pbseqlib →
0~20160705-1 →
armhf → 2016-10-30 20:21:51
sbuild (Debian sbuild) 0.71.0 (24 Aug 2016) on bm-wb-03
+==============================================================================+
| pbseqlib 0~20160705-1 (armhf) Sun, 30 Oct 2016 19:43:05 +0000 |
+==============================================================================+
Package: pbseqlib
Version: 0~20160705-1
Source Version: 0~20160705-1
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-1a8a2d19-a7d9-4130-95ff-faef4775e4b5' 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 [9413 kB]
Get:3 http://172.17.0.1/private stretch-staging/main armhf Packages [11.4 MB]
Fetched 20.8 MB in 22s (906 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 0~20160705-1 (dsc) [2433 B]
Get:2 http://172.17.0.1/private stretch-staging/main pbseqlib 0~20160705-1 (tar) [1343 kB]
Get:3 http://172.17.0.1/private stretch-staging/main pbseqlib 0~20160705-1 (diff) [4696 B]
Fetched 1350 kB in 0s (4873 kB/s)
Download complete and in download only mode
I: NOTICE: Log filtering will replace 'build/pbseqlib-9X0Te5/pbseqlib-0~20160705' with '<<PKGBUILDDIR>>'
I: NOTICE: Log filtering will replace 'build/pbseqlib-9X0Te5' 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-HnRFTO/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-HnRFTO/gpg/pubring.kbx' created
gpg: /<<BUILDDIR>>/resolver-HnRFTO/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-HnRFTO/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-HnRFTO/apt_archive ./ Release [957 B]
Get:3 copy:/<<BUILDDIR>>/resolver-HnRFTO/apt_archive ./ Release.gpg [342 B]
Get:4 copy:/<<BUILDDIR>>/resolver-HnRFTO/apt_archive ./ Sources [349 B]
Get:5 copy:/<<BUILDDIR>>/resolver-HnRFTO/apt_archive ./ Packages [432 B]
Fetched 2080 B in 0s (3394 B/s)
Reading package lists...
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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:
dirmngr fuse2fs gnupg-l10n kbd libffi6 libfuse2 libgnutls30 libhogweed4
libldap-2.4-2 libnettle6 libp11-kit0 libsasl2-2 libsasl2-modules
libsasl2-modules-db libssl1.0.2 libtasn1-6 manpages netbase psmisc
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 1 not upgraded.
Need to get 768 B of archives.
After this operation, 0 B of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-HnRFTO/apt_archive ./ sbuild-build-depends-core-dummy 0.invalid.0 [768 B]
debconf: delaying package configuration, since apt-utils is not installed
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(Reading database ... 13408 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 (>= 9), dh-exec, python, zlib1g-dev, libhdf5-dev, libboost-dev, libhts-dev, libgtest-dev
Filtered Build-Depends: debhelper (>= 9), dh-exec, python, zlib1g-dev, libhdf5-dev, libboost-dev, libhts-dev, libgtest-dev
dpkg-deb: building package 'sbuild-build-depends-pbseqlib-dummy' in '/<<BUILDDIR>>/resolver-HnRFTO/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-HnRFTO/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-HnRFTO/apt_archive ./ Release [963 B]
Get:3 copy:/<<BUILDDIR>>/resolver-HnRFTO/apt_archive ./ Release.gpg [342 B]
Get:4 copy:/<<BUILDDIR>>/resolver-HnRFTO/apt_archive ./ Sources [531 B]
Get:5 copy:/<<BUILDDIR>>/resolver-HnRFTO/apt_archive ./ Packages [608 B]
Fetched 2444 B in 0s (3957 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:
dirmngr fuse2fs gnupg-l10n kbd libfuse2 libsasl2-modules manpages netbase
psmisc
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
groff-base hdf5-helpers intltool-debian libaec-dev libaec0
libarchive-zip-perl libboost-dev libboost1.61-dev libbsd0 libcroco3
libcurl3-gnutls libexpat1 libfile-stripnondeterminism-perl libgfortran3
libglib2.0-0 libgssapi-krb5-2 libgtest-dev libhdf5-10 libhdf5-cpp-11
libhdf5-dev libhts-dev libhts1 libicu57 libjpeg-dev libjpeg62-turbo
libjpeg62-turbo-dev libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0
libmagic-mgc libmagic1 libnghttp2-14 libpipeline1 libpython-stdlib
libpython2.7-minimal libpython2.7-stdlib libreadline6 librtmp1 libsigsegv2
libssh2-1 libsz2 libtimedate-perl libtool libunistring0 libxml2 m4 man-db
mime-support po-debconf python python-minimal python2.7 python2.7-minimal
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 libboost1.61-doc libboost-atomic1.61-dev
libboost-chrono1.61-dev libboost-context1.61-dev libboost-coroutine1.61-dev
libboost-date-time1.61-dev libboost-exception1.61-dev
libboost-filesystem1.61-dev libboost-graph1.61-dev
libboost-graph-parallel1.61-dev libboost-iostreams1.61-dev
libboost-locale1.61-dev libboost-log1.61-dev libboost-math1.61-dev
libboost-mpi1.61-dev libboost-mpi-python1.61-dev
libboost-program-options1.61-dev libboost-python1.61-dev
libboost-random1.61-dev libboost-regex1.61-dev
libboost-serialization1.61-dev libboost-signals1.61-dev
libboost-system1.61-dev libboost-test1.61-dev libboost-thread1.61-dev
libboost-timer1.61-dev libboost-wave1.61-dev libboost1.61-tools-dev
libmpfrc++-dev libntl-dev 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 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
groff-base hdf5-helpers intltool-debian libaec-dev libaec0
libarchive-zip-perl libboost-dev libboost1.61-dev libbsd0 libcroco3
libcurl3-gnutls libexpat1 libfile-stripnondeterminism-perl libgfortran3
libglib2.0-0 libgssapi-krb5-2 libgtest-dev libhdf5-10 libhdf5-cpp-11
libhdf5-dev libhts-dev libhts1 libicu57 libjpeg-dev libjpeg62-turbo
libjpeg62-turbo-dev libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0
libmagic-mgc libmagic1 libnghttp2-14 libpipeline1 libpython-stdlib
libpython2.7-minimal libpython2.7-stdlib libreadline6 librtmp1 libsigsegv2
libssh2-1 libsz2 libtimedate-perl 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
0 upgraded, 68 newly installed, 0 to remove and 1 not upgraded.
Need to get 39.1 MB/39.2 MB of archives.
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Get:1 copy:/<<BUILDDIR>>/resolver-HnRFTO/apt_archive ./ sbuild-build-depends-pbseqlib-dummy 0.invalid.0 [806 B]
Get:2 http://172.17.0.1/private stretch-staging/main armhf groff-base armhf 1.22.3-8 [1087 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 9.0.11 [177 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 man-db armhf 2.7.5-1 [975 kB]
Get:7 http://172.17.0.1/private stretch-staging/main armhf libpython2.7-minimal armhf 2.7.12-3 [388 kB]
Get:8 http://172.17.0.1/private stretch-staging/main armhf python2.7-minimal armhf 2.7.12-3 [1174 kB]
Get:9 http://172.17.0.1/private stretch-staging/main armhf python-minimal armhf 2.7.11-2 [40.3 kB]
Get:10 http://172.17.0.1/private stretch-staging/main armhf mime-support all 3.60 [36.7 kB]
Get:11 http://172.17.0.1/private stretch-staging/main armhf libexpat1 armhf 2.2.0-1 [61.7 kB]
Get:12 http://172.17.0.1/private stretch-staging/main armhf libpython2.7-stdlib armhf 2.7.12-3 [1843 kB]
Get:13 http://172.17.0.1/private stretch-staging/main armhf python2.7 armhf 2.7.12-3 [279 kB]
Get:14 http://172.17.0.1/private stretch-staging/main armhf libpython-stdlib armhf 2.7.11-2 [19.8 kB]
Get:15 http://172.17.0.1/private stretch-staging/main armhf python armhf 2.7.11-2 [153 kB]
Get:16 http://172.17.0.1/private stretch-staging/main armhf libmagic-mgc armhf 1:5.28-4 [210 kB]
Get:17 http://172.17.0.1/private stretch-staging/main armhf libmagic1 armhf 1:5.28-4 [104 kB]
Get:18 http://172.17.0.1/private stretch-staging/main armhf file armhf 1:5.28-4 [62.7 kB]
Get:19 http://172.17.0.1/private stretch-staging/main armhf gettext-base armhf 0.19.8.1-1 [117 kB]
Get:20 http://172.17.0.1/private stretch-staging/main armhf libkeyutils1 armhf 1.5.9-9 [11.9 kB]
Get:21 http://172.17.0.1/private stretch-staging/main armhf libkrb5support0 armhf 1.14.3+dfsg-2 [57.5 kB]
Get:22 http://172.17.0.1/private stretch-staging/main armhf libk5crypto3 armhf 1.14.3+dfsg-2 [110 kB]
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Get:25 http://172.17.0.1/private stretch-staging/main armhf libicu57 armhf 57.1-4 [7407 kB]
Get:26 http://172.17.0.1/private stretch-staging/main armhf libxml2 armhf 2.9.4+dfsg1-2 [805 kB]
Get:27 http://172.17.0.1/private stretch-staging/main armhf libsigsegv2 armhf 2.10-5 [28.4 kB]
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Get:33 http://172.17.0.1/private stretch-staging/main armhf libtool all 2.4.6-2 [545 kB]
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Get:36 http://172.17.0.1/private stretch-staging/main armhf libfile-stripnondeterminism-perl all 0.028-1 [14.6 kB]
Get:37 http://172.17.0.1/private stretch-staging/main armhf libtimedate-perl all 2.3000-2 [42.2 kB]
Get:38 http://172.17.0.1/private stretch-staging/main armhf dh-strip-nondeterminism all 0.028-1 [9020 B]
Get:39 http://172.17.0.1/private stretch-staging/main armhf libglib2.0-0 armhf 2.50.0-2+rpi1 [2523 kB]
Get:40 http://172.17.0.1/private stretch-staging/main armhf libcroco3 armhf 0.6.11-2 [131 kB]
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Get:42 http://172.17.0.1/private stretch-staging/main armhf gettext armhf 0.19.8.1-1 [1433 kB]
Get:43 http://172.17.0.1/private stretch-staging/main armhf intltool-debian all 0.35.0+20060710.4 [26.3 kB]
Get:44 http://172.17.0.1/private stretch-staging/main armhf po-debconf all 1.0.20 [247 kB]
Get:45 http://172.17.0.1/private stretch-staging/main armhf debhelper all 10.2.2 [826 kB]
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Get:48 http://172.17.0.1/private stretch-staging/main armhf libboost1.61-dev armhf 1.61.0+dfsg-3 [6843 kB]
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Get:50 http://172.17.0.1/private stretch-staging/main armhf libnghttp2-14 armhf 1.15.0-1 [72.6 kB]
Get:51 http://172.17.0.1/private stretch-staging/main armhf librtmp1 armhf 2.4+20151223.gitfa8646d.1-1 [54.2 kB]
Get:52 http://172.17.0.1/private stretch-staging/main armhf libssh2-1 armhf 1.7.0-1 [125 kB]
Get:53 http://172.17.0.1/private stretch-staging/main armhf libcurl3-gnutls armhf 7.50.1-1 [248 kB]
Get:54 http://172.17.0.1/private stretch-staging/main armhf libgfortran3 armhf 6.2.0-6+rpi1 [165 kB]
Get:55 http://172.17.0.1/private stretch-staging/main armhf libgtest-dev armhf 1.7.0-4 [200 kB]
Get:56 http://172.17.0.1/private stretch-staging/main armhf libsz2 armhf 0.3.2-1 [5836 B]
Get:57 http://172.17.0.1/private stretch-staging/main armhf libhdf5-10 armhf 1.8.16+docs-8+b1 [977 kB]
Get:58 http://172.17.0.1/private stretch-staging/main armhf libhdf5-cpp-11 armhf 1.8.16+docs-8+b1 [116 kB]
Get:59 http://172.17.0.1/private stretch-staging/main armhf zlib1g-dev armhf 1:1.2.8.dfsg-2+b1 [197 kB]
Get:60 http://172.17.0.1/private stretch-staging/main armhf libjpeg62-turbo armhf 1:1.5.1-2 [109 kB]
Get:61 http://172.17.0.1/private stretch-staging/main armhf libjpeg62-turbo-dev armhf 1:1.5.1-2 [181 kB]
Get:62 http://172.17.0.1/private stretch-staging/main armhf libjpeg-dev all 1:1.5.1-2 [56.1 kB]
Get:63 http://172.17.0.1/private stretch-staging/main armhf libaec-dev armhf 0.3.2-1 [17.6 kB]
Get:64 http://172.17.0.1/private stretch-staging/main armhf libhdf5-dev armhf 1.8.16+docs-8+b1 [5530 kB]
Get:65 http://172.17.0.1/private stretch-staging/main armhf libhts1 armhf 1.3.1-3+rpi1 [216 kB]
Get:66 http://172.17.0.1/private stretch-staging/main armhf libhts-dev armhf 1.3.1-3+rpi1 [270 kB]
Get:67 http://172.17.0.1/private stretch-staging/main armhf dh-exec armhf 0.23 [24.9 kB]
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Setting up libglib2.0-0:armhf (2.50.0-2+rpi1) ...
No schema files found: doing nothing.
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Setting up libpipeline1:armhf (1.4.1-2) ...
Setting up librtmp1:armhf (2.4+20151223.gitfa8646d.1-1) ...
Setting up m4 (1.4.17-5) ...
Setting up libicu57:armhf (57.1-4) ...
Setting up libboost1.61-dev:armhf (1.61.0+dfsg-3) ...
Setting up libbsd0:armhf (0.8.3-1) ...
Setting up libxml2:armhf (2.9.4+dfsg1-2) ...
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Setting up libmagic1:armhf (1:5.28-4) ...
Setting up libcroco3:armhf (0.6.11-2) ...
Setting up libssh2-1:armhf (1.7.0-1) ...
Processing triggers for libc-bin (2.24-5+rpi1) ...
Setting up autotools-dev (20160430.1) ...
Setting up libunistring0:armhf (0.9.6+really0.9.3-0.1) ...
Setting up libgtest-dev:armhf (1.7.0-4) ...
Setting up libboost-dev:armhf (1.61.0.2) ...
Setting up libjpeg62-turbo-dev:armhf (1:1.5.1-2) ...
Setting up libkeyutils1:armhf (1.5.9-9) ...
Setting up bsdmainutils (9.0.11) ...
update-alternatives: using /usr/bin/bsd-write to provide /usr/bin/write (write) in auto mode
update-alternatives: using /usr/bin/bsd-from to provide /usr/bin/from (from) in auto mode
Setting up hdf5-helpers (1.8.16+docs-8+b1) ...
Setting up autopoint (0.19.8.1-1) ...
Setting up libreadline6:armhf (6.3-9) ...
Setting up libsz2:armhf (0.3.2-1) ...
Setting up zlib1g-dev:armhf (1:1.2.8.dfsg-2+b1) ...
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Setting up libhdf5-10:armhf (1.8.16+docs-8+b1) ...
Setting up libhdf5-cpp-11:armhf (1.8.16+docs-8+b1) ...
Setting up gettext (0.19.8.1-1) ...
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Setting up libhdf5-dev (1.8.16+docs-8+b1) ...
update-alternatives: using /usr/lib/arm-linux-gnueabihf/pkgconfig/hdf5-serial.pc to provide /usr/lib/arm-linux-gnueabihf/pkgconfig/hdf5.pc (hdf5.pc) in auto mode
Setting up autoconf (2.69-10) ...
Setting up file (1:5.28-4) ...
Setting up libkrb5support0:armhf (1.14.3+dfsg-2) ...
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Setting up libjpeg-dev (1:1.5.1-2) ...
Setting up automake (1:1.15-4) ...
update-alternatives: using /usr/bin/automake-1.15 to provide /usr/bin/automake (automake) in auto mode
Setting up man-db (2.7.5-1) ...
Not building database; man-db/auto-update is not 'true'.
Setting up libpython2.7-stdlib:armhf (2.7.12-3) ...
Setting up libtool (2.4.6-2) ...
Setting up libk5crypto3:armhf (1.14.3+dfsg-2) ...
Setting up po-debconf (1.0.20) ...
Setting up python2.7 (2.7.12-3) ...
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Setting up libkrb5-3:armhf (1.14.3+dfsg-2) ...
Setting up python (2.7.11-2) ...
Setting up libgssapi-krb5-2:armhf (1.14.3+dfsg-2) ...
Setting up libcurl3-gnutls:armhf (7.50.1-1) ...
Setting up libhts1:armhf (1.3.1-3+rpi1) ...
Setting up libhts-dev:armhf (1.3.1-3+rpi1) ...
Setting up dh-autoreconf (12) ...
Setting up dh-strip-nondeterminism (0.028-1) ...
Setting up debhelper (10.2.2) ...
Setting up dh-exec (0.23) ...
Setting up sbuild-build-depends-pbseqlib-dummy (0.invalid.0) ...
Processing triggers for libc-bin (2.24-5+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_2.27-9 dpkg-dev_1.18.10 g++-6_6.2.0-6+rpi1 gcc-6_6.2.0-6+rpi1 libc6-dev_2.24-5+rpi1 libstdc++-6-dev_6.2.0-6+rpi1 libstdc++6_6.2.0-6+rpi1 linux-libc-dev_3.18.5-1~exp1+rpi19+stretch
Package versions: adduser_3.115 apt_1.3.1 autoconf_2.69-10 automake_1:1.15-4 autopoint_0.19.8.1-1 autotools-dev_20160430.1 base-files_9.6+rpi1 base-passwd_3.5.40 bash_4.4-1 binutils_2.27-9 bsdmainutils_9.0.11 bsdutils_1:2.28.2-1 build-essential_12.2 bzip2_1.0.6-8 coreutils_8.25-2 cpio_2.11+dfsg-5 cpp_4:6.1.1-1 cpp-6_6.2.0-6+rpi1 dash_0.5.8-2.3 debconf_1.5.59 debfoster_2.7-2.1 debhelper_10.2.2 debianutils_4.8 dh-autoreconf_12 dh-exec_0.23 dh-strip-nondeterminism_0.028-1 diffutils_1:3.5-1 dirmngr_2.1.15-4 dmsetup_2:1.02.133-1 dpkg_1.18.10 dpkg-dev_1.18.10 e2fslibs_1.43.3-1 e2fsprogs_1.43.3-1 fakeroot_1.21-2 file_1:5.28-4 findutils_4.6.0+git+20160703-2 fuse2fs_1.43.3-1 g++_4:6.1.1-1 g++-6_6.2.0-6+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_6.2.0-6+rpi1 gcc-6-base_6.2.0-6+rpi1 gettext_0.19.8.1-1 gettext-base_0.19.8.1-1 gnupg_2.1.15-4 gnupg-agent_2.1.15-4 gnupg-l10n_2.1.15-4 gpgv_2.1.15-4 grep_2.26-1 groff-base_1.22.3-8 gzip_1.6-5 hdf5-helpers_1.8.16+docs-8+b1 hostname_3.18 init_1.45 init-system-helpers_1.45 initscripts_2.88dsf-59.8 insserv_1.14.0-5.4 intltool-debian_0.35.0+20060710.4 kbd_2.0.3-2 klibc-utils_2.0.4-9+rpi1 kmod_22-1.1 libacl1_2.2.52-3 libaec-dev_0.3.2-1 libaec0_0.3.2-1 libapparmor1_2.10.95-5 libapt-pkg5.0_1.3.1 libarchive-zip-perl_1.59-1 libasan3_6.2.0-6+rpi1 libassuan0_2.4.3-1 libatomic1_6.2.0-6+rpi1 libattr1_1:2.4.47-2 libaudit-common_1:2.6.7-1 libaudit1_1:2.6.7-1 libblkid1_2.28.2-1 libboost-dev_1.61.0.2 libboost1.61-dev_1.61.0+dfsg-3 libbsd0_0.8.3-1 libbz2-1.0_1.0.6-8 libc-bin_2.24-5+rpi1 libc-dev-bin_2.24-5+rpi1 libc6_2.24-5+rpi1 libc6-dev_2.24-5+rpi1 libcap-ng0_0.7.7-3 libcap2_1:2.25-1 libcap2-bin_1:2.25-1 libcc1-0_6.2.0-6+rpi1 libcomerr2_1.43.3-1 libcroco3_0.6.11-2 libcryptsetup4_2:1.7.2-5 libcurl3-gnutls_7.50.1-1 libdb5.3_5.3.28-12 libdbus-1-3_1.10.12-1 libdebconfclient0_0.218 libdevmapper1.02.1_2:1.02.133-1 libdpkg-perl_1.18.10 libdrm2_2.4.71-1 libexpat1_2.2.0-1 libfakeroot_1.21-2 libfdisk1_2.28.2-1 libffi6_3.2.1-6 libfile-stripnondeterminism-perl_0.028-1 libfuse2_2.9.7-1 libgc1c2_1:7.4.2-8 libgcc-6-dev_6.2.0-6+rpi1 libgcc1_1:6.2.0-6+rpi1 libgcrypt20_1.7.3-2 libgdbm3_1.8.3-14 libgfortran3_6.2.0-6+rpi1 libglib2.0-0_2.50.0-2+rpi1 libgmp10_2:6.1.1+dfsg-1 libgnutls30_3.5.5-2 libgomp1_6.2.0-6+rpi1 libgpg-error0_1.24-1 libgssapi-krb5-2_1.14.3+dfsg-2 libgtest-dev_1.7.0-4 libhdf5-10_1.8.16+docs-8+b1 libhdf5-cpp-11_1.8.16+docs-8+b1 libhdf5-dev_1.8.16+docs-8+b1 libhogweed4_3.3-1 libhts-dev_1.3.1-3+rpi1 libhts1_1.3.1-3+rpi1 libicu57_57.1-4 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_1.14.3+dfsg-2 libkeyutils1_1.5.9-9 libklibc_2.0.4-9+rpi1 libkmod2_22-1.1 libkrb5-3_1.14.3+dfsg-2 libkrb5support0_1.14.3+dfsg-2 libksba8_1.3.5-2 libldap-2.4-2_2.4.42+dfsg-2+rpi1+b3 liblz4-1_0.0~r131-2 liblzma5_5.2.2-1.2 libmagic-mgc_1:5.28-4 libmagic1_1:5.28-4 libmount1_2.28.2-1 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_1.15.0-1 libnpth0_1.2-3 libp11-kit0_0.23.2-5 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 libpcre3_2:8.39-2 libperl5.24_5.24.1~rc3-3 libpipeline1_1.4.1-2 libplymouth4_0.9.2-3 libpng12-0_1.2.54-6 libprocps6_2:3.3.12-2 libpython-stdlib_2.7.11-2 libpython2.7-minimal_2.7.12-3 libpython2.7-stdlib_2.7.12-3 libreadline6_6.3-9 libreadline7_7.0-1 librtmp1_2.4+20151223.gitfa8646d.1-1 libsasl2-2_2.1.26.dfsg1-15 libsasl2-modules_2.1.26.dfsg1-15 libsasl2-modules-db_2.1.26.dfsg1-15 libseccomp2_2.3.1-2 libselinux1_2.5-3 libsemanage-common_2.5-1 libsemanage1_2.5-1 libsepol1_2.5-1 libsigsegv2_2.10-5 libsmartcols1_2.28.2-1 libsqlite3-0_3.14.2-1 libss2_1.43.3-1 libssh2-1_1.7.0-1 libssl1.0.2_1.0.2j-1 libstdc++-6-dev_6.2.0-6+rpi1 libstdc++6_6.2.0-6+rpi1 libsystemd0_231-9 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_6.2.0-6+rpi1 libudev1_231-9 libunistring0_0.9.6+really0.9.3-0.1 libusb-0.1-4_2:0.1.12-30 libustr-1.0-1_1.0.4-5 libuuid1_2.28.2-1 libxml2_2.9.4+dfsg1-2 linux-libc-dev_3.18.5-1~exp1+rpi19+stretch login_1:4.2-3.2 lsb-base_9.20160629+rpi1 m4_1.4.17-5 make_4.1-9 makedev_2.3.1-93 man-db_2.7.5-1 manpages_4.08-1 mawk_1.3.3-17 mime-support_3.60 mount_2.28.2-1 multiarch-support_2.24-5+rpi1 ncurses-base_6.0+20160917-1 ncurses-bin_6.0+20160917-1 netbase_5.3 passwd_1:4.2-3.2 patch_2.7.5-1 perl_5.24.1~rc3-3 perl-base_5.24.1~rc3-3 perl-modules-5.24_5.24.1~rc3-3 pinentry-curses_0.9.7-6 po-debconf_1.0.20 procps_2:3.3.12-2 psmisc_22.21-2.1 python_2.7.11-2 python-minimal_2.7.11-2 python2.7_2.7.12-3 python2.7-minimal_2.7.12-3 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_231-9 systemd-sysv_231-9 sysv-rc_2.88dsf-59.8 sysvinit-utils_2.88dsf-59.8 tar_1.29b-1 tzdata_2016h-1 udev_231-9 util-linux_2.28.2-1 xz-utils_5.2.2-1.2 zlib1g_1:1.2.8.dfsg-2+b1 zlib1g-dev_1:1.2.8.dfsg-2+b1
+------------------------------------------------------------------------------+
| Build |
+------------------------------------------------------------------------------+
Unpack source
-------------
gpgv: unknown type of key resource 'trustedkeys.kbx'
gpgv: keyblock resource '/sbuild-nonexistent/.gnupg/trustedkeys.kbx': General error
gpgv: Signature made Mon Oct 24 01:49:54 2016 UTC
gpgv: using RSA key 59B2306F3AF9DDC1
gpgv: Can't check signature: No public key
dpkg-source: warning: failed to verify signature on ./pbseqlib_0~20160705-1.dsc
dpkg-source: info: extracting pbseqlib in /<<PKGBUILDDIR>>
dpkg-source: info: unpacking pbseqlib_0~20160705.orig.tar.gz
dpkg-source: info: unpacking pbseqlib_0~20160705-1.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-1a8a2d19-a7d9-4130-95ff-faef4775e4b5
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 0~20160705-1
dpkg-buildpackage: info: source distribution unstable
dpkg-source --before-build pbseqlib-0~20160705
dpkg-buildpackage: info: host architecture armhf
fakeroot debian/rules clean
dh clean --parallel
dh_testdir -O--parallel
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 -O--parallel
debian/rules build-arch
dh build-arch --parallel
dh_testdir -a -O--parallel
dh_update_autotools_config -a -O--parallel
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'
"""
"""
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
HDF5_INC:=/usr/include/hdf5/serial
HDF5_LIB:=/usr/lib/arm-linux-gnueabihf/hdf5/serial
LIBPBDATA_INC ?=../pbdata
LIBPBIHDF_INC ?=../hdf
LIBBLASR_INC ?=../alignment
LIBPBDATA_LIB ?=../pbdata
LIBPBIHDF_LIB ?=../hdf
LIBBLASR_LIB ?=../alignment
# Use PREFIX dir, if available.
INCLUDES += ${PREFIX_INC}
LIBS += ${PREFIX_LIB}
"""
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
dh_auto_build -a -O--parallel
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
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
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 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
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
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 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
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
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
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 HDFFile.cpp -o HDFFile.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 HDFScanDataReader.cpp -o HDFScanDataReader.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 HDFAlnInfoGroup.cpp -o HDFAlnInfoGroup.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 HDFRegionsWriter.cpp -o HDFRegionsWriter.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 HDFScanDataWriter.cpp -o HDFScanDataWriter.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 HDFNewBasReader.cpp -o HDFNewBasReader.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 HDFPulseWriter.cpp -o HDFPulseWriter.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 HDFGroup.cpp -o HDFGroup.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 HDFUtils.cpp -o HDFUtils.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 HDFAlnGroupGroup.cpp -o HDFAlnGroupGroup.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 HDFData.cpp -o HDFData.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 HDFZMWWriter.cpp -o HDFZMWWriter.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 HDFPulseH5Writer.cpp -o HDFPulseH5Writer.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 BufferedHDF2DArray.cpp -o BufferedHDF2DArray.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 -fPIC -c HDFAttributable.cpp -o HDFAttributable.shared.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 -fPIC -c HDFBaxWriter.cpp -o HDFBaxWriter.shared.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 -fPIC -c HDFWriterBase.cpp -o HDFWriterBase.shared.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 -fPIC -c DatasetCollection.cpp -o DatasetCollection.shared.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 -fPIC -c HDFRegionTableReader.cpp -o HDFRegionTableReader.shared.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 -fPIC -c BufferedHDFArray.cpp -o BufferedHDFArray.shared.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 -fPIC -c HDFAtom.cpp -o HDFAtom.shared.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 -fPIC -c HDFCmpExperimentGroup.cpp -o HDFCmpExperimentGroup.shared.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 -fPIC -c HDFZMWMetricsWriter.cpp -o HDFZMWMetricsWriter.shared.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 -fPIC -c HDFPulseDataFile.cpp -o HDFPulseDataFile.shared.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 -fPIC -c HDFPulseCallsWriter.cpp -o HDFPulseCallsWriter.shared.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 -fPIC -c HDFCmpSupportedFields.cpp -o HDFCmpSupportedFields.shared.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 -fPIC -c HDFBaseCallsWriter.cpp -o HDFBaseCallsWriter.shared.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 -fPIC -c HDFZMWReader.cpp -o HDFZMWReader.shared.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 -fPIC -c HDFFile.cpp -o HDFFile.shared.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 -fPIC -c HDFScanDataReader.cpp -o HDFScanDataReader.shared.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 -fPIC -c HDFAlnInfoGroup.cpp -o HDFAlnInfoGroup.shared.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 -fPIC -c HDFRegionsWriter.cpp -o HDFRegionsWriter.shared.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 -fPIC -c HDFScanDataWriter.cpp -o HDFScanDataWriter.shared.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 -fPIC -c HDFNewBasReader.cpp -o HDFNewBasReader.shared.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 -fPIC -c HDFPulseWriter.cpp -o HDFPulseWriter.shared.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 -fPIC -c HDFGroup.cpp -o HDFGroup.shared.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 -fPIC -c HDFUtils.cpp -o HDFUtils.shared.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 -fPIC -c HDFAlnGroupGroup.cpp -o HDFAlnGroupGroup.shared.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 -fPIC -c HDFData.cpp -o HDFData.shared.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 -fPIC -c HDFZMWWriter.cpp -o HDFZMWWriter.shared.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 -fPIC -c HDFPulseH5Writer.cpp -o HDFPulseH5Writer.shared.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 -fPIC -c BufferedHDF2DArray.cpp -o BufferedHDF2DArray.shared.o
ar rc libpbihdf.a HDFAttributable.o HDFBaxWriter.o HDFWriterBase.o DatasetCollection.o HDFRegionTableReader.o BufferedHDFArray.o HDFAtom.o HDFCmpExperimentGroup.o HDFZMWMetricsWriter.o HDFPulseDataFile.o HDFPulseCallsWriter.o HDFCmpSupportedFields.o HDFBaseCallsWriter.o HDFZMWReader.o HDFFile.o HDFScanDataReader.o HDFAlnInfoGroup.o HDFRegionsWriter.o HDFScanDataWriter.o HDFNewBasReader.o HDFPulseWriter.o HDFGroup.o HDFUtils.o HDFAlnGroupGroup.o HDFData.o HDFZMWWriter.o HDFPulseH5Writer.o BufferedHDF2DArray.o
g++ -shared -Wl,-z,relro -L/usr/lib -L../pbdata -L/usr/lib/arm-linux-gnueabihf/hdf5/serial -o libpbihdf.so -Wl,-soname,libpbihdf.so HDFAttributable.shared.o HDFBaxWriter.shared.o HDFWriterBase.shared.o DatasetCollection.shared.o HDFRegionTableReader.shared.o BufferedHDFArray.shared.o HDFAtom.shared.o HDFCmpExperimentGroup.shared.o HDFZMWMetricsWriter.shared.o HDFPulseDataFile.shared.o HDFPulseCallsWriter.shared.o HDFCmpSupportedFields.shared.o HDFBaseCallsWriter.shared.o HDFZMWReader.shared.o HDFFile.shared.o HDFScanDataReader.shared.o HDFAlnInfoGroup.shared.o HDFRegionsWriter.shared.o HDFScanDataWriter.shared.o HDFNewBasReader.shared.o HDFPulseWriter.shared.o HDFGroup.shared.o HDFUtils.shared.o HDFAlnGroupGroup.shared.o HDFData.shared.o HDFZMWWriter.shared.o HDFPulseH5Writer.shared.o BufferedHDF2DArray.shared.o -lpbdata -lhdf5 -lhdf5_cpp
make[3]: Leaving directory '/<<PKGBUILDDIR>>/hdf'
make[2]: Leaving directory '/<<PKGBUILDDIR>>'
make libblasr
make[2]: Entering directory '/<<PKGBUILDDIR>>'
make -C /<<PKGBUILDDIR>>//alignment all
make[3]: Entering directory '/<<PKGBUILDDIR>>/alignment'
g++ -std=c++11 -pedantic -Wno-long-long -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 MappingMetrics.cpp -o MappingMetrics.o
g++ -std=c++11 -pedantic -Wno-long-long -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 algorithms/alignment/AlignmentUtils.cpp -o AlignmentUtils.o
g++ -std=c++11 -pedantic -Wno-long-long -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 algorithms/alignment/BaseScoreFunction.cpp -o BaseScoreFunction.o
g++ -std=c++11 -pedantic -Wno-long-long -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 algorithms/alignment/ExtendAlign.cpp -o ExtendAlign.o
g++ -std=c++11 -pedantic -Wno-long-long -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 algorithms/alignment/GuidedAlign.cpp -o GuidedAlign.o
g++ -std=c++11 -pedantic -Wno-long-long -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 algorithms/alignment/IDSScoreFunction.cpp -o IDSScoreFunction.o
g++ -std=c++11 -pedantic -Wno-long-long -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 algorithms/alignment/KBandAlign.cpp -o KBandAlign.o
g++ -std=c++11 -pedantic -Wno-long-long -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 algorithms/alignment/QualityValueScoreFunction.cpp -o QualityValueScoreFunction.o
g++ -std=c++11 -pedantic -Wno-long-long -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 algorithms/alignment/ScoreMatrices.cpp -o ScoreMatrices.o
g++ -std=c++11 -pedantic -Wno-long-long -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 algorithms/alignment/StringToScoreMatrix.cpp -o StringToScoreMatrix.o
g++ -std=c++11 -pedantic -Wno-long-long -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 algorithms/alignment/sdp/SDPFragment.cpp -o SDPFragment.o
g++ -std=c++11 -pedantic -Wno-long-long -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 algorithms/alignment/sdp/SparseDynamicProgramming.cpp -o SparseDynamicProgramming.o
g++ -std=c++11 -pedantic -Wno-long-long -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 algorithms/anchoring/BWTSearch.cpp -o BWTSearch.o
g++ -std=c++11 -pedantic -Wno-long-long -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 algorithms/anchoring/ClusterProbability.cpp -o ClusterProbability.o
g++ -std=c++11 -pedantic -Wno-long-long -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 algorithms/anchoring/Coordinate.cpp -o Coordinate.o
g++ -std=c++11 -pedantic -Wno-long-long -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 algorithms/anchoring/FindMaxInterval.cpp -o FindMaxInterval.o
g++ -std=c++11 -pedantic -Wno-long-long -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 algorithms/sorting/DifferenceCovers.cpp -o DifferenceCovers.o
g++ -std=c++11 -pedantic -Wno-long-long -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 algorithms/sorting/LightweightSuffixArray.cpp -o LightweightSuffixArray.o
g++ -std=c++11 -pedantic -Wno-long-long -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 algorithms/sorting/MultikeyQuicksort.cpp -o MultikeyQuicksort.o
g++ -std=c++11 -pedantic -Wno-long-long -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 algorithms/sorting/qsufsort.cpp -o qsufsort.o
g++ -std=c++11 -pedantic -Wno-long-long -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 datastructures/alignment/Alignment.cpp -o Alignment.o
g++ -std=c++11 -pedantic -Wno-long-long -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 datastructures/alignment/AlignmentCandidate.cpp -o AlignmentCandidate.o
g++ -std=c++11 -pedantic -Wno-long-long -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 datastructures/alignment/AlignmentContext.cpp -o AlignmentContext.o
g++ -std=c++11 -pedantic -Wno-long-long -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 datastructures/alignment/AlignmentMap.cpp -o AlignmentMap.o
g++ -std=c++11 -pedantic -Wno-long-long -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 datastructures/alignment/AlignmentStats.cpp -o AlignmentStats.o
g++ -std=c++11 -pedantic -Wno-long-long -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 datastructures/alignment/CmpFile.cpp -o CmpFile.o
g++ -std=c++11 -pedantic -Wno-long-long -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 datastructures/alignment/FilterCriteria.cpp -o FilterCriteria.o
g++ -std=c++11 -pedantic -Wno-long-long -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 datastructures/alignment/SAMToAlignmentCandidateAdapter.cpp -o SAMToAlignmentCandidateAdapter.o
g++ -std=c++11 -pedantic -Wno-long-long -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 datastructures/alignmentset/SAMQVConversion.cpp -o SAMQVConversion.o
g++ -std=c++11 -pedantic -Wno-long-long -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 datastructures/alignmentset/SAMSupplementalQVList.cpp -o SAMSupplementalQVList.o
g++ -std=c++11 -pedantic -Wno-long-long -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 datastructures/anchoring/AnchorParameters.cpp -o AnchorParameters.o
g++ -std=c++11 -pedantic -Wno-long-long -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 datastructures/anchoring/ClusterList.cpp -o ClusterList.o
g++ -std=c++11 -pedantic -Wno-long-long -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 datastructures/anchoring/MatchPos.cpp -o MatchPos.o
g++ -std=c++11 -pedantic -Wno-long-long -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 datastructures/anchoring/WeightedInterval.cpp -o WeightedInterval.o
g++ -std=c++11 -pedantic -Wno-long-long -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 files/BaseSequenceIO.cpp -o BaseSequenceIO.o
g++ -std=c++11 -pedantic -Wno-long-long -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 files/CCSIterator.cpp -o CCSIterator.o
g++ -std=c++11 -pedantic -Wno-long-long -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 files/FragmentCCSIterator.cpp -o FragmentCCSIterator.o
g++ -std=c++11 -pedantic -Wno-long-long -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 files/ReaderAgglomerate.cpp -o ReaderAgglomerate.o
g++ -std=c++11 -pedantic -Wno-long-long -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 format/CompareSequencesPrinter.cpp -o CompareSequencesPrinter.o
files/ReaderAgglomerate.cpp: In member function 'int ReaderAgglomerate::Initialize(bool)':
files/ReaderAgglomerate.cpp:203:40: warning: unused parameter 'unrolled_mode' [-Wunused-parameter]
int ReaderAgglomerate::Initialize(bool unrolled_mode) {
^~~~~~~~~~~~~
g++ -std=c++11 -pedantic -Wno-long-long -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 format/IntervalPrinter.cpp -o IntervalPrinter.o
g++ -std=c++11 -pedantic -Wno-long-long -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 format/SAMHeaderPrinter.cpp -o SAMHeaderPrinter.o
g++ -std=c++11 -pedantic -Wno-long-long -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 format/SAMPrinter.cpp -o SAMPrinter.o
g++ -std=c++11 -pedantic -Wno-long-long -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 format/SummaryPrinter.cpp -o SummaryPrinter.o
g++ -std=c++11 -pedantic -Wno-long-long -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 query/PbiFilterZmwGroupQuery.cpp -o PbiFilterZmwGroupQuery.o
g++ -std=c++11 -pedantic -Wno-long-long -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 query/SequentialZmwGroupQuery.cpp -o SequentialZmwGroupQuery.o
g++ -std=c++11 -pedantic -Wno-long-long -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 qvs/QualityValueProfile.cpp -o QualityValueProfile.o
g++ -std=c++11 -pedantic -Wno-long-long -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 simulator/ContextSample.cpp -o ContextSample.o
g++ -std=c++11 -pedantic -Wno-long-long -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 simulator/ContextSet.cpp -o ContextSet.o
g++ -std=c++11 -pedantic -Wno-long-long -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 simulator/LengthHistogram.cpp -o LengthHistogram.o
g++ -std=c++11 -pedantic -Wno-long-long -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 simulator/QualitySample.cpp -o QualitySample.o
g++ -std=c++11 -pedantic -Wno-long-long -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 statistics/LookupAnchorDistribution.cpp -o LookupAnchorDistribution.o
g++ -std=c++11 -pedantic -Wno-long-long -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 statistics/StatUtils.cpp -o StatUtils.o
g++ -std=c++11 -pedantic -Wno-long-long -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 statistics/cdfs.cpp -o cdfs.o
g++ -std=c++11 -pedantic -Wno-long-long -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 statistics/pdfs.cpp -o pdfs.o
g++ -std=c++11 -pedantic -Wno-long-long -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 tuples/BaseTuple.cpp -o BaseTuple.o
g++ -std=c++11 -pedantic -Wno-long-long -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 tuples/DNATuple.cpp -o DNATuple.o
g++ -std=c++11 -pedantic -Wno-long-long -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 tuples/TupleMetrics.cpp -o TupleMetrics.o
g++ -std=c++11 -pedantic -Wno-long-long -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 utils/FileOfFileNames.cpp -o FileOfFileNames.o
g++ -std=c++11 -pedantic -Wno-long-long -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 utils/FileUtils.cpp -o FileUtils.o
g++ -std=c++11 -pedantic -Wno-long-long -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 utils/LogUtils.cpp -o LogUtils.o
g++ -std=c++11 -pedantic -Wno-long-long -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 utils/PhredUtils.cpp -o PhredUtils.o
g++ -std=c++11 -pedantic -Wno-long-long -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 utils/RangeUtils.cpp -o RangeUtils.o
g++ -std=c++11 -pedantic -Wno-long-long -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 utils/RegionUtils.cpp -o RegionUtils.o
g++ -std=c++11 -pedantic -Wno-long-long -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 -fPIC -c MappingMetrics.cpp -o MappingMetrics.shared.o
g++ -std=c++11 -pedantic -Wno-long-long -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 -fPIC -c algorithms/alignment/AlignmentUtils.cpp -o AlignmentUtils.shared.o
g++ -std=c++11 -pedantic -Wno-long-long -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 -fPIC -c algorithms/alignment/BaseScoreFunction.cpp -o BaseScoreFunction.shared.o
g++ -std=c++11 -pedantic -Wno-long-long -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 -fPIC -c algorithms/alignment/ExtendAlign.cpp -o ExtendAlign.shared.o
g++ -std=c++11 -pedantic -Wno-long-long -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 -fPIC -c algorithms/alignment/GuidedAlign.cpp -o GuidedAlign.shared.o
g++ -std=c++11 -pedantic -Wno-long-long -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 -fPIC -c algorithms/alignment/IDSScoreFunction.cpp -o IDSScoreFunction.shared.o
g++ -std=c++11 -pedantic -Wno-long-long -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 -fPIC -c algorithms/alignment/KBandAlign.cpp -o KBandAlign.shared.o
g++ -std=c++11 -pedantic -Wno-long-long -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 -fPIC -c algorithms/alignment/QualityValueScoreFunction.cpp -o QualityValueScoreFunction.shared.o
g++ -std=c++11 -pedantic -Wno-long-long -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 -fPIC -c algorithms/alignment/ScoreMatrices.cpp -o ScoreMatrices.shared.o
g++ -std=c++11 -pedantic -Wno-long-long -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 -fPIC -c algorithms/alignment/StringToScoreMatrix.cpp -o StringToScoreMatrix.shared.o
g++ -std=c++11 -pedantic -Wno-long-long -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 -fPIC -c algorithms/alignment/sdp/SDPFragment.cpp -o SDPFragment.shared.o
g++ -std=c++11 -pedantic -Wno-long-long -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 -fPIC -c algorithms/alignment/sdp/SparseDynamicProgramming.cpp -o SparseDynamicProgramming.shared.o
g++ -std=c++11 -pedantic -Wno-long-long -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 -fPIC -c algorithms/anchoring/BWTSearch.cpp -o BWTSearch.shared.o
g++ -std=c++11 -pedantic -Wno-long-long -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 -fPIC -c algorithms/anchoring/ClusterProbability.cpp -o ClusterProbability.shared.o
g++ -std=c++11 -pedantic -Wno-long-long -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 -fPIC -c algorithms/anchoring/Coordinate.cpp -o Coordinate.shared.o
g++ -std=c++11 -pedantic -Wno-long-long -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 -fPIC -c algorithms/anchoring/FindMaxInterval.cpp -o FindMaxInterval.shared.o
g++ -std=c++11 -pedantic -Wno-long-long -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 -fPIC -c algorithms/sorting/DifferenceCovers.cpp -o DifferenceCovers.shared.o
g++ -std=c++11 -pedantic -Wno-long-long -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 -fPIC -c algorithms/sorting/LightweightSuffixArray.cpp -o LightweightSuffixArray.shared.o
g++ -std=c++11 -pedantic -Wno-long-long -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 -fPIC -c algorithms/sorting/MultikeyQuicksort.cpp -o MultikeyQuicksort.shared.o
g++ -std=c++11 -pedantic -Wno-long-long -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 -fPIC -c algorithms/sorting/qsufsort.cpp -o qsufsort.shared.o
g++ -std=c++11 -pedantic -Wno-long-long -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 -fPIC -c datastructures/alignment/Alignment.cpp -o Alignment.shared.o
g++ -std=c++11 -pedantic -Wno-long-long -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 -fPIC -c datastructures/alignment/AlignmentCandidate.cpp -o AlignmentCandidate.shared.o
g++ -std=c++11 -pedantic -Wno-long-long -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 -fPIC -c datastructures/alignment/AlignmentContext.cpp -o AlignmentContext.shared.o
g++ -std=c++11 -pedantic -Wno-long-long -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 -fPIC -c datastructures/alignment/AlignmentMap.cpp -o AlignmentMap.shared.o
g++ -std=c++11 -pedantic -Wno-long-long -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 -fPIC -c datastructures/alignment/AlignmentStats.cpp -o AlignmentStats.shared.o
g++ -std=c++11 -pedantic -Wno-long-long -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 -fPIC -c datastructures/alignment/CmpFile.cpp -o CmpFile.shared.o
g++ -std=c++11 -pedantic -Wno-long-long -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 -fPIC -c datastructures/alignment/FilterCriteria.cpp -o FilterCriteria.shared.o
g++ -std=c++11 -pedantic -Wno-long-long -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 -fPIC -c datastructures/alignment/SAMToAlignmentCandidateAdapter.cpp -o SAMToAlignmentCandidateAdapter.shared.o
g++ -std=c++11 -pedantic -Wno-long-long -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 -fPIC -c datastructures/alignmentset/SAMQVConversion.cpp -o SAMQVConversion.shared.o
g++ -std=c++11 -pedantic -Wno-long-long -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 -fPIC -c datastructures/alignmentset/SAMSupplementalQVList.cpp -o SAMSupplementalQVList.shared.o
g++ -std=c++11 -pedantic -Wno-long-long -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 -fPIC -c datastructures/anchoring/AnchorParameters.cpp -o AnchorParameters.shared.o
g++ -std=c++11 -pedantic -Wno-long-long -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 -fPIC -c datastructures/anchoring/ClusterList.cpp -o ClusterList.shared.o
g++ -std=c++11 -pedantic -Wno-long-long -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 -fPIC -c datastructures/anchoring/MatchPos.cpp -o MatchPos.shared.o
g++ -std=c++11 -pedantic -Wno-long-long -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 -fPIC -c datastructures/anchoring/WeightedInterval.cpp -o WeightedInterval.shared.o
g++ -std=c++11 -pedantic -Wno-long-long -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 -fPIC -c files/BaseSequenceIO.cpp -o BaseSequenceIO.shared.o
g++ -std=c++11 -pedantic -Wno-long-long -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 -fPIC -c files/CCSIterator.cpp -o CCSIterator.shared.o
g++ -std=c++11 -pedantic -Wno-long-long -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 -fPIC -c files/FragmentCCSIterator.cpp -o FragmentCCSIterator.shared.o
g++ -std=c++11 -pedantic -Wno-long-long -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 -fPIC -c files/ReaderAgglomerate.cpp -o ReaderAgglomerate.shared.o
g++ -std=c++11 -pedantic -Wno-long-long -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 -fPIC -c format/CompareSequencesPrinter.cpp -o CompareSequencesPrinter.shared.o
g++ -std=c++11 -pedantic -Wno-long-long -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 -fPIC -c format/IntervalPrinter.cpp -o IntervalPrinter.shared.o
g++ -std=c++11 -pedantic -Wno-long-long -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 -fPIC -c format/SAMHeaderPrinter.cpp -o SAMHeaderPrinter.shared.o
g++ -std=c++11 -pedantic -Wno-long-long -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 -fPIC -c format/SAMPrinter.cpp -o SAMPrinter.shared.o
files/ReaderAgglomerate.cpp: In member function 'int ReaderAgglomerate::Initialize(bool)':
files/ReaderAgglomerate.cpp:203:40: warning: unused parameter 'unrolled_mode' [-Wunused-parameter]
int ReaderAgglomerate::Initialize(bool unrolled_mode) {
^~~~~~~~~~~~~
g++ -std=c++11 -pedantic -Wno-long-long -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 -fPIC -c format/SummaryPrinter.cpp -o SummaryPrinter.shared.o
g++ -std=c++11 -pedantic -Wno-long-long -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 -fPIC -c query/PbiFilterZmwGroupQuery.cpp -o PbiFilterZmwGroupQuery.shared.o
g++ -std=c++11 -pedantic -Wno-long-long -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 -fPIC -c query/SequentialZmwGroupQuery.cpp -o SequentialZmwGroupQuery.shared.o
g++ -std=c++11 -pedantic -Wno-long-long -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 -fPIC -c qvs/QualityValueProfile.cpp -o QualityValueProfile.shared.o
g++ -std=c++11 -pedantic -Wno-long-long -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 -fPIC -c simulator/ContextSample.cpp -o ContextSample.shared.o
g++ -std=c++11 -pedantic -Wno-long-long -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 -fPIC -c simulator/ContextSet.cpp -o ContextSet.shared.o
g++ -std=c++11 -pedantic -Wno-long-long -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 -fPIC -c simulator/LengthHistogram.cpp -o LengthHistogram.shared.o
g++ -std=c++11 -pedantic -Wno-long-long -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 -fPIC -c simulator/QualitySample.cpp -o QualitySample.shared.o
g++ -std=c++11 -pedantic -Wno-long-long -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 -fPIC -c statistics/LookupAnchorDistribution.cpp -o LookupAnchorDistribution.shared.o
g++ -std=c++11 -pedantic -Wno-long-long -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 -fPIC -c statistics/StatUtils.cpp -o StatUtils.shared.o
g++ -std=c++11 -pedantic -Wno-long-long -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 -fPIC -c statistics/cdfs.cpp -o cdfs.shared.o
g++ -std=c++11 -pedantic -Wno-long-long -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 -fPIC -c statistics/pdfs.cpp -o pdfs.shared.o
g++ -std=c++11 -pedantic -Wno-long-long -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 -fPIC -c tuples/BaseTuple.cpp -o BaseTuple.shared.o
g++ -std=c++11 -pedantic -Wno-long-long -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 -fPIC -c tuples/DNATuple.cpp -o DNATuple.shared.o
g++ -std=c++11 -pedantic -Wno-long-long -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 -fPIC -c tuples/TupleMetrics.cpp -o TupleMetrics.shared.o
g++ -std=c++11 -pedantic -Wno-long-long -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 -fPIC -c utils/FileOfFileNames.cpp -o FileOfFileNames.shared.o
g++ -std=c++11 -pedantic -Wno-long-long -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 -fPIC -c utils/FileUtils.cpp -o FileUtils.shared.o
g++ -std=c++11 -pedantic -Wno-long-long -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 -fPIC -c utils/LogUtils.cpp -o LogUtils.shared.o
g++ -std=c++11 -pedantic -Wno-long-long -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 -fPIC -c utils/PhredUtils.cpp -o PhredUtils.shared.o
g++ -std=c++11 -pedantic -Wno-long-long -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 -fPIC -c utils/RangeUtils.cpp -o RangeUtils.shared.o
g++ -std=c++11 -pedantic -Wno-long-long -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 -fPIC -c utils/RegionUtils.cpp -o RegionUtils.shared.o
ar rc libblasr.a MappingMetrics.o AlignmentUtils.o BaseScoreFunction.o ExtendAlign.o GuidedAlign.o IDSScoreFunction.o KBandAlign.o QualityValueScoreFunction.o ScoreMatrices.o StringToScoreMatrix.o SDPFragment.o SparseDynamicProgramming.o BWTSearch.o ClusterProbability.o Coordinate.o FindMaxInterval.o DifferenceCovers.o LightweightSuffixArray.o MultikeyQuicksort.o qsufsort.o Alignment.o AlignmentCandidate.o AlignmentContext.o AlignmentMap.o AlignmentStats.o CmpFile.o FilterCriteria.o SAMToAlignmentCandidateAdapter.o SAMQVConversion.o SAMSupplementalQVList.o AnchorParameters.o ClusterList.o MatchPos.o WeightedInterval.o BaseSequenceIO.o CCSIterator.o FragmentCCSIterator.o ReaderAgglomerate.o CompareSequencesPrinter.o IntervalPrinter.o SAMHeaderPrinter.o SAMPrinter.o SummaryPrinter.o PbiFilterZmwGroupQuery.o SequentialZmwGroupQuery.o QualityValueProfile.o ContextSample.o ContextSet.o LengthHistogram.o QualitySample.o LookupAnchorDistribution.o StatUtils.o cdfs.o pdfs.o BaseTuple.o DNATuple.o TupleMetrics.o FileOfFileNames.o FileUtils.o LogUtils.o PhredUtils.o RangeUtils.o RegionUtils.o
g++ -shared -Wl,-z,relro -L/usr/lib -L../pbdata -L../hdf -L/usr/lib/arm-linux-gnueabihf/hdf5/serial -o libblasr.so -Wl,-soname,libblasr.so MappingMetrics.shared.o AlignmentUtils.shared.o BaseScoreFunction.shared.o ExtendAlign.shared.o GuidedAlign.shared.o IDSScoreFunction.shared.o KBandAlign.shared.o QualityValueScoreFunction.shared.o ScoreMatrices.shared.o StringToScoreMatrix.shared.o SDPFragment.shared.o SparseDynamicProgramming.shared.o BWTSearch.shared.o ClusterProbability.shared.o Coordinate.shared.o FindMaxInterval.shared.o DifferenceCovers.shared.o LightweightSuffixArray.shared.o MultikeyQuicksort.shared.o qsufsort.shared.o Alignment.shared.o AlignmentCandidate.shared.o AlignmentContext.shared.o AlignmentMap.shared.o AlignmentStats.shared.o CmpFile.shared.o FilterCriteria.shared.o SAMToAlignmentCandidateAdapter.shared.o SAMQVConversion.shared.o SAMSupplementalQVList.shared.o AnchorParameters.shared.o ClusterList.shared.o MatchPos.shared.o WeightedInterval.shared.o BaseSequenceIO.shared.o CCSIterator.shared.o FragmentCCSIterator.shared.o ReaderAgglomerate.shared.o CompareSequencesPrinter.shared.o IntervalPrinter.shared.o SAMHeaderPrinter.shared.o SAMPrinter.shared.o SummaryPrinter.shared.o PbiFilterZmwGroupQuery.shared.o SequentialZmwGroupQuery.shared.o QualityValueProfile.shared.o ContextSample.shared.o ContextSet.shared.o LengthHistogram.shared.o QualitySample.shared.o LookupAnchorDistribution.shared.o StatUtils.shared.o cdfs.shared.o pdfs.shared.o BaseTuple.shared.o DNATuple.shared.o TupleMetrics.shared.o FileOfFileNames.shared.o FileUtils.shared.o LogUtils.shared.o PhredUtils.shared.o RangeUtils.shared.o RegionUtils.shared.o -lpbdata -lpbihdf
make[3]: Leaving directory '/<<PKGBUILDDIR>>/alignment'
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debian/rules override_dh_auto_test
make[1]: Entering directory '/<<PKGBUILDDIR>>'
/usr/bin/make -k gtest
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make[3]: Entering directory '/<<PKGBUILDDIR>>/unittest'
make[3]: *** No rule to make target 'gtest-all.o', needed by 'libblasr-test-runner'.
make[3]: *** No rule to make target 'gtest_main.o', needed by 'libblasr-test-runner'.
g++ -O3 -std=c++11 -Wno-div-by-zero -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/<<PKGBUILDDIR>>/unittest/ -I/<<PKGBUILDDIR>>/unittest//../alignment -I/usr/include -I../alignment -I../hdf -I../pbdata -I/usr/include/hdf5/serial -c -o CCSSequence_gtest.o /<<PKGBUILDDIR>>/unittest/pbdata/CCSSequence_gtest.cpp
g++ -O3 -std=c++11 -Wno-div-by-zero -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/<<PKGBUILDDIR>>/unittest/ -I/<<PKGBUILDDIR>>/unittest//../alignment -I/usr/include -I../alignment -I../hdf -I../pbdata -I/usr/include/hdf5/serial -c -o SeqUtils_gtest.o /<<PKGBUILDDIR>>/unittest/pbdata/SeqUtils_gtest.cpp
g++ -O3 -std=c++11 -Wno-div-by-zero -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/<<PKGBUILDDIR>>/unittest/ -I/<<PKGBUILDDIR>>/unittest//../alignment -I/usr/include -I../alignment -I../hdf -I../pbdata -I/usr/include/hdf5/serial -c -o SMRTSequence_gtest.o /<<PKGBUILDDIR>>/unittest/pbdata/SMRTSequence_gtest.cpp
g++ -O3 -std=c++11 -Wno-div-by-zero -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/<<PKGBUILDDIR>>/unittest/ -I/<<PKGBUILDDIR>>/unittest//../alignment -I/usr/include -I../alignment -I../hdf -I../pbdata -I/usr/include/hdf5/serial -c -o defs_gtest.o /<<PKGBUILDDIR>>/unittest/pbdata/defs_gtest.cpp
g++ -O3 -std=c++11 -Wno-div-by-zero -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/<<PKGBUILDDIR>>/unittest/ -I/<<PKGBUILDDIR>>/unittest//../alignment -I/usr/include -I../alignment -I../hdf -I../pbdata -I/usr/include/hdf5/serial -c -o NucConversion_gtest.o /<<PKGBUILDDIR>>/unittest/pbdata/NucConversion_gtest.cpp
g++ -O3 -std=c++11 -Wno-div-by-zero -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/<<PKGBUILDDIR>>/unittest/ -I/<<PKGBUILDDIR>>/unittest//../alignment -I/usr/include -I../alignment -I../hdf -I../pbdata -I/usr/include/hdf5/serial -c -o DNASequence_gtest.o /<<PKGBUILDDIR>>/unittest/pbdata/DNASequence_gtest.cpp
g++ -O3 -std=c++11 -Wno-div-by-zero -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/<<PKGBUILDDIR>>/unittest/ -I/<<PKGBUILDDIR>>/unittest//../alignment -I/usr/include -I../alignment -I../hdf -I../pbdata -I/usr/include/hdf5/serial -c -o VectorUtils_gtest.o /<<PKGBUILDDIR>>/unittest/pbdata/VectorUtils_gtest.cpp
g++ -O3 -std=c++11 -Wno-div-by-zero -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/<<PKGBUILDDIR>>/unittest/ -I/<<PKGBUILDDIR>>/unittest//../alignment -I/usr/include -I../alignment -I../hdf -I../pbdata -I/usr/include/hdf5/serial -c -o ScanData_gtest.o /<<PKGBUILDDIR>>/unittest/pbdata/ScanData_gtest.cpp
g++ -O3 -std=c++11 -Wno-div-by-zero -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/<<PKGBUILDDIR>>/unittest/ -I/<<PKGBUILDDIR>>/unittest//../alignment -I/usr/include -I../alignment -I../hdf -I../pbdata -I/usr/include/hdf5/serial -c -o ChangeListID_gtest.o /<<PKGBUILDDIR>>/unittest/pbdata/ChangeListID_gtest.cpp
g++ -O3 -std=c++11 -Wno-div-by-zero -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/<<PKGBUILDDIR>>/unittest/ -I/<<PKGBUILDDIR>>/unittest//../alignment -I/usr/include -I../alignment -I../hdf -I../pbdata -I/usr/include/hdf5/serial -c -o FASTQReader_gtest.o /<<PKGBUILDDIR>>/unittest/pbdata/FASTQReader_gtest.cpp
g++ -O3 -std=c++11 -Wno-div-by-zero -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/<<PKGBUILDDIR>>/unittest/ -I/<<PKGBUILDDIR>>/unittest//../alignment -I/usr/include -I../alignment -I../hdf -I../pbdata -I/usr/include/hdf5/serial -c -o utils_gtest.o /<<PKGBUILDDIR>>/unittest/pbdata/utils_gtest.cpp
g++ -O3 -std=c++11 -Wno-div-by-zero -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/<<PKGBUILDDIR>>/unittest/ -I/<<PKGBUILDDIR>>/unittest//../alignment -I/usr/include -I../alignment -I../hdf -I../pbdata -I/usr/include/hdf5/serial -c -o FASTASequence_gtest.o /<<PKGBUILDDIR>>/unittest/pbdata/FASTASequence_gtest.cpp
g++ -O3 -std=c++11 -Wno-div-by-zero -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/<<PKGBUILDDIR>>/unittest/ -I/<<PKGBUILDDIR>>/unittest//../alignment -I/usr/include -I../alignment -I../hdf -I../pbdata -I/usr/include/hdf5/serial -c -o FASTAReader_gtest.o /<<PKGBUILDDIR>>/unittest/pbdata/FASTAReader_gtest.cpp
g++ -O3 -std=c++11 -Wno-div-by-zero -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/<<PKGBUILDDIR>>/unittest/ -I/<<PKGBUILDDIR>>/unittest//../alignment -I/usr/include -I../alignment -I../hdf -I../pbdata -I/usr/include/hdf5/serial -c -o StringUtils_gtest.o /<<PKGBUILDDIR>>/unittest/pbdata/StringUtils_gtest.cpp
g++ -O3 -std=c++11 -Wno-div-by-zero -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/<<PKGBUILDDIR>>/unittest/ -I/<<PKGBUILDDIR>>/unittest//../alignment -I/usr/include -I../alignment -I../hdf -I../pbdata -I/usr/include/hdf5/serial -c -o SMRTTitle_gtest.o /<<PKGBUILDDIR>>/unittest/pbdata/utils/SMRTTitle_gtest.cpp
g++ -O3 -std=c++11 -Wno-div-by-zero -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/<<PKGBUILDDIR>>/unittest/ -I/<<PKGBUILDDIR>>/unittest//../alignment -I/usr/include -I../alignment -I../hdf -I../pbdata -I/usr/include/hdf5/serial -c -o TitleTable_gtest.o /<<PKGBUILDDIR>>/unittest/pbdata/metagenome/TitleTable_gtest.cpp
g++ -O3 -std=c++11 -Wno-div-by-zero -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/<<PKGBUILDDIR>>/unittest/ -I/<<PKGBUILDDIR>>/unittest//../alignment -I/usr/include -I../alignment -I../hdf -I../pbdata -I/usr/include/hdf5/serial -c -o RefInfo_gtest.o /<<PKGBUILDDIR>>/unittest/pbdata/saf/RefInfo_gtest.cpp
g++ -O3 -std=c++11 -Wno-div-by-zero -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/<<PKGBUILDDIR>>/unittest/ -I/<<PKGBUILDDIR>>/unittest//../alignment -I/usr/include -I../alignment -I../hdf -I../pbdata -I/usr/include/hdf5/serial -c -o AlnGroup_gtest.o /<<PKGBUILDDIR>>/unittest/pbdata/saf/AlnGroup_gtest.cpp
g++ -O3 -std=c++11 -Wno-div-by-zero -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/<<PKGBUILDDIR>>/unittest/ -I/<<PKGBUILDDIR>>/unittest//../alignment -I/usr/include -I../alignment -I../hdf -I../pbdata -I/usr/include/hdf5/serial -c -o MovieInfo_gtest.o /<<PKGBUILDDIR>>/unittest/pbdata/saf/MovieInfo_gtest.cpp
g++ -O3 -std=c++11 -Wno-div-by-zero -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/<<PKGBUILDDIR>>/unittest/ -I/<<PKGBUILDDIR>>/unittest//../alignment -I/usr/include -I../alignment -I../hdf -I../pbdata -I/usr/include/hdf5/serial -c -o RegionAnnotations_gtest.o /<<PKGBUILDDIR>>/unittest/pbdata/reads/RegionAnnotations_gtest.cpp
g++ -O3 -std=c++11 -Wno-div-by-zero -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/<<PKGBUILDDIR>>/unittest/ -I/<<PKGBUILDDIR>>/unittest//../alignment -I/usr/include -I../alignment -I../hdf -I../pbdata -I/usr/include/hdf5/serial -c -o ReadType_gtest.o /<<PKGBUILDDIR>>/unittest/pbdata/reads/ReadType_gtest.cpp
g++ -O3 -std=c++11 -Wno-div-by-zero -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/<<PKGBUILDDIR>>/unittest/ -I/<<PKGBUILDDIR>>/unittest//../alignment -I/usr/include -I../alignment -I../hdf -I../pbdata -I/usr/include/hdf5/serial -c -o RegionTypeMap_gtest.o /<<PKGBUILDDIR>>/unittest/pbdata/reads/RegionTypeMap_gtest.cpp
g++ -O3 -std=c++11 -Wno-div-by-zero -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/<<PKGBUILDDIR>>/unittest/ -I/<<PKGBUILDDIR>>/unittest//../alignment -I/usr/include -I../alignment -I../hdf -I../pbdata -I/usr/include/hdf5/serial -c -o QualityValueVector_gtest.o /<<PKGBUILDDIR>>/unittest/pbdata/qvs/QualityValueVector_gtest.cpp
g++ -O3 -std=c++11 -Wno-div-by-zero -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/<<PKGBUILDDIR>>/unittest/ -I/<<PKGBUILDDIR>>/unittest//../alignment -I/usr/include -I../alignment -I../hdf -I../pbdata -I/usr/include/hdf5/serial -c -o HDFScanDataReader_gtest.o /<<PKGBUILDDIR>>/unittest/hdf/HDFScanDataReader_gtest.cpp
g++ -O3 -std=c++11 -Wno-div-by-zero -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/<<PKGBUILDDIR>>/unittest/ -I/<<PKGBUILDDIR>>/unittest//../alignment -I/usr/include -I../alignment -I../hdf -I../pbdata -I/usr/include/hdf5/serial -c -o HDF2DArray_gtest.o /<<PKGBUILDDIR>>/unittest/hdf/HDF2DArray_gtest.cpp
g++ -O3 -std=c++11 -Wno-div-by-zero -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/<<PKGBUILDDIR>>/unittest/ -I/<<PKGBUILDDIR>>/unittest//../alignment -I/usr/include -I../alignment -I../hdf -I../pbdata -I/usr/include/hdf5/serial -c -o HDFScanDataWriter_gtest.o /<<PKGBUILDDIR>>/unittest/hdf/HDFScanDataWriter_gtest.cpp
g++ -O3 -std=c++11 -Wno-div-by-zero -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/<<PKGBUILDDIR>>/unittest/ -I/<<PKGBUILDDIR>>/unittest//../alignment -I/usr/include -I../alignment -I../hdf -I../pbdata -I/usr/include/hdf5/serial -c -o HDFCCSReader_gtest.o /<<PKGBUILDDIR>>/unittest/hdf/HDFCCSReader_gtest.cpp
g++ -O3 -std=c++11 -Wno-div-by-zero -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/<<PKGBUILDDIR>>/unittest/ -I/<<PKGBUILDDIR>>/unittest//../alignment -I/usr/include -I../alignment -I../hdf -I../pbdata -I/usr/include/hdf5/serial -c -o HDFUtils_gtest.o /<<PKGBUILDDIR>>/unittest/hdf/HDFUtils_gtest.cpp
g++ -O3 -std=c++11 -Wno-div-by-zero -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/<<PKGBUILDDIR>>/unittest/ -I/<<PKGBUILDDIR>>/unittest//../alignment -I/usr/include -I../alignment -I../hdf -I../pbdata -I/usr/include/hdf5/serial -c -o HDFPlsReader_gtest.o /<<PKGBUILDDIR>>/unittest/hdf/HDFPlsReader_gtest.cpp
g++ -O3 -std=c++11 -Wno-div-by-zero -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/<<PKGBUILDDIR>>/unittest/ -I/<<PKGBUILDDIR>>/unittest//../alignment -I/usr/include -I../alignment -I../hdf -I../pbdata -I/usr/include/hdf5/serial -c -o HDFBasReader_gtest.o /<<PKGBUILDDIR>>/unittest/hdf/HDFBasReader_gtest.cpp
g++ -O3 -std=c++11 -Wno-div-by-zero -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/<<PKGBUILDDIR>>/unittest/ -I/<<PKGBUILDDIR>>/unittest//../alignment -I/usr/include -I../alignment -I../hdf -I../pbdata -I/usr/include/hdf5/serial -c -o HDFZMWReader_gtest.o /<<PKGBUILDDIR>>/unittest/hdf/HDFZMWReader_gtest.cpp
g++ -O3 -std=c++11 -Wno-div-by-zero -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/<<PKGBUILDDIR>>/unittest/ -I/<<PKGBUILDDIR>>/unittest//../alignment -I/usr/include -I../alignment -I../hdf -I../pbdata -I/usr/include/hdf5/serial -c -o RangeUtils_gtest.o /<<PKGBUILDDIR>>/unittest/alignment/utils/RangeUtils_gtest.cpp
g++ -O3 -std=c++11 -Wno-div-by-zero -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/<<PKGBUILDDIR>>/unittest/ -I/<<PKGBUILDDIR>>/unittest//../alignment -I/usr/include -I../alignment -I../hdf -I../pbdata -I/usr/include/hdf5/serial -c -o FileUtils_gtest.o /<<PKGBUILDDIR>>/unittest/alignment/utils/FileUtils_gtest.cpp
g++ -O3 -std=c++11 -Wno-div-by-zero -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/<<PKGBUILDDIR>>/unittest/ -I/<<PKGBUILDDIR>>/unittest//../alignment -I/usr/include -I../alignment -I../hdf -I../pbdata -I/usr/include/hdf5/serial -c -o RegionUtils_gtest.o /<<PKGBUILDDIR>>/unittest/alignment/utils/RegionUtils_gtest.cpp
g++ -O3 -std=c++11 -Wno-div-by-zero -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/<<PKGBUILDDIR>>/unittest/ -I/<<PKGBUILDDIR>>/unittest//../alignment -I/usr/include -I../alignment -I../hdf -I../pbdata -I/usr/include/hdf5/serial -c -o PbiFilterZmwGroupQuery_gtest.o /<<PKGBUILDDIR>>/unittest/alignment/query/PbiFilterZmwGroupQuery_gtest.cpp
/<<PKGBUILDDIR>>/unittest/alignment/query/PbiFilterZmwGroupQuery_gtest.cpp:5:17: error: 'PacBio' is not a namespace-name
using namespace PacBio;
^~~~~~
/<<PKGBUILDDIR>>/unittest/alignment/query/PbiFilterZmwGroupQuery_gtest.cpp:5:23: error: expected namespace-name before ';' token
using namespace PacBio;
^
/<<PKGBUILDDIR>>/unittest/alignment/query/PbiFilterZmwGroupQuery_gtest.cpp:6:17: error: 'PacBio' has not been declared
using namespace PacBio::BAM;
^~~~~~
/<<PKGBUILDDIR>>/unittest/alignment/query/PbiFilterZmwGroupQuery_gtest.cpp:6:25: error: 'BAM' is not a namespace-name
using namespace PacBio::BAM;
^~~
/<<PKGBUILDDIR>>/unittest/alignment/query/PbiFilterZmwGroupQuery_gtest.cpp:6:28: error: expected namespace-name before ';' token
using namespace PacBio::BAM;
^
In file included from /usr/include/gtest/gtest.h:58:0,
from /<<PKGBUILDDIR>>/unittest/alignment/query/PbiFilterZmwGroupQuery_gtest.cpp:2:
/<<PKGBUILDDIR>>/unittest/alignment/query/PbiFilterZmwGroupQuery_gtest.cpp: In function 'void TestPbiFilterZmwGroupQuery(const string&, const std::vector<unsigned int>&, uint32_t, uint32_t)':
/<<PKGBUILDDIR>>/unittest/alignment/query/PbiFilterZmwGroupQuery_gtest.cpp:20:9: error: 'PbiFilterZmwGroupQuery' was not declared in this scope
PbiFilterZmwGroupQuery qQuery(fn);
^
/<<PKGBUILDDIR>>/unittest/alignment/query/PbiFilterZmwGroupQuery_gtest.cpp:23:27: error: 'BamRecord' was not declared in this scope
for (const vector<BamRecord>& records : qQuery)
^
/<<PKGBUILDDIR>>/unittest/alignment/query/PbiFilterZmwGroupQuery_gtest.cpp:23:36: error: template argument 1 is invalid
for (const vector<BamRecord>& records : qQuery)
^
/<<PKGBUILDDIR>>/unittest/alignment/query/PbiFilterZmwGroupQuery_gtest.cpp:23:36: error: template argument 2 is invalid
/<<PKGBUILDDIR>>/unittest/alignment/query/PbiFilterZmwGroupQuery_gtest.cpp:23:49: error: 'qQuery' was not declared in this scope
for (const vector<BamRecord>& records : qQuery)
^
/<<PKGBUILDDIR>>/unittest/alignment/query/PbiFilterZmwGroupQuery_gtest.cpp:25:38: error: request for member 'size' in 'records', which is of non-class type 'const int'
counts.push_back(records.size());
^
/<<PKGBUILDDIR>>/unittest/alignment/query/PbiFilterZmwGroupQuery_gtest.cpp:26:31: error: request for member 'size' in 'records', which is of non-class type 'const int'
EXPECT_GT(records.size(), 0);
^
/<<PKGBUILDDIR>>/unittest/alignment/query/PbiFilterZmwGroupQuery_gtest.cpp:27:41: error: invalid types 'const int[int]' for array subscript
string movieName = records[0].MovieName();
^
/<<PKGBUILDDIR>>/unittest/alignment/query/PbiFilterZmwGroupQuery_gtest.cpp:28:44: error: invalid types 'const int[int]' for array subscript
uint32_t holeNumber = records[0].HoleNumber();
^
/<<PKGBUILDDIR>>/unittest/alignment/query/PbiFilterZmwGroupQuery_gtest.cpp:31:24: error: 'BamRecord' does not name a type
for (const BamRecord & record: records) {
^
/<<PKGBUILDDIR>>/unittest/alignment/query/PbiFilterZmwGroupQuery_gtest.cpp:35:9: error: expected ';' before '}' token
}
^
/<<PKGBUILDDIR>>/unittest/alignment/query/PbiFilterZmwGroupQuery_gtest.cpp:35:9: error: expected primary-expression before '}' token
/<<PKGBUILDDIR>>/unittest/alignment/query/PbiFilterZmwGroupQuery_gtest.cpp:35:9: error: expected ';' before '}' token
/<<PKGBUILDDIR>>/unittest/alignment/query/PbiFilterZmwGroupQuery_gtest.cpp:35:9: error: expected primary-expression before '}' token
/<<PKGBUILDDIR>>/unittest/alignment/query/PbiFilterZmwGroupQuery_gtest.cpp:35:9: error: expected ')' before '}' token
/<<PKGBUILDDIR>>/unittest/alignment/query/PbiFilterZmwGroupQuery_gtest.cpp:35:9: error: expected primary-expression before '}' token
/<<PKGBUILDDIR>>/unittest/alignment/query/PbiFilterZmwGroupQuery_gtest.cpp: In function 'void TestNoneConstPbiFilterZmwGroupQuery(const string&, const std::vector<unsigned int>&, uint32_t, uint32_t)':
/<<PKGBUILDDIR>>/unittest/alignment/query/PbiFilterZmwGroupQuery_gtest.cpp:49:9: error: 'PbiFilterZmwGroupQuery' was not declared in this scope
PbiFilterZmwGroupQuery qQuery(fn);
^
/<<PKGBUILDDIR>>/unittest/alignment/query/PbiFilterZmwGroupQuery_gtest.cpp:52:21: error: 'BamRecord' was not declared in this scope
for (vector<BamRecord>& records : qQuery) {
^
/<<PKGBUILDDIR>>/unittest/alignment/query/PbiFilterZmwGroupQuery_gtest.cpp:52:30: error: template argument 1 is invalid
for (vector<BamRecord>& records : qQuery) {
^
/<<PKGBUILDDIR>>/unittest/alignment/query/PbiFilterZmwGroupQuery_gtest.cpp:52:30: error: template argument 2 is invalid
/<<PKGBUILDDIR>>/unittest/alignment/query/PbiFilterZmwGroupQuery_gtest.cpp:52:43: error: 'qQuery' was not declared in this scope
for (vector<BamRecord>& records : qQuery) {
^
/<<PKGBUILDDIR>>/unittest/alignment/query/PbiFilterZmwGroupQuery_gtest.cpp:53:38: error: request for member 'size' in 'records', which is of non-class type 'int'
counts.push_back(records.size());
^
/<<PKGBUILDDIR>>/unittest/alignment/query/PbiFilterZmwGroupQuery_gtest.cpp:54:31: error: request for member 'size' in 'records', which is of non-class type 'int'
EXPECT_GT(records.size(), 0);
^
/<<PKGBUILDDIR>>/unittest/alignment/query/PbiFilterZmwGroupQuery_gtest.cpp:55:41: error: invalid types 'int[int]' for array subscript
string movieName = records[0].MovieName();
^
/<<PKGBUILDDIR>>/unittest/alignment/query/PbiFilterZmwGroupQuery_gtest.cpp:56:44: error: invalid types 'int[int]' for array subscript
uint32_t holeNumber = records[0].HoleNumber();
^
/<<PKGBUILDDIR>>/unittest/alignment/query/PbiFilterZmwGroupQuery_gtest.cpp:59:36: error: found ':' in nested-name-specifier, expected '::'
for (BamRecord & record: records) {
^
/<<PKGBUILDDIR>>/unittest/alignment/query/PbiFilterZmwGroupQuery_gtest.cpp:59:30: error: 'record' has not been declared
for (BamRecord & record: records) {
^
/<<PKGBUILDDIR>>/unittest/alignment/query/PbiFilterZmwGroupQuery_gtest.cpp:63:9: error: expected primary-expression before '}' token
}
^
/<<PKGBUILDDIR>>/unittest/alignment/query/PbiFilterZmwGroupQuery_gtest.cpp:63:9: error: expected ';' before '}' token
/<<PKGBUILDDIR>>/unittest/alignment/query/PbiFilterZmwGroupQuery_gtest.cpp:63:9: error: expected primary-expression before '}' token
/<<PKGBUILDDIR>>/unittest/alignment/query/PbiFilterZmwGroupQuery_gtest.cpp:63:9: error: expected ')' before '}' token
/<<PKGBUILDDIR>>/unittest/alignment/query/PbiFilterZmwGroupQuery_gtest.cpp:63:9: error: expected primary-expression before '}' token
makefile:110: recipe for target 'PbiFilterZmwGroupQuery_gtest.o' failed
make[3]: *** [PbiFilterZmwGroupQuery_gtest.o] Error 1
g++ -O3 -std=c++11 -Wno-div-by-zero -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/<<PKGBUILDDIR>>/unittest/ -I/<<PKGBUILDDIR>>/unittest//../alignment -I/usr/include -I../alignment -I../hdf -I../pbdata -I/usr/include/hdf5/serial -c -o SequentialZmwGroupQuery_gtest.o /<<PKGBUILDDIR>>/unittest/alignment/query/SequentialZmwGroupQuery_gtest.cpp
/<<PKGBUILDDIR>>/unittest/alignment/query/SequentialZmwGroupQuery_gtest.cpp:5:17: error: 'PacBio' is not a namespace-name
using namespace PacBio;
^~~~~~
/<<PKGBUILDDIR>>/unittest/alignment/query/SequentialZmwGroupQuery_gtest.cpp:5:23: error: expected namespace-name before ';' token
using namespace PacBio;
^
/<<PKGBUILDDIR>>/unittest/alignment/query/SequentialZmwGroupQuery_gtest.cpp:6:17: error: 'PacBio' has not been declared
using namespace PacBio::BAM;
^~~~~~
/<<PKGBUILDDIR>>/unittest/alignment/query/SequentialZmwGroupQuery_gtest.cpp:6:25: error: 'BAM' is not a namespace-name
using namespace PacBio::BAM;
^~~
/<<PKGBUILDDIR>>/unittest/alignment/query/SequentialZmwGroupQuery_gtest.cpp:6:28: error: expected namespace-name before ';' token
using namespace PacBio::BAM;
^
In file included from /usr/include/gtest/gtest.h:58:0,
from /<<PKGBUILDDIR>>/unittest/alignment/query/SequentialZmwGroupQuery_gtest.cpp:2:
/<<PKGBUILDDIR>>/unittest/alignment/query/SequentialZmwGroupQuery_gtest.cpp: In function 'void TestSequentialZmwGroupQuery(const string&, const std::vector<int>&)':
/<<PKGBUILDDIR>>/unittest/alignment/query/SequentialZmwGroupQuery_gtest.cpp:19:9: error: 'SequentialZmwGroupQuery' was not declared in this scope
SequentialZmwGroupQuery qQuery(fn);
^
/<<PKGBUILDDIR>>/unittest/alignment/query/SequentialZmwGroupQuery_gtest.cpp:20:27: error: 'BamRecord' was not declared in this scope
for (const vector<BamRecord>& records : qQuery)
^
/<<PKGBUILDDIR>>/unittest/alignment/query/SequentialZmwGroupQuery_gtest.cpp:20:36: error: template argument 1 is invalid
for (const vector<BamRecord>& records : qQuery)
^
/<<PKGBUILDDIR>>/unittest/alignment/query/SequentialZmwGroupQuery_gtest.cpp:20:36: error: template argument 2 is invalid
/<<PKGBUILDDIR>>/unittest/alignment/query/SequentialZmwGroupQuery_gtest.cpp:20:49: error: 'qQuery' was not declared in this scope
for (const vector<BamRecord>& records : qQuery)
^
/<<PKGBUILDDIR>>/unittest/alignment/query/SequentialZmwGroupQuery_gtest.cpp:22:38: error: request for member 'size' in 'records', which is of non-class type 'const int'
counts.push_back(records.size());
^
/<<PKGBUILDDIR>>/unittest/alignment/query/SequentialZmwGroupQuery_gtest.cpp:23:31: error: request for member 'size' in 'records', which is of non-class type 'const int'
EXPECT_GT(records.size(), 0);
^
/<<PKGBUILDDIR>>/unittest/alignment/query/SequentialZmwGroupQuery_gtest.cpp:24:41: error: invalid types 'const int[int]' for array subscript
string movieName = records[0].MovieName();
^
/<<PKGBUILDDIR>>/unittest/alignment/query/SequentialZmwGroupQuery_gtest.cpp:25:44: error: invalid types 'const int[int]' for array subscript
uint32_t holeNumber = records[0].HoleNumber();
^
/<<PKGBUILDDIR>>/unittest/alignment/query/SequentialZmwGroupQuery_gtest.cpp:26:24: error: 'BamRecord' does not name a type
for (const BamRecord & record: records) {
^
/<<PKGBUILDDIR>>/unittest/alignment/query/SequentialZmwGroupQuery_gtest.cpp:30:9: error: expected ';' before '}' token
}
^
/<<PKGBUILDDIR>>/unittest/alignment/query/SequentialZmwGroupQuery_gtest.cpp:30:9: error: expected primary-expression before '}' token
/<<PKGBUILDDIR>>/unittest/alignment/query/SequentialZmwGroupQuery_gtest.cpp:30:9: error: expected ';' before '}' token
/<<PKGBUILDDIR>>/unittest/alignment/query/SequentialZmwGroupQuery_gtest.cpp:30:9: error: expected primary-expression before '}' token
/<<PKGBUILDDIR>>/unittest/alignment/query/SequentialZmwGroupQuery_gtest.cpp:30:9: error: expected ')' before '}' token
/<<PKGBUILDDIR>>/unittest/alignment/query/SequentialZmwGroupQuery_gtest.cpp:30:9: error: expected primary-expression before '}' token
/<<PKGBUILDDIR>>/unittest/alignment/query/SequentialZmwGroupQuery_gtest.cpp: In function 'void TestNoneConstSequentialZmwGroupQuery(const string&, const std::vector<int>&)':
/<<PKGBUILDDIR>>/unittest/alignment/query/SequentialZmwGroupQuery_gtest.cpp:42:9: error: 'SequentialZmwGroupQuery' was not declared in this scope
SequentialZmwGroupQuery qQuery(fn);
^
/<<PKGBUILDDIR>>/unittest/alignment/query/SequentialZmwGroupQuery_gtest.cpp:43:21: error: 'BamRecord' was not declared in this scope
for (vector<BamRecord>& records : qQuery) {
^
/<<PKGBUILDDIR>>/unittest/alignment/query/SequentialZmwGroupQuery_gtest.cpp:43:30: error: template argument 1 is invalid
for (vector<BamRecord>& records : qQuery) {
^
/<<PKGBUILDDIR>>/unittest/alignment/query/SequentialZmwGroupQuery_gtest.cpp:43:30: error: template argument 2 is invalid
/<<PKGBUILDDIR>>/unittest/alignment/query/SequentialZmwGroupQuery_gtest.cpp:43:43: error: 'qQuery' was not declared in this scope
for (vector<BamRecord>& records : qQuery) {
^
/<<PKGBUILDDIR>>/unittest/alignment/query/SequentialZmwGroupQuery_gtest.cpp:44:38: error: request for member 'size' in 'records', which is of non-class type 'int'
counts.push_back(records.size());
^
/<<PKGBUILDDIR>>/unittest/alignment/query/SequentialZmwGroupQuery_gtest.cpp:45:31: error: request for member 'size' in 'records', which is of non-class type 'int'
EXPECT_GT(records.size(), 0);
^
/<<PKGBUILDDIR>>/unittest/alignment/query/SequentialZmwGroupQuery_gtest.cpp:46:41: error: invalid types 'int[int]' for array subscript
string movieName = records[0].MovieName();
^
/<<PKGBUILDDIR>>/unittest/alignment/query/SequentialZmwGroupQuery_gtest.cpp:47:44: error: invalid types 'int[int]' for array subscript
uint32_t holeNumber = records[0].HoleNumber();
^
/<<PKGBUILDDIR>>/unittest/alignment/query/SequentialZmwGroupQuery_gtest.cpp:48:36: error: found ':' in nested-name-specifier, expected '::'
for (BamRecord & record: records) {
^
/<<PKGBUILDDIR>>/unittest/alignment/query/SequentialZmwGroupQuery_gtest.cpp:48:30: error: 'record' has not been declared
for (BamRecord & record: records) {
^
/<<PKGBUILDDIR>>/unittest/alignment/query/SequentialZmwGroupQuery_gtest.cpp:52:9: error: expected primary-expression before '}' token
}
^
/<<PKGBUILDDIR>>/unittest/alignment/query/SequentialZmwGroupQuery_gtest.cpp:52:9: error: expected ';' before '}' token
/<<PKGBUILDDIR>>/unittest/alignment/query/SequentialZmwGroupQuery_gtest.cpp:52:9: error: expected primary-expression before '}' token
/<<PKGBUILDDIR>>/unittest/alignment/query/SequentialZmwGroupQuery_gtest.cpp:52:9: error: expected ')' before '}' token
/<<PKGBUILDDIR>>/unittest/alignment/query/SequentialZmwGroupQuery_gtest.cpp:52:9: error: expected primary-expression before '}' token
makefile:110: recipe for target 'SequentialZmwGroupQuery_gtest.o' failed
make[3]: *** [SequentialZmwGroupQuery_gtest.o] Error 1
g++ -O3 -std=c++11 -Wno-div-by-zero -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/<<PKGBUILDDIR>>/unittest/ -I/<<PKGBUILDDIR>>/unittest//../alignment -I/usr/include -I../alignment -I../hdf -I../pbdata -I/usr/include/hdf5/serial -c -o AlignmentMap_gtest.o /<<PKGBUILDDIR>>/unittest/alignment/datastructures/alignment/AlignmentMap_gtest.cpp
g++ -O3 -std=c++11 -Wno-div-by-zero -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/<<PKGBUILDDIR>>/unittest/ -I/<<PKGBUILDDIR>>/unittest//../alignment -I/usr/include -I../alignment -I../hdf -I../pbdata -I/usr/include/hdf5/serial -c -o CmpIndexedStringTable_gtest.o /<<PKGBUILDDIR>>/unittest/alignment/datastructures/alignment/CmpIndexedStringTable_gtest.cpp
g++ -O3 -std=c++11 -Wno-div-by-zero -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/<<PKGBUILDDIR>>/unittest/ -I/<<PKGBUILDDIR>>/unittest//../alignment -I/usr/include -I../alignment -I../hdf -I../pbdata -I/usr/include/hdf5/serial -c -o CCSIterator_gtest.o /<<PKGBUILDDIR>>/unittest/alignment/files/CCSIterator_gtest.cpp
g++ -O3 -std=c++11 -Wno-div-by-zero -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/<<PKGBUILDDIR>>/unittest/ -I/<<PKGBUILDDIR>>/unittest//../alignment -I/usr/include -I../alignment -I../hdf -I../pbdata -I/usr/include/hdf5/serial -c -o ReaderAgglomerate_gtest.o /<<PKGBUILDDIR>>/unittest/alignment/files/ReaderAgglomerate_gtest.cpp
g++ -O3 -std=c++11 -Wno-div-by-zero -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/<<PKGBUILDDIR>>/unittest/ -I/<<PKGBUILDDIR>>/unittest//../alignment -I/usr/include -I../alignment -I../hdf -I../pbdata -I/usr/include/hdf5/serial -c -o FragmentCCSIterator_other_gtest.o /<<PKGBUILDDIR>>/unittest/alignment/files/FragmentCCSIterator_other_gtest.cpp
g++ -O3 -std=c++11 -Wno-div-by-zero -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/<<PKGBUILDDIR>>/unittest/ -I/<<PKGBUILDDIR>>/unittest//../alignment -I/usr/include -I../alignment -I../hdf -I../pbdata -I/usr/include/hdf5/serial -c -o FragmentCCSIterator_gtest.o /<<PKGBUILDDIR>>/unittest/alignment/files/FragmentCCSIterator_gtest.cpp
g++ -O3 -std=c++11 -Wno-div-by-zero -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/<<PKGBUILDDIR>>/unittest/ -I/<<PKGBUILDDIR>>/unittest//../alignment -I/usr/include -I../alignment -I../hdf -I../pbdata -I/usr/include/hdf5/serial -c -o SAMPrinter_gtest.o /<<PKGBUILDDIR>>/unittest/alignment/format/SAMPrinter_gtest.cpp
In file included from /<<PKGBUILDDIR>>/unittest//../alignment/format/SAMPrinter.hpp:4:0,
from /<<PKGBUILDDIR>>/unittest/alignment/format/SAMPrinter_gtest.cpp:24:
/usr/include/c++/6/sstream:300:7: error: 'struct std::__cxx11::basic_stringbuf<_CharT, _Traits, _Alloc>::__xfer_bufptrs' redeclared with different access
struct __xfer_bufptrs
^~~~~~
makefile:110: recipe for target 'SAMPrinter_gtest.o' failed
make[3]: *** [SAMPrinter_gtest.o] Error 1
make[3]: Target 'gtest' not remade because of errors.
make[3]: Leaving directory '/<<PKGBUILDDIR>>/unittest'
makefile:27: recipe for target 'gtest' failed
make[2]: *** [gtest] Error 2
make[2]: Leaving directory '/<<PKGBUILDDIR>>'
debian/rules:24: recipe for target 'override_dh_auto_test' failed
make[1]: [override_dh_auto_test] Error 2 (ignored)
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
fakeroot debian/rules binary-arch
dh binary-arch --parallel
dh_testroot -a -O--parallel
dh_prep -a -O--parallel
debian/rules override_dh_auto_install
make[1]: Entering directory '/<<PKGBUILDDIR>>'
mkdir -p debian/libpbdata-dev/usr/include/pbseq
cp -r pbdata debian/libpbdata-dev/usr/include/pbseq/
mkdir -p debian/libpbihdf-dev/usr/include/pbseq/
cp -r hdf debian/libpbihdf-dev/usr/include/pbseq/
mkdir -p debian/libblasr-dev/usr/include/pbseq/
cp -r alignment debian/libblasr-dev/usr/include/pbseq/
find -L debian/*/usr/include/ -type f -regextype posix-egrep -not -regex '.*(hpp|h)$' -delete
find debian/*/usr/include/ -name "*.mk" -delete
dh_auto_install
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
dh_install -a -O--parallel
dh_installdocs -a -O--parallel
dh_installchangelogs -a -O--parallel
dh_perl -a -O--parallel
dh_link -a -O--parallel
dh_strip_nondeterminism -a -O--parallel
dh_compress -a -O--parallel
dh_fixperms -a -O--parallel
dh_strip -a -O--parallel
dh_makeshlibs -a -O--parallel
dh_shlibdeps -a -O--parallel
dpkg-shlibdeps: warning: symbol __aeabi_atexit@CXXABI_ARM_1.3.3 used by debian/libpbdata/usr/lib/arm-linux-gnueabihf/libpbdata.so found in none of the libraries
dpkg-shlibdeps: warning: couldn't find library libpbdata.so needed by debian/libpbihdf/usr/lib/arm-linux-gnueabihf/libpbihdf.so (ELF format: 'elf32-littlearm'; RPATH: '')
dpkg-shlibdeps: warning: couldn't find library libpbdata.so needed by debian/libblasr/usr/lib/arm-linux-gnueabihf/libblasr.so (ELF format: 'elf32-littlearm'; RPATH: '')
dpkg-shlibdeps: warning: couldn't find library libpbihdf.so needed by debian/libblasr/usr/lib/arm-linux-gnueabihf/libblasr.so (ELF format: 'elf32-littlearm'; RPATH: '')
dh_installdeb -a -O--parallel
dh_gencontrol -a -O--parallel
dpkg-gencontrol: warning: File::FcntlLock not available; using flock which is not NFS-safe
dpkg-gencontrol: warning: File::FcntlLock not available; using flock which is not NFS-safe
dpkg-gencontrol: warning: File::FcntlLock not available; using flock which is not NFS-safe
dpkg-gencontrol: warning: File::FcntlLock not available; using flock which is not NFS-safe
dpkg-gencontrol: warning: File::FcntlLock not available; using flock which is not NFS-safe
dpkg-gencontrol: warning: File::FcntlLock not available; using flock which is not NFS-safe
dpkg-gencontrol: warning: File::FcntlLock not available; using flock which is not NFS-safe
dpkg-gencontrol: warning: File::FcntlLock not available; using flock which is not NFS-safe
dpkg-gencontrol: warning: File::FcntlLock not available; using flock which is not NFS-safe
dh_md5sums -a -O--parallel
dh_builddeb -a -O--parallel
dpkg-deb: building package 'libpbihdf-dev' in '../libpbihdf-dev_0~20160705-1_armhf.deb'.
dpkg-deb: building package 'libpbdata-dbgsym' in '../libpbdata-dbgsym_0~20160705-1_armhf.deb'.
dpkg-deb: building package 'libpbihdf-dbgsym' in '../libpbihdf-dbgsym_0~20160705-1_armhf.deb'.
dpkg-deb: building package 'libpbdata-dev' in '../libpbdata-dev_0~20160705-1_armhf.deb'.
dpkg-deb: building package 'libblasr-dev' in '../libblasr-dev_0~20160705-1_armhf.deb'.
dpkg-deb: building package 'libpbihdf' in '../libpbihdf_0~20160705-1_armhf.deb'.
dpkg-deb: building package 'libpbdata' in '../libpbdata_0~20160705-1_armhf.deb'.
dpkg-deb: building package 'libblasr-dbgsym' in '../libblasr-dbgsym_0~20160705-1_armhf.deb'.
dpkg-deb: building package 'libblasr' in '../libblasr_0~20160705-1_armhf.deb'.
dpkg-genchanges --build=any -mRaspbian wandboard test autobuilder <root@raspbian.org> >../pbseqlib_0~20160705-1_armhf.changes
dpkg-genchanges: info: binary-only arch-specific upload (source code and arch-indep packages not included)
dpkg-source --after-build pbseqlib-0~20160705
dpkg-buildpackage: info: binary-only upload (no source included)
--------------------------------------------------------------------------------
Build finished at 2016-10-30T20:18:58Z
Finished
--------
I: Built successfully
+------------------------------------------------------------------------------+
| Post Build Chroot |
+------------------------------------------------------------------------------+
+------------------------------------------------------------------------------+
| Changes |
+------------------------------------------------------------------------------+
pbseqlib_0~20160705-1_armhf.changes:
------------------------------------
Format: 1.8
Date: Sun, 23 Oct 2016 18:17:42 -0700
Source: pbseqlib
Binary: libpbseq libpbseq-dev libpbdata-dev libpbdata libpbihdf-dev libpbihdf libblasr-dev libblasr
Architecture: armhf
Version: 0~20160705-1
Distribution: stretch-staging
Urgency: medium
Maintainer: Raspbian wandboard test autobuilder <root@raspbian.org>
Changed-By: Afif Elghraoui <afif@debian.org>
Description:
libblasr - tools for aligning PacBio reads to target sequences
libblasr-dev - tools for aligning PacBio reads to target sequences (development
libpbdata - tools for handling PacBio sequences
libpbdata-dev - tools for handling PacBio sequences (development files)
libpbihdf - tools for handling PacBio hdf5 files
libpbihdf-dev - tools for handling PacBio hdf5 files (development files)
libpbseq - library for analyzing PacBio sequencing data
libpbseq-dev - library for analyzing PacBio sequencing data (development files)
Changes:
pbseqlib (0~20160705-1) unstable; urgency=medium
.
* Imported Upstream version 0~20160705
(upstream git 0ae1691)
- Drop patches
- Fix "clean" target
* Move header files to avoid breaking relative paths
* Bump Standards-Version to 3.9.8
* Don't put libpbseq in Metapackages section
* Use encrypted protocols for VCS
* Update email address and copyright years
* Use O3 optimization
* Use dh-exec to handle library installation
* Install libraries to main ldpath and add ld triggers
* Remove unnecessary definition in d/rules
* Remove obsolete lintian overrides
* Add README.source to explain relationship with reverse-dependencies
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Files:
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33b3131aa7ac561a1fb9daed9277417a 792044 libs optional libblasr_0~20160705-1_armhf.deb
26f2bf010cd8ce3aa48cdea17b0d0e16 1548344 debug extra libpbdata-dbgsym_0~20160705-1_armhf.deb
d98bbff34b6e15e591fab684fb1f93d2 174994 libdevel optional libpbdata-dev_0~20160705-1_armhf.deb
a1958fe18547c3ca77a17d4e803b5dc2 103786 libs optional libpbdata_0~20160705-1_armhf.deb
2017ee363708a646942ac710f6c75e56 1472026 debug extra libpbihdf-dbgsym_0~20160705-1_armhf.deb
a28410a5fc759c26816267970edd6e34 193270 libdevel optional libpbihdf-dev_0~20160705-1_armhf.deb
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+------------------------------------------------------------------------------+
| Package contents |
+------------------------------------------------------------------------------+
libblasr-dbgsym_0~20160705-1_armhf.deb
--------------------------------------
new debian package, version 2.0.
size 2944398 bytes: control archive=521 bytes.
460 bytes, 14 lines control
106 bytes, 1 lines md5sums
Package: libblasr-dbgsym
Source: pbseqlib
Version: 0~20160705-1
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 2996
Depends: libblasr (= 0~20160705-1)
Section: debug
Priority: extra
Multi-Arch: same
Homepage: https://github.com/PacificBiosciences/blasr_libcpp
Description: Debug symbols for libblasr
Auto-Built-Package: debug-symbols
Build-Ids: d81978bfbd32e4d4392148e7addbd5fb24607926
drwxr-xr-x root/root 0 2016-10-24 01:17 ./
drwxr-xr-x root/root 0 2016-10-24 01:17 ./usr/
drwxr-xr-x root/root 0 2016-10-24 01:17 ./usr/lib/
drwxr-xr-x root/root 0 2016-10-24 01:17 ./usr/lib/debug/
drwxr-xr-x root/root 0 2016-10-24 01:17 ./usr/lib/debug/.build-id/
drwxr-xr-x root/root 0 2016-10-24 01:17 ./usr/lib/debug/.build-id/d8/
-rw-r--r-- root/root 3057200 2016-10-24 01:17 ./usr/lib/debug/.build-id/d8/1978bfbd32e4d4392148e7addbd5fb24607926.debug
drwxr-xr-x root/root 0 2016-10-24 01:17 ./usr/share/
drwxr-xr-x root/root 0 2016-10-24 01:17 ./usr/share/doc/
lrwxrwxrwx root/root 0 2016-10-24 01:17 ./usr/share/doc/libblasr-dbgsym -> libblasr
libblasr-dev_0~20160705-1_armhf.deb
-----------------------------------
new debian package, version 2.0.
size 1627476 bytes: control archive=5683 bytes.
720 bytes, 18 lines control
16167 bytes, 167 lines md5sums
Package: libblasr-dev
Source: pbseqlib
Version: 0~20160705-1
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 6205
Depends: libblasr (= 0~20160705-1)
Section: libdevel
Priority: optional
Multi-Arch: same
Homepage: https://github.com/PacificBiosciences/blasr_libcpp
Description: tools for aligning PacBio reads to target sequences (development files)
Blasr_libcpp is a library used by blasr and other executables such as
samtoh5, loadPulses for analyzing PacBio sequences. This library contains
three sub-libraries, including pbdata, hdf and alignment.
.
This package contains the header files and static library for the alignment
sublibrary.
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-rw-r--r-- root/root 4674 2016-07-18 00:26 ./usr/share/doc/libblasr-dev/copyright
libblasr_0~20160705-1_armhf.deb
-------------------------------
new debian package, version 2.0.
size 792044 bytes: control archive=784 bytes.
738 bytes, 17 lines control
218 bytes, 3 lines md5sums
26 bytes, 1 lines triggers
Package: libblasr
Source: pbseqlib
Version: 0~20160705-1
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 2148
Depends: libc6 (>= 2.17), libgcc1 (>= 1:3.5), libstdc++6 (>= 5.2), libpbdata (= 0~20160705-1), libpbihdf (= 0~20160705-1)
Section: libs
Priority: optional
Multi-Arch: same
Homepage: https://github.com/PacificBiosciences/blasr_libcpp
Description: tools for aligning PacBio reads to target sequences
Blasr_libcpp is a library used by blasr and other executables such as
samtoh5, loadPulses for analyzing PacBio sequences. This library contains
three sub-libraries, including pbdata, hdf and alignment.
.
This package contains the alignment sublibrary.
drwxr-xr-x root/root 0 2016-10-24 01:17 ./
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-rw-r--r-- root/root 4674 2016-07-18 00:26 ./usr/share/doc/libblasr/copyright
libpbdata-dbgsym_0~20160705-1_armhf.deb
---------------------------------------
new debian package, version 2.0.
size 1548344 bytes: control archive=524 bytes.
463 bytes, 14 lines control
106 bytes, 1 lines md5sums
Package: libpbdata-dbgsym
Source: pbseqlib
Version: 0~20160705-1
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 1600
Depends: libpbdata (= 0~20160705-1)
Section: debug
Priority: extra
Multi-Arch: same
Homepage: https://github.com/PacificBiosciences/blasr_libcpp
Description: Debug symbols for libpbdata
Auto-Built-Package: debug-symbols
Build-Ids: 98075e1df06287be19fe897e49d320a2ebdeb793
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lrwxrwxrwx root/root 0 2016-10-24 01:17 ./usr/share/doc/libpbdata-dbgsym -> libpbdata
libpbdata-dev_0~20160705-1_armhf.deb
------------------------------------
new debian package, version 2.0.
size 174994 bytes: control archive=3210 bytes.
703 bytes, 18 lines control
6871 bytes, 86 lines md5sums
Package: libpbdata-dev
Source: pbseqlib
Version: 0~20160705-1
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 1023
Depends: libpbdata (= 0~20160705-1)
Section: libdevel
Priority: optional
Multi-Arch: same
Homepage: https://github.com/PacificBiosciences/blasr_libcpp
Description: tools for handling PacBio sequences (development files)
Blasr_libcpp is a library used by blasr and other executables such as
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.
This package contains the header files and static library for the pbdata
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libpbdata_0~20160705-1_armhf.deb
--------------------------------
new debian package, version 2.0.
size 103786 bytes: control archive=753 bytes.
662 bytes, 17 lines control
221 bytes, 3 lines md5sums
26 bytes, 1 lines triggers
Package: libpbdata
Source: pbseqlib
Version: 0~20160705-1
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 339
Depends: libc6 (>= 2.4), libgcc1 (>= 1:3.5), libstdc++6 (>= 5.2)
Section: libs
Priority: optional
Multi-Arch: same
Homepage: https://github.com/PacificBiosciences/blasr_libcpp
Description: tools for handling PacBio sequences
Blasr_libcpp is a library used by blasr and other executables such as
samtoh5, loadPulses for analyzing PacBio sequences. This library contains
three sub-libraries, including pbdata, hdf and alignment.
.
This package contains the pbdata sublibrary.
drwxr-xr-x root/root 0 2016-10-24 01:17 ./
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libpbihdf-dbgsym_0~20160705-1_armhf.deb
---------------------------------------
new debian package, version 2.0.
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463 bytes, 14 lines control
106 bytes, 1 lines md5sums
Package: libpbihdf-dbgsym
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Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 1548
Depends: libpbihdf (= 0~20160705-1)
Section: debug
Priority: extra
Multi-Arch: same
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Description: Debug symbols for libpbihdf
Auto-Built-Package: debug-symbols
Build-Ids: 5b70539c4848b99bb6d4ed9c72724067391415d3
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drwxr-xr-x root/root 0 2016-10-24 01:17 ./usr/share/
drwxr-xr-x root/root 0 2016-10-24 01:17 ./usr/share/doc/
lrwxrwxrwx root/root 0 2016-10-24 01:17 ./usr/share/doc/libpbihdf-dbgsym -> libpbihdf
libpbihdf-dev_0~20160705-1_armhf.deb
------------------------------------
new debian package, version 2.0.
size 193270 bytes: control archive=2217 bytes.
701 bytes, 18 lines control
4232 bytes, 56 lines md5sums
Package: libpbihdf-dev
Source: pbseqlib
Version: 0~20160705-1
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 1471
Depends: libpbihdf (= 0~20160705-1)
Section: libdevel
Priority: optional
Multi-Arch: same
Homepage: https://github.com/PacificBiosciences/blasr_libcpp
Description: tools for handling PacBio hdf5 files (development files)
Blasr_libcpp is a library used by blasr and other executables such as
samtoh5, loadPulses for analyzing PacBio sequences. This library contains
three sub-libraries, including pbdata, hdf and alignment.
.
This package contains the header files and static library for the hdf
sublibrary.
drwxr-xr-x root/root 0 2016-10-24 01:17 ./
drwxr-xr-x root/root 0 2016-10-24 01:17 ./usr/
drwxr-xr-x root/root 0 2016-10-24 01:17 ./usr/include/
drwxr-xr-x root/root 0 2016-10-24 01:17 ./usr/include/pbseq/
drwxr-xr-x root/root 0 2016-10-24 01:17 ./usr/include/pbseq/hdf/
-rw-r--r-- root/root 5238 2016-10-24 01:17 ./usr/include/pbseq/hdf/BufferedHDF2DArray.hpp
-rw-r--r-- root/root 12125 2016-10-24 01:17 ./usr/include/pbseq/hdf/BufferedHDF2DArrayImpl.hpp
-rw-r--r-- root/root 7555 2016-10-24 01:17 ./usr/include/pbseq/hdf/BufferedHDFArray.hpp
-rw-r--r-- root/root 13156 2016-10-24 01:17 ./usr/include/pbseq/hdf/BufferedHDFArrayImpl.hpp
-rw-r--r-- root/root 964 2016-10-24 01:17 ./usr/include/pbseq/hdf/DatasetCollection.hpp
-rw-r--r-- root/root 942 2016-10-24 01:17 ./usr/include/pbseq/hdf/DatasetCollectionImpl.hpp
-rw-r--r-- root/root 645 2016-10-24 01:17 ./usr/include/pbseq/hdf/HDF2DArray.hpp
-rw-r--r-- root/root 1001 2016-10-24 01:17 ./usr/include/pbseq/hdf/HDFAlnGroup.hpp
-rw-r--r-- root/root 481 2016-10-24 01:17 ./usr/include/pbseq/hdf/HDFAlnGroupGroup.hpp
-rw-r--r-- root/root 1151 2016-10-24 01:17 ./usr/include/pbseq/hdf/HDFAlnInfoGroup.hpp
-rw-r--r-- root/root 2340 2016-10-24 01:17 ./usr/include/pbseq/hdf/HDFArray.hpp
-rw-r--r-- root/root 5549 2016-10-24 01:17 ./usr/include/pbseq/hdf/HDFAtom.hpp
-rw-r--r-- root/root 563 2016-10-24 01:17 ./usr/include/pbseq/hdf/HDFAttributable.hpp
-rw-r--r-- root/root 41200 2016-10-24 01:17 ./usr/include/pbseq/hdf/HDFBasReader.hpp
-rw-r--r-- root/root 12384 2016-10-24 01:17 ./usr/include/pbseq/hdf/HDFBasWriter.hpp
-rw-r--r-- root/root 6361 2016-10-24 01:17 ./usr/include/pbseq/hdf/HDFBaseCallsWriter.hpp
-rw-r--r-- root/root 3549 2016-10-24 01:17 ./usr/include/pbseq/hdf/HDFBaxWriter.hpp
-rw-r--r-- root/root 9158 2016-10-24 01:17 ./usr/include/pbseq/hdf/HDFCCSReader.hpp
-rw-r--r-- root/root 930 2016-10-24 01:17 ./usr/include/pbseq/hdf/HDFCmpData.hpp
-rw-r--r-- root/root 2462 2016-10-24 01:17 ./usr/include/pbseq/hdf/HDFCmpExperimentGroup.hpp
-rw-r--r-- root/root 35501 2016-10-24 01:17 ./usr/include/pbseq/hdf/HDFCmpFile.hpp
-rw-r--r-- root/root 28427 2016-10-24 01:17 ./usr/include/pbseq/hdf/HDFCmpReader.hpp
-rw-r--r-- root/root 3444 2016-10-24 01:17 ./usr/include/pbseq/hdf/HDFCmpRefAlignmentGroup.hpp
-rw-r--r-- root/root 1753 2016-10-24 01:17 ./usr/include/pbseq/hdf/HDFCmpRootGroup.hpp
-rw-r--r-- root/root 228 2016-10-24 01:17 ./usr/include/pbseq/hdf/HDFCmpSupportedFields.hpp
-rw-r--r-- root/root 153 2016-10-24 01:17 ./usr/include/pbseq/hdf/HDFCommonFG.hpp
-rw-r--r-- root/root 92 2016-10-24 01:17 ./usr/include/pbseq/hdf/HDFConfig.hpp
-rw-r--r-- root/root 1479 2016-10-24 01:17 ./usr/include/pbseq/hdf/HDFData.hpp
-rw-r--r-- root/root 715 2016-10-24 01:17 ./usr/include/pbseq/hdf/HDFFile.hpp
-rw-r--r-- root/root 1635 2016-10-24 01:17 ./usr/include/pbseq/hdf/HDFFileLogGroup.hpp
-rw-r--r-- root/root 735 2016-10-24 01:17 ./usr/include/pbseq/hdf/HDFGroup.hpp
-rw-r--r-- root/root 1931 2016-10-24 01:17 ./usr/include/pbseq/hdf/HDFMovieInfoGroup.hpp
-rw-r--r-- root/root 839 2016-10-24 01:17 ./usr/include/pbseq/hdf/HDFNewBasReader.hpp
-rw-r--r-- root/root 20980 2016-10-24 01:17 ./usr/include/pbseq/hdf/HDFPlsReader.hpp
-rw-r--r-- root/root 5898 2016-10-24 01:17 ./usr/include/pbseq/hdf/HDFPlsWriter.hpp
-rw-r--r-- root/root 8071 2016-10-24 01:17 ./usr/include/pbseq/hdf/HDFPulseCallsWriter.hpp
-rw-r--r-- root/root 1713 2016-10-24 01:17 ./usr/include/pbseq/hdf/HDFPulseDataFile.hpp
-rw-r--r-- root/root 3437 2016-10-24 01:17 ./usr/include/pbseq/hdf/HDFPulseWriter.hpp
-rw-r--r-- root/root 1683 2016-10-24 01:17 ./usr/include/pbseq/hdf/HDFRefGroupGroup.hpp
-rw-r--r-- root/root 2647 2016-10-24 01:17 ./usr/include/pbseq/hdf/HDFRefInfoGroup.hpp
-rw-r--r-- root/root 1317 2016-10-24 01:17 ./usr/include/pbseq/hdf/HDFRegionTableReader.hpp
-rw-r--r-- root/root 3878 2016-10-24 01:17 ./usr/include/pbseq/hdf/HDFRegionTableWriter.hpp
-rw-r--r-- root/root 1937 2016-10-24 01:17 ./usr/include/pbseq/hdf/HDFRegionsWriter.hpp
-rw-r--r-- root/root 1892 2016-10-24 01:17 ./usr/include/pbseq/hdf/HDFSMRTSequenceReader.hpp
-rw-r--r-- root/root 3339 2016-10-24 01:17 ./usr/include/pbseq/hdf/HDFScanDataReader.hpp
-rw-r--r-- root/root 2341 2016-10-24 01:17 ./usr/include/pbseq/hdf/HDFScanDataWriter.hpp
-rw-r--r-- root/root 452 2016-10-24 01:17 ./usr/include/pbseq/hdf/HDFSentinalFile.hpp
-rw-r--r-- root/root 1635 2016-10-24 01:17 ./usr/include/pbseq/hdf/HDFUtils.hpp
-rw-r--r-- root/root 985 2016-10-24 01:17 ./usr/include/pbseq/hdf/HDFWriteBuffer.hpp
-rw-r--r-- root/root 5388 2016-10-24 01:17 ./usr/include/pbseq/hdf/HDFWriterBase.hpp
-rw-r--r-- root/root 2054 2016-10-24 01:17 ./usr/include/pbseq/hdf/HDFZMWMetricsWriter.hpp
-rw-r--r-- root/root 993 2016-10-24 01:17 ./usr/include/pbseq/hdf/HDFZMWReader.hpp
-rw-r--r-- root/root 4036 2016-10-24 01:17 ./usr/include/pbseq/hdf/HDFZMWWriter.hpp
drwxr-xr-x root/root 0 2016-10-24 01:17 ./usr/lib/
drwxr-xr-x root/root 0 2016-10-24 01:17 ./usr/lib/arm-linux-gnueabihf/
-rw-r--r-- root/root 1185570 2016-10-24 01:17 ./usr/lib/arm-linux-gnueabihf/libpbihdf.a
drwxr-xr-x root/root 0 2016-10-24 01:17 ./usr/share/
drwxr-xr-x root/root 0 2016-10-24 01:17 ./usr/share/doc/
drwxr-xr-x root/root 0 2016-10-24 01:17 ./usr/share/doc/libpbihdf-dev/
-rw-r--r-- root/root 677 2016-10-24 01:17 ./usr/share/doc/libpbihdf-dev/changelog.Debian.gz
-rw-r--r-- root/root 4674 2016-07-18 00:26 ./usr/share/doc/libpbihdf-dev/copyright
libpbihdf_0~20160705-1_armhf.deb
--------------------------------
new debian package, version 2.0.
size 103032 bytes: control archive=787 bytes.
728 bytes, 17 lines control
221 bytes, 3 lines md5sums
26 bytes, 1 lines triggers
Package: libpbihdf
Source: pbseqlib
Version: 0~20160705-1
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 391
Depends: libc6 (>= 2.4), libgcc1 (>= 1:3.5), libhdf5-10, libhdf5-cpp-11 (>= 1.8.16), libstdc++6 (>= 5.2), libpbdata (= 0~20160705-1)
Section: libs
Priority: optional
Multi-Arch: same
Homepage: https://github.com/PacificBiosciences/blasr_libcpp
Description: tools for handling PacBio hdf5 files
Blasr_libcpp is a library used by blasr and other executables such as
samtoh5, loadPulses for analyzing PacBio sequences. This library contains
three sub-libraries, including pbdata, hdf and alignment.
.
This package contains the hdf sublibrary.
drwxr-xr-x root/root 0 2016-10-24 01:17 ./
drwxr-xr-x root/root 0 2016-10-24 01:17 ./usr/
drwxr-xr-x root/root 0 2016-10-24 01:17 ./usr/lib/
drwxr-xr-x root/root 0 2016-10-24 01:17 ./usr/lib/arm-linux-gnueabihf/
-rw-r--r-- root/root 384352 2016-10-24 01:17 ./usr/lib/arm-linux-gnueabihf/libpbihdf.so
drwxr-xr-x root/root 0 2016-10-24 01:17 ./usr/share/
drwxr-xr-x root/root 0 2016-10-24 01:17 ./usr/share/doc/
drwxr-xr-x root/root 0 2016-10-24 01:17 ./usr/share/doc/libpbihdf/
-rw-r--r-- root/root 677 2016-10-24 01:17 ./usr/share/doc/libpbihdf/changelog.Debian.gz
-rw-r--r-- root/root 4674 2016-07-18 00:26 ./usr/share/doc/libpbihdf/copyright
+------------------------------------------------------------------------------+
| Post Build |
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| Cleanup |
+------------------------------------------------------------------------------+
Purging /<<BUILDDIR>>
Not cleaning session: cloned chroot in use
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| Summary |
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Build Architecture: armhf
Build-Space: 180196
Build-Time: 1709
Distribution: stretch-staging
Host Architecture: armhf
Install-Time: 400
Job: pbseqlib_0~20160705-1
Machine Architecture: armhf
Package: pbseqlib
Package-Time: 2153
Source-Version: 0~20160705-1
Space: 180196
Status: successful
Version: 0~20160705-1
--------------------------------------------------------------------------------
Finished at 2016-10-30T20:18:58Z
Build needed 00:35:53, 180196k disc space