIGNSTATS_IGNORE -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/external/vcflib -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/external/freebayes/src -I/usr/include/jsoncpp -I/usr/include/bamtools -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/FlowDistEval -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/EnsembleEval -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Bookkeeping -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Reads -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Splice -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Filter -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/realignment -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/file-io -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/BaseCaller -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/Calibration -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/Util -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o CMakeFiles/tvcassembly.dir/VariantCaller/SampleManager.cpp.o -c /<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/SampleManager.cpp
[ 10%] Building CXX object CMakeFiles/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]
36 | arma::set_stream_err1(null_ostream);
| ^~~~~~~~~~~~~~~
In file included from /usr/include/armadillo:364,
from /<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/VariantCaller.cpp:12:
/usr/include/armadillo_bits/debug.hpp:90:1: note: declared here
90 | set_stream_err1(std::ostream& user_stream)
| ^~~~~~~~~~~~~~~
/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/VariantCaller.cpp:36:37: warning: 'void arma::set_stream_err1(std::ostream&)' is deprecated [-Wdeprecated-declarations]
36 | arma::set_stream_err1(null_ostream);
| ^
In file included from /usr/include/armadillo:364,
from /<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/VariantCaller.cpp:12:
/usr/include/armadillo_bits/debug.hpp:90:1: note: declared here
90 | set_stream_err1(std::ostream& user_stream)
| ^~~~~~~~~~~~~~~
/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/VariantCaller.cpp:36:37: warning: 'void arma::set_stream_err1(std::ostream&)' is deprecated [-Wdeprecated-declarations]
36 | arma::set_stream_err1(null_ostream);
| ^
In file included from /usr/include/armadillo:364,
from /<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/VariantCaller.cpp:12:
/usr/include/armadillo_bits/debug.hpp:90:1: note: declared here
90 | set_stream_err1(std::ostream& user_stream)
| ^~~~~~~~~~~~~~~
/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/VariantCaller.cpp:37:9: warning: 'void arma::set_stream_err2(std::ostream&)' is deprecated [-Wdeprecated-declarations]
37 | arma::set_stream_err2(null_ostream);
| ^~~~~~~~~~~~~~~
In file included from /usr/include/armadillo:364,
from /<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/VariantCaller.cpp:12:
/usr/include/armadillo_bits/debug.hpp:101:1: note: declared here
101 | set_stream_err2(std::ostream& user_stream)
| ^~~~~~~~~~~~~~~
/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/VariantCaller.cpp:37:37: warning: 'void arma::set_stream_err2(std::ostream&)' is deprecated [-Wdeprecated-declarations]
37 | arma::set_stream_err2(null_ostream);
| ^
In file included from /usr/include/armadillo:364,
from /<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/VariantCaller.cpp:12:
/usr/include/armadillo_bits/debug.hpp:101:1: note: declared here
101 | set_stream_err2(std::ostream& user_stream)
| ^~~~~~~~~~~~~~~
/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/VariantCaller.cpp:37:37: warning: 'void arma::set_stream_err2(std::ostream&)' is deprecated [-Wdeprecated-declarations]
37 | arma::set_stream_err2(null_ostream);
| ^
In file included from /usr/include/armadillo:364,
from /<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/VariantCaller.cpp:12:
/usr/include/armadillo_bits/debug.hpp:101:1: note: declared here
101 | set_stream_err2(std::ostream& user_stream)
| ^~~~~~~~~~~~~~~
[ 12%] 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
/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/tvcutils/validate_bed.cpp: In function 'bool load_and_validate_bed(const string&, ReferenceReader&, BedFile&, Json::Value&, bool)':
/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/tvcutils/validate_bed.cpp:861:26: warning: '%s' directive writing up to 65535 bytes into a region of size 1024 [-Wformat-overflow=]
783 | fields[0] = line;
| ~~~~
......
861 | sprintf(buffer, "%s:%ld-%ld", fields[0], bed_line.start+1, bed_line.end);
| ^~
/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/tvcutils/validate_bed.cpp:861:25: note: directive argument in the range [-2147483647, 2147483647]
861 | sprintf(buffer, "%s:%ld-%ld", fields[0], bed_line.start+1, bed_line.end);
| ^~~~~~~~~~~~
In file included from /usr/include/stdio.h:867,
from /usr/include/c++/9/cstdio:42,
from /usr/include/c++/9/ext/string_conversions.h:43,
from /usr/include/c++/9/bits/basic_string.h:6493,
from /usr/include/c++/9/string:55,
from /<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/tvcutils/validate_bed.cpp:5:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:36:34: note: '__builtin___sprintf_chk' output between 5 and 65560 bytes into a destination of size 1024
36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
| ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
37 | __bos (__s), __fmt, __va_arg_pack ());
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
[ 14%] Building CXX object CMakeFiles/tvcassembly.dir/Util/OptArgs.cpp.o
/usr/bin/c++ -DALIGNSTATS_IGNORE -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/external/vcflib -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/external/freebayes/src -I/usr/include/jsoncpp -I/usr/include/bamtools -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/FlowDistEval -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/EnsembleEval -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Bookkeeping -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Reads -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Splice -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Filter -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/realignment -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/file-io -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/BaseCaller -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/Calibration -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/Util -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg -g -O2 -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
[ 15%] Building CXX object CMakeFiles/tvcassembly.dir/Util/Utils.cpp.o
/usr/bin/c++ -DALIGNSTATS_IGNORE -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/external/vcflib -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/external/freebayes/src -I/usr/include/jsoncpp -I/usr/include/bamtools -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/FlowDistEval -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/EnsembleEval -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Bookkeeping -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Reads -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Splice -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Filter -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/realignment -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/file-io -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/BaseCaller -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/Calibration -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/Util -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg -g -O2 -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
In file included from /usr/include/c++/9/vector:72,
from /<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/Util/OptArgs.h:11,
from /<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/Util/OptArgs.cpp:4:
/usr/include/c++/9/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++/9/bits/vector.tcc:426:7: 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
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc: In member function 'void OptArgs::StringToDoubleVector(std::vector<double>&, const string&, const string&, char)':
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
In file included from /usr/include/string.h:495,
from /usr/include/c++/9/cstring:42,
from /<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/Util/Utils.cpp:12:
In function 'char* strncpy(char*, const char*, size_t)',
inlined from 'char* GetProcessParam(const char*, const char*)' at /<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/Util/Utils.cpp:503:15:
/usr/include/arm-linux-gnueabihf/bits/string_fortified.h:106:34: warning: 'char* __builtin_strncpy(char*, const char*, unsigned int)' specified bound depends on the length of the source argument [-Wstringop-overflow=]
106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
| ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/Util/Utils.cpp: In function 'char* GetProcessParam(const char*, const char*)':
/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/Util/Utils.cpp:503:37: note: length computed here
503 | strncpy (keyword, buf, strlen (buf)-1);
| ~~~~~~~^~~~~
[ 17%] Building CXX object CMakeFiles/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
[ 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/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
[ 21%] 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
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[ 23%] Built target tvcassembly
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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/TargetsManager.cpp.o -c /<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/TargetsManager.cpp
[ 26%] 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
[ 28%] 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
[ 29%] 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
[ 31%] 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
In file included from /usr/include/c++/9/vector:72,
from /<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/Util/OptArgs.h:11,
from /<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/Util/OptArgs.cpp:4:
/usr/include/c++/9/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++/9/bits/vector.tcc:426:7: 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
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc: In member function 'void OptArgs::StringToDoubleVector(std::vector<double>&, const string&, const string&, char)':
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
[ 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/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
[ 35%] 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
[ 37%] 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
In file included from /usr/include/c++/9/vector:72,
from /<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/tvcutils/unify_vcf.cpp:13:
/usr/include/c++/9/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++/9/bits/vector.tcc:426:7: 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
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/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++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<markov_state*, std::vector<markov_state> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
[ 39%] 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
[ 40%] 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
In file included from /usr/include/c++/9/vector:72,
from /<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Bookkeeping/InputStructures.h:12,
from /<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Bookkeeping/InputStructures.cpp:7:
/usr/include/c++/9/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++/9/bits/vector.tcc:426:7: 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
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:67,
from /<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Bookkeeping/InputStructures.h:12,
from /<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Bookkeeping/InputStructures.cpp:7:
/usr/include/c++/9/bits/stl_vector.h: In constructor 'PersistingThreadObjects::PersistingThreadObjects(const InputStructures&)':
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<DPTreephaser*, std::vector<DPTreephaser> >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
[ 42%] Building CXX object CMakeFiles/tvc.dir/VariantCaller/Reads/ExtendedReadInfo.cpp.o
/usr/bin/c++ -DALIGNSTATS_IGNORE -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/external/vcflib -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/external/freebayes/src -I/usr/include/jsoncpp -I/usr/include/bamtools -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/FlowDistEval -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/EnsembleEval -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Bookkeeping -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Reads -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Splice -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Filter -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/realignment -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/file-io -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/BaseCaller -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/Calibration -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/Util -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o CMakeFiles/tvc.dir/VariantCaller/Reads/ExtendedReadInfo.cpp.o -c /<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Reads/ExtendedReadInfo.cpp
[ 43%] 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
[ 45%] 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
[ 46%] 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
[ 48%] 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
[ 50%] 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
[ 51%] 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
[ 53%] 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
[ 54%] 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
[ 56%] Building C object CMakeFiles/tvcutils.dir/external/vcflib/tabixpp/bgzf.c.o
/usr/bin/cc -DALIGNSTATS_IGNORE -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/external/vcflib -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/external/freebayes/src -I/usr/include/jsoncpp -I/usr/include/bamtools -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/FlowDistEval -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/EnsembleEval -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Bookkeeping -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Reads -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Splice -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Filter -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/realignment -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/file-io -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/BaseCaller -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/Calibration -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/Util -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o CMakeFiles/tvcutils.dir/external/vcflib/tabixpp/bgzf.c.o -c /<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/external/vcflib/tabixpp/bgzf.c
/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/external/vcflib/tabixpp/bgzf.c: In function '_bgzf_check_EOF':
/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/external/vcflib/tabixpp/bgzf.c:678:2: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
678 | fread(buf, 1, 28, fp->file);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
[ 57%] Building CXX object CMakeFiles/tvc.dir/VariantCaller/Filter/VariantAssist.cpp.o
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/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Filter/VariantAssist.cpp: In function 'double VariantAssist::MannWhitneyU(std::vector<float>&, std::vector<float>&, bool)':
/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Filter/VariantAssist.cpp:191:36: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'std::vector<float>::size_type' {aka 'unsigned int'} [-Wformat=]
191 | fprintf(stdout, "ref.size()=%lu; ", ref.size());
| ~~^ ~~~~~~~~~~
| | |
| | std::vector<float>::size_type {aka unsigned int}
| long unsigned int
| %u
/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Filter/VariantAssist.cpp:192:36: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'std::vector<float>::size_type' {aka 'unsigned int'} [-Wformat=]
192 | fprintf(stdout, "var.size()=%lu; ", var.size());
| ~~^ ~~~~~~~~~~
| | |
| | std::vector<float>::size_type {aka unsigned int}
| long unsigned int
| %u
/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Filter/VariantAssist.cpp:193:37: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'std::vector<double>::size_type' {aka 'unsigned int'} [-Wformat=]
193 | fprintf(stdout, "both.size()=%lu; ", both.size());
| ~~^ ~~~~~~~~~~~
| | |
| | std::vector<double>::size_type {aka unsigned int}
| long unsigned int
| %u
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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/HypothesisEvaluator.cpp.o -c /<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/HypothesisEvaluator.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/EnsembleEval/DiagnosticJSON.cpp.o -c /<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/EnsembleEval/DiagnosticJSON.cpp
[ 65%] Building CXX object CMakeFiles/tvc.dir/VariantCaller/EnsembleEval/BiasGenerator.cpp.o
/usr/bin/c++ -DALIGNSTATS_IGNORE -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/external/vcflib -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/external/freebayes/src -I/usr/include/jsoncpp -I/usr/include/bamtools -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/FlowDistEval -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/EnsembleEval -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Bookkeeping -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Reads -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Splice -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Filter -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/realignment -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/file-io -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/BaseCaller -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/Calibration -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/Util -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o CMakeFiles/tvc.dir/VariantCaller/EnsembleEval/BiasGenerator.cpp.o -c /<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/EnsembleEval/BiasGenerator.cpp
[ 67%] Building CXX object CMakeFiles/tvc.dir/VariantCaller/EnsembleEval/SigmaGenerator.cpp.o
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[ 68%] Building CXX object CMakeFiles/tvc.dir/VariantCaller/EnsembleEval/SkewGenerator.cpp.o
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[ 76%] Building CXX object CMakeFiles/tvc.dir/external/vcflib/Variant.cpp.o
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[ 78%] Building CXX object CMakeFiles/tvc.dir/external/vcflib/split.cpp.o
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[ 79%] Building CXX object CMakeFiles/tvc.dir/external/vcflib/tabixpp/tabix.cpp.o
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[ 81%] Building C object CMakeFiles/tvc.dir/external/vcflib/tabixpp/index.c.o
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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]
678 | fread(buf, 1, 28, fp->file);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
[ 84%] Building CXX object CMakeFiles/tvc.dir/external/freebayes/src/AlleleParser.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
In file included from /usr/include/c++/9/vector:72,
from /<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/Util/OptArgs.h:11,
from /<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/Util/OptArgs.cpp:4:
/usr/include/c++/9/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++/9/bits/vector.tcc:426:7: 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
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
[ 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
/usr/include/c++/9/bits/vector.tcc: In member function 'void OptArgs::StringToDoubleVector(std::vector<double>&, const string&, const string&, char)':
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
[ 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
[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'
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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 0.02 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 0.12 sec
Start 7: tvcutils_unify_vcf_call
4/8 Test #6: tvcutils_validate_bed_call ....................... Passed 0.04 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 5.82 sec
8/8 Test #3: tvc_test_4_threads_sse_off_with_parameter_file ... Passed 5.89 sec
100% tests passed, 0 tests failed out of 8
Total Test time (real) = 5.92 sec
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create-stamp debian/debhelper-build-stamp
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/tvcassembly.dir/build.make CMakeFiles/tvcassembly.dir/depend
make -f CMakeFiles/tvc.dir/build.make CMakeFiles/tvc.dir/depend
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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'
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[ 10%] Built target tvcassembly
make[3]: Entering directory '/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/obj-arm-linux-gnueabihf'
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[ 31%] Built target tvcutils
[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_dwz -a
dh_strip -a
dh_makeshlibs -a
dh_shlibdeps -a
dpkg-shlibdeps: warning: debian/tvc/usr/bin/tvcassembly contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/tvc/usr/bin/tvcutils contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/tvc/usr/bin/tvc contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/tvc/usr/bin/tvcassembly debian/tvc/usr/bin/tvcutils debian/tvc/usr/bin/tvc were not linked against ld-linux-armhf.so.3 (they use none of the library's symbols)
dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/tvc/usr/bin/tvcutils debian/tvc/usr/bin/tvc were not linked against libdisorder.so.0 (they use none of the library's symbols)
dh_installdeb -a
dh_gencontrol -a
dh_md5sums -a
dh_builddeb -a
dpkg-deb: building package 'tvc-dbgsym' in '../tvc-dbgsym_5.0.3+git20151221.80e144e+dfsg-3_armhf.deb'.
dpkg-deb: building package 'tvc' in '../tvc_5.0.3+git20151221.80e144e+dfsg-3_armhf.deb'.
dpkg-genbuildinfo --build=any
dpkg-genchanges --build=any -mRaspbian wandboard test autobuilder <root@raspbian.org> >../tvc_5.0.3+git20151221.80e144e+dfsg-3_armhf.changes
dpkg-genchanges: info: binary-only arch-specific upload (source code and arch-indep packages not included)
dpkg-source --after-build .
dpkg-buildpackage: info: binary-only upload (no source included)
--------------------------------------------------------------------------------
Build finished at 2020-03-06T11:27:57Z
Finished
--------
I: Built successfully
+------------------------------------------------------------------------------+
| Post Build Chroot |
+------------------------------------------------------------------------------+
+------------------------------------------------------------------------------+
| Changes |
+------------------------------------------------------------------------------+
tvc_5.0.3+git20151221.80e144e+dfsg-3_armhf.changes:
---------------------------------------------------
Format: 1.8
Date: Sun, 01 Mar 2020 15:57:45 +1100
Source: tvc
Binary: tvc tvc-dbgsym
Architecture: armhf
Version: 5.0.3+git20151221.80e144e+dfsg-3
Distribution: bullseye-staging
Urgency: medium
Maintainer: Raspbian wandboard test autobuilder <root@raspbian.org>
Changed-By: Stuart Prescott <stuart@debian.org>
Description:
tvc - genetic variant caller for Ion Torrent sequencing platforms
Closes: 945720
Changes:
tvc (5.0.3+git20151221.80e144e+dfsg-3) unstable; urgency=medium
.
* Team upload.
* Use Python 3 in scripts (Closes: #945720).
* Add Rules-Requires-Root: no.
* Update Standards-Version to 4.5.0 (no changes required).
* Switch to debhelper-compat (= 12).
Checksums-Sha1:
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aa88fdd22037392c744d985dc51154fb9598f1ab 6938 tvc_5.0.3+git20151221.80e144e+dfsg-3_armhf.buildinfo
aaaf8f546a9b408872765c9145e93460a7219735 944032 tvc_5.0.3+git20151221.80e144e+dfsg-3_armhf.deb
Checksums-Sha256:
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dc090dcc3b58ca85cfa811a897fee9b4e98dce2046fa5e793e973903cc9bfe5b 6938 tvc_5.0.3+git20151221.80e144e+dfsg-3_armhf.buildinfo
ba2f82b8f20316a28d67cc80d34d8f64e59e36fb34b9f78b60e0406618dd4a4a 944032 tvc_5.0.3+git20151221.80e144e+dfsg-3_armhf.deb
Files:
ddff08a5b4720b089a5c9b1fe6857c9e 10338184 debug optional tvc-dbgsym_5.0.3+git20151221.80e144e+dfsg-3_armhf.deb
8e3f82ef49e825a1976a5c0644453a09 6938 science optional tvc_5.0.3+git20151221.80e144e+dfsg-3_armhf.buildinfo
5541d0098447177915ee62666adaab69 944032 science optional tvc_5.0.3+git20151221.80e144e+dfsg-3_armhf.deb
+------------------------------------------------------------------------------+
| Package contents |
+------------------------------------------------------------------------------+
tvc-dbgsym_5.0.3+git20151221.80e144e+dfsg-3_armhf.deb
-----------------------------------------------------
new Debian package, version 2.0.
size 10338184 bytes: control archive=708 bytes.
488 bytes, 12 lines control
401 bytes, 4 lines md5sums
Package: tvc-dbgsym
Source: tvc
Version: 5.0.3+git20151221.80e144e+dfsg-3
Auto-Built-Package: debug-symbols
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 10464
Depends: tvc (= 5.0.3+git20151221.80e144e+dfsg-3)
Section: debug
Priority: optional
Description: debug symbols for tvc
Build-Ids: 017615d03848f0b9cf2caf8e20f26a44d8e3d77e 15ac15b4f35e355e0c2e96c1d5920936529d0785 e596abff604845c54530c1980f78ce4a340cd83c
drwxr-xr-x root/root 0 2020-03-01 04:57 ./
drwxr-xr-x root/root 0 2020-03-01 04:57 ./usr/
drwxr-xr-x root/root 0 2020-03-01 04:57 ./usr/lib/
drwxr-xr-x root/root 0 2020-03-01 04:57 ./usr/lib/debug/
drwxr-xr-x root/root 0 2020-03-01 04:57 ./usr/lib/debug/.build-id/
drwxr-xr-x root/root 0 2020-03-01 04:57 ./usr/lib/debug/.build-id/01/
-rw-r--r-- root/root 7027760 2020-03-01 04:57 ./usr/lib/debug/.build-id/01/7615d03848f0b9cf2caf8e20f26a44d8e3d77e.debug
drwxr-xr-x root/root 0 2020-03-01 04:57 ./usr/lib/debug/.build-id/15/
-rw-r--r-- root/root 2435464 2020-03-01 04:57 ./usr/lib/debug/.build-id/15/ac15b4f35e355e0c2e96c1d5920936529d0785.debug
drwxr-xr-x root/root 0 2020-03-01 04:57 ./usr/lib/debug/.build-id/e5/
-rw-r--r-- root/root 786896 2020-03-01 04:57 ./usr/lib/debug/.build-id/e5/96abff604845c54530c1980f78ce4a340cd83c.debug
drwxr-xr-x root/root 0 2020-03-01 04:57 ./usr/lib/debug/.dwz/
drwxr-xr-x root/root 0 2020-03-01 04:57 ./usr/lib/debug/.dwz/arm-linux-gnueabihf/
-rw-r--r-- root/root 448012 2020-03-01 04:57 ./usr/lib/debug/.dwz/arm-linux-gnueabihf/tvc.debug
drwxr-xr-x root/root 0 2020-03-01 04:57 ./usr/share/
drwxr-xr-x root/root 0 2020-03-01 04:57 ./usr/share/doc/
lrwxrwxrwx root/root 0 2020-03-01 04:57 ./usr/share/doc/tvc-dbgsym -> tvc
tvc_5.0.3+git20151221.80e144e+dfsg-3_armhf.deb
----------------------------------------------
new Debian package, version 2.0.
size 944032 bytes: control archive=1676 bytes.
992 bytes, 16 lines control
2459 bytes, 28 lines md5sums
Package: tvc
Version: 5.0.3+git20151221.80e144e+dfsg-3
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 2977
Depends: libarmadillo9 (>= 1:9.800.4+dfsg), libbamtools2.5.1 (>= 2.5.1+dfsg), libc6 (>= 2.29), libdisorder0 (>= 0.0.2), libgcc-s1 (>= 3.5), libjsoncpp1 (>= 1.7.4), libsmithwaterman0 (>= 0.0+git20160702.2610e25), libstdc++6 (>= 9), zlib1g (>= 1:1.1.4), python3
Section: science
Priority: optional
Homepage: http://ioncommunity.thermofisher.com
Description: genetic variant caller for Ion Torrent sequencing platforms
Torrent Variant Caller (TVC) is a genetic variant caller for
Ion Torrent sequencing platforms, and is specially optimized to exploit the
underlying flow signal information in the statistical model
to evaluate variants. Torrent Variant Caller is designed to call
single-nucleotide polymorphisms (SNPs), multi-nucleotide polymorphisms (MNPs),
insertions, deletions, and block substitutions.
drwxr-xr-x root/root 0 2020-03-01 04:57 ./
drwxr-xr-x root/root 0 2020-03-01 04:57 ./usr/
drwxr-xr-x root/root 0 2020-03-01 04:57 ./usr/bin/
-rwxr-xr-x root/root 905248 2020-03-01 04:57 ./usr/bin/tvc
-rwxr-xr-x root/root 174412 2020-03-01 04:57 ./usr/bin/tvcassembly
-rwxr-xr-x root/root 518764 2020-03-01 04:57 ./usr/bin/tvcutils
-rwxr-xr-x root/root 12985 2020-03-01 04:57 ./usr/bin/variant_caller_pipeline.py
drwxr-xr-x root/root 0 2020-03-01 04:57 ./usr/share/
drwxr-xr-x root/root 0 2020-03-01 04:57 ./usr/share/TVC/
drwxr-xr-x root/root 0 2020-03-01 04:57 ./usr/share/TVC/examples/
drwxr-xr-x root/root 0 2020-03-01 04:57 ./usr/share/TVC/examples/example1/
drwxr-xr-x root/root 0 2020-03-01 04:57 ./usr/share/TVC/examples/example1/expected/
-rw-r--r-- root/root 6876 2015-12-21 20:38 ./usr/share/TVC/examples/example1/expected/TSVC_variants.vcf
-rw-r--r-- root/root 6479 2015-12-21 20:38 ./usr/share/TVC/examples/example1/expected/small_variants.vcf
-rw-r--r-- root/root 108 2015-12-21 20:38 ./usr/share/TVC/examples/example1/reference.dict
-rw-r--r-- root/root 3400 2015-12-21 20:38 ./usr/share/TVC/examples/example1/reference.fasta
-rw-r--r-- root/root 22 2015-12-21 20:38 ./usr/share/TVC/examples/example1/reference.fasta.fai
-rw-r--r-- root/root 225904 2015-12-21 20:38 ./usr/share/TVC/examples/example1/test.bam
-rw-r--r-- root/root 96 2015-12-21 20:38 ./usr/share/TVC/examples/example1/test.bam.bai
-rw-r--r-- root/root 13 2015-12-21 20:38 ./usr/share/TVC/examples/example1/test.bed
-rw-r--r-- root/root 13 2015-12-21 20:38 ./usr/share/TVC/examples/example1/test_merged_plain.bed
-rw-r--r-- root/root 13 2015-12-21 20:38 ./usr/share/TVC/examples/example1/test_original.bed
-rw-r--r-- root/root 70 2015-12-21 20:38 ./usr/share/TVC/examples/example1/test_unmerged_detail.bed
drwxr-xr-x root/root 0 2020-03-01 04:57 ./usr/share/TVC/pluginMedia/
drwxr-xr-x root/root 0 2020-03-01 04:57 ./usr/share/TVC/pluginMedia/parameter_sets/
-rw-r--r-- root/root 2809 2015-12-21 20:38 ./usr/share/TVC/pluginMedia/parameter_sets/ampliseq_germline_lowstringency_pgm_parameters.json
-rw-r--r-- root/root 2926 2015-12-21 20:38 ./usr/share/TVC/pluginMedia/parameter_sets/ampliseq_somatic_lowstringency_pgm_parameters.json
-rw-r--r-- root/root 2826 2015-12-21 20:38 ./usr/share/TVC/pluginMedia/parameter_sets/ampliseqexome_germline_lowstringency_p1_parameters.json
-rw-r--r-- root/root 2918 2015-12-21 20:38 ./usr/share/TVC/pluginMedia/parameter_sets/ampliseqexome_somatic_lowstringency_p1_parameters.json
-rw-r--r-- root/root 3062 2015-12-21 20:38 ./usr/share/TVC/pluginMedia/parameter_sets/ocp_somatic_lowstringency_pgm_parameters.json
-rw-r--r-- root/root 2628 2015-12-21 20:38 ./usr/share/TVC/pluginMedia/parameter_sets/pgx4_germline_lowstringency_pgm_parameters.json
-rw-r--r-- root/root 2757 2015-12-21 20:38 ./usr/share/TVC/pluginMedia/parameter_sets/targetseq_germline_lowstringency_p1_parameters.json
drwxr-xr-x root/root 0 2020-03-01 04:57 ./usr/share/TVC/sse/
-rw-r--r-- root/root 683778 2015-12-21 20:38 ./usr/share/TVC/sse/ampliseqexome_germline_p1_hiq_motifset.txt
-rw-r--r-- root/root 451754 2015-12-21 20:38 ./usr/share/TVC/sse/motifset.txt
drwxr-xr-x root/root 0 2020-03-01 04:57 ./usr/share/doc/
drwxr-xr-x root/root 0 2020-03-01 04:57 ./usr/share/doc/tvc/
-rw-r--r-- root/root 1078 2020-03-01 04:46 ./usr/share/doc/tvc/README.Debian
-rw-r--r-- root/root 1180 2020-03-01 04:57 ./usr/share/doc/tvc/changelog.Debian.gz
-rw-r--r-- root/root 2939 2020-03-01 04:46 ./usr/share/doc/tvc/copyright
drwxr-xr-x root/root 0 2020-03-01 04:57 ./usr/share/lintian/
drwxr-xr-x root/root 0 2020-03-01 04:57 ./usr/share/lintian/overrides/
-rw-r--r-- root/root 135 2020-03-01 04:46 ./usr/share/lintian/overrides/tvc
+------------------------------------------------------------------------------+
| Post Build |
+------------------------------------------------------------------------------+
+------------------------------------------------------------------------------+
| Cleanup |
+------------------------------------------------------------------------------+
Purging /<<BUILDDIR>>
Not cleaning session: cloned chroot in use
+------------------------------------------------------------------------------+
| Summary |
+------------------------------------------------------------------------------+
Build Architecture: armhf
Build-Space: 150836
Build-Time: 755
Distribution: bullseye-staging
Host Architecture: armhf
Install-Time: 790
Job: tvc_5.0.3+git20151221.80e144e+dfsg-3
Machine Architecture: armhf
Package: tvc
Package-Time: 1596
Source-Version: 5.0.3+git20151221.80e144e+dfsg-3
Space: 150836
Status: successful
Version: 5.0.3+git20151221.80e144e+dfsg-3
--------------------------------------------------------------------------------
Finished at 2020-03-06T11:27:57Z
Build needed 00:26:36, 150836k disc space