pbseqlib →
0~20161219-2+b1 →
armhf → 2018-12-19 17:39:24
sbuild (Debian sbuild) 0.71.0 (24 Aug 2016) on bm-wb-01
+==============================================================================+
| pbseqlib 0~20161219-2+b1 (armhf) Wed, 19 Dec 2018 17:17:34 +0000 |
+==============================================================================+
Package: pbseqlib
Version: 0~20161219-2+b1
Source Version: 0~20161219-2
Distribution: buster-staging
Machine Architecture: armhf
Host Architecture: armhf
Build Architecture: armhf
I: NOTICE: Log filtering will replace 'var/run/schroot/mount/buster-staging-armhf-sbuild-d69f5afd-13b4-4bd8-9749-5d880d6872a2' with '<<CHROOT>>'
+------------------------------------------------------------------------------+
| Update chroot |
+------------------------------------------------------------------------------+
Get:1 http://172.17.0.1/private buster-staging InRelease [11.3 kB]
Get:2 http://172.17.0.1/private buster-staging/main Sources [11.3 MB]
Get:3 http://172.17.0.1/private buster-staging/main armhf Packages [13.0 MB]
Fetched 24.3 MB in 28s (874 kB/s)
Reading package lists...
+------------------------------------------------------------------------------+
| Fetch source files |
+------------------------------------------------------------------------------+
Check APT
---------
Checking available source versions...
Download source files with APT
------------------------------
Reading package lists...
NOTICE: 'pbseqlib' packaging is maintained in the 'Git' version control system at:
https://anonscm.debian.org/git/debian-med/pbseqlib.git
Please use:
git clone https://anonscm.debian.org/git/debian-med/pbseqlib.git
to retrieve the latest (possibly unreleased) updates to the package.
Need to get 1351 kB of source archives.
Get:1 http://172.17.0.1/private buster-staging/main pbseqlib 0~20161219-2 (dsc) [2498 B]
Get:2 http://172.17.0.1/private buster-staging/main pbseqlib 0~20161219-2 (tar) [1343 kB]
Get:3 http://172.17.0.1/private buster-staging/main pbseqlib 0~20161219-2 (diff) [5780 B]
Fetched 1351 kB in 0s (5650 kB/s)
Download complete and in download only mode
I: NOTICE: Log filtering will replace 'build/pbseqlib-zdHVoA/pbseqlib-0~20161219' with '<<PKGBUILDDIR>>'
I: NOTICE: Log filtering will replace 'build/pbseqlib-zdHVoA' 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-2UWkWS/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-2UWkWS/gpg/pubring.kbx' created
gpg: /<<BUILDDIR>>/resolver-2UWkWS/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-2UWkWS/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-2UWkWS/apt_archive ./ Release [957 B]
Get:3 copy:/<<BUILDDIR>>/resolver-2UWkWS/apt_archive ./ Release.gpg [370 B]
Ign:3 copy:/<<BUILDDIR>>/resolver-2UWkWS/apt_archive ./ Release.gpg
Get:4 copy:/<<BUILDDIR>>/resolver-2UWkWS/apt_archive ./ Sources [349 B]
Get:5 copy:/<<BUILDDIR>>/resolver-2UWkWS/apt_archive ./ Packages [433 B]
Fetched 2109 B in 1s (2589 B/s)
Reading package lists...
W: copy:///<<BUILDDIR>>/resolver-2UWkWS/apt_archive/./Release.gpg: The key(s) in the keyring /etc/apt/trusted.gpg.d/sbuild-build-depends-archive.gpg are ignored as the file is not readable by user '_apt' executing apt-key.
W: GPG error: copy:/<<BUILDDIR>>/resolver-2UWkWS/apt_archive ./ Release: The following signatures couldn't be verified because the public key is not available: NO_PUBKEY 35506D9A48F77B2E
Reading package lists...
Install core build dependencies (apt-based resolver)
----------------------------------------------------
Installing build dependencies
Reading package lists...
Building dependency tree...
Reading state information...
The following packages were automatically installed and are no longer required:
ca-certificates e2fsprogs-l10n krb5-locales libgpg-error-l10n
libsasl2-modules libssl1.1 openssl
Use 'apt autoremove' to remove them.
The following NEW packages will be installed:
sbuild-build-depends-core-dummy
0 upgraded, 1 newly installed, 0 to remove and 17 not upgraded.
Need to get 852 B of archives.
After this operation, 0 B of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-2UWkWS/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 ... 15636 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) ...
+------------------------------------------------------------------------------+
| Check architectures |
+------------------------------------------------------------------------------+
Arch check ok (armhf included in any all)
+------------------------------------------------------------------------------+
| Install package build dependencies |
+------------------------------------------------------------------------------+
Setup apt archive
-----------------
Merged Build-Depends: debhelper (>= 10), dh-exec, python, zlib1g-dev, libhdf5-dev, libboost-dev, libpbbam-dev, libhts-dev, libgtest-dev
Filtered Build-Depends: debhelper (>= 10), dh-exec, python, zlib1g-dev, libhdf5-dev, libboost-dev, libpbbam-dev, libhts-dev, libgtest-dev
dpkg-deb: building package 'sbuild-build-depends-pbseqlib-dummy' in '/<<BUILDDIR>>/resolver-2UWkWS/apt_archive/sbuild-build-depends-pbseqlib-dummy.deb'.
dpkg-scanpackages: warning: Packages in archive but missing from override file:
dpkg-scanpackages: warning: sbuild-build-depends-core-dummy sbuild-build-depends-pbseqlib-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-2UWkWS/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-2UWkWS/apt_archive ./ Release [963 B]
Get:3 copy:/<<BUILDDIR>>/resolver-2UWkWS/apt_archive ./ Release.gpg [370 B]
Ign:3 copy:/<<BUILDDIR>>/resolver-2UWkWS/apt_archive ./ Release.gpg
Get:4 copy:/<<BUILDDIR>>/resolver-2UWkWS/apt_archive ./ Sources [546 B]
Get:5 copy:/<<BUILDDIR>>/resolver-2UWkWS/apt_archive ./ Packages [617 B]
Fetched 2496 B in 1s (3642 B/s)
Reading package lists...
W: copy:///<<BUILDDIR>>/resolver-2UWkWS/apt_archive/./Release.gpg: The key(s) in the keyring /etc/apt/trusted.gpg.d/sbuild-build-depends-archive.gpg are ignored as the file is not readable by user '_apt' executing apt-key.
W: GPG error: copy:/<<BUILDDIR>>/resolver-2UWkWS/apt_archive ./ Release: The following signatures couldn't be verified because the public key is not available: NO_PUBKEY 35506D9A48F77B2E
Reading package lists...
Install pbseqlib build dependencies (apt-based resolver)
--------------------------------------------------------
Installing build dependencies
Reading package lists...
Building dependency tree...
Reading state information...
The following packages were automatically installed and are no longer required:
ca-certificates e2fsprogs-l10n krb5-locales libgpg-error-l10n
libsasl2-modules openssl
Use 'apt autoremove' to remove them.
The following additional packages will be installed:
autoconf automake autopoint autotools-dev bsdmainutils cpp-8 debhelper
dh-autoreconf dh-exec dh-strip-nondeterminism dwz file g++-8 gcc-8
gcc-8-base gettext gettext-base googletest groff-base hdf5-helpers
intltool-debian libaec-dev libaec0 libarchive-zip-perl libasan5 libatomic1
libboost-dev libboost1.67-dev libbsd0 libcc1-0 libcroco3 libcurl3-gnutls
libelf1 libexpat1 libfile-stripnondeterminism-perl libgcc-8-dev libgcc1
libgfortran5 libglib2.0-0 libgomp1 libgtest-dev libhdf5-103 libhdf5-cpp-103
libhdf5-dev libhts-dev libhts2 libicu63 libjpeg-dev libjpeg62-turbo
libjpeg62-turbo-dev liblzma-dev libmagic-mgc libmagic1 libnghttp2-14
libpbbam libpbbam-dev libpipeline1 libpsl5 libpython-stdlib
libpython2-stdlib libpython2.7-minimal libpython2.7-stdlib librtmp1
libsigsegv2 libssh2-1 libssl-dev libstdc++-8-dev libstdc++6 libsz2 libtool
libubsan1 libxml2 m4 man-db mime-support po-debconf python python-minimal
python2 python2-minimal python2.7 python2.7-minimal zlib1g-dev
Suggested packages:
autoconf-archive gnu-standards autoconf-doc wamerican | wordlist whois
vacation gcc-8-locales dh-make gcc-8-doc libstdc++6-8-dbg libgcc1-dbg
libgomp1-dbg libitm1-dbg libatomic1-dbg libasan5-dbg liblsan0-dbg
libtsan0-dbg libubsan1-dbg libmpx2-dbg libquadmath0-dbg gettext-doc
libasprintf-dev libgettextpo-dev groff libboost-doc libboost1.67-doc
libboost-atomic1.67-dev libboost-chrono1.67-dev libboost-container1.67-dev
libboost-context1.67-dev libboost-coroutine1.67-dev
libboost-date-time1.67-dev libboost-exception1.67-dev libboost-fiber1.67-dev
libboost-filesystem1.67-dev libboost-graph1.67-dev
libboost-graph-parallel1.67-dev libboost-iostreams1.67-dev
libboost-locale1.67-dev libboost-log1.67-dev libboost-math1.67-dev
libboost-mpi1.67-dev libboost-mpi-python1.67-dev libboost-numpy1.67-dev
libboost-program-options1.67-dev libboost-python1.67-dev
libboost-random1.67-dev libboost-regex1.67-dev
libboost-serialization1.67-dev libboost-signals1.67-dev
libboost-stacktrace1.67-dev libboost-system1.67-dev libboost-test1.67-dev
libboost-thread1.67-dev libboost-timer1.67-dev libboost-type-erasure1.67-dev
libboost-wave1.67-dev libboost1.67-tools-dev libmpfrc++-dev libntl-dev
libhdf5-doc liblzma-doc libssl-doc libstdc++-8-doc libtool-doc gfortran
| fortran95-compiler gcj-jdk m4-doc apparmor less www-browser
libmail-box-perl python-doc python-tk python2-doc python2.7-doc
binfmt-support
Recommended packages:
curl | wget | lynx libarchive-cpio-perl libglib2.0-data shared-mime-info
xdg-user-dirs publicsuffix libltdl-dev libmail-sendmail-perl
The following NEW packages will be installed:
autoconf automake autopoint autotools-dev bsdmainutils debhelper
dh-autoreconf dh-exec dh-strip-nondeterminism dwz file gettext gettext-base
googletest groff-base hdf5-helpers intltool-debian libaec-dev libaec0
libarchive-zip-perl libboost-dev libboost1.67-dev libbsd0 libcroco3
libcurl3-gnutls libelf1 libexpat1 libfile-stripnondeterminism-perl
libgfortran5 libglib2.0-0 libgtest-dev libhdf5-103 libhdf5-cpp-103
libhdf5-dev libhts-dev libhts2 libicu63 libjpeg-dev libjpeg62-turbo
libjpeg62-turbo-dev liblzma-dev libmagic-mgc libmagic1 libnghttp2-14
libpbbam libpbbam-dev libpipeline1 libpsl5 libpython-stdlib
libpython2-stdlib libpython2.7-minimal libpython2.7-stdlib librtmp1
libsigsegv2 libssh2-1 libssl-dev libsz2 libtool libxml2 m4 man-db
mime-support po-debconf python python-minimal python2 python2-minimal
python2.7 python2.7-minimal sbuild-build-depends-pbseqlib-dummy zlib1g-dev
The following packages will be upgraded:
cpp-8 g++-8 gcc-8 gcc-8-base libasan5 libatomic1 libcc1-0 libgcc-8-dev
libgcc1 libgomp1 libstdc++-8-dev libstdc++6 libubsan1
13 upgraded, 71 newly installed, 0 to remove and 4 not upgraded.
Need to get 62.7 MB of archives.
After this operation, 265 MB of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-2UWkWS/apt_archive ./ sbuild-build-depends-pbseqlib-dummy 0.invalid.0 [904 B]
Get:2 http://172.17.0.1/private buster-staging/main armhf libbsd0 armhf 0.9.1-1 [104 kB]
Get:3 http://172.17.0.1/private buster-staging/main armhf bsdmainutils armhf 11.1.2 [182 kB]
Get:4 http://172.17.0.1/private buster-staging/main armhf libcc1-0 armhf 8.2.0-12+rpi1 [30.1 kB]
Get:5 http://172.17.0.1/private buster-staging/main armhf gcc-8-base armhf 8.2.0-12+rpi1 [188 kB]
Get:6 http://172.17.0.1/private buster-staging/main armhf libgcc1 armhf 1:8.2.0-12+rpi1 [36.6 kB]
Get:7 http://172.17.0.1/private buster-staging/main armhf libgomp1 armhf 8.2.0-12+rpi1 [63.9 kB]
Get:8 http://172.17.0.1/private buster-staging/main armhf libatomic1 armhf 8.2.0-12+rpi1 [8108 B]
Get:9 http://172.17.0.1/private buster-staging/main armhf libasan5 armhf 8.2.0-12+rpi1 [318 kB]
Get:10 http://172.17.0.1/private buster-staging/main armhf libubsan1 armhf 8.2.0-12+rpi1 [104 kB]
Get:11 http://172.17.0.1/private buster-staging/main armhf g++-8 armhf 8.2.0-12+rpi1 [5942 kB]
Get:12 http://172.17.0.1/private buster-staging/main armhf libstdc++-8-dev armhf 8.2.0-12+rpi1 [1565 kB]
Get:13 http://172.17.0.1/private buster-staging/main armhf libgcc-8-dev armhf 8.2.0-12+rpi1 [3743 kB]
Get:14 http://172.17.0.1/private buster-staging/main armhf gcc-8 armhf 8.2.0-12+rpi1 [5848 kB]
Get:15 http://172.17.0.1/private buster-staging/main armhf cpp-8 armhf 8.2.0-12+rpi1 [5475 kB]
Get:16 http://172.17.0.1/private buster-staging/main armhf libstdc++6 armhf 8.2.0-12+rpi1 [326 kB]
Get:17 http://172.17.0.1/private buster-staging/main armhf groff-base armhf 1.22.3-10 [1005 kB]
Get:18 http://172.17.0.1/private buster-staging/main armhf libpipeline1 armhf 1.5.0-2 [25.1 kB]
Get:19 http://172.17.0.1/private buster-staging/main armhf man-db armhf 2.8.4-3 [1160 kB]
Get:20 http://172.17.0.1/private buster-staging/main armhf libpython2.7-minimal armhf 2.7.15-5 [394 kB]
Get:21 http://172.17.0.1/private buster-staging/main armhf python2.7-minimal armhf 2.7.15-5 [1089 kB]
Get:22 http://172.17.0.1/private buster-staging/main armhf python2-minimal armhf 2.7.15-3 [41.3 kB]
Get:23 http://172.17.0.1/private buster-staging/main armhf python-minimal armhf 2.7.15-3 [20.9 kB]
Get:24 http://172.17.0.1/private buster-staging/main armhf mime-support all 3.61 [37.1 kB]
Get:25 http://172.17.0.1/private buster-staging/main armhf libexpat1 armhf 2.2.6-1 [76.8 kB]
Get:26 http://172.17.0.1/private buster-staging/main armhf libpython2.7-stdlib armhf 2.7.15-5 [1844 kB]
Get:27 http://172.17.0.1/private buster-staging/main armhf python2.7 armhf 2.7.15-5 [299 kB]
Get:28 http://172.17.0.1/private buster-staging/main armhf libpython2-stdlib armhf 2.7.15-3 [20.7 kB]
Get:29 http://172.17.0.1/private buster-staging/main armhf libpython-stdlib armhf 2.7.15-3 [20.7 kB]
Get:30 http://172.17.0.1/private buster-staging/main armhf python2 armhf 2.7.15-3 [41.5 kB]
Get:31 http://172.17.0.1/private buster-staging/main armhf python armhf 2.7.15-3 [22.7 kB]
Get:32 http://172.17.0.1/private buster-staging/main armhf libmagic-mgc armhf 1:5.34-2 [239 kB]
Get:33 http://172.17.0.1/private buster-staging/main armhf libmagic1 armhf 1:5.34-2 [107 kB]
Get:34 http://172.17.0.1/private buster-staging/main armhf file armhf 1:5.34-2 [65.0 kB]
Get:35 http://172.17.0.1/private buster-staging/main armhf gettext-base armhf 0.19.8.1-9 [117 kB]
Get:36 http://172.17.0.1/private buster-staging/main armhf libsigsegv2 armhf 2.12-2 [32.3 kB]
Get:37 http://172.17.0.1/private buster-staging/main armhf m4 armhf 1.4.18-2 [185 kB]
Get:38 http://172.17.0.1/private buster-staging/main armhf autoconf all 2.69-11 [341 kB]
Get:39 http://172.17.0.1/private buster-staging/main armhf autotools-dev all 20180224.1 [77.0 kB]
Get:40 http://172.17.0.1/private buster-staging/main armhf automake all 1:1.16.1-4 [771 kB]
Get:41 http://172.17.0.1/private buster-staging/main armhf autopoint all 0.19.8.1-9 [434 kB]
Get:42 http://172.17.0.1/private buster-staging/main armhf libtool all 2.4.6-6 [547 kB]
Get:43 http://172.17.0.1/private buster-staging/main armhf dh-autoreconf all 19 [16.9 kB]
Get:44 http://172.17.0.1/private buster-staging/main armhf libarchive-zip-perl all 1.64-1 [96.8 kB]
Get:45 http://172.17.0.1/private buster-staging/main armhf libfile-stripnondeterminism-perl all 1.0.0-1 [19.5 kB]
Get:46 http://172.17.0.1/private buster-staging/main armhf dh-strip-nondeterminism all 1.0.0-1 [12.5 kB]
Get:47 http://172.17.0.1/private buster-staging/main armhf libelf1 armhf 0.170-0.5 [160 kB]
Get:48 http://172.17.0.1/private buster-staging/main armhf dwz armhf 0.12-3 [66.0 kB]
Get:49 http://172.17.0.1/private buster-staging/main armhf libglib2.0-0 armhf 2.58.1-2 [1051 kB]
Get:50 http://172.17.0.1/private buster-staging/main armhf libicu63 armhf 63.1-5 [7976 kB]
Get:51 http://172.17.0.1/private buster-staging/main armhf libxml2 armhf 2.9.4+dfsg1-7+b1 [570 kB]
Get:52 http://172.17.0.1/private buster-staging/main armhf libcroco3 armhf 0.6.12-2 [132 kB]
Get:53 http://172.17.0.1/private buster-staging/main armhf gettext armhf 0.19.8.1-9 [1219 kB]
Get:54 http://172.17.0.1/private buster-staging/main armhf intltool-debian all 0.35.0+20060710.4 [26.3 kB]
Get:55 http://172.17.0.1/private buster-staging/main armhf po-debconf all 1.0.21 [248 kB]
Get:56 http://172.17.0.1/private buster-staging/main armhf debhelper all 11.5.4 [1003 kB]
Get:57 http://172.17.0.1/private buster-staging/main armhf googletest armhf 1.8.0-10.1 [648 kB]
Get:58 http://172.17.0.1/private buster-staging/main armhf hdf5-helpers armhf 1.10.4+repack-1 [33.0 kB]
Get:59 http://172.17.0.1/private buster-staging/main armhf libaec0 armhf 1.0.2-1 [21.3 kB]
Get:60 http://172.17.0.1/private buster-staging/main armhf libsz2 armhf 1.0.2-1 [6640 B]
Get:61 http://172.17.0.1/private buster-staging/main armhf libaec-dev armhf 1.0.2-1 [19.1 kB]
Get:62 http://172.17.0.1/private buster-staging/main armhf libboost1.67-dev armhf 1.67.0-11 [8386 kB]
Get:63 http://172.17.0.1/private buster-staging/main armhf libboost-dev armhf 1.67.0.1+b1 [4140 B]
Get:64 http://172.17.0.1/private buster-staging/main armhf libnghttp2-14 armhf 1.35.1-1 [70.8 kB]
Get:65 http://172.17.0.1/private buster-staging/main armhf libpsl5 armhf 0.20.2-2 [52.6 kB]
Get:66 http://172.17.0.1/private buster-staging/main armhf librtmp1 armhf 2.4+20151223.gitfa8646d.1-2 [54.0 kB]
Get:67 http://172.17.0.1/private buster-staging/main armhf libssh2-1 armhf 1.8.0-2 [125 kB]
Get:68 http://172.17.0.1/private buster-staging/main armhf libcurl3-gnutls armhf 7.62.0-1 [284 kB]
Get:69 http://172.17.0.1/private buster-staging/main armhf libgfortran5 armhf 8.2.0-12+rpi1 [205 kB]
Get:70 http://172.17.0.1/private buster-staging/main armhf libgtest-dev armhf 1.8.0-10.1 [203 kB]
Get:71 http://172.17.0.1/private buster-staging/main armhf libhdf5-103 armhf 1.10.4+repack-1 [1258 kB]
Get:72 http://172.17.0.1/private buster-staging/main armhf libhdf5-cpp-103 armhf 1.10.4+repack-1 [118 kB]
Get:73 http://172.17.0.1/private buster-staging/main armhf zlib1g-dev armhf 1:1.2.11.dfsg-1 [206 kB]
Get:74 http://172.17.0.1/private buster-staging/main armhf libjpeg62-turbo armhf 1:1.5.2-2+b1 [110 kB]
Get:75 http://172.17.0.1/private buster-staging/main armhf libjpeg62-turbo-dev armhf 1:1.5.2-2+b1 [179 kB]
Get:76 http://172.17.0.1/private buster-staging/main armhf libjpeg-dev all 1:1.5.2-2 [57.5 kB]
Get:77 http://172.17.0.1/private buster-staging/main armhf libhdf5-dev armhf 1.10.4+repack-1 [2220 kB]
Get:78 http://172.17.0.1/private buster-staging/main armhf libhts2 armhf 1.7-2 [259 kB]
Get:79 http://172.17.0.1/private buster-staging/main armhf liblzma-dev armhf 5.2.2-1.3 [284 kB]
Get:80 http://172.17.0.1/private buster-staging/main armhf libhts-dev armhf 1.7-2 [329 kB]
Get:81 http://172.17.0.1/private buster-staging/main armhf libpbbam armhf 0.7.4+ds-1+rpi1+b1 [395 kB]
Get:82 http://172.17.0.1/private buster-staging/main armhf libssl-dev armhf 1.1.1a-1 [1556 kB]
Get:83 http://172.17.0.1/private buster-staging/main armhf libpbbam-dev armhf 0.7.4+ds-1+rpi1+b1 [90.2 kB]
Get:84 http://172.17.0.1/private buster-staging/main armhf dh-exec armhf 0.23+b8 [25.3 kB]
debconf: delaying package configuration, since apt-utils is not installed
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+------------------------------------------------------------------------------+
| Build environment |
+------------------------------------------------------------------------------+
Kernel: Linux 4.9.0-0.bpo.1-armmp armhf (armv7l)
Toolchain package versions: binutils_2.31.1-10+rpi1 dpkg-dev_1.19.2 g++-8_8.2.0-12+rpi1 gcc-8_8.2.0-12+rpi1 libc6-dev_2.28-2 libstdc++-8-dev_8.2.0-12+rpi1 libstdc++6_8.2.0-12+rpi1 linux-libc-dev_4.18.20-2+rpi1
Package versions: adduser_3.118 apt_1.8.0~alpha2 autoconf_2.69-11 automake_1:1.16.1-4 autopoint_0.19.8.1-9 autotools-dev_20180224.1 base-files_10.1+rpi1 base-passwd_3.5.45 bash_4.4.18-3.1 binutils_2.31.1-10+rpi1 binutils-arm-linux-gnueabihf_2.31.1-10+rpi1 binutils-common_2.31.1-10+rpi1 bsdmainutils_11.1.2 bsdutils_1:2.33-0.2 build-essential_12.5 bzip2_1.0.6-9 ca-certificates_20170717 coreutils_8.30-1 cpio_2.12+dfsg-6 cpp_4:8.2.0-2+rpi1 cpp-8_8.2.0-12+rpi1 dash_0.5.10.2-2 debconf_1.5.69 debhelper_11.5.4 debianutils_4.8.6 dh-autoreconf_19 dh-exec_0.23+b8 dh-strip-nondeterminism_1.0.0-1 diffutils_1:3.6-1 dirmngr_2.2.11-1 dmsetup_2:1.02.145-4.1+b5 dpkg_1.19.2 dpkg-dev_1.19.2 dwz_0.12-3 e2fslibs_1.44.4-2 e2fsprogs_1.44.4-2 e2fsprogs-l10n_1.44.4-2 fakeroot_1.23-1 fdisk_2.33-0.2 file_1:5.34-2 findutils_4.6.0+git+20181018-1 g++_4:8.2.0-2+rpi1 g++-8_8.2.0-12+rpi1 gcc_4:8.2.0-2+rpi1 gcc-4.6-base_4.6.4-5+rpi1 gcc-4.7-base_4.7.3-11+rpi1 gcc-4.8-base_4.8.5-4 gcc-4.9-base_4.9.4-2+rpi1+b19 gcc-5-base_5.5.0-8 gcc-8_8.2.0-12+rpi1 gcc-8-base_8.2.0-12+rpi1 gettext_0.19.8.1-9 gettext-base_0.19.8.1-9 gnupg_2.2.11-1 gnupg-agent_2.2.11-1 gnupg-l10n_2.2.11-1 gnupg-utils_2.2.11-1 googletest_1.8.0-10.1 gpg_2.2.11-1 gpg-agent_2.2.11-1 gpg-wks-client_2.2.11-1 gpg-wks-server_2.2.11-1 gpgconf_2.2.11-1 gpgsm_2.2.11-1 gpgv_2.2.11-1 grep_3.1-2 groff-base_1.22.3-10 gzip_1.9-2.1 hdf5-helpers_1.10.4+repack-1 hostname_3.21 inetutils-ping_2:1.9.4-5 init-system-helpers_1.56 initramfs-tools_0.132 initramfs-tools-core_0.132 intltool-debian_0.35.0+20060710.4 klibc-utils_2.0.4-14+rpi1 kmod_25-2 krb5-locales_1.16.1-1 libacl1_2.2.52-3 libaec-dev_1.0.2-1 libaec0_1.0.2-1 libapparmor1_2.13.1-3+b1 libapt-pkg5.0_1.8.0~alpha2 libarchive-zip-perl_1.64-1 libargon2-1_0~20171227-0.1 libasan5_8.2.0-12+rpi1 libassuan0_2.5.1-2 libatomic1_8.2.0-12+rpi1 libattr1_1:2.4.47-2 libaudit-common_1:2.8.4-2 libaudit1_1:2.8.4-2 libbinutils_2.31.1-10+rpi1 libblkid1_2.33-0.2 libboost-dev_1.67.0.1+b1 libboost1.67-dev_1.67.0-11 libbsd0_0.9.1-1 libbz2-1.0_1.0.6-9 libc-bin_2.28-2 libc-dev-bin_2.28-2 libc6_2.28-2 libc6-dev_2.28-2 libcap-ng0_0.7.9-1 libcap2_1:2.25-1.2 libcc1-0_8.2.0-12+rpi1 libcom-err2_1.44.4-2 libcroco3_0.6.12-2 libcryptsetup12_2:2.0.6-1 libcryptsetup4_2:1.7.5-1 libcurl3-gnutls_7.62.0-1 libdb5.3_5.3.28+dfsg1-0.2 libdbus-1-3_1.12.12-1 libdebconfclient0_0.245 libdevmapper1.02.1_2:1.02.145-4.1+b5 libdpkg-perl_1.19.2 libdrm-common_2.4.95-1+rpi1 libdrm2_2.4.95-1+rpi1 libelf1_0.170-0.5 libexpat1_2.2.6-1 libext2fs2_1.44.4-2 libfakeroot_1.23-1 libfdisk1_2.33-0.2 libffi6_3.2.1-9 libfile-stripnondeterminism-perl_1.0.0-1 libgcc-8-dev_8.2.0-12+rpi1 libgcc1_1:8.2.0-12+rpi1 libgcrypt20_1.8.4-4 libgdbm-compat4_1.18.1-2 libgdbm3_1.8.3-14 libgdbm6_1.18.1-2 libgfortran5_8.2.0-12+rpi1 libglib2.0-0_2.58.1-2 libgmp10_2:6.1.2+dfsg-4 libgnutls30_3.5.19-1+b1 libgomp1_8.2.0-12+rpi1 libgpg-error-l10n_1.32-3 libgpg-error0_1.32-3 libgssapi-krb5-2_1.16.1-1 libgtest-dev_1.8.0-10.1 libhdf5-103_1.10.4+repack-1 libhdf5-cpp-103_1.10.4+repack-1 libhdf5-dev_1.10.4+repack-1 libhogweed4_3.4.1~rc1-1 libhts-dev_1.7-2 libhts2_1.7-2 libicu63_63.1-5 libidn11_1.33-2.2 libidn2-0_2.0.5-1 libip4tc0_1.8.2-2+b1 libisl19_0.20-2 libjpeg-dev_1:1.5.2-2 libjpeg62-turbo_1:1.5.2-2+b1 libjpeg62-turbo-dev_1:1.5.2-2+b1 libjson-c3_0.12.1-1.3 libk5crypto3_1.16.1-1 libkeyutils1_1.5.9-9.3 libklibc_2.0.4-14+rpi1 libkmod2_25-2 libkrb5-3_1.16.1-1 libkrb5support0_1.16.1-1 libksba8_1.3.5-2 libldap-2.4-2_2.4.46+dfsg-5+rpi1+b1 libldap-common_2.4.46+dfsg-5+rpi1 liblz4-1_1.8.2-1+rpi1 liblzma-dev_5.2.2-1.3 liblzma5_5.2.2-1.3 libmagic-mgc_1:5.34-2 libmagic1_1:5.34-2 libmount1_2.33-0.2 libmpc3_1.1.0-1 libmpfr6_4.0.1-2 libncurses5_6.1+20181013-1 libncurses6_6.1+20181013-1 libncursesw5_6.1+20181013-1 libncursesw6_6.1+20181013-1 libnettle6_3.4.1~rc1-1 libnghttp2-14_1.35.1-1 libnpth0_1.6-1 libp11-kit0_0.23.14-2 libpam-modules_1.1.8-3.8 libpam-modules-bin_1.1.8-3.8 libpam-runtime_1.1.8-3.8 libpam0g_1.1.8-3.8 libpbbam_0.7.4+ds-1+rpi1+b1 libpbbam-dev_0.7.4+ds-1+rpi1+b1 libpcre3_2:8.39-11+rpi1 libperl5.24_5.24.1-7 libperl5.28_5.28.1-3 libpipeline1_1.5.0-2 libplymouth4_0.9.4-1 libpng16-16_1.6.34-2+rpi1 libprocps7_2:3.3.15-2 libpsl5_0.20.2-2 libpython-stdlib_2.7.15-3 libpython2-stdlib_2.7.15-3 libpython2.7-minimal_2.7.15-5 libpython2.7-stdlib_2.7.15-5 libreadline7_7.0-5 librtmp1_2.4+20151223.gitfa8646d.1-2 libsasl2-2_2.1.27~rc8-1 libsasl2-modules_2.1.27~rc8-1 libsasl2-modules-db_2.1.27~rc8-1 libseccomp2_2.3.3-3 libselinux1_2.8-1 libsemanage-common_2.8-1 libsemanage1_2.8-1 libsepol1_2.8-1 libsigsegv2_2.12-2 libsmartcols1_2.33-0.2 libsqlite3-0_3.26.0-3 libss2_1.44.4-2 libssh2-1_1.8.0-2 libssl-dev_1.1.1a-1 libssl1.1_1.1.1a-1 libstdc++-8-dev_8.2.0-12+rpi1 libstdc++6_8.2.0-12+rpi1 libsystemd0_239-15+rpi1 libsz2_1.0.2-1 libtasn1-6_4.13-3 libtinfo5_6.1+20181013-1 libtinfo6_6.1+20181013-1 libtool_2.4.6-6 libubsan1_8.2.0-12+rpi1 libudev1_239-15+rpi1 libunistring2_0.9.10-1 libustr-1.0-1_1.0.4-6 libuuid1_2.33-0.2 libxml2_2.9.4+dfsg1-7+b1 libzstd1_1.3.5+dfsg-1+rpi1 linux-base_4.5 linux-libc-dev_4.18.20-2+rpi1 login_1:4.5-1.1 lsb-base_10.2018112800+rpi1 m4_1.4.18-2 make_4.2.1-1.2 makedev_2.3.1-94 man-db_2.8.4-3 mawk_1.3.3-17 mime-support_3.61 mount_2.33-0.2 multiarch-support_2.28-2 nano_3.2-1 ncurses-base_6.1+20181013-1 ncurses-bin_6.1+20181013-1 netbase_5.5 openssl_1.1.1a-1 passwd_1:4.5-1.1 patch_2.7.6-3 perl_5.28.1-3 perl-base_5.28.1-3 perl-modules-5.24_5.24.1-7 perl-modules-5.28_5.28.1-3 pinentry-curses_1.1.0-1 plymouth_0.9.4-1 po-debconf_1.0.21 procps_2:3.3.15-2 python_2.7.15-3 python-minimal_2.7.15-3 python2_2.7.15-3 python2-minimal_2.7.15-3 python2.7_2.7.15-5 python2.7-minimal_2.7.15-5 raspbian-archive-keyring_20120528.2 readline-common_7.0-5 sbuild-build-depends-core-dummy_0.invalid.0 sbuild-build-depends-pbseqlib-dummy_0.invalid.0 sed_4.5-2 sensible-utils_0.0.12 systemd_239-15+rpi1 sysvinit-utils_2.93-1 tar_1.30+dfsg-3+rpi1 tzdata_2018g-1 udev_239-15+rpi1 util-linux_2.33-0.2 xz-utils_5.2.2-1.3 zlib1g_1:1.2.11.dfsg-1 zlib1g-dev_1:1.2.11.dfsg-1
+------------------------------------------------------------------------------+
| Build |
+------------------------------------------------------------------------------+
Unpack source
-------------
gpgv: unknown type of key resource 'trustedkeys.kbx'
gpgv: keyblock resource '/sbuild-nonexistent/.gnupg/trustedkeys.kbx': General error
gpgv: Signature made Fri Nov 10 03:51:02 2017 UTC
gpgv: using RSA key EAB723A266F627E68055615F59B2306F3AF9DDC1
gpgv: issuer "afif@debian.org"
gpgv: Can't check signature: No public key
dpkg-source: warning: failed to verify signature on ./pbseqlib_0~20161219-2.dsc
dpkg-source: info: extracting pbseqlib in /<<PKGBUILDDIR>>
dpkg-source: info: unpacking pbseqlib_0~20161219.orig.tar.gz
dpkg-source: info: unpacking pbseqlib_0~20161219-2.debian.tar.xz
dpkg-source: info: using patch list from debian/patches/series
dpkg-source: info: applying hdf5-1.10.1-support.patch
Check disc space
----------------
Sufficient free space for build
Hack binNMU version
-------------------
Created changelog entry for binNMU version 0~20161219-2+b1
User Environment
----------------
APT_CONFIG=/var/lib/sbuild/apt.conf
DEB_BUILD_OPTIONS=parallel=4
HOME=/sbuild-nonexistent
LC_ALL=POSIX
LOGNAME=buildd
PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games
SCHROOT_ALIAS_NAME=buster-staging-armhf-sbuild
SCHROOT_CHROOT_NAME=buster-staging-armhf-sbuild
SCHROOT_COMMAND=env
SCHROOT_GID=109
SCHROOT_GROUP=buildd
SCHROOT_SESSION_ID=buster-staging-armhf-sbuild-d69f5afd-13b4-4bd8-9749-5d880d6872a2
SCHROOT_UID=104
SCHROOT_USER=buildd
SHELL=/bin/sh
TERM=linux
USER=buildd
dpkg-buildpackage
-----------------
dpkg-buildpackage: info: source package pbseqlib
dpkg-buildpackage: info: source version 0~20161219-2+b1
dpkg-buildpackage: info: source distribution buster-staging
dpkg-source --before-build .
dpkg-buildpackage: info: host architecture armhf
fakeroot debian/rules clean
dh clean
debian/rules override_dh_auto_clean
make[1]: Entering directory '/<<PKGBUILDDIR>>'
dh_auto_clean
make -j4 clean
make[2]: Entering directory '/<<PKGBUILDDIR>>'
make -C /<<PKGBUILDDIR>>//pbdata clean
make[3]: Entering directory '/<<PKGBUILDDIR>>/pbdata'
rm -f libpbdata.a libpbdata.so *.o *.d
make[3]: Leaving directory '/<<PKGBUILDDIR>>/pbdata'
make -C /<<PKGBUILDDIR>>//hdf clean
make[3]: Entering directory '/<<PKGBUILDDIR>>/hdf'
rm -f libpbihdf.a libpbihdf.so *.o *.d
make[3]: Leaving directory '/<<PKGBUILDDIR>>/hdf'
make -C /<<PKGBUILDDIR>>//alignment clean
make[3]: Entering directory '/<<PKGBUILDDIR>>/alignment'
rm -f libblasr.a libblasr.so *.o *.d
make[3]: Leaving directory '/<<PKGBUILDDIR>>/alignment'
make -C /<<PKGBUILDDIR>>//unittest clean
make[3]: Entering directory '/<<PKGBUILDDIR>>/unittest'
rm -f -r *.o libblasr-test-runner
make[3]: Leaving directory '/<<PKGBUILDDIR>>/unittest'
make[2]: Leaving directory '/<<PKGBUILDDIR>>'
find -name defines.mk -delete
rm -f pbdata/libconfig.h
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
dh_clean
debian/rules build-arch
dh build-arch
dh_update_autotools_config -a
dh_autoreconf -a
debian/rules override_dh_auto_configure
make[1]: Entering directory '/<<PKGBUILDDIR>>'
./configure.py PREFIX=/usr/
uname -s
uname='Linux'
writing to '/<<PKGBUILDDIR>>/pbdata/libconfig.h'
"""
#define USE_PBBAM
"""
writing to 'defines.mk'
"""
CXXFLAGS := -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3
PREFIX_INC := /usr/include
PREFIX_LIB := /usr/lib
SH_LIB_EXT := .so
GTEST_INC ?= /usr/include
GTEST_SRCDIR ?= /usr/src/gtest
HDF5_INC ?= /usr/include/hdf5/serial
HDF5_LIB ?= /usr/lib/arm-linux-gnueabihf/hdf5/serial
LIBBLASR_INC ?= ../alignment
LIBBLASR_LIB ?= ../alignment/
LIBPBDATA_INC ?= ../pbdata
LIBPBDATA_LIB ?= ../pbdata/
LIBPBIHDF_INC ?= ../hdf
LIBPBIHDF_LIB ?= ../hdf/
SHELL ?= bash
# Use PREFIX dir, if available.
INCLUDES += ${PREFIX_INC}
LIBS += ${PREFIX_LIB}
"""
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
dh_auto_build -a
make -j4
make[1]: Entering directory '/<<PKGBUILDDIR>>'
make libpbdata
make[2]: Entering directory '/<<PKGBUILDDIR>>'
make -C /<<PKGBUILDDIR>>//pbdata libconfig.h
make[3]: Entering directory '/<<PKGBUILDDIR>>/pbdata'
make[3]: 'libconfig.h' is up to date.
make[3]: Leaving directory '/<<PKGBUILDDIR>>/pbdata'
make -C /<<PKGBUILDDIR>>//pbdata all
make[3]: Entering directory '/<<PKGBUILDDIR>>/pbdata'
g++ -std=c++11 -pedantic -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I/usr/include -c CCSSequence.cpp -o CCSSequence.o
g++ -std=c++11 -pedantic -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I/usr/include -c ChangeListID.cpp -o ChangeListID.o
g++ -std=c++11 -pedantic -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I/usr/include -c CommandLineParser.cpp -o CommandLineParser.o
g++ -std=c++11 -pedantic -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I/usr/include -c DNASequence.cpp -o DNASequence.o
g++ -std=c++11 -pedantic -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I/usr/include -c FASTAReader.cpp -o FASTAReader.o
CommandLineParser.cpp: In member function 'CommandLineParser::ErrorValue CommandLineParser::ParseOption(int, int&, int, char**)':
CommandLineParser.cpp:362:5: warning: 'ev' may be used uninitialized in this function [-Wmaybe-uninitialized]
if (ev == CLGood) {
^~
g++ -std=c++11 -pedantic -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I/usr/include -c FASTASequence.cpp -o FASTASequence.o
g++ -std=c++11 -pedantic -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I/usr/include -c FASTQReader.cpp -o FASTQReader.o
g++ -std=c++11 -pedantic -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I/usr/include -c FASTQSequence.cpp -o FASTQSequence.o
g++ -std=c++11 -pedantic -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I/usr/include -c GFFFile.cpp -o GFFFile.o
g++ -std=c++11 -pedantic -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I/usr/include -c MD5Utils.cpp -o MD5Utils.o
g++ -std=c++11 -pedantic -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I/usr/include -c NucConversion.cpp -o NucConversion.o
g++ -std=c++11 -pedantic -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I/usr/include -c PackedDNASequence.cpp -o PackedDNASequence.o
g++ -std=c++11 -pedantic -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I/usr/include -c ReverseCompressIndex.cpp -o ReverseCompressIndex.o
g++ -std=c++11 -pedantic -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I/usr/include -c SMRTSequence.cpp -o SMRTSequence.o
g++ -std=c++11 -pedantic -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I/usr/include -c StringUtils.cpp -o StringUtils.o
g++ -std=c++11 -pedantic -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I/usr/include -c alignment/CmpAlignment.cpp -o CmpAlignment.o
g++ -std=c++11 -pedantic -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I/usr/include -c amos/AfgBasWriter.cpp -o AfgBasWriter.o
g++ -std=c++11 -pedantic -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I/usr/include -c loadpulses/MetricField.cpp -o MetricField.o
g++ -std=c++11 -pedantic -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I/usr/include -c loadpulses/MovieAlnIndexLookupTable.cpp -o MovieAlnIndexLookupTable.o
g++ -std=c++11 -pedantic -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I/usr/include -c metagenome/TitleTable.cpp -o TitleTable.o
g++ -std=c++11 -pedantic -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I/usr/include -c qvs/QualityTransform.cpp -o QualityTransform.o
g++ -std=c++11 -pedantic -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I/usr/include -c qvs/QualityValue.cpp -o QualityValue.o
g++ -std=c++11 -pedantic -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I/usr/include -c reads/AcqParams.cpp -o AcqParams.o
g++ -std=c++11 -pedantic -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I/usr/include -c reads/BaseFile.cpp -o BaseFile.o
g++ -std=c++11 -pedantic -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I/usr/include -c reads/HoleXY.cpp -o HoleXY.o
g++ -std=c++11 -pedantic -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I/usr/include -c reads/PulseBaseCommon.cpp -o PulseBaseCommon.o
g++ -std=c++11 -pedantic -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I/usr/include -c reads/PulseFile.cpp -o PulseFile.o
g++ -std=c++11 -pedantic -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I/usr/include -c reads/ReadType.cpp -o ReadType.o
g++ -std=c++11 -pedantic -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I/usr/include -c reads/RegionAnnotation.cpp -o RegionAnnotation.o
g++ -std=c++11 -pedantic -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I/usr/include -c reads/RegionAnnotations.cpp -o RegionAnnotations.o
g++ -std=c++11 -pedantic -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I/usr/include -c reads/RegionTable.cpp -o RegionTable.o
g++ -std=c++11 -pedantic -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I/usr/include -c reads/RegionTypeMap.cpp -o RegionTypeMap.o
g++ -std=c++11 -pedantic -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I/usr/include -c reads/ScanData.cpp -o ScanData.o
g++ -std=c++11 -pedantic -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I/usr/include -c reads/ZMWGroupEntry.cpp -o ZMWGroupEntry.o
g++ -std=c++11 -pedantic -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I/usr/include -c saf/AlnGroup.cpp -o AlnGroup.o
g++ -std=c++11 -pedantic -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I/usr/include -c saf/MovieInfo.cpp -o MovieInfo.o
g++ -std=c++11 -pedantic -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I/usr/include -c saf/RefGroup.cpp -o RefGroup.o
g++ -std=c++11 -pedantic -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I/usr/include -c saf/RefInfo.cpp -o RefInfo.o
g++ -std=c++11 -pedantic -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I/usr/include -c sam/ReadGroup.cpp -o ReadGroup.o
g++ -std=c++11 -pedantic -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I/usr/include -c sam/ReferenceSequence.cpp -o ReferenceSequence.o
g++ -std=c++11 -pedantic -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I/usr/include -c sam/SAMAlignment.cpp -o SAMAlignment.o
g++ -std=c++11 -pedantic -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I/usr/include -c sam/SAMHeader.cpp -o SAMHeader.o
g++ -std=c++11 -pedantic -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I/usr/include -c sam/SAMKeywordValuePair.cpp -o SAMKeywordValuePair.o
g++ -std=c++11 -pedantic -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I/usr/include -c utils/BitUtils.cpp -o BitUtils.o
g++ -std=c++11 -pedantic -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I/usr/include -c utils/SMRTReadUtils.cpp -o SMRTReadUtils.o
sam/SAMAlignment.cpp: In member function 'bool SAMAlignment::StoreValues(std::__cxx11::string&, int)':
sam/SAMAlignment.cpp:110:139: warning: 'field' may be used uninitialized in this function [-Wmaybe-uninitialized]
std::cout << "Error parsing alignment line " << lineNumber << ". Missing or error in field " << SAMAlignmentRequiredFieldNames[field] << std::endl;
^
g++ -std=c++11 -pedantic -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I/usr/include -c utils/SMRTTitle.cpp -o SMRTTitle.o
g++ -std=c++11 -pedantic -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I/usr/include -c utils/TimeUtils.cpp -o TimeUtils.o
g++ -std=c++11 -pedantic -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I/usr/include -fPIC -c CCSSequence.cpp -o CCSSequence.shared.o
g++ -std=c++11 -pedantic -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I/usr/include -fPIC -c ChangeListID.cpp -o ChangeListID.shared.o
g++ -std=c++11 -pedantic -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I/usr/include -fPIC -c CommandLineParser.cpp -o CommandLineParser.shared.o
g++ -std=c++11 -pedantic -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I/usr/include -fPIC -c DNASequence.cpp -o DNASequence.shared.o
CommandLineParser.cpp: In member function 'CommandLineParser::ErrorValue CommandLineParser::ParseOption(int, int&, int, char**)':
CommandLineParser.cpp:365:12: warning: 'ev' may be used uninitialized in this function [-Wmaybe-uninitialized]
return ev;
^~
g++ -std=c++11 -pedantic -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I/usr/include -fPIC -c FASTAReader.cpp -o FASTAReader.shared.o
g++ -std=c++11 -pedantic -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I/usr/include -fPIC -c FASTASequence.cpp -o FASTASequence.shared.o
g++ -std=c++11 -pedantic -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I/usr/include -fPIC -c FASTQReader.cpp -o FASTQReader.shared.o
g++ -std=c++11 -pedantic -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I/usr/include -fPIC -c FASTQSequence.cpp -o FASTQSequence.shared.o
g++ -std=c++11 -pedantic -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I/usr/include -fPIC -c GFFFile.cpp -o GFFFile.shared.o
g++ -std=c++11 -pedantic -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I/usr/include -fPIC -c MD5Utils.cpp -o MD5Utils.shared.o
g++ -std=c++11 -pedantic -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I/usr/include -fPIC -c NucConversion.cpp -o NucConversion.shared.o
g++ -std=c++11 -pedantic -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I/usr/include -fPIC -c PackedDNASequence.cpp -o PackedDNASequence.shared.o
g++ -std=c++11 -pedantic -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I/usr/include -fPIC -c ReverseCompressIndex.cpp -o ReverseCompressIndex.shared.o
g++ -std=c++11 -pedantic -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I/usr/include -fPIC -c SMRTSequence.cpp -o SMRTSequence.shared.o
g++ -std=c++11 -pedantic -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I/usr/include -fPIC -c StringUtils.cpp -o StringUtils.shared.o
g++ -std=c++11 -pedantic -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I/usr/include -fPIC -c alignment/CmpAlignment.cpp -o CmpAlignment.shared.o
g++ -std=c++11 -pedantic -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I/usr/include -fPIC -c amos/AfgBasWriter.cpp -o AfgBasWriter.shared.o
g++ -std=c++11 -pedantic -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I/usr/include -fPIC -c loadpulses/MetricField.cpp -o MetricField.shared.o
g++ -std=c++11 -pedantic -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I/usr/include -fPIC -c loadpulses/MovieAlnIndexLookupTable.cpp -o MovieAlnIndexLookupTable.shared.o
g++ -std=c++11 -pedantic -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I/usr/include -fPIC -c metagenome/TitleTable.cpp -o TitleTable.shared.o
g++ -std=c++11 -pedantic -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I/usr/include -fPIC -c qvs/QualityTransform.cpp -o QualityTransform.shared.o
g++ -std=c++11 -pedantic -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I/usr/include -fPIC -c qvs/QualityValue.cpp -o QualityValue.shared.o
g++ -std=c++11 -pedantic -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I/usr/include -fPIC -c reads/AcqParams.cpp -o AcqParams.shared.o
g++ -std=c++11 -pedantic -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I/usr/include -fPIC -c reads/BaseFile.cpp -o BaseFile.shared.o
g++ -std=c++11 -pedantic -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I/usr/include -fPIC -c reads/HoleXY.cpp -o HoleXY.shared.o
g++ -std=c++11 -pedantic -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I/usr/include -fPIC -c reads/PulseBaseCommon.cpp -o PulseBaseCommon.shared.o
g++ -std=c++11 -pedantic -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I/usr/include -fPIC -c reads/PulseFile.cpp -o PulseFile.shared.o
g++ -std=c++11 -pedantic -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I/usr/include -fPIC -c reads/ReadType.cpp -o ReadType.shared.o
g++ -std=c++11 -pedantic -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I/usr/include -fPIC -c reads/RegionAnnotation.cpp -o RegionAnnotation.shared.o
g++ -std=c++11 -pedantic -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I/usr/include -fPIC -c reads/RegionAnnotations.cpp -o RegionAnnotations.shared.o
g++ -std=c++11 -pedantic -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I/usr/include -fPIC -c reads/RegionTable.cpp -o RegionTable.shared.o
g++ -std=c++11 -pedantic -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I/usr/include -fPIC -c reads/RegionTypeMap.cpp -o RegionTypeMap.shared.o
g++ -std=c++11 -pedantic -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I/usr/include -fPIC -c reads/ScanData.cpp -o ScanData.shared.o
g++ -std=c++11 -pedantic -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I/usr/include -fPIC -c reads/ZMWGroupEntry.cpp -o ZMWGroupEntry.shared.o
g++ -std=c++11 -pedantic -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I/usr/include -fPIC -c saf/AlnGroup.cpp -o AlnGroup.shared.o
g++ -std=c++11 -pedantic -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I/usr/include -fPIC -c saf/MovieInfo.cpp -o MovieInfo.shared.o
g++ -std=c++11 -pedantic -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I/usr/include -fPIC -c saf/RefGroup.cpp -o RefGroup.shared.o
g++ -std=c++11 -pedantic -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I/usr/include -fPIC -c saf/RefInfo.cpp -o RefInfo.shared.o
g++ -std=c++11 -pedantic -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I/usr/include -fPIC -c sam/ReadGroup.cpp -o ReadGroup.shared.o
g++ -std=c++11 -pedantic -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I/usr/include -fPIC -c sam/ReferenceSequence.cpp -o ReferenceSequence.shared.o
g++ -std=c++11 -pedantic -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I/usr/include -fPIC -c sam/SAMAlignment.cpp -o SAMAlignment.shared.o
g++ -std=c++11 -pedantic -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I/usr/include -fPIC -c sam/SAMHeader.cpp -o SAMHeader.shared.o
g++ -std=c++11 -pedantic -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I/usr/include -fPIC -c sam/SAMKeywordValuePair.cpp -o SAMKeywordValuePair.shared.o
g++ -std=c++11 -pedantic -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I/usr/include -fPIC -c utils/BitUtils.cpp -o BitUtils.shared.o
g++ -std=c++11 -pedantic -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I/usr/include -fPIC -c utils/SMRTReadUtils.cpp -o SMRTReadUtils.shared.o
g++ -std=c++11 -pedantic -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I/usr/include -fPIC -c utils/SMRTTitle.cpp -o SMRTTitle.shared.o
sam/SAMAlignment.cpp: In member function 'bool SAMAlignment::StoreValues(std::__cxx11::string&, int)':
sam/SAMAlignment.cpp:110:139: warning: 'field' may be used uninitialized in this function [-Wmaybe-uninitialized]
std::cout << "Error parsing alignment line " << lineNumber << ". Missing or error in field " << SAMAlignmentRequiredFieldNames[field] << std::endl;
^
g++ -std=c++11 -pedantic -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I/usr/include -fPIC -c utils/TimeUtils.cpp -o TimeUtils.shared.o
ar rc libpbdata.a CCSSequence.o ChangeListID.o CommandLineParser.o DNASequence.o FASTAReader.o FASTASequence.o FASTQReader.o FASTQSequence.o GFFFile.o MD5Utils.o NucConversion.o PackedDNASequence.o ReverseCompressIndex.o SMRTSequence.o StringUtils.o CmpAlignment.o AfgBasWriter.o MetricField.o MovieAlnIndexLookupTable.o TitleTable.o QualityTransform.o QualityValue.o AcqParams.o BaseFile.o HoleXY.o PulseBaseCommon.o PulseFile.o ReadType.o RegionAnnotation.o RegionAnnotations.o RegionTable.o RegionTypeMap.o ScanData.o ZMWGroupEntry.o AlnGroup.o MovieInfo.o RefGroup.o RefInfo.o ReadGroup.o ReferenceSequence.o SAMAlignment.o SAMHeader.o SAMKeywordValuePair.o BitUtils.o SMRTReadUtils.o SMRTTitle.o TimeUtils.o
g++ -shared -Wl,-z,relro -L/usr/lib -o libpbdata.so -Wl,-soname,libpbdata.so CCSSequence.shared.o ChangeListID.shared.o CommandLineParser.shared.o DNASequence.shared.o FASTAReader.shared.o FASTASequence.shared.o FASTQReader.shared.o FASTQSequence.shared.o GFFFile.shared.o MD5Utils.shared.o NucConversion.shared.o PackedDNASequence.shared.o ReverseCompressIndex.shared.o SMRTSequence.shared.o StringUtils.shared.o CmpAlignment.shared.o AfgBasWriter.shared.o MetricField.shared.o MovieAlnIndexLookupTable.shared.o TitleTable.shared.o QualityTransform.shared.o QualityValue.shared.o AcqParams.shared.o BaseFile.shared.o HoleXY.shared.o PulseBaseCommon.shared.o PulseFile.shared.o ReadType.shared.o RegionAnnotation.shared.o RegionAnnotations.shared.o RegionTable.shared.o RegionTypeMap.shared.o ScanData.shared.o ZMWGroupEntry.shared.o AlnGroup.shared.o MovieInfo.shared.o RefGroup.shared.o RefInfo.shared.o ReadGroup.shared.o ReferenceSequence.shared.o SAMAlignment.shared.o SAMHeader.shared.o SAMKeywordValuePair.shared.o BitUtils.shared.o SMRTReadUtils.shared.o SMRTTitle.shared.o TimeUtils.shared.o -lpbbam
make[3]: Leaving directory '/<<PKGBUILDDIR>>/pbdata'
make[2]: Leaving directory '/<<PKGBUILDDIR>>'
make libpbihdf
make[2]: Entering directory '/<<PKGBUILDDIR>>'
make -C /<<PKGBUILDDIR>>//hdf all
make[3]: Entering directory '/<<PKGBUILDDIR>>/hdf'
g++ -std=c++11 -pedantic -Wall -Wextra -Wno-overloaded-virtual -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I/usr/include -I/usr/include/hdf5/serial -c HDFAttributable.cpp -o HDFAttributable.o
g++ -std=c++11 -pedantic -Wall -Wextra -Wno-overloaded-virtual -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I/usr/include -I/usr/include/hdf5/serial -c HDFBaxWriter.cpp -o HDFBaxWriter.o
g++ -std=c++11 -pedantic -Wall -Wextra -Wno-overloaded-virtual -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I/usr/include -I/usr/include/hdf5/serial -c HDFWriterBase.cpp -o HDFWriterBase.o
g++ -std=c++11 -pedantic -Wall -Wextra -Wno-overloaded-virtual -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I/usr/include -I/usr/include/hdf5/serial -c DatasetCollection.cpp -o DatasetCollection.o
HDFAttributable.cpp: In member function 'int HDFAttributable::ContainsAttribute(const string&)':
HDFAttributable.cpp:37:28: warning: catching polymorphic type 'class H5::Exception' by value [-Wcatch-value=]
} catch (H5::Exception e) {
^
g++ -std=c++11 -pedantic -Wall -Wextra -Wno-overloaded-virtual -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I/usr/include -I/usr/include/hdf5/serial -c HDFRegionTableReader.cpp -o HDFRegionTableReader.o
g++ -std=c++11 -pedantic -Wall -Wextra -Wno-overloaded-virtual -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I/usr/include -I/usr/include/hdf5/serial -c BufferedHDFArray.cpp -o BufferedHDFArray.o
In file included from BufferedHDFArray.hpp:213,
from HDFWriterBase.hpp:14,
from HDFWriterBase.cpp:3:
BufferedHDFArrayImpl.hpp: In member function 'void BufferedHDFArray<T>::Flush(bool, DSLength)':
BufferedHDFArrayImpl.hpp:143:11: error: 'class H5::DataSetIException' has no member named 'printError'; did you mean 'printErrorStack'?
e.printError();
^~~~~~~~~~
printErrorStack
BufferedHDFArrayImpl.hpp: In member function 'int BufferedHDFArray<T>::UpdateH5Dataspace()':
BufferedHDFArrayImpl.hpp:295:11: error: 'class H5::DataSetIException' has no member named 'printError'; did you mean 'printErrorStack'?
e.printError();
^~~~~~~~~~
printErrorStack
BufferedHDFArrayImpl.hpp:332:11: error: 'class H5::Exception' has no member named 'printError'; did you mean 'printErrorStack'?
e.printError();
^~~~~~~~~~
printErrorStack
BufferedHDFArrayImpl.hpp: In member function 'int BufferedHDFArray<T>::Resize(DSLength)':
BufferedHDFArrayImpl.hpp:354:11: error: 'class H5::DataSetIException' has no member named 'printError'; did you mean 'printErrorStack'?
e.printError();
^~~~~~~~~~
printErrorStack
In file included from BufferedHDFArray.hpp:213,
from HDFWriterBase.hpp:14,
from HDFBaxWriter.hpp:13,
from HDFBaxWriter.cpp:3:
BufferedHDFArrayImpl.hpp: In member function 'void BufferedHDFArray<T>::Flush(bool, DSLength)':
BufferedHDFArrayImpl.hpp:143:11: error: 'class H5::DataSetIException' has no member named 'printError'; did you mean 'printErrorStack'?
e.printError();
^~~~~~~~~~
printErrorStack
BufferedHDFArrayImpl.hpp: In member function 'int BufferedHDFArray<T>::UpdateH5Dataspace()':
BufferedHDFArrayImpl.hpp:295:11: error: 'class H5::DataSetIException' has no member named 'printError'; did you mean 'printErrorStack'?
e.printError();
^~~~~~~~~~
printErrorStack
BufferedHDFArrayImpl.hpp:332:11: error: 'class H5::Exception' has no member named 'printError'; did you mean 'printErrorStack'?
e.printError();
^~~~~~~~~~
printErrorStack
BufferedHDFArrayImpl.hpp: In member function 'int BufferedHDFArray<T>::Resize(DSLength)':
BufferedHDFArrayImpl.hpp:354:11: error: 'class H5::DataSetIException' has no member named 'printError'; did you mean 'printErrorStack'?
e.printError();
^~~~~~~~~~
printErrorStack
In file included from BufferedHDFArray.hpp:213,
from HDFArray.hpp:11,
from HDFRegionTableReader.hpp:11,
from HDFRegionTableReader.cpp:2:
BufferedHDFArrayImpl.hpp: In member function 'void BufferedHDFArray<T>::Flush(bool, DSLength)':
BufferedHDFArrayImpl.hpp:143:11: error: 'class H5::DataSetIException' has no member named 'printError'; did you mean 'printErrorStack'?
e.printError();
^~~~~~~~~~
printErrorStack
BufferedHDFArrayImpl.hpp: In member function 'int BufferedHDFArray<T>::UpdateH5Dataspace()':
BufferedHDFArrayImpl.hpp:295:11: error: 'class H5::DataSetIException' has no member named 'printError'; did you mean 'printErrorStack'?
e.printError();
^~~~~~~~~~
printErrorStack
BufferedHDFArrayImpl.hpp:332:11: error: 'class H5::Exception' has no member named 'printError'; did you mean 'printErrorStack'?
e.printError();
^~~~~~~~~~
printErrorStack
BufferedHDFArrayImpl.hpp: In member function 'int BufferedHDFArray<T>::Resize(DSLength)':
BufferedHDFArrayImpl.hpp:354:11: error: 'class H5::DataSetIException' has no member named 'printError'; did you mean 'printErrorStack'?
e.printError();
^~~~~~~~~~
printErrorStack
In file included from BufferedHDFArray.hpp:213,
from BufferedHDFArray.cpp:1:
BufferedHDFArrayImpl.hpp: In member function 'void BufferedHDFArray<T>::Flush(bool, DSLength)':
BufferedHDFArrayImpl.hpp:143:11: error: 'class H5::DataSetIException' has no member named 'printError'; did you mean 'printErrorStack'?
e.printError();
^~~~~~~~~~
printErrorStack
BufferedHDFArrayImpl.hpp: In member function 'int BufferedHDFArray<T>::UpdateH5Dataspace()':
BufferedHDFArrayImpl.hpp:295:11: error: 'class H5::DataSetIException' has no member named 'printError'; did you mean 'printErrorStack'?
e.printError();
^~~~~~~~~~
printErrorStack
BufferedHDFArrayImpl.hpp:332:11: error: 'class H5::Exception' has no member named 'printError'; did you mean 'printErrorStack'?
e.printError();
^~~~~~~~~~
printErrorStack
BufferedHDFArrayImpl.hpp: In member function 'int BufferedHDFArray<T>::Resize(DSLength)':
BufferedHDFArrayImpl.hpp:354:11: error: 'class H5::DataSetIException' has no member named 'printError'; did you mean 'printErrorStack'?
e.printError();
^~~~~~~~~~
printErrorStack
In file included from HDFWriterBase.hpp:13,
from HDFWriterBase.cpp:3:
HDFAtom.hpp: In instantiation of 'int HDFAtom<T>::Initialize(H5::Group&, const string&) [with T = std::vector<std::__cxx11::basic_string<char> >; std::__cxx11::string = std::__cxx11::basic_string<char>]':
HDFAtom.hpp:39:53: required from 'int HDFAtom<T>::Initialize(HDFGroup&, const string&) [with T = std::vector<std::__cxx11::basic_string<char> >; std::__cxx11::string = std::__cxx11::basic_string<char>]'
HDFAtom.hpp:38:9: required from here
HDFAtom.hpp:50:9: warning: catching polymorphic type 'class H5::Exception' by value [-Wcatch-value=]
catch (H5::Exception e) {
^~~~~
make[3]: *** [/<<PKGBUILDDIR>>/hdf//../rules.mk:20: HDFWriterBase.o] Error 1
make[3]: *** Waiting for unfinished jobs....
make[3]: *** [/<<PKGBUILDDIR>>/hdf//../rules.mk:20: HDFBaxWriter.o] Error 1
In file included from HDFRegionTableReader.hpp:13,
from HDFRegionTableReader.cpp:2:
HDFAtom.hpp: In instantiation of 'int HDFAtom<T>::Initialize(H5::Group&, const string&) [with T = std::vector<std::__cxx11::basic_string<char> >; std::__cxx11::string = std::__cxx11::basic_string<char>]':
HDFAtom.hpp:39:53: required from 'int HDFAtom<T>::Initialize(HDFGroup&, const string&) [with T = std::vector<std::__cxx11::basic_string<char> >; std::__cxx11::string = std::__cxx11::basic_string<char>]'
HDFAtom.hpp:38:9: required from here
HDFAtom.hpp:50:9: warning: catching polymorphic type 'class H5::Exception' by value [-Wcatch-value=]
catch (H5::Exception e) {
^~~~~
make[3]: *** [/<<PKGBUILDDIR>>/hdf//../rules.mk:20: HDFRegionTableReader.o] Error 1
make[3]: *** [/<<PKGBUILDDIR>>/hdf//../rules.mk:20: BufferedHDFArray.o] Error 1
make[3]: Leaving directory '/<<PKGBUILDDIR>>/hdf'
make[2]: *** [makefile:21: libpbihdf] Error 2
make[2]: Leaving directory '/<<PKGBUILDDIR>>'
make[1]: *** [makefile:9: all] Error 2
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
dh_auto_build: make -j4 returned exit code 2
make: *** [debian/rules:23: build-arch] Error 2
dpkg-buildpackage: error: debian/rules build-arch subprocess returned exit status 2
--------------------------------------------------------------------------------
Build finished at 2018-12-19T17:39:19Z
Finished
--------
+------------------------------------------------------------------------------+
| Cleanup |
+------------------------------------------------------------------------------+
Purging /<<BUILDDIR>>
Not cleaning session: cloned chroot in use
E: Build failure (dpkg-buildpackage died)
+------------------------------------------------------------------------------+
| Summary |
+------------------------------------------------------------------------------+
Build Architecture: armhf
Build-Space: 0
Build-Time: 548
Distribution: buster-staging
Fail-Stage: build
Host Architecture: armhf
Install-Time: 701
Job: pbseqlib_0~20161219-2
Machine Architecture: armhf
Package: pbseqlib
Package-Time: 1305
Source-Version: 0~20161219-2
Space: 0
Status: failed
Version: 0~20161219-2+b1
--------------------------------------------------------------------------------
Finished at 2018-12-19T17:39:19Z
Build needed 00:00:00, 0k disc space