pbseqlib →
0~20161219-1 →
armhf → 2017-01-11 00:12:38
sbuild (Debian sbuild) 0.71.0 (24 Aug 2016) on bm-wb-02
+==============================================================================+
| pbseqlib 0~20161219-1 (armhf) Tue, 10 Jan 2017 23:51:08 +0000 |
+==============================================================================+
Package: pbseqlib
Version: 0~20161219-1
Source Version: 0~20161219-1
Distribution: stretch-staging
Machine Architecture: armhf
Host Architecture: armhf
Build Architecture: armhf
I: NOTICE: Log filtering will replace 'var/lib/schroot/mount/stretch-staging-armhf-sbuild-c49d5e69-120d-47f1-9ae9-eee931e9ef66' with '<<CHROOT>>'
+------------------------------------------------------------------------------+
| Update chroot |
+------------------------------------------------------------------------------+
Get:1 http://172.17.0.1/private stretch-staging InRelease [11.3 kB]
Get:2 http://172.17.0.1/private stretch-staging/main Sources [9727 kB]
Get:3 http://172.17.0.1/private stretch-staging/main armhf Packages [11.7 MB]
Fetched 21.4 MB in 26s (820 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: '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 1350 kB of source archives.
Get:1 http://172.17.0.1/private stretch-staging/main pbseqlib 0~20161219-1 (dsc) [2448 B]
Get:2 http://172.17.0.1/private stretch-staging/main pbseqlib 0~20161219-1 (tar) [1343 kB]
Get:3 http://172.17.0.1/private stretch-staging/main pbseqlib 0~20161219-1 (diff) [4760 B]
Fetched 1350 kB in 0s (5915 kB/s)
Download complete and in download only mode
I: NOTICE: Log filtering will replace 'build/pbseqlib-P3KTYq/pbseqlib-0~20161219' with '<<PKGBUILDDIR>>'
I: NOTICE: Log filtering will replace 'build/pbseqlib-P3KTYq' 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-vyo6lf/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-vyo6lf/gpg/pubring.kbx' created
gpg: /<<BUILDDIR>>/resolver-vyo6lf/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-vyo6lf/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-vyo6lf/apt_archive ./ Release [957 B]
Get:3 copy:/<<BUILDDIR>>/resolver-vyo6lf/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-vyo6lf/apt_archive ./ Sources [349 B]
Get:5 copy:/<<BUILDDIR>>/resolver-vyo6lf/apt_archive ./ Packages [433 B]
Fetched 2109 B in 0s (3455 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:
fuse2fs gnupg-l10n libfuse2 manpages
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 56 not upgraded.
Need to get 772 B of archives.
After this operation, 0 B of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-vyo6lf/apt_archive ./ sbuild-build-depends-core-dummy 0.invalid.0 [772 B]
debconf: delaying package configuration, since apt-utils is not installed
Fetched 772 B in 0s (43.0 kB/s)
Selecting previously unselected package sbuild-build-depends-core-dummy.
(Reading database ... 13928 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 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-vyo6lf/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-vyo6lf/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-vyo6lf/apt_archive ./ Release [963 B]
Get:3 copy:/<<BUILDDIR>>/resolver-vyo6lf/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-vyo6lf/apt_archive ./ Sources [536 B]
Get:5 copy:/<<BUILDDIR>>/resolver-vyo6lf/apt_archive ./ Packages [616 B]
Fetched 2485 B in 0s (4163 B/s)
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
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:
fuse2fs gnupg-l10n libfuse2 manpages
Use 'apt autoremove' to remove them.
The following additional packages will be installed:
autoconf automake autopoint autotools-dev bsdmainutils debhelper
dh-autoreconf dh-exec dh-strip-nondeterminism file gettext gettext-base
googletest groff-base hdf5-helpers intltool-debian libaec-dev libaec0
libarchive-zip-perl libboost-dev libboost1.62-dev libbsd0 libcroco3
libcurl3-gnutls libexpat1 libffi6 libfile-stripnondeterminism-perl
libgfortran3 libglib2.0-0 libgnutls30 libgssapi-krb5-2 libgtest-dev
libhdf5-100 libhdf5-cpp-100 libhdf5-dev libhogweed4 libhts-dev libhts1
libicu57 libjpeg-dev libjpeg62-turbo libjpeg62-turbo-dev libk5crypto3
libkeyutils1 libkrb5-3 libkrb5support0 libldap-2.4-2 libldap-common
libmagic-mgc libmagic1 libnettle6 libnghttp2-14 libp11-kit0 libpbbam
libpbbam-dev libpipeline1 libpython-stdlib libpython2.7-minimal
libpython2.7-stdlib librtmp1 libsasl2-2 libsasl2-modules-db libsigsegv2
libssh2-1 libssl1.0.2 libssl1.1 libsz2 libtasn1-6 libtool libunistring0
libxml2 m4 man-db mime-support po-debconf python python-minimal python2.7
python2.7-minimal zlib1g zlib1g-dev
Suggested packages:
autoconf-archive gnu-standards autoconf-doc wamerican | wordlist whois
vacation dh-make gettext-doc libasprintf-dev libgettextpo-dev groff
libboost-doc libboost1.62-doc libboost-atomic1.62-dev
libboost-chrono1.62-dev libboost-context1.62-dev libboost-coroutine1.62-dev
libboost-date-time1.62-dev libboost-exception1.62-dev libboost-fiber1.62-dev
libboost-filesystem1.62-dev libboost-graph1.62-dev
libboost-graph-parallel1.62-dev libboost-iostreams1.62-dev
libboost-locale1.62-dev libboost-log1.62-dev libboost-math1.62-dev
libboost-mpi1.62-dev libboost-mpi-python1.62-dev
libboost-program-options1.62-dev libboost-python1.62-dev
libboost-random1.62-dev libboost-regex1.62-dev
libboost-serialization1.62-dev libboost-signals1.62-dev
libboost-system1.62-dev libboost-test1.62-dev libboost-thread1.62-dev
libboost-timer1.62-dev libboost-type-erasure1.62-dev libboost-wave1.62-dev
libboost1.62-tools-dev libmpfrc++-dev libntl-dev gnutls-bin krb5-doc
krb5-user libhdf5-doc libtool-doc gfortran | fortran95-compiler gcj-jdk less
www-browser libmail-box-perl python-doc python-tk python2.7-doc
binfmt-support
Recommended packages:
curl | wget | lynx-cur ca-certificates libglib2.0-data shared-mime-info
xdg-user-dirs krb5-locales libsasl2-modules libltdl-dev xml-core
libmail-sendmail-perl
The following NEW packages will be installed:
autoconf automake autopoint autotools-dev bsdmainutils debhelper
dh-autoreconf dh-exec dh-strip-nondeterminism file gettext gettext-base
googletest groff-base hdf5-helpers intltool-debian libaec-dev libaec0
libarchive-zip-perl libboost-dev libboost1.62-dev libbsd0 libcroco3
libcurl3-gnutls libexpat1 libffi6 libfile-stripnondeterminism-perl
libgfortran3 libglib2.0-0 libgnutls30 libgssapi-krb5-2 libgtest-dev
libhdf5-100 libhdf5-cpp-100 libhdf5-dev libhogweed4 libhts-dev libhts1
libicu57 libjpeg-dev libjpeg62-turbo libjpeg62-turbo-dev libk5crypto3
libkeyutils1 libkrb5-3 libkrb5support0 libldap-2.4-2 libldap-common
libmagic-mgc libmagic1 libnettle6 libnghttp2-14 libp11-kit0 libpbbam
libpbbam-dev libpipeline1 libpython-stdlib libpython2.7-minimal
libpython2.7-stdlib librtmp1 libsasl2-2 libsasl2-modules-db libsigsegv2
libssh2-1 libssl1.0.2 libssl1.1 libsz2 libtasn1-6 libtool libunistring0
libxml2 m4 man-db mime-support po-debconf python python-minimal python2.7
python2.7-minimal sbuild-build-depends-pbseqlib-dummy zlib1g-dev
The following packages will be upgraded:
zlib1g
1 upgraded, 81 newly installed, 0 to remove and 55 not upgraded.
Need to get 39.3 MB/40.6 MB of archives.
After this operation, 235 MB of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-vyo6lf/apt_archive ./ sbuild-build-depends-pbseqlib-dummy 0.invalid.0 [824 B]
Get:2 http://172.17.0.1/private stretch-staging/main armhf groff-base armhf 1.22.3-9 [1005 kB]
Get:3 http://172.17.0.1/private stretch-staging/main armhf libbsd0 armhf 0.8.3-1 [89.0 kB]
Get:4 http://172.17.0.1/private stretch-staging/main armhf bsdmainutils armhf 9.0.12 [178 kB]
Get:5 http://172.17.0.1/private stretch-staging/main armhf libpipeline1 armhf 1.4.1-2 [23.7 kB]
Get:6 http://172.17.0.1/private stretch-staging/main armhf zlib1g armhf 1:1.2.8.dfsg-4 [81.6 kB]
Get:7 http://172.17.0.1/private stretch-staging/main armhf man-db armhf 2.7.6.1-2 [1014 kB]
Get:8 http://172.17.0.1/private stretch-staging/main armhf libpython2.7-minimal armhf 2.7.13-1 [389 kB]
Get:9 http://172.17.0.1/private stretch-staging/main armhf python2.7-minimal armhf 2.7.13-1 [1180 kB]
Get:10 http://172.17.0.1/private stretch-staging/main armhf python-minimal armhf 2.7.13-1 [40.5 kB]
Get:11 http://172.17.0.1/private stretch-staging/main armhf mime-support all 3.60 [36.7 kB]
Get:12 http://172.17.0.1/private stretch-staging/main armhf libexpat1 armhf 2.2.0-1 [61.7 kB]
Get:13 http://172.17.0.1/private stretch-staging/main armhf libssl1.1 armhf 1.1.0c-2 [1101 kB]
Get:14 http://172.17.0.1/private stretch-staging/main armhf libpython2.7-stdlib armhf 2.7.13-1 [1828 kB]
Get:15 http://172.17.0.1/private stretch-staging/main armhf python2.7 armhf 2.7.13-1 [285 kB]
Get:16 http://172.17.0.1/private stretch-staging/main armhf libpython-stdlib armhf 2.7.13-1 [19.9 kB]
Get:17 http://172.17.0.1/private stretch-staging/main armhf python armhf 2.7.13-1 [154 kB]
Get:18 http://172.17.0.1/private stretch-staging/main armhf libmagic-mgc armhf 1:5.29-2 [221 kB]
Get:19 http://172.17.0.1/private stretch-staging/main armhf libmagic1 armhf 1:5.29-2 [104 kB]
Get:20 http://172.17.0.1/private stretch-staging/main armhf file armhf 1:5.29-2 [63.1 kB]
Get:21 http://172.17.0.1/private stretch-staging/main armhf gettext-base armhf 0.19.8.1-1 [117 kB]
Get:22 http://172.17.0.1/private stretch-staging/main armhf libp11-kit0 armhf 0.23.3-2 [94.4 kB]
Get:23 http://172.17.0.1/private stretch-staging/main armhf libgnutls30 armhf 3.5.7-3 [816 kB]
Get:24 http://172.17.0.1/private stretch-staging/main armhf libkeyutils1 armhf 1.5.9-9 [11.9 kB]
Get:25 http://172.17.0.1/private stretch-staging/main armhf libkrb5support0 armhf 1.15-1 [57.9 kB]
Get:26 http://172.17.0.1/private stretch-staging/main armhf libk5crypto3 armhf 1.15-1 [115 kB]
Get:27 http://172.17.0.1/private stretch-staging/main armhf libkrb5-3 armhf 1.15-1 [262 kB]
Get:28 http://172.17.0.1/private stretch-staging/main armhf libgssapi-krb5-2 armhf 1.15-1 [132 kB]
Get:29 http://172.17.0.1/private stretch-staging/main armhf libsasl2-modules-db armhf 2.1.27~101-g0780600+dfsg-1 [66.7 kB]
Get:30 http://172.17.0.1/private stretch-staging/main armhf libsasl2-2 armhf 2.1.27~101-g0780600+dfsg-1 [97.9 kB]
Get:31 http://172.17.0.1/private stretch-staging/main armhf libldap-common all 2.4.44+dfsg-2+rpi1 [84.5 kB]
Get:32 http://172.17.0.1/private stretch-staging/main armhf libldap-2.4-2 armhf 2.4.44+dfsg-2+rpi1 [195 kB]
Get:33 http://172.17.0.1/private stretch-staging/main armhf libicu57 armhf 57.1-5 [7427 kB]
Get:34 http://172.17.0.1/private stretch-staging/main armhf libxml2 armhf 2.9.4+dfsg1-2.1 [804 kB]
Get:35 http://172.17.0.1/private stretch-staging/main armhf libsigsegv2 armhf 2.10-5 [28.4 kB]
Get:36 http://172.17.0.1/private stretch-staging/main armhf m4 armhf 1.4.17-5 [239 kB]
Get:37 http://172.17.0.1/private stretch-staging/main armhf autoconf all 2.69-10 [338 kB]
Get:38 http://172.17.0.1/private stretch-staging/main armhf autotools-dev all 20161112.1 [73.4 kB]
Get:39 http://172.17.0.1/private stretch-staging/main armhf automake all 1:1.15-5 [733 kB]
Get:40 http://172.17.0.1/private stretch-staging/main armhf autopoint all 0.19.8.1-1 [433 kB]
Get:41 http://172.17.0.1/private stretch-staging/main armhf libtool all 2.4.6-2 [545 kB]
Get:42 http://172.17.0.1/private stretch-staging/main armhf dh-autoreconf all 12 [15.8 kB]
Get:43 http://172.17.0.1/private stretch-staging/main armhf libarchive-zip-perl all 1.59-1 [95.5 kB]
Get:44 http://172.17.0.1/private stretch-staging/main armhf libfile-stripnondeterminism-perl all 0.029-2 [15.3 kB]
Get:45 http://172.17.0.1/private stretch-staging/main armhf dh-strip-nondeterminism all 0.029-2 [9330 B]
Get:46 http://172.17.0.1/private stretch-staging/main armhf libglib2.0-0 armhf 2.50.2-2 [2527 kB]
Get:47 http://172.17.0.1/private stretch-staging/main armhf libcroco3 armhf 0.6.11-2 [131 kB]
Get:48 http://172.17.0.1/private stretch-staging/main armhf libunistring0 armhf 0.9.6+really0.9.3-0.1 [252 kB]
Get:49 http://172.17.0.1/private stretch-staging/main armhf gettext armhf 0.19.8.1-1 [1433 kB]
Get:50 http://172.17.0.1/private stretch-staging/main armhf intltool-debian all 0.35.0+20060710.4 [26.3 kB]
Get:51 http://172.17.0.1/private stretch-staging/main armhf po-debconf all 1.0.20 [247 kB]
Get:52 http://172.17.0.1/private stretch-staging/main armhf debhelper all 10.2.2 [826 kB]
Get:53 http://172.17.0.1/private stretch-staging/main armhf googletest armhf 1.8.0-5 [652 kB]
Get:54 http://172.17.0.1/private stretch-staging/main armhf hdf5-helpers armhf 1.10.0-patch1+docs-3 [35.9 kB]
Get:55 http://172.17.0.1/private stretch-staging/main armhf libaec0 armhf 0.3.2-1 [19.4 kB]
Get:56 http://172.17.0.1/private stretch-staging/main armhf libboost1.62-dev armhf 1.62.0+dfsg-4 [7009 kB]
Get:57 http://172.17.0.1/private stretch-staging/main armhf libboost-dev armhf 1.62.0.1 [3632 B]
Get:58 http://172.17.0.1/private stretch-staging/main armhf libnghttp2-14 armhf 1.17.0-1 [70.1 kB]
Get:59 http://172.17.0.1/private stretch-staging/main armhf librtmp1 armhf 2.4+20151223.gitfa8646d.1-1 [54.2 kB]
Get:60 http://172.17.0.1/private stretch-staging/main armhf libssh2-1 armhf 1.7.0-1 [125 kB]
Get:61 http://172.17.0.1/private stretch-staging/main armhf libcurl3-gnutls armhf 7.51.0-1 [254 kB]
Get:62 http://172.17.0.1/private stretch-staging/main armhf libgfortran3 armhf 6.2.1-5+rpi1 [166 kB]
Get:63 http://172.17.0.1/private stretch-staging/main armhf libsz2 armhf 0.3.2-1 [5836 B]
Get:64 http://172.17.0.1/private stretch-staging/main armhf libhdf5-100 armhf 1.10.0-patch1+docs-3 [1203 kB]
Get:65 http://172.17.0.1/private stretch-staging/main armhf libhdf5-cpp-100 armhf 1.10.0-patch1+docs-3 [118 kB]
Get:66 http://172.17.0.1/private stretch-staging/main armhf zlib1g-dev armhf 1:1.2.8.dfsg-4 [198 kB]
Get:67 http://172.17.0.1/private stretch-staging/main armhf libjpeg62-turbo armhf 1:1.5.1-2 [109 kB]
Get:68 http://172.17.0.1/private stretch-staging/main armhf libjpeg62-turbo-dev armhf 1:1.5.1-2 [181 kB]
Get:69 http://172.17.0.1/private stretch-staging/main armhf libjpeg-dev all 1:1.5.1-2 [56.1 kB]
Get:70 http://172.17.0.1/private stretch-staging/main armhf libaec-dev armhf 0.3.2-1 [17.6 kB]
Get:71 http://172.17.0.1/private stretch-staging/main armhf libhdf5-dev armhf 1.10.0-patch1+docs-3 [2093 kB]
Get:72 http://172.17.0.1/private stretch-staging/main armhf libhts1 armhf 1.3.2-1+rpi1 [215 kB]
Get:73 http://172.17.0.1/private stretch-staging/main armhf libhts-dev armhf 1.3.2-1+rpi1 [270 kB]
Get:74 http://172.17.0.1/private stretch-staging/main armhf libpbbam armhf 0.1.0~20150813+git4e9e417+dfsg-1 [270 kB]
Get:75 http://172.17.0.1/private stretch-staging/main armhf libpbbam-dev armhf 0.1.0~20150813+git4e9e417+dfsg-1 [52.0 kB]
Get:76 http://172.17.0.1/private stretch-staging/main armhf dh-exec armhf 0.23 [24.9 kB]
Get:77 http://172.17.0.1/private stretch-staging/main armhf libgtest-dev armhf 1.8.0-5 [4848 B]
debconf: delaying package configuration, since apt-utils is not installed
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Processing triggers for libc-bin (2.24-7+rpi1) ...
W: No sandbox user '_apt' on the system, can not drop privileges
+------------------------------------------------------------------------------+
| Build environment |
+------------------------------------------------------------------------------+
Kernel: Linux 3.19.0-trunk-armmp armhf (armv7l)
Toolchain package versions: binutils_2.27.51.20161127-1 dpkg-dev_1.18.15 g++-6_6.2.1-5+rpi1 gcc-6_6.2.1-5+rpi1 libc6-dev_2.24-7+rpi1 libstdc++-4.9-dev_4.9.3-14 libstdc++-6-dev_6.2.1-5+rpi1 libstdc++6_6.2.1-5+rpi1 linux-libc-dev_3.18.5-1~exp1+rpi19+stretch
Package versions: acl_2.2.52-3 adduser_3.115 apt_1.4~beta1 autoconf_2.69-10 automake_1:1.15-5 autopoint_0.19.8.1-1 autotools-dev_20161112.1 base-files_9.7+rpi1 base-passwd_3.5.41 bash_4.4-2 binutils_2.27.51.20161127-1 bsdmainutils_9.0.12 bsdutils_1:2.29-1 build-essential_12.2 bzip2_1.0.6-8 coreutils_8.25-2 cpio_2.11+dfsg-6 cpp_4:6.1.1-1 cpp-6_6.2.1-5+rpi1 dash_0.5.8-2.3 debconf_1.5.59 debfoster_2.7-2.1 debhelper_10.2.2 debianutils_4.8.1 dh-autoreconf_12 dh-exec_0.23 dh-strip-nondeterminism_0.029-2 diffutils_1:3.5-1 dmsetup_2:1.02.136-1 dpkg_1.18.15 dpkg-dev_1.18.15 e2fslibs_1.43.3-1 e2fsprogs_1.43.3-1 fakeroot_1.21-2 file_1:5.29-2 findutils_4.6.0+git+20161106-1 fuse2fs_1.43.3-1 g++_4:6.1.1-1 g++-6_6.2.1-5+rpi1 gcc_4:6.1.1-1 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_4.9.3-14 gcc-6_6.2.1-5+rpi1 gcc-6-base_6.2.1-5+rpi1 gettext_0.19.8.1-1 gettext-base_0.19.8.1-1 gnupg_2.1.16-2 gnupg-agent_2.1.16-2 gnupg-l10n_2.1.16-2 googletest_1.8.0-5 gpgv_2.1.16-2 grep_2.26-1 groff-base_1.22.3-9 gzip_1.6-5 hdf5-helpers_1.10.0-patch1+docs-3 hostname_3.18 init_1.46 init-system-helpers_1.46 initscripts_2.88dsf-59.8 insserv_1.14.0-5.4 intltool-debian_0.35.0+20060710.4 klibc-utils_2.0.4-9+rpi1 kmod_23-1 libacl1_2.2.52-3 libaec-dev_0.3.2-1 libaec0_0.3.2-1 libapparmor1_2.10.95-6 libapt-pkg4.12_1.0.9.10 libapt-pkg5.0_1.4~beta1 libarchive-zip-perl_1.59-1 libasan1_4.9.3-14 libasan3_6.2.1-5+rpi1 libassuan0_2.4.3-2 libatomic1_6.2.1-5+rpi1 libattr1_1:2.4.47-2 libaudit-common_1:2.6.7-1 libaudit1_1:2.6.7-1 libblkid1_2.29-1 libboost-dev_1.62.0.1 libboost1.62-dev_1.62.0+dfsg-4 libbsd0_0.8.3-1 libbz2-1.0_1.0.6-8 libc-bin_2.24-7+rpi1 libc-dev-bin_2.24-7+rpi1 libc6_2.24-7+rpi1 libc6-dev_2.24-7+rpi1 libcap-ng0_0.7.7-3 libcap2_1:2.25-1 libcap2-bin_1:2.25-1 libcc1-0_6.2.1-5+rpi1 libcomerr2_1.43.3-1 libcroco3_0.6.11-2 libcryptsetup4_2:1.7.3-2 libcurl3-gnutls_7.51.0-1 libdb5.3_5.3.28-12 libdbus-1-3_1.10.14-1 libdebconfclient0_0.218 libdevmapper1.02.1_2:1.02.136-1 libdpkg-perl_1.18.15 libdrm2_2.4.74-1 libexpat1_2.2.0-1 libfakeroot_1.21-2 libfdisk1_2.29-1 libffi6_3.2.1-6 libfile-stripnondeterminism-perl_0.029-2 libfuse2_2.9.7-1 libgc1c2_1:7.4.2-8 libgcc-4.9-dev_4.9.3-14 libgcc-6-dev_6.2.1-5+rpi1 libgcc1_1:6.2.1-5+rpi1 libgcrypt20_1.7.3-2 libgdbm3_1.8.3-14 libgfortran3_6.2.1-5+rpi1 libglib2.0-0_2.50.2-2 libgmp10_2:6.1.1+dfsg-1 libgnutls30_3.5.7-3 libgomp1_6.2.1-5+rpi1 libgpg-error0_1.25-1 libgssapi-krb5-2_1.15-1 libgtest-dev_1.8.0-5 libhdf5-100_1.10.0-patch1+docs-3 libhdf5-cpp-100_1.10.0-patch1+docs-3 libhdf5-dev_1.10.0-patch1+docs-3 libhogweed4_3.3-1 libhts-dev_1.3.2-1+rpi1 libhts1_1.3.2-1+rpi1 libicu57_57.1-5 libidn11_1.33-1 libip4tc0_1.6.0-4 libisl15_0.17.1-1 libjpeg-dev_1:1.5.1-2 libjpeg62-turbo_1:1.5.1-2 libjpeg62-turbo-dev_1:1.5.1-2 libk5crypto3_1.15-1 libkeyutils1_1.5.9-9 libklibc_2.0.4-9+rpi1 libkmod2_23-1 libkrb5-3_1.15-1 libkrb5support0_1.15-1 libksba8_1.3.5-2 libldap-2.4-2_2.4.44+dfsg-2+rpi1 libldap-common_2.4.44+dfsg-2+rpi1 liblz4-1_0.0~r131-2 liblzma5_5.2.2-1.2 libmagic-mgc_1:5.29-2 libmagic1_1:5.29-2 libmount1_2.29-1 libmpc3_1.0.3-1 libmpfr4_3.1.5-1 libncurses5_6.0+20160917-1 libncursesw5_6.0+20160917-1 libnettle6_3.3-1 libnghttp2-14_1.17.0-1 libnpth0_1.3-1 libp11-kit0_0.23.3-2 libpam-modules_1.1.8-3.3 libpam-modules-bin_1.1.8-3.3 libpam-runtime_1.1.8-3.3 libpam0g_1.1.8-3.3 libpbbam_0.1.0~20150813+git4e9e417+dfsg-1 libpbbam-dev_0.1.0~20150813+git4e9e417+dfsg-1 libpcre3_2:8.39-2 libperl5.24_5.24.1~rc4-1 libpipeline1_1.4.1-2 libpng12-0_1.2.54-6 libprocps3_2:3.3.9-9 libprocps6_2:3.3.12-3 libpython-stdlib_2.7.13-1 libpython2.7-minimal_2.7.13-1 libpython2.7-stdlib_2.7.13-1 libreadline7_7.0-1 librtmp1_2.4+20151223.gitfa8646d.1-1 libsasl2-2_2.1.27~101-g0780600+dfsg-1 libsasl2-modules-db_2.1.27~101-g0780600+dfsg-1 libseccomp2_2.3.1-2.1 libselinux1_2.6-3 libsemanage-common_2.6-1 libsemanage1_2.6-1 libsepol1_2.6-1 libsigsegv2_2.10-5 libslang2_2.3.1-5 libsmartcols1_2.29-1 libsqlite3-0_3.15.2-1 libss2_1.43.3-1 libssh2-1_1.7.0-1 libssl1.0.2_1.0.2j-4 libssl1.1_1.1.0c-2 libstdc++-4.9-dev_4.9.3-14 libstdc++-6-dev_6.2.1-5+rpi1 libstdc++6_6.2.1-5+rpi1 libsystemd0_232-6 libsz2_0.3.2-1 libtasn1-6_4.9-4 libtimedate-perl_2.3000-2 libtinfo5_6.0+20160917-1 libtool_2.4.6-2 libubsan0_6.2.1-5+rpi1 libudev1_232-6 libunistring0_0.9.6+really0.9.3-0.1 libusb-0.1-4_2:0.1.12-30 libustr-1.0-1_1.0.4-6 libuuid1_2.29-1 libxml2_2.9.4+dfsg1-2.1 linux-libc-dev_3.18.5-1~exp1+rpi19+stretch login_1:4.2-3.3 lsb-base_9.20161125+rpi1 m4_1.4.17-5 make_4.1-9 makedev_2.3.1-93 man-db_2.7.6.1-2 manpages_4.08-1 mawk_1.3.3-17 mime-support_3.60 mount_2.29-1 multiarch-support_2.24-7+rpi1 nano_2.7.1-1 ncurses-base_6.0+20160917-1 ncurses-bin_6.0+20160917-1 passwd_1:4.2-3.3 patch_2.7.5-1 perl_5.24.1~rc4-1 perl-base_5.24.1~rc4-1 perl-modules-5.24_5.24.1~rc4-1 pinentry-curses_0.9.7-9 po-debconf_1.0.20 procps_2:3.3.12-3 python_2.7.13-1 python-minimal_2.7.13-1 python2.7_2.7.13-1 python2.7-minimal_2.7.13-1 raspbian-archive-keyring_20120528.2 readline-common_7.0-1 sbuild-build-depends-core-dummy_0.invalid.0 sbuild-build-depends-pbseqlib-dummy_0.invalid.0 sed_4.2.2-8 sensible-utils_0.0.9 startpar_0.59-3.1 systemd_232-6 systemd-sysv_232-6 sysv-rc_2.88dsf-59.8 sysvinit-utils_2.88dsf-59.8 tar_1.29b-1.1 tzdata_2016j-2 udev_232-6 util-linux_2.29-1 xz-utils_5.2.2-1.2 zlib1g_1:1.2.8.dfsg-4 zlib1g-dev_1:1.2.8.dfsg-4
+------------------------------------------------------------------------------+
| Build |
+------------------------------------------------------------------------------+
Unpack source
-------------
gpgv: unknown type of key resource 'trustedkeys.kbx'
gpgv: keyblock resource '/sbuild-nonexistent/.gnupg/trustedkeys.kbx': General error
gpgv: Signature made Tue Dec 20 08:59:01 2016 UTC
gpgv: using RSA key 59B2306F3AF9DDC1
gpgv: Can't check signature: No public key
dpkg-source: warning: failed to verify signature on ./pbseqlib_0~20161219-1.dsc
dpkg-source: info: extracting pbseqlib in /<<PKGBUILDDIR>>
dpkg-source: info: unpacking pbseqlib_0~20161219.orig.tar.gz
dpkg-source: info: unpacking pbseqlib_0~20161219-1.debian.tar.xz
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=root
PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games
SCHROOT_ALIAS_NAME=stretch-staging-armhf-sbuild
SCHROOT_CHROOT_NAME=stretch-staging-armhf-sbuild
SCHROOT_COMMAND=env
SCHROOT_GID=109
SCHROOT_GROUP=buildd
SCHROOT_SESSION_ID=stretch-staging-armhf-sbuild-c49d5e69-120d-47f1-9ae9-eee931e9ef66
SCHROOT_UID=104
SCHROOT_USER=buildd
SHELL=/bin/sh
TERM=xterm
USER=buildd
dpkg-buildpackage
-----------------
dpkg-buildpackage: info: source package pbseqlib
dpkg-buildpackage: info: source version 0~20161219-1
dpkg-buildpackage: info: source distribution unstable
dpkg-source --before-build pbseqlib-0~20161219
dpkg-buildpackage: info: host architecture armhf
fakeroot debian/rules clean
dh clean
dh_testdir
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_autoreconf_clean
dh_clean
debian/rules build-arch
dh build-arch
dh_testdir -a
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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -I/usr/include -c utils/SMRTReadUtils.cpp -o SMRTReadUtils.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 -I/usr/include -c utils/SMRTTitle.cpp -o SMRTTitle.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 -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 -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 -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 -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 -I/usr/include -fPIC -c DNASequence.cpp -o DNASequence.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 -I/usr/include -fPIC -c FASTAReader.cpp -o FASTAReader.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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -I/usr/include -I/usr/include/hdf5/serial -c DatasetCollection.cpp -o DatasetCollection.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 -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 -I/usr/include -I/usr/include/hdf5/serial -c BufferedHDFArray.cpp -o BufferedHDFArray.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 -I/usr/include -I/usr/include/hdf5/serial -c HDFAtom.cpp -o HDFAtom.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 -I/usr/include -I/usr/include/hdf5/serial -c HDFCmpExperimentGroup.cpp -o HDFCmpExperimentGroup.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 -I/usr/include -I/usr/include/hdf5/serial -c HDFZMWMetricsWriter.cpp -o HDFZMWMetricsWriter.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 -I/usr/include -I/usr/include/hdf5/serial -c HDFPulseDataFile.cpp -o HDFPulseDataFile.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 -I/usr/include -I/usr/include/hdf5/serial -c HDFPulseCallsWriter.cpp -o HDFPulseCallsWriter.o
In file included from HDFPulseCallsWriter.cpp:7:0:
HDFPulseCallsWriter.hpp: In member function 'bool HDFPulseCallsWriter::HasStartFrame() const':
HDFPulseCallsWriter.hpp:194:17: error: 'START_FRAME' is not a member of 'PacBio::BAM::BaseFeature'
{return (_HasQV(PacBio::BAM::BaseFeature::START_FRAME) and
^~~~~~
HDFPulseCallsWriter.cpp: At global scope:
HDFPulseCallsWriter.cpp:18:7: error: 'START_FRAME' is not a member of 'PacBio::BAM::BaseFeature'
, PacBio::BAM::BaseFeature::START_FRAME
^~~~~~
HDFPulseCallsWriter.cpp:20:1: error: could not convert '{PULSE_CALL, LABEL_QV, PKMID, PKMEAN, PULSE_MERGE_QV, ALT_LABEL, ALT_LABEL_QV, <expression error>, PULSE_CALL_WIDTH}' from '<brace-enclosed initializer list>' to 'const std::vector<PacBio::BAM::BaseFeature>'
};
^
HDFPulseCallsWriter.cpp: In constructor 'HDFPulseCallsWriter::HDFPulseCallsWriter(const string&, HDFGroup&, const std::map<char, unsigned int>&, const string&, const std::vector<PacBio::BAM::BaseFeature>&)':
HDFPulseCallsWriter.cpp:64:20: error: 'START_FRAME' is not a member of 'PacBio::BAM::BaseFeature'
if (not _HasQV(PacBio::BAM::BaseFeature::START_FRAME)) {
^~~~~~
HDFPulseCallsWriter.cpp: In member function 'bool HDFPulseCallsWriter::InitializeQVGroups()':
HDFPulseCallsWriter.cpp:234:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (_HasQV(PacBio::BAM::BaseFeature::PULSE_CALL))
^~
HDFPulseCallsWriter.cpp:236:9: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'if'
ret *= isPulseArray_.Initialize(pulsecallsGroup_, PacBio::GroupNames::ispulse);
^~~
HDFPulseCallsWriter.cpp:245:16: error: 'START_FRAME' is not a member of 'PacBio::BAM::BaseFeature'
if (_HasQV(PacBio::BAM::BaseFeature::START_FRAME))
^~~~~~
HDFPulseCallsWriter.cpp: In member function 'bool HDFPulseCallsWriter::_WriteStartFrame(const PacBio::BAM::BamRecord&)':
HDFPulseCallsWriter.cpp:420:18: error: 'const class PacBio::BAM::BamRecord' has no member named 'HasStartFrame'; did you mean 'HasPreBaseFrames'?
if (read.HasStartFrame()) {
^~~~~~~~~~~~~
HDFPulseCallsWriter.cpp:421:53: error: 'const class PacBio::BAM::BamRecord' has no member named 'StartFrame'
const std::vector<uint32_t> data = read.StartFrame();
^~~~~~~~~~
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 -I/usr/include -I/usr/include/hdf5/serial -c HDFCmpSupportedFields.cpp -o HDFCmpSupportedFields.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 -I/usr/include -I/usr/include/hdf5/serial -c HDFBaseCallsWriter.cpp -o HDFBaseCallsWriter.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 -I/usr/include -I/usr/include/hdf5/serial -c HDFZMWReader.cpp -o HDFZMWReader.o
/<<PKGBUILDDIR>>/hdf//../rules.mk:20: recipe for target 'HDFPulseCallsWriter.o' failed
make[3]: *** [HDFPulseCallsWriter.o] Error 1
make[3]: *** Waiting for unfinished jobs....
make[3]: Leaving directory '/<<PKGBUILDDIR>>/hdf'
makefile:21: recipe for target 'libpbihdf' failed
make[2]: *** [libpbihdf] Error 2
make[2]: Leaving directory '/<<PKGBUILDDIR>>'
makefile:8: recipe for target 'all' failed
make[1]: *** [all] Error 2
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
dh_auto_build: make -j4 returned exit code 2
debian/rules:17: recipe for target 'build-arch' failed
make: *** [build-arch] Error 2
dpkg-buildpackage: error: debian/rules build-arch gave error exit status 2
--------------------------------------------------------------------------------
Build finished at 2017-01-11T00:10:01Z
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: 588
Distribution: stretch-staging
Fail-Stage: build
Host Architecture: armhf
Install-Time: 489
Job: pbseqlib_0~20161219-1
Machine Architecture: armhf
Package: pbseqlib
Package-Time: 1133
Source-Version: 0~20161219-1
Space: 0
Status: failed
Version: 0~20161219-1
--------------------------------------------------------------------------------
Finished at 2017-01-11T00:10:01Z
Build needed 00:00:00, 0k disc space