Build log for pbseqlib (0~20151014+gitbe5d1bf-2) on armhf

pbseqlib → 0~20151014+gitbe5d1bf-2 → armhf → 2015-12-19 21:15:53

sbuild (Debian sbuild) 0.65.2 (24 Mar 2015) on testwandboard

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║ pbseqlib 0~20151014+gitbe5d1bf-2 (armhf)                   19 Dec 2015 20:45 ║
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Package: pbseqlib
Version: 0~20151014+gitbe5d1bf-2
Source Version: 0~20151014+gitbe5d1bf-2
Distribution: stretch-staging
Machine Architecture: armhf
Host Architecture: armhf
Build Architecture: armhf

I: NOTICE: Log filtering will replace 'build/pbseqlib-rzkFT5/pbseqlib-0~20151014+gitbe5d1bf' with '«PKGBUILDDIR»'
I: NOTICE: Log filtering will replace 'build/pbseqlib-rzkFT5' with '«BUILDDIR»'
I: NOTICE: Log filtering will replace 'var/lib/schroot/mount/stretch-staging-armhf-sbuild-18ca301b-2ad6-4286-a9fd-fdfb98be69b9' with '«CHROOT»'

┌──────────────────────────────────────────────────────────────────────────────┐
│ Update chroot                                                                │
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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 [8541 kB]
Get:3 http://172.17.0.1/private stretch-staging/main armhf Packages [10.5 MB]
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│ Fetch source files                                                           │
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Check APT
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Reading package lists...
Building dependency tree...
Reading state information...
NOTICE: 'pbseqlib' packaging is maintained in the 'Git' version control system at:
git://anonscm.debian.org/debian-med/pbseqlib.git
Please use:
git clone git://anonscm.debian.org/debian-med/pbseqlib.git
to retrieve the latest (possibly unreleased) updates to the package.
Need to get 1294 kB of source archives.
Get:1 http://172.17.0.1/private stretch-staging/main pbseqlib 0~20151014+gitbe5d1bf-2 (dsc) [2504 B]
Get:2 http://172.17.0.1/private stretch-staging/main pbseqlib 0~20151014+gitbe5d1bf-2 (tar) [1286 kB]
Get:3 http://172.17.0.1/private stretch-staging/main pbseqlib 0~20151014+gitbe5d1bf-2 (diff) [5224 B]
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Merged Build-Depends: build-essential, fakeroot
Filtered Build-Depends: build-essential, fakeroot
dpkg-deb: building package 'sbuild-build-depends-core-dummy' in '/«BUILDDIR»/resolver-w0sr2n/apt_archive/sbuild-build-depends-core-dummy.deb'.
OK
Get:1 file:/«BUILDDIR»/resolver-w0sr2n/apt_archive ./ InRelease
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Get:3 file:/«BUILDDIR»/resolver-w0sr2n/apt_archive ./ Release.gpg [299 B]
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Get:4 file:/«BUILDDIR»/resolver-w0sr2n/apt_archive ./ Sources [188 B]
Get:5 file:/«BUILDDIR»/resolver-w0sr2n/apt_archive ./ Packages [507 B]
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┌──────────────────────────────────────────────────────────────────────────────┐
│ Install core build dependencies (apt-based resolver)                         │
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Installing build dependencies
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The following NEW packages will be installed:
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Merged Build-Depends: libc6-dev | libc-dev, gcc (>= 4:4.9.1), g++ (>= 4:4.9.1), make, dpkg-dev (>= 1.17.11), debhelper (>= 9), python, zlib1g-dev, libhdf5-dev, libboost-dev, libhts-dev, libgtest-dev
Filtered Build-Depends: libc6-dev, gcc (>= 4:4.9.1), g++ (>= 4:4.9.1), make, dpkg-dev (>= 1.17.11), debhelper (>= 9), python, zlib1g-dev, libhdf5-dev, libboost-dev, libhts-dev, libgtest-dev
dpkg-deb: building package 'sbuild-build-depends-pbseqlib-dummy' in '/«BUILDDIR»/resolver-hWyTsS/apt_archive/sbuild-build-depends-pbseqlib-dummy.deb'.
OK
Get:1 file:/«BUILDDIR»/resolver-hWyTsS/apt_archive ./ InRelease
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Get:3 file:/«BUILDDIR»/resolver-hWyTsS/apt_archive ./ Release.gpg [299 B]
Get:3 file:/«BUILDDIR»/resolver-hWyTsS/apt_archive ./ Release.gpg [299 B]
Get:4 file:/«BUILDDIR»/resolver-hWyTsS/apt_archive ./ Sources [327 B]
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┌──────────────────────────────────────────────────────────────────────────────┐
│ Install pbseqlib build dependencies (apt-based resolver)                     │
└──────────────────────────────────────────────────────────────────────────────┘

Installing build dependencies
Reading package lists...
Building dependency tree...
Reading state information...
The following additional packages will be installed:
  bsdmainutils debhelper dh-strip-nondeterminism file gettext gettext-base
  groff-base hdf5-helpers intltool-debian libarchive-zip-perl libboost-dev
  libboost1.58-dev libcroco3 libexpat1 libffi6
  libfile-stripnondeterminism-perl libgfortran3 libglib2.0-0 libgtest-dev
  libhdf5-10 libhdf5-cpp-11 libhdf5-dev libhts-dev libhts1 libicu55
  libjpeg-dev libjpeg62-turbo libjpeg62-turbo-dev libmagic1 libpipeline1
  libpython-stdlib libpython2.7-minimal libpython2.7-stdlib libsqlite3-0
  libssl1.0.2 libtimedate-perl libunistring0 libxml2 man-db mime-support
  po-debconf python python-minimal python2.7 python2.7-minimal zlib1g-dev
Suggested packages:
  wamerican | wordlist whois vacation dh-make gettext-doc autopoint
  libasprintf-dev libgettextpo-dev groff libboost-doc libboost1.58-doc
  libboost-atomic1.58-dev libboost-chrono1.58-dev libboost-context1.58-dev
  libboost-coroutine1.58-dev libboost-date-time1.58-dev
  libboost-exception1.58-dev libboost-filesystem1.58-dev
  libboost-graph1.58-dev libboost-graph-parallel1.58-dev
  libboost-iostreams1.58-dev libboost-locale1.58-dev libboost-log1.58-dev
  libboost-math1.58-dev libboost-mpi1.58-dev libboost-mpi-python1.58-dev
  libboost-program-options1.58-dev libboost-python1.58-dev
  libboost-random1.58-dev libboost-regex1.58-dev
  libboost-serialization1.58-dev libboost-signals1.58-dev
  libboost-system1.58-dev libboost-test1.58-dev libboost-thread1.58-dev
  libboost-timer1.58-dev libboost-wave1.58-dev libboost1.58-tools-dev
  libmpfrc++-dev libntl-dev libhdf5-doc less www-browser libmail-box-perl
  python-doc python-tk python2.7-doc binfmt-support
Recommended packages:
  curl | wget | lynx-cur libglib2.0-data shared-mime-info xdg-user-dirs
  xml-core libmail-sendmail-perl
The following NEW packages will be installed:
  bsdmainutils debhelper dh-strip-nondeterminism file gettext gettext-base
  groff-base hdf5-helpers intltool-debian libarchive-zip-perl libboost-dev
  libboost1.58-dev libcroco3 libexpat1 libffi6
  libfile-stripnondeterminism-perl libgfortran3 libglib2.0-0 libgtest-dev
  libhdf5-10 libhdf5-cpp-11 libhdf5-dev libhts-dev libhts1 libicu55
  libjpeg-dev libjpeg62-turbo libjpeg62-turbo-dev libmagic1 libpipeline1
  libpython-stdlib libpython2.7-minimal libpython2.7-stdlib libsqlite3-0
  libssl1.0.2 libtimedate-perl libunistring0 libxml2 man-db mime-support
  po-debconf python python-minimal python2.7 python2.7-minimal
  sbuild-build-depends-pbseqlib-dummy zlib1g-dev
0 upgraded, 47 newly installed, 0 to remove and 1 not upgraded.
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Get:1 file:/«BUILDDIR»/resolver-hWyTsS/apt_archive ./ sbuild-build-depends-pbseqlib-dummy 0.invalid.0 [846 B]
Get:2 http://172.17.0.1/private stretch-staging/main armhf groff-base armhf 1.22.3-4 [1084 kB]
Get:3 http://172.17.0.1/private stretch-staging/main armhf bsdmainutils armhf 9.0.6 [177 kB]
Get:4 http://172.17.0.1/private stretch-staging/main armhf libpipeline1 armhf 1.4.1-1 [23.9 kB]
Get:5 http://172.17.0.1/private stretch-staging/main armhf man-db armhf 2.7.5-1 [975 kB]
Get:6 http://172.17.0.1/private stretch-staging/main armhf libpython2.7-minimal armhf 2.7.11-2 [380 kB]
Get:7 http://172.17.0.1/private stretch-staging/main armhf python2.7-minimal armhf 2.7.11-2 [1081 kB]
Get:8 http://172.17.0.1/private stretch-staging/main armhf python-minimal armhf 2.7.11-1 [40.0 kB]
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Get:27 http://172.17.0.1/private stretch-staging/main armhf intltool-debian all 0.35.0+20060710.4 [26.3 kB]
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Get:40 http://172.17.0.1/private stretch-staging/main armhf libhdf5-cpp-11 armhf 1.8.16+docs-1 [115 kB]
Get:41 http://172.17.0.1/private stretch-staging/main armhf zlib1g-dev armhf 1:1.2.8.dfsg-2+b1 [197 kB]
Get:42 http://172.17.0.1/private stretch-staging/main armhf libjpeg62-turbo armhf 1:1.4.1-2 [103 kB]
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Processing triggers for libc-bin (2.21-4) ...
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update-alternatives: using /usr/bin/bsd-write to provide /usr/bin/write (write) in auto mode
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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
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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_2.25.90.20151209-1 dpkg-dev_1.18.3 g++-5_5.3.1-3+rpi1 gcc-5_5.3.1-3+rpi1 libc6-dev_2.21-4 libstdc++-5-dev_5.3.1-3+rpi1 libstdc++6_5.3.1-3+rpi1 linux-libc-dev_3.18.5-1~exp1+rpi19+stretch
Package versions: adduser_3.113+nmu3 apt_1.1.4 base-files_9.4+rpi1 base-passwd_3.5.38 bash_4.3-14 binutils_2.25.90.20151209-1 bsdmainutils_9.0.6 bsdutils_1:2.27.1-1 build-essential_11.7 bzip2_1.0.6-8 coreutils_8.23-4 cpio_2.11+dfsg-4.1 cpp_4:5.2.1-4+rpi3 cpp-5_5.3.1-3+rpi1 dash_0.5.7-4 debconf_1.5.58 debconf-i18n_1.5.58 debfoster_2.7-2 debhelper_9.20151126 debianutils_4.5.1 dh-strip-nondeterminism_0.014-1 diffutils_1:3.3-2 dmsetup_2:1.02.110-2 dpkg_1.18.3 dpkg-dev_1.18.3 e2fslibs_1.42.13-1 e2fsprogs_1.42.13-1 fakeroot_1.20.2-1 file_1:5.25-2 findutils_4.4.2-10 g++_4:5.2.1-4+rpi3 g++-5_5.3.1-3+rpi1 gcc_4:5.2.1-4+rpi3 gcc-4.6-base_4.6.4-5+rpi1 gcc-4.7-base_4.7.3-11+rpi1 gcc-4.8-base_4.8.5-1+b1 gcc-4.9-base_4.9.3-5+b1 gcc-5_5.3.1-3+rpi1 gcc-5-base_5.3.1-3+rpi1 gettext_0.19.6-1 gettext-base_0.19.6-1 gnupg_1.4.19-6 gpgv_1.4.19-6 grep_2.22-1 groff-base_1.22.3-4 gzip_1.6-4 hdf5-helpers_1.8.16+docs-1 hostname_3.16 init_1.24 init-system-helpers_1.24 initramfs-tools_0.120 initscripts_2.88dsf-59.2 insserv_1.14.0-5 intltool-debian_0.35.0+20060710.4 klibc-utils_2.0.4-4+rpi1 kmod_21-1 libacl1_2.2.52-2 libapparmor1_2.10-2+b2 libapt-pkg4.16_1.0.10.2 libapt-pkg5.0_1.1.4 libarchive-zip-perl_1.55-1 libasan2_5.3.1-3+rpi1 libatomic1_5.3.1-3+rpi1 libattr1_1:2.4.47-2 libaudit-common_1:2.4.4-4 libaudit1_1:2.4.4-4 libblkid1_2.27.1-1 libboost-dev_1.58.0.1 libboost1.58-dev_1.58.0+dfsg-4.1 libbz2-1.0_1.0.6-8 libc-bin_2.21-4 libc-dev-bin_2.21-4 libc6_2.21-4 libc6-dev_2.21-4 libcap2_1:2.24-12 libcap2-bin_1:2.24-12 libcc1-0_5.3.1-3+rpi1 libcomerr2_1.42.13-1 libcroco3_0.6.9-1 libcryptsetup4_2:1.6.6-5 libdb5.3_5.3.28-11 libdbus-1-3_1.10.6-1 libdebconfclient0_0.200 libdevmapper1.02.1_2:1.02.110-2 libdpkg-perl_1.18.3 libdrm2_2.4.65-3 libexpat1_2.1.0-7 libfakeroot_1.20.2-1 libfdisk1_2.27.1-1 libffi6_3.2.1-3 libfile-stripnondeterminism-perl_0.014-1 libgc1c2_1:7.4.2-7.3 libgcc-5-dev_5.3.1-3+rpi1 libgcc1_1:5.3.1-3+rpi1 libgcrypt20_1.6.4-3 libgdbm3_1.8.3-13.1 libgfortran3_5.3.1-3+rpi1 libglib2.0-0_2.46.2-1 libgmp10_2:6.1.0+dfsg-2 libgomp1_5.3.1-3+rpi1 libgpg-error0_1.20-1 libgtest-dev_1.7.0-4 libhdf5-10_1.8.16+docs-1 libhdf5-cpp-11_1.8.16+docs-1 libhdf5-dev_1.8.16+docs-1 libhts-dev_1.2.1-1+rpi1 libhts1_1.2.1-1+rpi1 libicu55_55.1-6 libisl13_0.14-2 libisl15_0.15-3 libjpeg-dev_1:1.4.1-2 libjpeg62-turbo_1:1.4.1-2 libjpeg62-turbo-dev_1:1.4.1-2 libklibc_2.0.4-4+rpi1 libkmod2_21-1 liblocale-gettext-perl_1.07-1 liblzma5_5.1.1alpha+20120614-2.1 libmagic1_1:5.25-2 libmount1_2.27.1-1 libmpc3_1.0.3-1 libmpfr4_3.1.3-1 libncurses5_6.0+20151024-2 libncursesw5_6.0+20151024-2 libpam-modules_1.1.8-3.1 libpam-modules-bin_1.1.8-3.1 libpam-runtime_1.1.8-3.1 libpam0g_1.1.8-3.1 libpcre3_2:8.35-8 libpipeline1_1.4.1-1 libplymouth4_0.9.2-3 libpng12-0_1.2.54-1 libprocps4_2:3.3.10-2 libpython-stdlib_2.7.11-1 libpython2.7-minimal_2.7.11-2 libpython2.7-stdlib_2.7.11-2 libreadline6_6.3-8+b3 libseccomp2_2.2.3-2 libselinux1_2.4-3 libsemanage-common_2.4-3 libsemanage1_2.4-3 libsepol1_2.4-2 libsmartcols1_2.27.1-1 libsqlite3-0_3.9.2-1 libss2_1.42.13-1 libssl1.0.2_1.0.2e-1 libstdc++-5-dev_5.3.1-3+rpi1 libstdc++6_5.3.1-3+rpi1 libsystemd0_228-2 libtext-charwidth-perl_0.04-7+b4 libtext-iconv-perl_1.7-5+b5 libtext-wrapi18n-perl_0.06-7.1 libtimedate-perl_2.3000-2 libtinfo5_6.0+20151024-2 libubsan0_5.3.1-3+rpi1 libudev1_228-2 libunistring0_0.9.3-5.2 libusb-0.1-4_2:0.1.12-27 libustr-1.0-1_1.0.4-5 libuuid1_2.27.1-1 libxml2_2.9.2+zdfsg1-4 linux-libc-dev_3.18.5-1~exp1+rpi19+stretch login_1:4.2-3.1 lsb-base_4.1+Debian13+rpi1+nmu1 make_4.0-8.2 makedev_2.3.1-93 man-db_2.7.5-1 manpages_3.74-1 mawk_1.3.3-17 mime-support_3.59 mount_2.27.1-1 multiarch-support_2.21-4 ncurses-base_6.0+20151024-2 ncurses-bin_6.0+20151024-2 passwd_1:4.2-3.1 patch_2.7.5-1 perl_5.20.2-6 perl-base_5.20.2-6 perl-modules_5.20.2-6 plymouth_0.9.2-3 po-debconf_1.0.18 procps_2:3.3.10-2 python_2.7.11-1 python-minimal_2.7.11-1 python2.7_2.7.11-2 python2.7-minimal_2.7.11-2 raspbian-archive-keyring_20120528.2 readline-common_6.3-8 sbuild-build-depends-core-dummy_0.invalid.0 sbuild-build-depends-pbseqlib-dummy_0.invalid.0 sed_4.2.2-6.1 sensible-utils_0.0.9 startpar_0.59-3 systemd_228-2 systemd-sysv_228-2 sysv-rc_2.88dsf-59.2 sysvinit-utils_2.88dsf-59.2 tar_1.28-2.1 tzdata_2015g-1 udev_228-2 util-linux_2.27.1-1 xz-utils_5.1.1alpha+20120614-2.1 zlib1g_1:1.2.8.dfsg-2+b1 zlib1g-dev_1:1.2.8.dfsg-2+b1

┌──────────────────────────────────────────────────────────────────────────────┐
│ Build                                                                        │
└──────────────────────────────────────────────────────────────────────────────┘


Unpack source
─────────────

gpgv: keyblock resource `/sbuild-nonexistent/.gnupg/trustedkeys.gpg': file open error
gpgv: Signature made Mon Dec 14 03:51:13 2015 UTC using RSA key ID AFE826FB
gpgv: Can't check signature: public key not found
dpkg-source: warning: failed to verify signature on ./pbseqlib_0~20151014+gitbe5d1bf-2.dsc
dpkg-source: info: extracting pbseqlib in pbseqlib-0~20151014+gitbe5d1bf
dpkg-source: info: unpacking pbseqlib_0~20151014+gitbe5d1bf.orig.tar.gz
dpkg-source: info: unpacking pbseqlib_0~20151014+gitbe5d1bf-2.debian.tar.xz
dpkg-source: info: applying external-gtest.patch
dpkg-source: info: applying exclude-pbbam.patch
dpkg-source: info: applying 32bit-narrowing-conversion.patch

Check disc space
────────────────

Sufficient free space for build

User Environment
────────────────

DEB_BUILD_OPTIONS=parallel=4
HOME=/sbuild-nonexistent
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-18ca301b-2ad6-4286-a9fd-fdfb98be69b9
SCHROOT_UID=104
SCHROOT_USER=buildd
SHELL=/bin/sh
TERM=xterm
USER=buildd

dpkg-buildpackage
─────────────────

dpkg-buildpackage: source package pbseqlib
dpkg-buildpackage: source version 0~20151014+gitbe5d1bf-2
dpkg-buildpackage: source distribution unstable
 dpkg-source --before-build pbseqlib-0~20151014+gitbe5d1bf
dpkg-buildpackage: host architecture armhf
 fakeroot debian/rules clean
dh clean --parallel
   dh_testdir -O--parallel
   debian/rules override_dh_auto_clean
make[1]: Entering directory '/«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf'
dh_auto_clean
	make -j4 clean
make[2]: Entering directory '/«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf'
make -C /«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf//pbdata clean
make[3]: Entering directory '/«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/pbdata'
rm -f libpbdata.a  libpbdata.so *.o *.d
make[3]: Leaving directory '/«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/pbdata'
make -C /«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf//hdf clean
make[3]: Entering directory '/«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/hdf'
rm -f libpbihdf.a libpbihdf.so *.o *.d
make[3]: Leaving directory '/«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/hdf'
make -C /«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf//alignment clean
make[3]: Entering directory '/«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/alignment'
rm -f libblasr.a libblasr.so *.o *.d
make[3]: Leaving directory '/«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/alignment'
make -C /«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf//unittest clean
make[3]: Entering directory '/«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/unittest'
rm -f -r  *.o test-runner
make[3]: Leaving directory '/«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/unittest'
make[2]: Leaving directory '/«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf'
rm -f					\
	debian/libpbdata*.install	\
	debian/libpbihdf*.install	\
	debian/libblasr*.install
make[1]: Leaving directory '/«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf'
   dh_clean -O--parallel
 debian/rules build-arch
dh build-arch --parallel
   dh_testdir -a -O--parallel
   debian/rules override_dh_auto_configure
make[1]: Entering directory '/«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf'
./configure.py PREFIX=/usr/
uname -s
uname='Linux'
writing to './libconfig.h'
"""

"""
writing to 'defines.mk'
"""

CXXFLAGS             := -g -O2 -fstack-protector-strong -Wformat -Werror=format-security
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
#CPPFLAGS+= -I../pbdata -I../hdf -I../alignment
LIBPBDATA_INC     ?=../pbdata
LIBPBIHDF_INC     ?=../hdf
LIBBLASR_INC      ?=../alignment
LIBPBDATA_LIB     ?=../pbdata
LIBPBIHDF_LIB     ?=../hdf
LIBBLASR_LIB      ?=../alignment

LIBCONFIG_H:=/«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/libconfig.h
# Use PREFIX dir, if available.
INCLUDES      += ${PREFIX_INC}
LIBS          += ${PREFIX_LIB}
"""
make[1]: Leaving directory '/«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf'
   dh_auto_build -a -O--parallel
	make -j4
make[1]: Entering directory '/«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf'
make libpbdata
make[2]: Entering directory '/«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf'
make -C /«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf//pbdata libconfig.h
make[3]: Entering directory '/«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/pbdata'
cp -af /«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/libconfig.h libconfig.h
make[3]: Leaving directory '/«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/pbdata'
make -C /«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf//pbdata all
make[3]: Entering directory '/«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/pbdata'
g++ -std=c++11 -pedantic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -I/usr/include -I/«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/pbdata -I/«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/pbdata/ -Imatrix -Ireads -Iqvs -Imetagenome -Isaf -Iutils -I../alignment -c CCSSequence.cpp -o CCSSequence.o
g++ -std=c++11 -pedantic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -I/usr/include -I/«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/pbdata -I/«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/pbdata/ -Imatrix -Ireads -Iqvs -Imetagenome -Isaf -Iutils -I../alignment -c ChangeListID.cpp -o ChangeListID.o
g++ -std=c++11 -pedantic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -I/usr/include -I/«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/pbdata -I/«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/pbdata/ -Imatrix -Ireads -Iqvs -Imetagenome -Isaf -Iutils -I../alignment -c CommandLineParser.cpp -o CommandLineParser.o
g++ -std=c++11 -pedantic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -I/usr/include -I/«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/pbdata -I/«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/pbdata/ -Imatrix -Ireads -Iqvs -Imetagenome -Isaf -Iutils -I../alignment -c DNASequence.cpp -o DNASequence.o
g++ -std=c++11 -pedantic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -I/usr/include -I/«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/pbdata -I/«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/pbdata/ -Imatrix -Ireads -Iqvs -Imetagenome -Isaf -Iutils -I../alignment -c FASTAReader.cpp -o FASTAReader.o
g++ -std=c++11 -pedantic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -I/usr/include -I/«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/pbdata -I/«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/pbdata/ -Imatrix -Ireads -Iqvs -Imetagenome -Isaf -Iutils -I../alignment -c FASTASequence.cpp -o FASTASequence.o
g++ -std=c++11 -pedantic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -I/usr/include -I/«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/pbdata -I/«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/pbdata/ -Imatrix -Ireads -Iqvs -Imetagenome -Isaf -Iutils -I../alignment -c FASTQReader.cpp -o FASTQReader.o
g++ -std=c++11 -pedantic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -I/usr/include -I/«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/pbdata -I/«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/pbdata/ -Imatrix -Ireads -Iqvs -Imetagenome -Isaf -Iutils -I../alignment -c FASTQSequence.cpp -o FASTQSequence.o
g++ -std=c++11 -pedantic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -I/usr/include -I/«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/pbdata -I/«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/pbdata/ -Imatrix -Ireads -Iqvs -Imetagenome -Isaf -Iutils -I../alignment -c GFFFile.cpp -o GFFFile.o
g++ -std=c++11 -pedantic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -I/usr/include -I/«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/pbdata -I/«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/pbdata/ -Imatrix -Ireads -Iqvs -Imetagenome -Isaf -Iutils -I../alignment -c MD5Utils.cpp -o MD5Utils.o
g++ -std=c++11 -pedantic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -I/usr/include -I/«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/pbdata -I/«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/pbdata/ -Imatrix -Ireads -Iqvs -Imetagenome -Isaf -Iutils -I../alignment -c NucConversion.cpp -o NucConversion.o
g++ -std=c++11 -pedantic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -I/usr/include -I/«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/pbdata -I/«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/pbdata/ -Imatrix -Ireads -Iqvs -Imetagenome -Isaf -Iutils -I../alignment -c PackedDNASequence.cpp -o PackedDNASequence.o
g++ -std=c++11 -pedantic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -I/usr/include -I/«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/pbdata -I/«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/pbdata/ -Imatrix -Ireads -Iqvs -Imetagenome -Isaf -Iutils -I../alignment -c ReverseCompressIndex.cpp -o ReverseCompressIndex.o
g++ -std=c++11 -pedantic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -I/usr/include -I/«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/pbdata -I/«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/pbdata/ -Imatrix -Ireads -Iqvs -Imetagenome -Isaf -Iutils -I../alignment -c SMRTSequence.cpp -o SMRTSequence.o
g++ -std=c++11 -pedantic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -I/usr/include -I/«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/pbdata -I/«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/pbdata/ -Imatrix -Ireads -Iqvs -Imetagenome -Isaf -Iutils -I../alignment -c StringUtils.cpp -o StringUtils.o
g++ -std=c++11 -pedantic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -I/usr/include -I/«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/pbdata -I/«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/pbdata/ -Imatrix -Ireads -Iqvs -Imetagenome -Isaf -Iutils -I../alignment -c /«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/pbdata/alignment/CmpAlignment.cpp -o CmpAlignment.o
g++ -std=c++11 -pedantic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -I/usr/include -I/«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/pbdata -I/«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/pbdata/ -Imatrix -Ireads -Iqvs -Imetagenome -Isaf -Iutils -I../alignment -c /«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/pbdata/amos/AfgBasWriter.cpp -o AfgBasWriter.o
g++ -std=c++11 -pedantic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -I/usr/include -I/«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/pbdata -I/«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/pbdata/ -Imatrix -Ireads -Iqvs -Imetagenome -Isaf -Iutils -I../alignment -c /«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/pbdata/loadpulses/MetricField.cpp -o MetricField.o
g++ -std=c++11 -pedantic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -I/usr/include -I/«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/pbdata -I/«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/pbdata/ -Imatrix -Ireads -Iqvs -Imetagenome -Isaf -Iutils -I../alignment -c /«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/pbdata/loadpulses/MovieAlnIndexLookupTable.cpp -o MovieAlnIndexLookupTable.o
g++ -std=c++11 -pedantic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -I/usr/include -I/«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/pbdata -I/«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/pbdata/ -Imatrix -Ireads -Iqvs -Imetagenome -Isaf -Iutils -I../alignment -c /«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/pbdata/metagenome/TitleTable.cpp -o TitleTable.o
g++ -std=c++11 -pedantic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -I/usr/include -I/«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/pbdata -I/«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/pbdata/ -Imatrix -Ireads -Iqvs -Imetagenome -Isaf -Iutils -I../alignment -c /«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/pbdata/qvs/QualityTransform.cpp -o QualityTransform.o
g++ -std=c++11 -pedantic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -I/usr/include -I/«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/pbdata -I/«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/pbdata/ -Imatrix -Ireads -Iqvs -Imetagenome -Isaf -Iutils -I../alignment -c /«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/pbdata/qvs/QualityValue.cpp -o QualityValue.o
g++ -std=c++11 -pedantic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -I/usr/include -I/«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/pbdata -I/«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/pbdata/ -Imatrix -Ireads -Iqvs -Imetagenome -Isaf -Iutils -I../alignment -c /«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/pbdata/reads/BaseFile.cpp -o BaseFile.o
g++ -std=c++11 -pedantic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -I/usr/include -I/«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/pbdata -I/«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/pbdata/ -Imatrix -Ireads -Iqvs -Imetagenome -Isaf -Iutils -I../alignment -c /«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/pbdata/reads/HoleXY.cpp -o HoleXY.o
g++ -std=c++11 -pedantic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -I/usr/include -I/«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/pbdata -I/«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/pbdata/ -Imatrix -Ireads -Iqvs -Imetagenome -Isaf -Iutils -I../alignment -c /«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/pbdata/reads/PulseBaseCommon.cpp -o PulseBaseCommon.o
g++ -std=c++11 -pedantic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -I/usr/include -I/«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/pbdata -I/«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/pbdata/ -Imatrix -Ireads -Iqvs -Imetagenome -Isaf -Iutils -I../alignment -c /«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/pbdata/reads/PulseFile.cpp -o PulseFile.o
g++ -std=c++11 -pedantic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -I/usr/include -I/«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/pbdata -I/«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/pbdata/ -Imatrix -Ireads -Iqvs -Imetagenome -Isaf -Iutils -I../alignment -c /«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/pbdata/reads/ReadType.cpp -o ReadType.o
g++ -std=c++11 -pedantic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -I/usr/include -I/«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/pbdata -I/«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/pbdata/ -Imatrix -Ireads -Iqvs -Imetagenome -Isaf -Iutils -I../alignment -c /«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/pbdata/reads/RegionAnnotation.cpp -o RegionAnnotation.o
g++ -std=c++11 -pedantic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -I/usr/include -I/«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/pbdata -I/«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/pbdata/ -Imatrix -Ireads -Iqvs -Imetagenome -Isaf -Iutils -I../alignment -c /«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/pbdata/reads/RegionAnnotations.cpp -o RegionAnnotations.o
g++ -std=c++11 -pedantic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -I/usr/include -I/«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/pbdata -I/«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/pbdata/ -Imatrix -Ireads -Iqvs -Imetagenome -Isaf -Iutils -I../alignment -c /«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/pbdata/reads/RegionTable.cpp -o RegionTable.o
g++ -std=c++11 -pedantic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -I/usr/include -I/«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/pbdata -I/«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/pbdata/ -Imatrix -Ireads -Iqvs -Imetagenome -Isaf -Iutils -I../alignment -c /«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/pbdata/reads/RegionTypeMap.cpp -o RegionTypeMap.o
g++ -std=c++11 -pedantic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -I/usr/include -I/«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/pbdata -I/«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/pbdata/ -Imatrix -Ireads -Iqvs -Imetagenome -Isaf -Iutils -I../alignment -c /«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/pbdata/reads/ScanData.cpp -o ScanData.o
g++ -std=c++11 -pedantic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -I/usr/include -I/«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/pbdata -I/«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/pbdata/ -Imatrix -Ireads -Iqvs -Imetagenome -Isaf -Iutils -I../alignment -c /«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/pbdata/reads/ZMWGroupEntry.cpp -o ZMWGroupEntry.o
g++ -std=c++11 -pedantic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -I/usr/include -I/«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/pbdata -I/«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/pbdata/ -Imatrix -Ireads -Iqvs -Imetagenome -Isaf -Iutils -I../alignment -c /«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/pbdata/saf/AlnGroup.cpp -o AlnGroup.o
g++ -std=c++11 -pedantic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -I/usr/include -I/«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/pbdata -I/«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/pbdata/ -Imatrix -Ireads -Iqvs -Imetagenome -Isaf -Iutils -I../alignment -c /«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/pbdata/saf/MovieInfo.cpp -o MovieInfo.o
g++ -std=c++11 -pedantic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -I/usr/include -I/«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/pbdata -I/«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/pbdata/ -Imatrix -Ireads -Iqvs -Imetagenome -Isaf -Iutils -I../alignment -c /«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/pbdata/saf/RefGroup.cpp -o RefGroup.o
g++ -std=c++11 -pedantic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -I/usr/include -I/«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/pbdata -I/«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/pbdata/ -Imatrix -Ireads -Iqvs -Imetagenome -Isaf -Iutils -I../alignment -c /«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/pbdata/saf/RefInfo.cpp -o RefInfo.o
g++ -std=c++11 -pedantic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -I/usr/include -I/«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/pbdata -I/«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/pbdata/ -Imatrix -Ireads -Iqvs -Imetagenome -Isaf -Iutils -I../alignment -c /«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/pbdata/sam/ReadGroup.cpp -o ReadGroup.o
g++ -std=c++11 -pedantic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -I/usr/include -I/«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/pbdata -I/«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/pbdata/ -Imatrix -Ireads -Iqvs -Imetagenome -Isaf -Iutils -I../alignment -c /«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/pbdata/sam/ReferenceSequence.cpp -o ReferenceSequence.o
g++ -std=c++11 -pedantic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -I/usr/include -I/«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/pbdata -I/«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/pbdata/ -Imatrix -Ireads -Iqvs -Imetagenome -Isaf -Iutils -I../alignment -c /«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/pbdata/sam/SAMAlignment.cpp -o SAMAlignment.o
g++ -std=c++11 -pedantic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -I/usr/include -I/«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/pbdata -I/«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/pbdata/ -Imatrix -Ireads -Iqvs -Imetagenome -Isaf -Iutils -I../alignment -c /«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/pbdata/sam/SAMHeader.cpp -o SAMHeader.o
g++ -std=c++11 -pedantic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -I/usr/include -I/«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/pbdata -I/«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/pbdata/ -Imatrix -Ireads -Iqvs -Imetagenome -Isaf -Iutils -I../alignment -c /«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/pbdata/sam/SAMKeywordValuePair.cpp -o SAMKeywordValuePair.o
g++ -std=c++11 -pedantic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -I/usr/include -I/«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/pbdata -I/«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/pbdata/ -Imatrix -Ireads -Iqvs -Imetagenome -Isaf -Iutils -I../alignment -c /«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/pbdata/utils/BitUtils.cpp -o BitUtils.o
g++ -std=c++11 -pedantic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -I/usr/include -I/«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/pbdata -I/«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/pbdata/ -Imatrix -Ireads -Iqvs -Imetagenome -Isaf -Iutils -I../alignment -c /«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/pbdata/utils/SMRTReadUtils.cpp -o SMRTReadUtils.o
g++ -std=c++11 -pedantic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -I/usr/include -I/«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/pbdata -I/«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/pbdata/ -Imatrix -Ireads -Iqvs -Imetagenome -Isaf -Iutils -I../alignment -c /«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/pbdata/utils/SMRTTitle.cpp -o SMRTTitle.o
g++ -std=c++11 -pedantic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -I/usr/include -I/«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/pbdata -I/«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/pbdata/ -Imatrix -Ireads -Iqvs -Imetagenome -Isaf -Iutils -I../alignment -fPIC -c CCSSequence.cpp -o CCSSequence.shared.o
g++ -std=c++11 -pedantic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -I/usr/include -I/«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/pbdata -I/«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/pbdata/ -Imatrix -Ireads -Iqvs -Imetagenome -Isaf -Iutils -I../alignment -fPIC -c ChangeListID.cpp -o ChangeListID.shared.o
g++ -std=c++11 -pedantic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -I/usr/include -I/«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/pbdata -I/«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/pbdata/ -Imatrix -Ireads -Iqvs -Imetagenome -Isaf -Iutils -I../alignment -fPIC -c CommandLineParser.cpp -o CommandLineParser.shared.o
g++ -std=c++11 -pedantic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -I/usr/include -I/«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/pbdata -I/«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/pbdata/ -Imatrix -Ireads -Iqvs -Imetagenome -Isaf -Iutils -I../alignment -fPIC -c DNASequence.cpp -o DNASequence.shared.o
g++ -std=c++11 -pedantic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -I/usr/include -I/«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/pbdata -I/«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/pbdata/ -Imatrix -Ireads -Iqvs -Imetagenome -Isaf -Iutils -I../alignment -fPIC -c FASTAReader.cpp -o FASTAReader.shared.o
g++ -std=c++11 -pedantic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -I/usr/include -I/«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/pbdata -I/«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/pbdata/ -Imatrix -Ireads -Iqvs -Imetagenome -Isaf -Iutils -I../alignment -fPIC -c FASTASequence.cpp -o FASTASequence.shared.o
g++ -std=c++11 -pedantic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -I/usr/include -I/«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/pbdata -I/«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/pbdata/ -Imatrix -Ireads -Iqvs -Imetagenome -Isaf -Iutils -I../alignment -fPIC -c FASTQReader.cpp -o FASTQReader.shared.o
g++ -std=c++11 -pedantic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -I/usr/include -I/«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/pbdata -I/«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/pbdata/ -Imatrix -Ireads -Iqvs -Imetagenome -Isaf -Iutils -I../alignment -fPIC -c FASTQSequence.cpp -o FASTQSequence.shared.o
g++ -std=c++11 -pedantic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -I/usr/include -I/«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/pbdata -I/«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/pbdata/ -Imatrix -Ireads -Iqvs -Imetagenome -Isaf -Iutils -I../alignment -fPIC -c GFFFile.cpp -o GFFFile.shared.o
g++ -std=c++11 -pedantic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -I/usr/include -I/«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/pbdata -I/«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/pbdata/ -Imatrix -Ireads -Iqvs -Imetagenome -Isaf -Iutils -I../alignment -fPIC -c MD5Utils.cpp -o MD5Utils.shared.o
g++ -std=c++11 -pedantic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -I/usr/include -I/«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/pbdata -I/«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/pbdata/ -Imatrix -Ireads -Iqvs -Imetagenome -Isaf -Iutils -I../alignment -fPIC -c NucConversion.cpp -o NucConversion.shared.o
g++ -std=c++11 -pedantic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -I/usr/include -I/«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/pbdata -I/«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/pbdata/ -Imatrix -Ireads -Iqvs -Imetagenome -Isaf -Iutils -I../alignment -fPIC -c PackedDNASequence.cpp -o PackedDNASequence.shared.o
g++ -std=c++11 -pedantic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -I/usr/include -I/«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/pbdata -I/«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/pbdata/ -Imatrix -Ireads -Iqvs -Imetagenome -Isaf -Iutils -I../alignment -fPIC -c ReverseCompressIndex.cpp -o ReverseCompressIndex.shared.o
g++ -std=c++11 -pedantic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -I/usr/include -I/«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/pbdata -I/«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/pbdata/ -Imatrix -Ireads -Iqvs -Imetagenome -Isaf -Iutils -I../alignment -fPIC -c SMRTSequence.cpp -o SMRTSequence.shared.o
g++ -std=c++11 -pedantic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -I/usr/include -I/«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/pbdata -I/«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/pbdata/ -Imatrix -Ireads -Iqvs -Imetagenome -Isaf -Iutils -I../alignment -fPIC -c StringUtils.cpp -o StringUtils.shared.o
g++ -std=c++11 -pedantic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -I/usr/include -I/«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/pbdata -I/«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/pbdata/ -Imatrix -Ireads -Iqvs -Imetagenome -Isaf -Iutils -I../alignment -fPIC -c /«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/pbdata/alignment/CmpAlignment.cpp -o CmpAlignment.shared.o
g++ -std=c++11 -pedantic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -I/usr/include -I/«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/pbdata -I/«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/pbdata/ -Imatrix -Ireads -Iqvs -Imetagenome -Isaf -Iutils -I../alignment -fPIC -c /«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/pbdata/amos/AfgBasWriter.cpp -o AfgBasWriter.shared.o
g++ -std=c++11 -pedantic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -I/usr/include -I/«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/pbdata -I/«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/pbdata/ -Imatrix -Ireads -Iqvs -Imetagenome -Isaf -Iutils -I../alignment -fPIC -c /«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/pbdata/loadpulses/MetricField.cpp -o MetricField.shared.o
g++ -std=c++11 -pedantic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -I/usr/include -I/«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/pbdata -I/«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/pbdata/ -Imatrix -Ireads -Iqvs -Imetagenome -Isaf -Iutils -I../alignment -fPIC -c /«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/pbdata/loadpulses/MovieAlnIndexLookupTable.cpp -o MovieAlnIndexLookupTable.shared.o
g++ -std=c++11 -pedantic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -I/usr/include -I/«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/pbdata -I/«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/pbdata/ -Imatrix -Ireads -Iqvs -Imetagenome -Isaf -Iutils -I../alignment -fPIC -c /«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/pbdata/metagenome/TitleTable.cpp -o TitleTable.shared.o
g++ -std=c++11 -pedantic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -I/usr/include -I/«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/pbdata -I/«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/pbdata/ -Imatrix -Ireads -Iqvs -Imetagenome -Isaf -Iutils -I../alignment -fPIC -c /«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/pbdata/qvs/QualityTransform.cpp -o QualityTransform.shared.o
g++ -std=c++11 -pedantic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -I/usr/include -I/«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/pbdata -I/«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/pbdata/ -Imatrix -Ireads -Iqvs -Imetagenome -Isaf -Iutils -I../alignment -fPIC -c /«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/pbdata/qvs/QualityValue.cpp -o QualityValue.shared.o
g++ -std=c++11 -pedantic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -I/usr/include -I/«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/pbdata -I/«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/pbdata/ -Imatrix -Ireads -Iqvs -Imetagenome -Isaf -Iutils -I../alignment -fPIC -c /«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/pbdata/reads/BaseFile.cpp -o BaseFile.shared.o
g++ -std=c++11 -pedantic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -I/usr/include -I/«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/pbdata -I/«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/pbdata/ -Imatrix -Ireads -Iqvs -Imetagenome -Isaf -Iutils -I../alignment -fPIC -c /«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/pbdata/reads/HoleXY.cpp -o HoleXY.shared.o
g++ -std=c++11 -pedantic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -I/usr/include -I/«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/pbdata -I/«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/pbdata/ -Imatrix -Ireads -Iqvs -Imetagenome -Isaf -Iutils -I../alignment -fPIC -c /«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/pbdata/reads/PulseBaseCommon.cpp -o PulseBaseCommon.shared.o
g++ -std=c++11 -pedantic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -I/usr/include -I/«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/pbdata -I/«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/pbdata/ -Imatrix -Ireads -Iqvs -Imetagenome -Isaf -Iutils -I../alignment -fPIC -c /«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/pbdata/reads/PulseFile.cpp -o PulseFile.shared.o
g++ -std=c++11 -pedantic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -I/usr/include -I/«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/pbdata -I/«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/pbdata/ -Imatrix -Ireads -Iqvs -Imetagenome -Isaf -Iutils -I../alignment -fPIC -c /«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/pbdata/reads/ReadType.cpp -o ReadType.shared.o
g++ -std=c++11 -pedantic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -I/usr/include -I/«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/pbdata -I/«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/pbdata/ -Imatrix -Ireads -Iqvs -Imetagenome -Isaf -Iutils -I../alignment -fPIC -c /«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/pbdata/reads/RegionAnnotation.cpp -o RegionAnnotation.shared.o
g++ -std=c++11 -pedantic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -I/usr/include -I/«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/pbdata -I/«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/pbdata/ -Imatrix -Ireads -Iqvs -Imetagenome -Isaf -Iutils -I../alignment -fPIC -c /«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/pbdata/reads/RegionAnnotations.cpp -o RegionAnnotations.shared.o
g++ -std=c++11 -pedantic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -I/usr/include -I/«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/pbdata -I/«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/pbdata/ -Imatrix -Ireads -Iqvs -Imetagenome -Isaf -Iutils -I../alignment -fPIC -c /«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/pbdata/reads/RegionTable.cpp -o RegionTable.shared.o
g++ -std=c++11 -pedantic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -I/usr/include -I/«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/pbdata -I/«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/pbdata/ -Imatrix -Ireads -Iqvs -Imetagenome -Isaf -Iutils -I../alignment -fPIC -c /«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/pbdata/reads/RegionTypeMap.cpp -o RegionTypeMap.shared.o
g++ -std=c++11 -pedantic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -I/usr/include -I/«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/pbdata -I/«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/pbdata/ -Imatrix -Ireads -Iqvs -Imetagenome -Isaf -Iutils -I../alignment -fPIC -c /«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/pbdata/reads/ScanData.cpp -o ScanData.shared.o
g++ -std=c++11 -pedantic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -I/usr/include -I/«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/pbdata -I/«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/pbdata/ -Imatrix -Ireads -Iqvs -Imetagenome -Isaf -Iutils -I../alignment -fPIC -c /«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/pbdata/reads/ZMWGroupEntry.cpp -o ZMWGroupEntry.shared.o
g++ -std=c++11 -pedantic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -I/usr/include -I/«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/pbdata -I/«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/pbdata/ -Imatrix -Ireads -Iqvs -Imetagenome -Isaf -Iutils -I../alignment -fPIC -c /«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/pbdata/saf/AlnGroup.cpp -o AlnGroup.shared.o
g++ -std=c++11 -pedantic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -I/usr/include -I/«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/pbdata -I/«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/pbdata/ -Imatrix -Ireads -Iqvs -Imetagenome -Isaf -Iutils -I../alignment -fPIC -c /«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/pbdata/saf/MovieInfo.cpp -o MovieInfo.shared.o
g++ -std=c++11 -pedantic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -I/usr/include -I/«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/pbdata -I/«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/pbdata/ -Imatrix -Ireads -Iqvs -Imetagenome -Isaf -Iutils -I../alignment -fPIC -c /«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/pbdata/saf/RefGroup.cpp -o RefGroup.shared.o
g++ -std=c++11 -pedantic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -I/usr/include -I/«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/pbdata -I/«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/pbdata/ -Imatrix -Ireads -Iqvs -Imetagenome -Isaf -Iutils -I../alignment -fPIC -c /«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/pbdata/saf/RefInfo.cpp -o RefInfo.shared.o
g++ -std=c++11 -pedantic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -I/usr/include -I/«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/pbdata -I/«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/pbdata/ -Imatrix -Ireads -Iqvs -Imetagenome -Isaf -Iutils -I../alignment -fPIC -c /«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/pbdata/sam/ReadGroup.cpp -o ReadGroup.shared.o
g++ -std=c++11 -pedantic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -I/usr/include -I/«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/pbdata -I/«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/pbdata/ -Imatrix -Ireads -Iqvs -Imetagenome -Isaf -Iutils -I../alignment -fPIC -c /«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/pbdata/sam/ReferenceSequence.cpp -o ReferenceSequence.shared.o
g++ -std=c++11 -pedantic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -I/usr/include -I/«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/pbdata -I/«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/pbdata/ -Imatrix -Ireads -Iqvs -Imetagenome -Isaf -Iutils -I../alignment -fPIC -c /«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/pbdata/sam/SAMAlignment.cpp -o SAMAlignment.shared.o
g++ -std=c++11 -pedantic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -I/usr/include -I/«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/pbdata -I/«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/pbdata/ -Imatrix -Ireads -Iqvs -Imetagenome -Isaf -Iutils -I../alignment -fPIC -c /«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/pbdata/sam/SAMHeader.cpp -o SAMHeader.shared.o
g++ -std=c++11 -pedantic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -I/usr/include -I/«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/pbdata -I/«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/pbdata/ -Imatrix -Ireads -Iqvs -Imetagenome -Isaf -Iutils -I../alignment -fPIC -c /«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/pbdata/sam/SAMKeywordValuePair.cpp -o SAMKeywordValuePair.shared.o
g++ -std=c++11 -pedantic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -I/usr/include -I/«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/pbdata -I/«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/pbdata/ -Imatrix -Ireads -Iqvs -Imetagenome -Isaf -Iutils -I../alignment -fPIC -c /«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/pbdata/utils/BitUtils.cpp -o BitUtils.shared.o
g++ -std=c++11 -pedantic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -I/usr/include -I/«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/pbdata -I/«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/pbdata/ -Imatrix -Ireads -Iqvs -Imetagenome -Isaf -Iutils -I../alignment -fPIC -c /«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/pbdata/utils/SMRTReadUtils.cpp -o SMRTReadUtils.shared.o
g++ -std=c++11 -pedantic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -I/usr/include -I/«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/pbdata -I/«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/pbdata/ -Imatrix -Ireads -Iqvs -Imetagenome -Isaf -Iutils -I../alignment -fPIC -c /«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/pbdata/utils/SMRTTitle.cpp -o SMRTTitle.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 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
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 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 
make[3]: Leaving directory '/«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/pbdata'
make[2]: Leaving directory '/«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf'
make libpbihdf
make[2]: Entering directory '/«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf'
make -C /«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf//hdf all
make[3]: Entering directory '/«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/hdf'
g++ -std=c++11 -pedantic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -I/usr/include -I../pbdata -I/usr/include/hdf5/serial -c HDFAttributable.cpp -o HDFAttributable.o
g++ -std=c++11 -pedantic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -I/usr/include -I../pbdata -I/usr/include/hdf5/serial -c HDFBaxWriter.cpp -o HDFBaxWriter.o
g++ -std=c++11 -pedantic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -I/usr/include -I../pbdata -I/usr/include/hdf5/serial -c HDFWriterBase.cpp -o HDFWriterBase.o
g++ -std=c++11 -pedantic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -I/usr/include -I../pbdata -I/usr/include/hdf5/serial -c DatasetCollection.cpp -o DatasetCollection.o
g++ -std=c++11 -pedantic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -I/usr/include -I../pbdata -I/usr/include/hdf5/serial -c HDFRegionTableReader.cpp -o HDFRegionTableReader.o
g++ -std=c++11 -pedantic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -I/usr/include -I../pbdata -I/usr/include/hdf5/serial -c BufferedHDFArray.cpp -o BufferedHDFArray.o
g++ -std=c++11 -pedantic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -I/usr/include -I../pbdata -I/usr/include/hdf5/serial -c HDFBasReader.cpp -o HDFBasReader.o
g++ -std=c++11 -pedantic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -I/usr/include -I../pbdata -I/usr/include/hdf5/serial -c HDFAtom.cpp -o HDFAtom.o
g++ -std=c++11 -pedantic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -I/usr/include -I../pbdata -I/usr/include/hdf5/serial -c HDFCmpExperimentGroup.cpp -o HDFCmpExperimentGroup.o
g++ -std=c++11 -pedantic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -I/usr/include -I../pbdata -I/usr/include/hdf5/serial -c HDFPulseDataFile.cpp -o HDFPulseDataFile.o
g++ -std=c++11 -pedantic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -I/usr/include -I../pbdata -I/usr/include/hdf5/serial -c HDFCmpSupportedFields.cpp -o HDFCmpSupportedFields.o
g++ -std=c++11 -pedantic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -I/usr/include -I../pbdata -I/usr/include/hdf5/serial -c HDFBaseCallsWriter.cpp -o HDFBaseCallsWriter.o
g++ -std=c++11 -pedantic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -I/usr/include -I../pbdata -I/usr/include/hdf5/serial -c HDFZMWReader.cpp -o HDFZMWReader.o
g++ -std=c++11 -pedantic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -I/usr/include -I../pbdata -I/usr/include/hdf5/serial -c HDFFile.cpp -o HDFFile.o
g++ -std=c++11 -pedantic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -I/usr/include -I../pbdata -I/usr/include/hdf5/serial -c HDFAlnInfoGroup.cpp -o HDFAlnInfoGroup.o
g++ -std=c++11 -pedantic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -I/usr/include -I../pbdata -I/usr/include/hdf5/serial -c HDFRegionsWriter.cpp -o HDFRegionsWriter.o
g++ -std=c++11 -pedantic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -I/usr/include -I../pbdata -I/usr/include/hdf5/serial -c HDFScanDataWriter.cpp -o HDFScanDataWriter.o
g++ -std=c++11 -pedantic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -I/usr/include -I../pbdata -I/usr/include/hdf5/serial -c HDFNewBasReader.cpp -o HDFNewBasReader.o
g++ -std=c++11 -pedantic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -I/usr/include -I../pbdata -I/usr/include/hdf5/serial -c HDFZMWMetricsWriter.cpp -o HDFZMWMetricsWriter.o
g++ -std=c++11 -pedantic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -I/usr/include -I../pbdata -I/usr/include/hdf5/serial -c HDFGroup.cpp -o HDFGroup.o
g++ -std=c++11 -pedantic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -I/usr/include -I../pbdata -I/usr/include/hdf5/serial -c HDFUtils.cpp -o HDFUtils.o
g++ -std=c++11 -pedantic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -I/usr/include -I../pbdata -I/usr/include/hdf5/serial -c HDFAlnGroupGroup.cpp -o HDFAlnGroupGroup.o
g++ -std=c++11 -pedantic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -I/usr/include -I../pbdata -I/usr/include/hdf5/serial -c HDFData.cpp -o HDFData.o
g++ -std=c++11 -pedantic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -I/usr/include -I../pbdata -I/usr/include/hdf5/serial -c HDFZMWWriter.cpp -o HDFZMWWriter.o
g++ -std=c++11 -pedantic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -I/usr/include -I../pbdata -I/usr/include/hdf5/serial -c HDFScanDataReader.cpp -o HDFScanDataReader.o
g++ -std=c++11 -pedantic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -I/usr/include -I../pbdata -I/usr/include/hdf5/serial -c BufferedHDF2DArray.cpp -o BufferedHDF2DArray.o
g++ -std=c++11 -pedantic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -I/usr/include -I../pbdata -I/usr/include/hdf5/serial -fPIC -c HDFAttributable.cpp -o HDFAttributable.shared.o
g++ -std=c++11 -pedantic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -I/usr/include -I../pbdata -I/usr/include/hdf5/serial -fPIC -c HDFBaxWriter.cpp -o HDFBaxWriter.shared.o
g++ -std=c++11 -pedantic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -I/usr/include -I../pbdata -I/usr/include/hdf5/serial -fPIC -c HDFWriterBase.cpp -o HDFWriterBase.shared.o
g++ -std=c++11 -pedantic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -I/usr/include -I../pbdata -I/usr/include/hdf5/serial -fPIC -c DatasetCollection.cpp -o DatasetCollection.shared.o
g++ -std=c++11 -pedantic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -I/usr/include -I../pbdata -I/usr/include/hdf5/serial -fPIC -c HDFRegionTableReader.cpp -o HDFRegionTableReader.shared.o
g++ -std=c++11 -pedantic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -I/usr/include -I../pbdata -I/usr/include/hdf5/serial -fPIC -c BufferedHDFArray.cpp -o BufferedHDFArray.shared.o
g++ -std=c++11 -pedantic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -I/usr/include -I../pbdata -I/usr/include/hdf5/serial -fPIC -c HDFBasReader.cpp -o HDFBasReader.shared.o
g++ -std=c++11 -pedantic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -I/usr/include -I../pbdata -I/usr/include/hdf5/serial -fPIC -c HDFAtom.cpp -o HDFAtom.shared.o
g++ -std=c++11 -pedantic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -I/usr/include -I../pbdata -I/usr/include/hdf5/serial -fPIC -c HDFCmpExperimentGroup.cpp -o HDFCmpExperimentGroup.shared.o
g++ -std=c++11 -pedantic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -I/usr/include -I../pbdata -I/usr/include/hdf5/serial -fPIC -c HDFPulseDataFile.cpp -o HDFPulseDataFile.shared.o
g++ -std=c++11 -pedantic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -I/usr/include -I../pbdata -I/usr/include/hdf5/serial -fPIC -c HDFCmpSupportedFields.cpp -o HDFCmpSupportedFields.shared.o
g++ -std=c++11 -pedantic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -I/usr/include -I../pbdata -I/usr/include/hdf5/serial -fPIC -c HDFBaseCallsWriter.cpp -o HDFBaseCallsWriter.shared.o
g++ -std=c++11 -pedantic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -I/usr/include -I../pbdata -I/usr/include/hdf5/serial -fPIC -c HDFZMWReader.cpp -o HDFZMWReader.shared.o
g++ -std=c++11 -pedantic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -I/usr/include -I../pbdata -I/usr/include/hdf5/serial -fPIC -c HDFFile.cpp -o HDFFile.shared.o
g++ -std=c++11 -pedantic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -I/usr/include -I../pbdata -I/usr/include/hdf5/serial -fPIC -c HDFAlnInfoGroup.cpp -o HDFAlnInfoGroup.shared.o
g++ -std=c++11 -pedantic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -I/usr/include -I../pbdata -I/usr/include/hdf5/serial -fPIC -c HDFRegionsWriter.cpp -o HDFRegionsWriter.shared.o
g++ -std=c++11 -pedantic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -I/usr/include -I../pbdata -I/usr/include/hdf5/serial -fPIC -c HDFScanDataWriter.cpp -o HDFScanDataWriter.shared.o
g++ -std=c++11 -pedantic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -I/usr/include -I../pbdata -I/usr/include/hdf5/serial -fPIC -c HDFNewBasReader.cpp -o HDFNewBasReader.shared.o
g++ -std=c++11 -pedantic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -I/usr/include -I../pbdata -I/usr/include/hdf5/serial -fPIC -c HDFZMWMetricsWriter.cpp -o HDFZMWMetricsWriter.shared.o
g++ -std=c++11 -pedantic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -I/usr/include -I../pbdata -I/usr/include/hdf5/serial -fPIC -c HDFGroup.cpp -o HDFGroup.shared.o
g++ -std=c++11 -pedantic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -I/usr/include -I../pbdata -I/usr/include/hdf5/serial -fPIC -c HDFUtils.cpp -o HDFUtils.shared.o
g++ -std=c++11 -pedantic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -I/usr/include -I../pbdata -I/usr/include/hdf5/serial -fPIC -c HDFAlnGroupGroup.cpp -o HDFAlnGroupGroup.shared.o
g++ -std=c++11 -pedantic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -I/usr/include -I../pbdata -I/usr/include/hdf5/serial -fPIC -c HDFData.cpp -o HDFData.shared.o
g++ -std=c++11 -pedantic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -I/usr/include -I../pbdata -I/usr/include/hdf5/serial -fPIC -c HDFZMWWriter.cpp -o HDFZMWWriter.shared.o
g++ -std=c++11 -pedantic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -I/usr/include -I../pbdata -I/usr/include/hdf5/serial -fPIC -c HDFScanDataReader.cpp -o HDFScanDataReader.shared.o
g++ -std=c++11 -pedantic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -I/usr/include -I../pbdata -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 HDFBasReader.o HDFAtom.o HDFCmpExperimentGroup.o HDFPulseDataFile.o HDFCmpSupportedFields.o HDFBaseCallsWriter.o HDFZMWReader.o HDFFile.o HDFAlnInfoGroup.o HDFRegionsWriter.o HDFScanDataWriter.o HDFNewBasReader.o HDFZMWMetricsWriter.o HDFGroup.o HDFUtils.o HDFAlnGroupGroup.o HDFData.o HDFZMWWriter.o HDFScanDataReader.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 HDFBasReader.shared.o HDFAtom.shared.o HDFCmpExperimentGroup.shared.o HDFPulseDataFile.shared.o HDFCmpSupportedFields.shared.o HDFBaseCallsWriter.shared.o HDFZMWReader.shared.o HDFFile.shared.o HDFAlnInfoGroup.shared.o HDFRegionsWriter.shared.o HDFScanDataWriter.shared.o HDFNewBasReader.shared.o HDFZMWMetricsWriter.shared.o HDFGroup.shared.o HDFUtils.shared.o HDFAlnGroupGroup.shared.o HDFData.shared.o HDFZMWWriter.shared.o HDFScanDataReader.shared.o BufferedHDF2DArray.shared.o -lpbdata -lhdf5 -lhdf5_cpp
make[3]: Leaving directory '/«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/hdf'
make[2]: Leaving directory '/«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf'
make libblasr
make[2]: Entering directory '/«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf'
make -C /«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf//alignment all
make[3]: Entering directory '/«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/alignment'
g++ -std=c++11 -pedantic -Wno-long-long -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -I/usr/include -I/«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/alignment/ -I../pbdata -I../hdf -I/usr/include/hdf5/serial -c MappingMetrics.cpp -o MappingMetrics.o
g++ -std=c++11 -pedantic -Wno-long-long -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -I/usr/include -I/«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/alignment/ -I../pbdata -I../hdf -I/usr/include/hdf5/serial -c /«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/alignment/algorithms/alignment/AlignmentUtils.cpp -o AlignmentUtils.o
g++ -std=c++11 -pedantic -Wno-long-long -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -I/usr/include -I/«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/alignment/ -I../pbdata -I../hdf -I/usr/include/hdf5/serial -c /«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/alignment/algorithms/alignment/BaseScoreFunction.cpp -o BaseScoreFunction.o
g++ -std=c++11 -pedantic -Wno-long-long -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -I/usr/include -I/«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/alignment/ -I../pbdata -I../hdf -I/usr/include/hdf5/serial -c /«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/alignment/algorithms/alignment/ExtendAlign.cpp -o ExtendAlign.o
g++ -std=c++11 -pedantic -Wno-long-long -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -I/usr/include -I/«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/alignment/ -I../pbdata -I../hdf -I/usr/include/hdf5/serial -c /«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/alignment/algorithms/alignment/GuidedAlign.cpp -o GuidedAlign.o
g++ -std=c++11 -pedantic -Wno-long-long -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -I/usr/include -I/«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/alignment/ -I../pbdata -I../hdf -I/usr/include/hdf5/serial -c /«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/alignment/algorithms/alignment/IDSScoreFunction.cpp -o IDSScoreFunction.o
g++ -std=c++11 -pedantic -Wno-long-long -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -I/usr/include -I/«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/alignment/ -I../pbdata -I../hdf -I/usr/include/hdf5/serial -c /«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/alignment/algorithms/alignment/KBandAlign.cpp -o KBandAlign.o
g++ -std=c++11 -pedantic -Wno-long-long -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -I/usr/include -I/«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/alignment/ -I../pbdata -I../hdf -I/usr/include/hdf5/serial -c /«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/alignment/algorithms/alignment/QualityValueScoreFunction.cpp -o QualityValueScoreFunction.o
g++ -std=c++11 -pedantic -Wno-long-long -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -I/usr/include -I/«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/alignment/ -I../pbdata -I../hdf -I/usr/include/hdf5/serial -c /«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/alignment/algorithms/alignment/ScoreMatrices.cpp -o ScoreMatrices.o
g++ -std=c++11 -pedantic -Wno-long-long -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -I/usr/include -I/«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/alignment/ -I../pbdata -I../hdf -I/usr/include/hdf5/serial -c /«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/alignment/algorithms/alignment/StringToScoreMatrix.cpp -o StringToScoreMatrix.o
g++ -std=c++11 -pedantic -Wno-long-long -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -I/usr/include -I/«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/alignment/ -I../pbdata -I../hdf -I/usr/include/hdf5/serial -c /«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/alignment/algorithms/alignment/sdp/SDPFragment.cpp -o SDPFragment.o
g++ -std=c++11 -pedantic -Wno-long-long -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -I/usr/include -I/«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/alignment/ -I../pbdata -I../hdf -I/usr/include/hdf5/serial -c /«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/alignment/algorithms/alignment/sdp/SparseDynamicProgramming.cpp -o SparseDynamicProgramming.o
g++ -std=c++11 -pedantic -Wno-long-long -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -I/usr/include -I/«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/alignment/ -I../pbdata -I../hdf -I/usr/include/hdf5/serial -c /«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/alignment/algorithms/anchoring/BWTSearch.cpp -o BWTSearch.o
g++ -std=c++11 -pedantic -Wno-long-long -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -I/usr/include -I/«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/alignment/ -I../pbdata -I../hdf -I/usr/include/hdf5/serial -c /«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/alignment/algorithms/anchoring/ClusterProbability.cpp -o ClusterProbability.o
g++ -std=c++11 -pedantic -Wno-long-long -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -I/usr/include -I/«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/alignment/ -I../pbdata -I../hdf -I/usr/include/hdf5/serial -c /«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/alignment/algorithms/anchoring/Coordinate.cpp -o Coordinate.o
g++ -std=c++11 -pedantic -Wno-long-long -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -I/usr/include -I/«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/alignment/ -I../pbdata -I../hdf -I/usr/include/hdf5/serial -c /«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/alignment/algorithms/anchoring/FindMaxInterval.cpp -o FindMaxInterval.o
g++ -std=c++11 -pedantic -Wno-long-long -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -I/usr/include -I/«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/alignment/ -I../pbdata -I../hdf -I/usr/include/hdf5/serial -c /«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/alignment/algorithms/sorting/DifferenceCovers.cpp -o DifferenceCovers.o
g++ -std=c++11 -pedantic -Wno-long-long -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -I/usr/include -I/«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/alignment/ -I../pbdata -I../hdf -I/usr/include/hdf5/serial -c /«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/alignment/algorithms/sorting/LightweightSuffixArray.cpp -o LightweightSuffixArray.o
g++ -std=c++11 -pedantic -Wno-long-long -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -I/usr/include -I/«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/alignment/ -I../pbdata -I../hdf -I/usr/include/hdf5/serial -c /«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/alignment/algorithms/sorting/MultikeyQuicksort.cpp -o MultikeyQuicksort.o
g++ -std=c++11 -pedantic -Wno-long-long -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -I/usr/include -I/«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/alignment/ -I../pbdata -I../hdf -I/usr/include/hdf5/serial -c /«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/alignment/algorithms/sorting/qsufsort.cpp -o qsufsort.o
g++ -std=c++11 -pedantic -Wno-long-long -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -I/usr/include -I/«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/alignment/ -I../pbdata -I../hdf -I/usr/include/hdf5/serial -c /«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/alignment/datastructures/alignment/Alignment.cpp -o Alignment.o
g++ -std=c++11 -pedantic -Wno-long-long -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -I/usr/include -I/«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/alignment/ -I../pbdata -I../hdf -I/usr/include/hdf5/serial -c /«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/alignment/datastructures/alignment/AlignmentCandidate.cpp -o AlignmentCandidate.o
g++ -std=c++11 -pedantic -Wno-long-long -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -I/usr/include -I/«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/alignment/ -I../pbdata -I../hdf -I/usr/include/hdf5/serial -c /«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/alignment/datastructures/alignment/AlignmentContext.cpp -o AlignmentContext.o
g++ -std=c++11 -pedantic -Wno-long-long -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -I/usr/include -I/«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/alignment/ -I../pbdata -I../hdf -I/usr/include/hdf5/serial -c /«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/alignment/datastructures/alignment/AlignmentMap.cpp -o AlignmentMap.o
g++ -std=c++11 -pedantic -Wno-long-long -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -I/usr/include -I/«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/alignment/ -I../pbdata -I../hdf -I/usr/include/hdf5/serial -c /«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/alignment/datastructures/alignment/AlignmentStats.cpp -o AlignmentStats.o
g++ -std=c++11 -pedantic -Wno-long-long -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -I/usr/include -I/«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/alignment/ -I../pbdata -I../hdf -I/usr/include/hdf5/serial -c /«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/alignment/datastructures/alignment/CmpFile.cpp -o CmpFile.o
g++ -std=c++11 -pedantic -Wno-long-long -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -I/usr/include -I/«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/alignment/ -I../pbdata -I../hdf -I/usr/include/hdf5/serial -c /«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/alignment/datastructures/alignment/FilterCriteria.cpp -o FilterCriteria.o
g++ -std=c++11 -pedantic -Wno-long-long -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -I/usr/include -I/«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/alignment/ -I../pbdata -I../hdf -I/usr/include/hdf5/serial -c /«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/alignment/datastructures/alignment/SAMToAlignmentCandidateAdapter.cpp -o SAMToAlignmentCandidateAdapter.o
g++ -std=c++11 -pedantic -Wno-long-long -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -I/usr/include -I/«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/alignment/ -I../pbdata -I../hdf -I/usr/include/hdf5/serial -c /«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/alignment/datastructures/alignmentset/SAMQVConversion.cpp -o SAMQVConversion.o
g++ -std=c++11 -pedantic -Wno-long-long -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -I/usr/include -I/«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/alignment/ -I../pbdata -I../hdf -I/usr/include/hdf5/serial -c /«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/alignment/datastructures/alignmentset/SAMSupplementalQVList.cpp -o SAMSupplementalQVList.o
g++ -std=c++11 -pedantic -Wno-long-long -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -I/usr/include -I/«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/alignment/ -I../pbdata -I../hdf -I/usr/include/hdf5/serial -c /«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/alignment/datastructures/anchoring/AnchorParameters.cpp -o AnchorParameters.o
g++ -std=c++11 -pedantic -Wno-long-long -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -I/usr/include -I/«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/alignment/ -I../pbdata -I../hdf -I/usr/include/hdf5/serial -c /«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/alignment/datastructures/anchoring/ClusterList.cpp -o ClusterList.o
g++ -std=c++11 -pedantic -Wno-long-long -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -I/usr/include -I/«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/alignment/ -I../pbdata -I../hdf -I/usr/include/hdf5/serial -c /«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/alignment/datastructures/anchoring/MatchPos.cpp -o MatchPos.o
g++ -std=c++11 -pedantic -Wno-long-long -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -I/usr/include -I/«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/alignment/ -I../pbdata -I../hdf -I/usr/include/hdf5/serial -c /«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/alignment/datastructures/anchoring/WeightedInterval.cpp -o WeightedInterval.o
g++ -std=c++11 -pedantic -Wno-long-long -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -I/usr/include -I/«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/alignment/ -I../pbdata -I../hdf -I/usr/include/hdf5/serial -c /«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/alignment/files/BaseSequenceIO.cpp -o BaseSequenceIO.o
g++ -std=c++11 -pedantic -Wno-long-long -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -I/usr/include -I/«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/alignment/ -I../pbdata -I../hdf -I/usr/include/hdf5/serial -c /«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/alignment/files/CCSIterator.cpp -o CCSIterator.o
g++ -std=c++11 -pedantic -Wno-long-long -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -I/usr/include -I/«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/alignment/ -I../pbdata -I../hdf -I/usr/include/hdf5/serial -c /«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/alignment/files/FragmentCCSIterator.cpp -o FragmentCCSIterator.o
g++ -std=c++11 -pedantic -Wno-long-long -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -I/usr/include -I/«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/alignment/ -I../pbdata -I../hdf -I/usr/include/hdf5/serial -c /«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/alignment/files/ReaderAgglomerate.cpp -o ReaderAgglomerate.o
g++ -std=c++11 -pedantic -Wno-long-long -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -I/usr/include -I/«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/alignment/ -I../pbdata -I../hdf -I/usr/include/hdf5/serial -c /«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/alignment/format/CompareSequencesPrinter.cpp -o CompareSequencesPrinter.o
g++ -std=c++11 -pedantic -Wno-long-long -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -I/usr/include -I/«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/alignment/ -I../pbdata -I../hdf -I/usr/include/hdf5/serial -c /«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/alignment/format/IntervalPrinter.cpp -o IntervalPrinter.o
g++ -std=c++11 -pedantic -Wno-long-long -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -I/usr/include -I/«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/alignment/ -I../pbdata -I../hdf -I/usr/include/hdf5/serial -c /«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/alignment/format/SAMHeaderPrinter.cpp -o SAMHeaderPrinter.o
g++ -std=c++11 -pedantic -Wno-long-long -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -I/usr/include -I/«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/alignment/ -I../pbdata -I../hdf -I/usr/include/hdf5/serial -c /«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/alignment/format/SAMPrinter.cpp -o SAMPrinter.o
g++ -std=c++11 -pedantic -Wno-long-long -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -I/usr/include -I/«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/alignment/ -I../pbdata -I../hdf -I/usr/include/hdf5/serial -c /«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/alignment/format/SummaryPrinter.cpp -o SummaryPrinter.o
g++ -std=c++11 -pedantic -Wno-long-long -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -I/usr/include -I/«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/alignment/ -I../pbdata -I../hdf -I/usr/include/hdf5/serial -c /«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/alignment/qvs/QualityValueProfile.cpp -o QualityValueProfile.o
g++ -std=c++11 -pedantic -Wno-long-long -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -I/usr/include -I/«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/alignment/ -I../pbdata -I../hdf -I/usr/include/hdf5/serial -c /«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/alignment/simulator/ContextSample.cpp -o ContextSample.o
g++ -std=c++11 -pedantic -Wno-long-long -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -I/usr/include -I/«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/alignment/ -I../pbdata -I../hdf -I/usr/include/hdf5/serial -c /«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/alignment/simulator/ContextSet.cpp -o ContextSet.o
g++ -std=c++11 -pedantic -Wno-long-long -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -I/usr/include -I/«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/alignment/ -I../pbdata -I../hdf -I/usr/include/hdf5/serial -c /«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/alignment/simulator/LengthHistogram.cpp -o LengthHistogram.o
g++ -std=c++11 -pedantic -Wno-long-long -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -I/usr/include -I/«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/alignment/ -I../pbdata -I../hdf -I/usr/include/hdf5/serial -c /«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/alignment/simulator/QualitySample.cpp -o QualitySample.o
g++ -std=c++11 -pedantic -Wno-long-long -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -I/usr/include -I/«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/alignment/ -I../pbdata -I../hdf -I/usr/include/hdf5/serial -c /«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/alignment/statistics/LookupAnchorDistribution.cpp -o LookupAnchorDistribution.o
g++ -std=c++11 -pedantic -Wno-long-long -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -I/usr/include -I/«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/alignment/ -I../pbdata -I../hdf -I/usr/include/hdf5/serial -c /«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/alignment/statistics/StatUtils.cpp -o StatUtils.o
g++ -std=c++11 -pedantic -Wno-long-long -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -I/usr/include -I/«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/alignment/ -I../pbdata -I../hdf -I/usr/include/hdf5/serial -c /«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/alignment/statistics/cdfs.cpp -o cdfs.o
g++ -std=c++11 -pedantic -Wno-long-long -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -I/usr/include -I/«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/alignment/ -I../pbdata -I../hdf -I/usr/include/hdf5/serial -c /«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/alignment/statistics/pdfs.cpp -o pdfs.o
g++ -std=c++11 -pedantic -Wno-long-long -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -I/usr/include -I/«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/alignment/ -I../pbdata -I../hdf -I/usr/include/hdf5/serial -c /«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/alignment/tuples/BaseTuple.cpp -o BaseTuple.o
g++ -std=c++11 -pedantic -Wno-long-long -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -I/usr/include -I/«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/alignment/ -I../pbdata -I../hdf -I/usr/include/hdf5/serial -c /«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/alignment/tuples/DNATuple.cpp -o DNATuple.o
g++ -std=c++11 -pedantic -Wno-long-long -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -I/usr/include -I/«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/alignment/ -I../pbdata -I../hdf -I/usr/include/hdf5/serial -c /«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/alignment/tuples/TupleMetrics.cpp -o TupleMetrics.o
g++ -std=c++11 -pedantic -Wno-long-long -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -I/usr/include -I/«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/alignment/ -I../pbdata -I../hdf -I/usr/include/hdf5/serial -c /«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/alignment/utils/FileOfFileNames.cpp -o FileOfFileNames.o
g++ -std=c++11 -pedantic -Wno-long-long -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -I/usr/include -I/«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/alignment/ -I../pbdata -I../hdf -I/usr/include/hdf5/serial -c /«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/alignment/utils/FileUtils.cpp -o FileUtils.o
g++ -std=c++11 -pedantic -Wno-long-long -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -I/usr/include -I/«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/alignment/ -I../pbdata -I../hdf -I/usr/include/hdf5/serial -c /«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/alignment/utils/LogUtils.cpp -o LogUtils.o
g++ -std=c++11 -pedantic -Wno-long-long -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -I/usr/include -I/«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/alignment/ -I../pbdata -I../hdf -I/usr/include/hdf5/serial -c /«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/alignment/utils/PhredUtils.cpp -o PhredUtils.o
g++ -std=c++11 -pedantic -Wno-long-long -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -I/usr/include -I/«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/alignment/ -I../pbdata -I../hdf -I/usr/include/hdf5/serial -c /«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/alignment/utils/RangeUtils.cpp -o RangeUtils.o
g++ -std=c++11 -pedantic -Wno-long-long -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -I/usr/include -I/«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/alignment/ -I../pbdata -I../hdf -I/usr/include/hdf5/serial -c /«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/alignment/utils/RegionUtils.cpp -o RegionUtils.o
g++ -std=c++11 -pedantic -Wno-long-long -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -I/usr/include -I/«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/alignment/ -I../pbdata -I../hdf -I/usr/include/hdf5/serial -c /«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/alignment/utils/TimeUtils.cpp -o TimeUtils.o
g++ -std=c++11 -pedantic -Wno-long-long -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -I/usr/include -I/«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/alignment/ -I../pbdata -I../hdf -I/usr/include/hdf5/serial -fPIC -c MappingMetrics.cpp -o MappingMetrics.shared.o
g++ -std=c++11 -pedantic -Wno-long-long -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -I/usr/include -I/«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/alignment/ -I../pbdata -I../hdf -I/usr/include/hdf5/serial -fPIC -c /«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/alignment/algorithms/alignment/AlignmentUtils.cpp -o AlignmentUtils.shared.o
g++ -std=c++11 -pedantic -Wno-long-long -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -I/usr/include -I/«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/alignment/ -I../pbdata -I../hdf -I/usr/include/hdf5/serial -fPIC -c /«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/alignment/algorithms/alignment/BaseScoreFunction.cpp -o BaseScoreFunction.shared.o
g++ -std=c++11 -pedantic -Wno-long-long -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -I/usr/include -I/«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/alignment/ -I../pbdata -I../hdf -I/usr/include/hdf5/serial -fPIC -c /«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/alignment/algorithms/alignment/ExtendAlign.cpp -o ExtendAlign.shared.o
g++ -std=c++11 -pedantic -Wno-long-long -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -I/usr/include -I/«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/alignment/ -I../pbdata -I../hdf -I/usr/include/hdf5/serial -fPIC -c /«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/alignment/algorithms/alignment/GuidedAlign.cpp -o GuidedAlign.shared.o
g++ -std=c++11 -pedantic -Wno-long-long -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -I/usr/include -I/«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/alignment/ -I../pbdata -I../hdf -I/usr/include/hdf5/serial -fPIC -c /«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/alignment/algorithms/alignment/IDSScoreFunction.cpp -o IDSScoreFunction.shared.o
g++ -std=c++11 -pedantic -Wno-long-long -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -I/usr/include -I/«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/alignment/ -I../pbdata -I../hdf -I/usr/include/hdf5/serial -fPIC -c /«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/alignment/algorithms/alignment/KBandAlign.cpp -o KBandAlign.shared.o
g++ -std=c++11 -pedantic -Wno-long-long -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -I/usr/include -I/«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/alignment/ -I../pbdata -I../hdf -I/usr/include/hdf5/serial -fPIC -c /«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/alignment/algorithms/alignment/QualityValueScoreFunction.cpp -o QualityValueScoreFunction.shared.o
g++ -std=c++11 -pedantic -Wno-long-long -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -I/usr/include -I/«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/alignment/ -I../pbdata -I../hdf -I/usr/include/hdf5/serial -fPIC -c /«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/alignment/algorithms/alignment/ScoreMatrices.cpp -o ScoreMatrices.shared.o
g++ -std=c++11 -pedantic -Wno-long-long -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -I/usr/include -I/«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/alignment/ -I../pbdata -I../hdf -I/usr/include/hdf5/serial -fPIC -c /«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/alignment/algorithms/alignment/StringToScoreMatrix.cpp -o StringToScoreMatrix.shared.o
g++ -std=c++11 -pedantic -Wno-long-long -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -I/usr/include -I/«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/alignment/ -I../pbdata -I../hdf -I/usr/include/hdf5/serial -fPIC -c /«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/alignment/algorithms/alignment/sdp/SDPFragment.cpp -o SDPFragment.shared.o
g++ -std=c++11 -pedantic -Wno-long-long -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -I/usr/include -I/«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/alignment/ -I../pbdata -I../hdf -I/usr/include/hdf5/serial -fPIC -c /«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/alignment/algorithms/alignment/sdp/SparseDynamicProgramming.cpp -o SparseDynamicProgramming.shared.o
g++ -std=c++11 -pedantic -Wno-long-long -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -I/usr/include -I/«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/alignment/ -I../pbdata -I../hdf -I/usr/include/hdf5/serial -fPIC -c /«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/alignment/algorithms/anchoring/BWTSearch.cpp -o BWTSearch.shared.o
g++ -std=c++11 -pedantic -Wno-long-long -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -I/usr/include -I/«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/alignment/ -I../pbdata -I../hdf -I/usr/include/hdf5/serial -fPIC -c /«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/alignment/algorithms/anchoring/ClusterProbability.cpp -o ClusterProbability.shared.o
g++ -std=c++11 -pedantic -Wno-long-long -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -I/usr/include -I/«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/alignment/ -I../pbdata -I../hdf -I/usr/include/hdf5/serial -fPIC -c /«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/alignment/algorithms/anchoring/Coordinate.cpp -o Coordinate.shared.o
g++ -std=c++11 -pedantic -Wno-long-long -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -I/usr/include -I/«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/alignment/ -I../pbdata -I../hdf -I/usr/include/hdf5/serial -fPIC -c /«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/alignment/algorithms/anchoring/FindMaxInterval.cpp -o FindMaxInterval.shared.o
g++ -std=c++11 -pedantic -Wno-long-long -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -I/usr/include -I/«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/alignment/ -I../pbdata -I../hdf -I/usr/include/hdf5/serial -fPIC -c /«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/alignment/algorithms/sorting/DifferenceCovers.cpp -o DifferenceCovers.shared.o
g++ -std=c++11 -pedantic -Wno-long-long -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -I/usr/include -I/«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/alignment/ -I../pbdata -I../hdf -I/usr/include/hdf5/serial -fPIC -c /«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/alignment/algorithms/sorting/LightweightSuffixArray.cpp -o LightweightSuffixArray.shared.o
g++ -std=c++11 -pedantic -Wno-long-long -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -I/usr/include -I/«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/alignment/ -I../pbdata -I../hdf -I/usr/include/hdf5/serial -fPIC -c /«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/alignment/algorithms/sorting/MultikeyQuicksort.cpp -o MultikeyQuicksort.shared.o
g++ -std=c++11 -pedantic -Wno-long-long -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -I/usr/include -I/«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/alignment/ -I../pbdata -I../hdf -I/usr/include/hdf5/serial -fPIC -c /«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/alignment/algorithms/sorting/qsufsort.cpp -o qsufsort.shared.o
g++ -std=c++11 -pedantic -Wno-long-long -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -I/usr/include -I/«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/alignment/ -I../pbdata -I../hdf -I/usr/include/hdf5/serial -fPIC -c /«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/alignment/datastructures/alignment/Alignment.cpp -o Alignment.shared.o
g++ -std=c++11 -pedantic -Wno-long-long -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -I/usr/include -I/«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/alignment/ -I../pbdata -I../hdf -I/usr/include/hdf5/serial -fPIC -c /«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/alignment/datastructures/alignment/AlignmentCandidate.cpp -o AlignmentCandidate.shared.o
g++ -std=c++11 -pedantic -Wno-long-long -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -I/usr/include -I/«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/alignment/ -I../pbdata -I../hdf -I/usr/include/hdf5/serial -fPIC -c /«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/alignment/datastructures/alignment/AlignmentContext.cpp -o AlignmentContext.shared.o
g++ -std=c++11 -pedantic -Wno-long-long -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -I/usr/include -I/«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/alignment/ -I../pbdata -I../hdf -I/usr/include/hdf5/serial -fPIC -c /«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/alignment/datastructures/alignment/AlignmentMap.cpp -o AlignmentMap.shared.o
g++ -std=c++11 -pedantic -Wno-long-long -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -I/usr/include -I/«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/alignment/ -I../pbdata -I../hdf -I/usr/include/hdf5/serial -fPIC -c /«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/alignment/datastructures/alignment/AlignmentStats.cpp -o AlignmentStats.shared.o
g++ -std=c++11 -pedantic -Wno-long-long -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -I/usr/include -I/«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/alignment/ -I../pbdata -I../hdf -I/usr/include/hdf5/serial -fPIC -c /«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/alignment/datastructures/alignment/CmpFile.cpp -o CmpFile.shared.o
g++ -std=c++11 -pedantic -Wno-long-long -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -I/usr/include -I/«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/alignment/ -I../pbdata -I../hdf -I/usr/include/hdf5/serial -fPIC -c /«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/alignment/datastructures/alignment/FilterCriteria.cpp -o FilterCriteria.shared.o
g++ -std=c++11 -pedantic -Wno-long-long -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -I/usr/include -I/«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/alignment/ -I../pbdata -I../hdf -I/usr/include/hdf5/serial -fPIC -c /«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/alignment/datastructures/alignment/SAMToAlignmentCandidateAdapter.cpp -o SAMToAlignmentCandidateAdapter.shared.o
g++ -std=c++11 -pedantic -Wno-long-long -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -I/usr/include -I/«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/alignment/ -I../pbdata -I../hdf -I/usr/include/hdf5/serial -fPIC -c /«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/alignment/datastructures/alignmentset/SAMQVConversion.cpp -o SAMQVConversion.shared.o
g++ -std=c++11 -pedantic -Wno-long-long -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -I/usr/include -I/«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/alignment/ -I../pbdata -I../hdf -I/usr/include/hdf5/serial -fPIC -c /«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/alignment/datastructures/alignmentset/SAMSupplementalQVList.cpp -o SAMSupplementalQVList.shared.o
g++ -std=c++11 -pedantic -Wno-long-long -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -I/usr/include -I/«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/alignment/ -I../pbdata -I../hdf -I/usr/include/hdf5/serial -fPIC -c /«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/alignment/datastructures/anchoring/AnchorParameters.cpp -o AnchorParameters.shared.o
g++ -std=c++11 -pedantic -Wno-long-long -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -I/usr/include -I/«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/alignment/ -I../pbdata -I../hdf -I/usr/include/hdf5/serial -fPIC -c /«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/alignment/datastructures/anchoring/ClusterList.cpp -o ClusterList.shared.o
g++ -std=c++11 -pedantic -Wno-long-long -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -I/usr/include -I/«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/alignment/ -I../pbdata -I../hdf -I/usr/include/hdf5/serial -fPIC -c /«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/alignment/datastructures/anchoring/MatchPos.cpp -o MatchPos.shared.o
g++ -std=c++11 -pedantic -Wno-long-long -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -I/usr/include -I/«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/alignment/ -I../pbdata -I../hdf -I/usr/include/hdf5/serial -fPIC -c /«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/alignment/datastructures/anchoring/WeightedInterval.cpp -o WeightedInterval.shared.o
g++ -std=c++11 -pedantic -Wno-long-long -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -I/usr/include -I/«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/alignment/ -I../pbdata -I../hdf -I/usr/include/hdf5/serial -fPIC -c /«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/alignment/files/BaseSequenceIO.cpp -o BaseSequenceIO.shared.o
g++ -std=c++11 -pedantic -Wno-long-long -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -I/usr/include -I/«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/alignment/ -I../pbdata -I../hdf -I/usr/include/hdf5/serial -fPIC -c /«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/alignment/files/CCSIterator.cpp -o CCSIterator.shared.o
g++ -std=c++11 -pedantic -Wno-long-long -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -I/usr/include -I/«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/alignment/ -I../pbdata -I../hdf -I/usr/include/hdf5/serial -fPIC -c /«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/alignment/files/FragmentCCSIterator.cpp -o FragmentCCSIterator.shared.o
g++ -std=c++11 -pedantic -Wno-long-long -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -I/usr/include -I/«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/alignment/ -I../pbdata -I../hdf -I/usr/include/hdf5/serial -fPIC -c /«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/alignment/files/ReaderAgglomerate.cpp -o ReaderAgglomerate.shared.o
g++ -std=c++11 -pedantic -Wno-long-long -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -I/usr/include -I/«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/alignment/ -I../pbdata -I../hdf -I/usr/include/hdf5/serial -fPIC -c /«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/alignment/format/CompareSequencesPrinter.cpp -o CompareSequencesPrinter.shared.o
g++ -std=c++11 -pedantic -Wno-long-long -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -I/usr/include -I/«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/alignment/ -I../pbdata -I../hdf -I/usr/include/hdf5/serial -fPIC -c /«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/alignment/format/IntervalPrinter.cpp -o IntervalPrinter.shared.o
g++ -std=c++11 -pedantic -Wno-long-long -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -I/usr/include -I/«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/alignment/ -I../pbdata -I../hdf -I/usr/include/hdf5/serial -fPIC -c /«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/alignment/format/SAMHeaderPrinter.cpp -o SAMHeaderPrinter.shared.o
g++ -std=c++11 -pedantic -Wno-long-long -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -I/usr/include -I/«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/alignment/ -I../pbdata -I../hdf -I/usr/include/hdf5/serial -fPIC -c /«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/alignment/format/SAMPrinter.cpp -o SAMPrinter.shared.o
g++ -std=c++11 -pedantic -Wno-long-long -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -I/usr/include -I/«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/alignment/ -I../pbdata -I../hdf -I/usr/include/hdf5/serial -fPIC -c /«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/alignment/format/SummaryPrinter.cpp -o SummaryPrinter.shared.o
g++ -std=c++11 -pedantic -Wno-long-long -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -I/usr/include -I/«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/alignment/ -I../pbdata -I../hdf -I/usr/include/hdf5/serial -fPIC -c /«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/alignment/qvs/QualityValueProfile.cpp -o QualityValueProfile.shared.o
g++ -std=c++11 -pedantic -Wno-long-long -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -I/usr/include -I/«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/alignment/ -I../pbdata -I../hdf -I/usr/include/hdf5/serial -fPIC -c /«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/alignment/simulator/ContextSample.cpp -o ContextSample.shared.o
g++ -std=c++11 -pedantic -Wno-long-long -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -I/usr/include -I/«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/alignment/ -I../pbdata -I../hdf -I/usr/include/hdf5/serial -fPIC -c /«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/alignment/simulator/ContextSet.cpp -o ContextSet.shared.o
g++ -std=c++11 -pedantic -Wno-long-long -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -I/usr/include -I/«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/alignment/ -I../pbdata -I../hdf -I/usr/include/hdf5/serial -fPIC -c /«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/alignment/simulator/LengthHistogram.cpp -o LengthHistogram.shared.o
g++ -std=c++11 -pedantic -Wno-long-long -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -I/usr/include -I/«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/alignment/ -I../pbdata -I../hdf -I/usr/include/hdf5/serial -fPIC -c /«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/alignment/simulator/QualitySample.cpp -o QualitySample.shared.o
g++ -std=c++11 -pedantic -Wno-long-long -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -I/usr/include -I/«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/alignment/ -I../pbdata -I../hdf -I/usr/include/hdf5/serial -fPIC -c /«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/alignment/statistics/LookupAnchorDistribution.cpp -o LookupAnchorDistribution.shared.o
g++ -std=c++11 -pedantic -Wno-long-long -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -I/usr/include -I/«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/alignment/ -I../pbdata -I../hdf -I/usr/include/hdf5/serial -fPIC -c /«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/alignment/statistics/StatUtils.cpp -o StatUtils.shared.o
g++ -std=c++11 -pedantic -Wno-long-long -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -I/usr/include -I/«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/alignment/ -I../pbdata -I../hdf -I/usr/include/hdf5/serial -fPIC -c /«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/alignment/statistics/cdfs.cpp -o cdfs.shared.o
g++ -std=c++11 -pedantic -Wno-long-long -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -I/usr/include -I/«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/alignment/ -I../pbdata -I../hdf -I/usr/include/hdf5/serial -fPIC -c /«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/alignment/statistics/pdfs.cpp -o pdfs.shared.o
g++ -std=c++11 -pedantic -Wno-long-long -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -I/usr/include -I/«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/alignment/ -I../pbdata -I../hdf -I/usr/include/hdf5/serial -fPIC -c /«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/alignment/tuples/BaseTuple.cpp -o BaseTuple.shared.o
g++ -std=c++11 -pedantic -Wno-long-long -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -I/usr/include -I/«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/alignment/ -I../pbdata -I../hdf -I/usr/include/hdf5/serial -fPIC -c /«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/alignment/tuples/DNATuple.cpp -o DNATuple.shared.o
g++ -std=c++11 -pedantic -Wno-long-long -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -I/usr/include -I/«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/alignment/ -I../pbdata -I../hdf -I/usr/include/hdf5/serial -fPIC -c /«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/alignment/tuples/TupleMetrics.cpp -o TupleMetrics.shared.o
g++ -std=c++11 -pedantic -Wno-long-long -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -I/usr/include -I/«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/alignment/ -I../pbdata -I../hdf -I/usr/include/hdf5/serial -fPIC -c /«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/alignment/utils/FileOfFileNames.cpp -o FileOfFileNames.shared.o
g++ -std=c++11 -pedantic -Wno-long-long -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -I/usr/include -I/«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/alignment/ -I../pbdata -I../hdf -I/usr/include/hdf5/serial -fPIC -c /«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/alignment/utils/FileUtils.cpp -o FileUtils.shared.o
g++ -std=c++11 -pedantic -Wno-long-long -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -I/usr/include -I/«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/alignment/ -I../pbdata -I../hdf -I/usr/include/hdf5/serial -fPIC -c /«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/alignment/utils/LogUtils.cpp -o LogUtils.shared.o
g++ -std=c++11 -pedantic -Wno-long-long -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -I/usr/include -I/«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/alignment/ -I../pbdata -I../hdf -I/usr/include/hdf5/serial -fPIC -c /«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/alignment/utils/PhredUtils.cpp -o PhredUtils.shared.o
g++ -std=c++11 -pedantic -Wno-long-long -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -I/usr/include -I/«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/alignment/ -I../pbdata -I../hdf -I/usr/include/hdf5/serial -fPIC -c /«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/alignment/utils/RangeUtils.cpp -o RangeUtils.shared.o
g++ -std=c++11 -pedantic -Wno-long-long -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -I/usr/include -I/«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/alignment/ -I../pbdata -I../hdf -I/usr/include/hdf5/serial -fPIC -c /«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/alignment/utils/RegionUtils.cpp -o RegionUtils.shared.o
g++ -std=c++11 -pedantic -Wno-long-long -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -I/usr/include -I/«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/alignment/ -I../pbdata -I../hdf -I/usr/include/hdf5/serial -fPIC -c /«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/alignment/utils/TimeUtils.cpp -o TimeUtils.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 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 TimeUtils.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 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 TimeUtils.shared.o -lpbdata -lpbihdf
make[3]: Leaving directory '/«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/alignment'
make[2]: Leaving directory '/«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf'
make[1]: Leaving directory '/«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf'
   debian/rules override_dh_auto_test
make[1]: Entering directory '/«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf'
/usr/bin/make -k gtest
make[2]: Entering directory '/«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf'
/usr/bin/make -C /«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf//unittest gtest
make[3]: Entering directory '/«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/unittest'
g++ -O3 -std=c++11 -Wno-div-by-zero  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security  -D_FORTIFY_SOURCE=2 -I/usr/include -I/«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/unittest/ -I/usr/include -I/usr/src/gtest -I../alignment -I../hdf -I../pbdata -I/usr/include/hdf5/serial  -c -o gtest-all.o /usr/src/gtest/src/gtest-all.cc
g++ -O3 -std=c++11 -Wno-div-by-zero  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security  -D_FORTIFY_SOURCE=2 -I/usr/include -I/«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/unittest/ -I/usr/include -I/usr/src/gtest -I../alignment -I../hdf -I../pbdata -I/usr/include/hdf5/serial  -c -o gtest_main.o /usr/src/gtest/src/gtest_main.cc
g++ -O3 -std=c++11 -Wno-div-by-zero  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security  -D_FORTIFY_SOURCE=2 -I/usr/include -I/«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/unittest/ -I/usr/include -I/usr/src/gtest -I../alignment -I../hdf -I../pbdata -I/usr/include/hdf5/serial  -c -o CCSSequence_gtest.o /«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/unittest/pbdata/CCSSequence_gtest.cpp
g++ -O3 -std=c++11 -Wno-div-by-zero  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security  -D_FORTIFY_SOURCE=2 -I/usr/include -I/«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/unittest/ -I/usr/include -I/usr/src/gtest -I../alignment -I../hdf -I../pbdata -I/usr/include/hdf5/serial  -c -o SeqUtils_gtest.o /«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/unittest/pbdata/SeqUtils_gtest.cpp
g++ -O3 -std=c++11 -Wno-div-by-zero  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security  -D_FORTIFY_SOURCE=2 -I/usr/include -I/«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/unittest/ -I/usr/include -I/usr/src/gtest -I../alignment -I../hdf -I../pbdata -I/usr/include/hdf5/serial  -c -o SMRTSequence_gtest.o /«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/unittest/pbdata/SMRTSequence_gtest.cpp
g++ -O3 -std=c++11 -Wno-div-by-zero  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security  -D_FORTIFY_SOURCE=2 -I/usr/include -I/«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/unittest/ -I/usr/include -I/usr/src/gtest -I../alignment -I../hdf -I../pbdata -I/usr/include/hdf5/serial  -c -o defs_gtest.o /«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/unittest/pbdata/defs_gtest.cpp
g++ -O3 -std=c++11 -Wno-div-by-zero  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security  -D_FORTIFY_SOURCE=2 -I/usr/include -I/«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/unittest/ -I/usr/include -I/usr/src/gtest -I../alignment -I../hdf -I../pbdata -I/usr/include/hdf5/serial  -c -o NucConversion_gtest.o /«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/unittest/pbdata/NucConversion_gtest.cpp
g++ -O3 -std=c++11 -Wno-div-by-zero  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security  -D_FORTIFY_SOURCE=2 -I/usr/include -I/«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/unittest/ -I/usr/include -I/usr/src/gtest -I../alignment -I../hdf -I../pbdata -I/usr/include/hdf5/serial  -c -o DNASequence_gtest.o /«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/unittest/pbdata/DNASequence_gtest.cpp
g++ -O3 -std=c++11 -Wno-div-by-zero  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security  -D_FORTIFY_SOURCE=2 -I/usr/include -I/«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/unittest/ -I/usr/include -I/usr/src/gtest -I../alignment -I../hdf -I../pbdata -I/usr/include/hdf5/serial  -c -o VectorUtils_gtest.o /«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/unittest/pbdata/VectorUtils_gtest.cpp
g++ -O3 -std=c++11 -Wno-div-by-zero  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security  -D_FORTIFY_SOURCE=2 -I/usr/include -I/«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/unittest/ -I/usr/include -I/usr/src/gtest -I../alignment -I../hdf -I../pbdata -I/usr/include/hdf5/serial  -c -o ScanData_gtest.o /«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/unittest/pbdata/ScanData_gtest.cpp
g++ -O3 -std=c++11 -Wno-div-by-zero  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security  -D_FORTIFY_SOURCE=2 -I/usr/include -I/«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/unittest/ -I/usr/include -I/usr/src/gtest -I../alignment -I../hdf -I../pbdata -I/usr/include/hdf5/serial  -c -o ChangeListID_gtest.o /«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/unittest/pbdata/ChangeListID_gtest.cpp
g++ -O3 -std=c++11 -Wno-div-by-zero  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security  -D_FORTIFY_SOURCE=2 -I/usr/include -I/«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/unittest/ -I/usr/include -I/usr/src/gtest -I../alignment -I../hdf -I../pbdata -I/usr/include/hdf5/serial  -c -o FASTQReader_gtest.o /«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/unittest/pbdata/FASTQReader_gtest.cpp
g++ -O3 -std=c++11 -Wno-div-by-zero  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security  -D_FORTIFY_SOURCE=2 -I/usr/include -I/«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/unittest/ -I/usr/include -I/usr/src/gtest -I../alignment -I../hdf -I../pbdata -I/usr/include/hdf5/serial  -c -o utils_gtest.o /«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/unittest/pbdata/utils_gtest.cpp
g++ -O3 -std=c++11 -Wno-div-by-zero  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security  -D_FORTIFY_SOURCE=2 -I/usr/include -I/«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/unittest/ -I/usr/include -I/usr/src/gtest -I../alignment -I../hdf -I../pbdata -I/usr/include/hdf5/serial  -c -o FASTASequence_gtest.o /«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/unittest/pbdata/FASTASequence_gtest.cpp
g++ -O3 -std=c++11 -Wno-div-by-zero  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security  -D_FORTIFY_SOURCE=2 -I/usr/include -I/«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/unittest/ -I/usr/include -I/usr/src/gtest -I../alignment -I../hdf -I../pbdata -I/usr/include/hdf5/serial  -c -o FASTAReader_gtest.o /«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/unittest/pbdata/FASTAReader_gtest.cpp
g++ -O3 -std=c++11 -Wno-div-by-zero  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security  -D_FORTIFY_SOURCE=2 -I/usr/include -I/«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/unittest/ -I/usr/include -I/usr/src/gtest -I../alignment -I../hdf -I../pbdata -I/usr/include/hdf5/serial  -c -o StringUtils_gtest.o /«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/unittest/pbdata/StringUtils_gtest.cpp
g++ -O3 -std=c++11 -Wno-div-by-zero  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security  -D_FORTIFY_SOURCE=2 -I/usr/include -I/«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/unittest/ -I/usr/include -I/usr/src/gtest -I../alignment -I../hdf -I../pbdata -I/usr/include/hdf5/serial  -c -o SMRTTitle_gtest.o /«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/unittest/pbdata/utils/SMRTTitle_gtest.cpp
g++ -O3 -std=c++11 -Wno-div-by-zero  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security  -D_FORTIFY_SOURCE=2 -I/usr/include -I/«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/unittest/ -I/usr/include -I/usr/src/gtest -I../alignment -I../hdf -I../pbdata -I/usr/include/hdf5/serial  -c -o TitleTable_gtest.o /«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/unittest/pbdata/metagenome/TitleTable_gtest.cpp
g++ -O3 -std=c++11 -Wno-div-by-zero  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security  -D_FORTIFY_SOURCE=2 -I/usr/include -I/«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/unittest/ -I/usr/include -I/usr/src/gtest -I../alignment -I../hdf -I../pbdata -I/usr/include/hdf5/serial  -c -o RefInfo_gtest.o /«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/unittest/pbdata/saf/RefInfo_gtest.cpp
g++ -O3 -std=c++11 -Wno-div-by-zero  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security  -D_FORTIFY_SOURCE=2 -I/usr/include -I/«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/unittest/ -I/usr/include -I/usr/src/gtest -I../alignment -I../hdf -I../pbdata -I/usr/include/hdf5/serial  -c -o AlnGroup_gtest.o /«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/unittest/pbdata/saf/AlnGroup_gtest.cpp
g++ -O3 -std=c++11 -Wno-div-by-zero  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security  -D_FORTIFY_SOURCE=2 -I/usr/include -I/«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/unittest/ -I/usr/include -I/usr/src/gtest -I../alignment -I../hdf -I../pbdata -I/usr/include/hdf5/serial  -c -o MovieInfo_gtest.o /«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/unittest/pbdata/saf/MovieInfo_gtest.cpp
g++ -O3 -std=c++11 -Wno-div-by-zero  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security  -D_FORTIFY_SOURCE=2 -I/usr/include -I/«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/unittest/ -I/usr/include -I/usr/src/gtest -I../alignment -I../hdf -I../pbdata -I/usr/include/hdf5/serial  -c -o RegionAnnotations_gtest.o /«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/unittest/pbdata/reads/RegionAnnotations_gtest.cpp
g++ -O3 -std=c++11 -Wno-div-by-zero  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security  -D_FORTIFY_SOURCE=2 -I/usr/include -I/«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/unittest/ -I/usr/include -I/usr/src/gtest -I../alignment -I../hdf -I../pbdata -I/usr/include/hdf5/serial  -c -o ReadType_gtest.o /«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/unittest/pbdata/reads/ReadType_gtest.cpp
g++ -O3 -std=c++11 -Wno-div-by-zero  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security  -D_FORTIFY_SOURCE=2 -I/usr/include -I/«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/unittest/ -I/usr/include -I/usr/src/gtest -I../alignment -I../hdf -I../pbdata -I/usr/include/hdf5/serial  -c -o RegionTypeMap_gtest.o /«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/unittest/pbdata/reads/RegionTypeMap_gtest.cpp
g++ -O3 -std=c++11 -Wno-div-by-zero  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security  -D_FORTIFY_SOURCE=2 -I/usr/include -I/«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/unittest/ -I/usr/include -I/usr/src/gtest -I../alignment -I../hdf -I../pbdata -I/usr/include/hdf5/serial  -c -o QualityValueVector_gtest.o /«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/unittest/pbdata/qvs/QualityValueVector_gtest.cpp
g++ -O3 -std=c++11 -Wno-div-by-zero  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security  -D_FORTIFY_SOURCE=2 -I/usr/include -I/«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/unittest/ -I/usr/include -I/usr/src/gtest -I../alignment -I../hdf -I../pbdata -I/usr/include/hdf5/serial  -c -o HDFScanDataReader_gtest.o /«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/unittest/hdf/HDFScanDataReader_gtest.cpp
g++ -O3 -std=c++11 -Wno-div-by-zero  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security  -D_FORTIFY_SOURCE=2 -I/usr/include -I/«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/unittest/ -I/usr/include -I/usr/src/gtest -I../alignment -I../hdf -I../pbdata -I/usr/include/hdf5/serial  -c -o HDF2DArray_gtest.o /«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/unittest/hdf/HDF2DArray_gtest.cpp
g++ -O3 -std=c++11 -Wno-div-by-zero  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security  -D_FORTIFY_SOURCE=2 -I/usr/include -I/«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/unittest/ -I/usr/include -I/usr/src/gtest -I../alignment -I../hdf -I../pbdata -I/usr/include/hdf5/serial  -c -o HDFScanDataWriter_gtest.o /«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/unittest/hdf/HDFScanDataWriter_gtest.cpp
g++ -O3 -std=c++11 -Wno-div-by-zero  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security  -D_FORTIFY_SOURCE=2 -I/usr/include -I/«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/unittest/ -I/usr/include -I/usr/src/gtest -I../alignment -I../hdf -I../pbdata -I/usr/include/hdf5/serial  -c -o HDFCCSReader_gtest.o /«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/unittest/hdf/HDFCCSReader_gtest.cpp
g++ -O3 -std=c++11 -Wno-div-by-zero  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security  -D_FORTIFY_SOURCE=2 -I/usr/include -I/«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/unittest/ -I/usr/include -I/usr/src/gtest -I../alignment -I../hdf -I../pbdata -I/usr/include/hdf5/serial  -c -o HDFUtils_gtest.o /«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/unittest/hdf/HDFUtils_gtest.cpp
g++ -O3 -std=c++11 -Wno-div-by-zero  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security  -D_FORTIFY_SOURCE=2 -I/usr/include -I/«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/unittest/ -I/usr/include -I/usr/src/gtest -I../alignment -I../hdf -I../pbdata -I/usr/include/hdf5/serial  -c -o HDFPlsReader_gtest.o /«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/unittest/hdf/HDFPlsReader_gtest.cpp
g++ -O3 -std=c++11 -Wno-div-by-zero  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security  -D_FORTIFY_SOURCE=2 -I/usr/include -I/«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/unittest/ -I/usr/include -I/usr/src/gtest -I../alignment -I../hdf -I../pbdata -I/usr/include/hdf5/serial  -c -o HDFBasReader_gtest.o /«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/unittest/hdf/HDFBasReader_gtest.cpp
g++ -O3 -std=c++11 -Wno-div-by-zero  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security  -D_FORTIFY_SOURCE=2 -I/usr/include -I/«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/unittest/ -I/usr/include -I/usr/src/gtest -I../alignment -I../hdf -I../pbdata -I/usr/include/hdf5/serial  -c -o HDFZMWReader_gtest.o /«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/unittest/hdf/HDFZMWReader_gtest.cpp
g++ -O3 -std=c++11 -Wno-div-by-zero  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security  -D_FORTIFY_SOURCE=2 -I/usr/include -I/«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/unittest/ -I/usr/include -I/usr/src/gtest -I../alignment -I../hdf -I../pbdata -I/usr/include/hdf5/serial  -c -o RangeUtils_gtest.o /«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/unittest/alignment/utils/RangeUtils_gtest.cpp
g++ -O3 -std=c++11 -Wno-div-by-zero  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security  -D_FORTIFY_SOURCE=2 -I/usr/include -I/«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/unittest/ -I/usr/include -I/usr/src/gtest -I../alignment -I../hdf -I../pbdata -I/usr/include/hdf5/serial  -c -o RegionUtils_gtest.o /«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/unittest/alignment/utils/RegionUtils_gtest.cpp
g++ -O3 -std=c++11 -Wno-div-by-zero  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security  -D_FORTIFY_SOURCE=2 -I/usr/include -I/«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/unittest/ -I/usr/include -I/usr/src/gtest -I../alignment -I../hdf -I../pbdata -I/usr/include/hdf5/serial  -c -o AlignmentMap_gtest.o /«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/unittest/alignment/datastructures/alignment/AlignmentMap_gtest.cpp
g++ -O3 -std=c++11 -Wno-div-by-zero  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security  -D_FORTIFY_SOURCE=2 -I/usr/include -I/«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/unittest/ -I/usr/include -I/usr/src/gtest -I../alignment -I../hdf -I../pbdata -I/usr/include/hdf5/serial  -c -o CmpIndexedStringTable_gtest.o /«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/unittest/alignment/datastructures/alignment/CmpIndexedStringTable_gtest.cpp
g++ -O3 -std=c++11 -Wno-div-by-zero  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security  -D_FORTIFY_SOURCE=2 -I/usr/include -I/«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/unittest/ -I/usr/include -I/usr/src/gtest -I../alignment -I../hdf -I../pbdata -I/usr/include/hdf5/serial  -c -o CCSIterator_gtest.o /«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/unittest/alignment/files/CCSIterator_gtest.cpp
g++ -O3 -std=c++11 -Wno-div-by-zero  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security  -D_FORTIFY_SOURCE=2 -I/usr/include -I/«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/unittest/ -I/usr/include -I/usr/src/gtest -I../alignment -I../hdf -I../pbdata -I/usr/include/hdf5/serial  -c -o FragmentCCSIterator_other_gtest.o /«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/unittest/alignment/files/FragmentCCSIterator_other_gtest.cpp
g++ -O3 -std=c++11 -Wno-div-by-zero  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security  -D_FORTIFY_SOURCE=2 -I/usr/include -I/«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/unittest/ -I/usr/include -I/usr/src/gtest -I../alignment -I../hdf -I../pbdata -I/usr/include/hdf5/serial  -c -o FragmentCCSIterator_gtest.o /«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/unittest/alignment/files/FragmentCCSIterator_gtest.cpp
g++ -L/usr/lib -L../alignment -L../hdf -L../pbdata -L/usr/lib/arm-linux-gnueabihf/hdf5/serial  -Wl,-z,relro   gtest-all.o gtest_main.o CCSSequence_gtest.o SeqUtils_gtest.o SMRTSequence_gtest.o defs_gtest.o NucConversion_gtest.o DNASequence_gtest.o VectorUtils_gtest.o ScanData_gtest.o ChangeListID_gtest.o FASTQReader_gtest.o utils_gtest.o FASTASequence_gtest.o FASTAReader_gtest.o StringUtils_gtest.o SMRTTitle_gtest.o TitleTable_gtest.o RefInfo_gtest.o AlnGroup_gtest.o MovieInfo_gtest.o RegionAnnotations_gtest.o ReadType_gtest.o RegionTypeMap_gtest.o QualityValueVector_gtest.o HDFScanDataReader_gtest.o HDF2DArray_gtest.o HDFScanDataWriter_gtest.o HDFCCSReader_gtest.o HDFUtils_gtest.o HDFPlsReader_gtest.o HDFBasReader_gtest.o HDFZMWReader_gtest.o RangeUtils_gtest.o RegionUtils_gtest.o AlignmentMap_gtest.o CmpIndexedStringTable_gtest.o CCSIterator_gtest.o FragmentCCSIterator_other_gtest.o FragmentCCSIterator_gtest.o -lblasr -lpbihdf -lpbdata -lhts -lhdf5_cpp -lhdf5 -lz -lpthread -ldl -lrt  -o test-runner
LD_LIBRARY_PATH=/usr/lib:../alignment:../hdf:../pbdata:/usr/lib/arm-linux-gnueabihf/hdf5/serial ./test-runner --gtest_output=xml:./xml/all.xml
Running main() from gtest_main.cc
[==========] Running 89 tests from 39 test cases.
[----------] Global test environment set-up.
[----------] 2 tests from CCSSequenceTest
[ RUN      ] CCSSequenceTest.Print
[       OK ] CCSSequenceTest.Print (1 ms)
[ RUN      ] CCSSequenceTest.Explode
[       OK ] CCSSequenceTest.Explode (0 ms)
[----------] 2 tests from CCSSequenceTest (1 ms total)

[----------] 3 tests from SeqUtils
[ RUN      ] SeqUtils.OnlyACTG
[       OK ] SeqUtils.OnlyACTG (0 ms)
[ RUN      ] SeqUtils.CountMasked
[       OK ] SeqUtils.CountMasked (0 ms)
[ RUN      ] SeqUtils.CountNotMasked
[       OK ] SeqUtils.CountNotMasked (0 ms)
[----------] 3 tests from SeqUtils (0 ms total)

[----------] 2 tests from SMRTSequenceTest
[ RUN      ] SMRTSequenceTest.Print
[       OK ] SMRTSequenceTest.Print (0 ms)
[ RUN      ] SMRTSequenceTest.GetDeletionQV
[       OK ] SMRTSequenceTest.GetDeletionQV (0 ms)
[----------] 2 tests from SMRTSequenceTest (1 ms total)

[----------] 3 tests from DefsTest
[ RUN      ] DefsTest.MIN
[       OK ] DefsTest.MIN (0 ms)
[ RUN      ] DefsTest.MAX
[       OK ] DefsTest.MAX (0 ms)
[ RUN      ] DefsTest.SWAP
[       OK ] DefsTest.SWAP (0 ms)
[----------] 3 tests from DefsTest (1 ms total)

[----------] 7 tests from NucConversion
[ RUN      ] NucConversion.ASCIITo2BIT
[       OK ] NucConversion.ASCIITo2BIT (0 ms)
[ RUN      ] NucConversion.ASCIITo3BIT
[       OK ] NucConversion.ASCIITo3BIT (0 ms)
[ RUN      ] NucConversion.ISACTG
[       OK ] NucConversion.ISACTG (0 ms)
[ RUN      ] NucConversion.ThreeBitToASCII
[       OK ] NucConversion.ThreeBitToASCII (0 ms)
[ RUN      ] NucConversion.AllToUpper
[       OK ] NucConversion.AllToUpper (0 ms)
[ RUN      ] NucConversion.AllToLower
[       OK ] NucConversion.AllToLower (1 ms)
[ RUN      ] NucConversion.ReverseComplementNuc
[       OK ] NucConversion.ReverseComplementNuc (0 ms)
[----------] 7 tests from NucConversion (2 ms total)

[----------] 7 tests from DNASequenceTest
[ RUN      ] DNASequenceTest.Constructor
[       OK ] DNASequenceTest.Constructor (0 ms)
[ RUN      ] DNASequenceTest.Append
[       OK ] DNASequenceTest.Append (0 ms)
[ RUN      ] DNASequenceTest.TakeOwnership
[       OK ] DNASequenceTest.TakeOwnership (0 ms)
[ RUN      ] DNASequenceTest.ShallowCopy
[       OK ] DNASequenceTest.ShallowCopy (0 ms)
[ RUN      ] DNASequenceTest.Copy
[       OK ] DNASequenceTest.Copy (0 ms)
[ RUN      ] DNASequenceTest.Allocate
[       OK ] DNASequenceTest.Allocate (0 ms)
[ RUN      ] DNASequenceTest.ReferenceSubstring
[       OK ] DNASequenceTest.ReferenceSubstring (0 ms)
[----------] 7 tests from DNASequenceTest (2 ms total)

[----------] 1 test from VectorUtils
[ RUN      ] VectorUtils.ClearMemory
[       OK ] VectorUtils.ClearMemory (0 ms)
[----------] 1 test from VectorUtils (1 ms total)

[----------] 1 test from ScanDataTest
[ RUN      ] ScanDataTest.GetMovieName
[       OK ] ScanDataTest.GetMovieName (0 ms)
[----------] 1 test from ScanDataTest (0 ms total)

[----------] 1 test from ChangeListID
[ RUN      ] ChangeListID.GetVersion
[       OK ] ChangeListID.GetVersion (1 ms)
[----------] 1 test from ChangeListID (1 ms total)

[----------] 1 test from FASTQReaderTest
[ RUN      ] FASTQReaderTest.GetNext
Could not open FASTA file /mnt/secondary-siv/testdata/BlasrTestData/utest/data/ccs_P4-C2/m130328_211423_ethan_c100499512550000001823070408081371_s1_p0.fastq
make[3]: *** [gtest] Error 1
makefile:106: recipe for target 'gtest' failed
make[3]: Leaving directory '/«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf/unittest'
make[2]: *** [gtest] Error 2
makefile:25: recipe for target 'gtest' failed
make[2]: Leaving directory '/«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf'
make[1]: [override_dh_auto_test] Error 2 (ignored)
debian/rules:23: recipe for target 'override_dh_auto_test' failed
make[1]: Leaving directory '/«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf'
 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 '/«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf'
mkdir -p debian/libpbdata-dev/usr/include/pbdata
cp -r pbdata/* debian/libpbdata-dev/usr/include/pbdata
mkdir -p debian/libpbihdf-dev/usr/include/pbihdf
cp -r hdf/* debian/libpbihdf-dev/usr/include/pbihdf
mkdir -p debian/libblasr-dev/usr/include/blasr
cp -r alignment/* debian/libblasr-dev/usr/include/blasr
find -L debian/*/usr/include/ -type f -regextype posix-egrep -not -regex '.*(hpp|h)$' -delete
find debian/*/usr/include/ -name "*.mk" -delete
for library in debian/lib*.install.in;				\
do								\
	sed 's/@MULTIARCH@/arm-linux-gnueabihf/g'		\
	    $library > debian/$(basename $library .in);	\
done
dh_auto_install
make[1]: Leaving directory '/«BUILDDIR»/pbseqlib-0~20151014+gitbe5d1bf'
   dh_install -a -O--parallel
   dh_installdocs -a -O--parallel
   dh_installchangelogs -a -O--parallel
   dh_lintian -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: debian/libpbdata/usr/lib/arm-linux-gnueabihf/pbdata/libpbdata.so contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: couldn't find library libpbdata.so needed by debian/libpbihdf/usr/lib/arm-linux-gnueabihf/pbihdf/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/blasr/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/blasr/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
   dh_md5sums -a -O--parallel
   dh_builddeb -a -O--parallel
dpkg-deb: building package 'libpbdata-dev' in '../libpbdata-dev_0~20151014+gitbe5d1bf-2_armhf.deb'.
dpkg-deb: building package 'libpbdata' in '../libpbdata_0~20151014+gitbe5d1bf-2_armhf.deb'.
dpkg-deb: building package 'libpbihdf-dev' in '../libpbihdf-dev_0~20151014+gitbe5d1bf-2_armhf.deb'.
dpkg-deb: building package 'libpbihdf' in '../libpbihdf_0~20151014+gitbe5d1bf-2_armhf.deb'.
dpkg-deb: building package 'libblasr-dev' in '../libblasr-dev_0~20151014+gitbe5d1bf-2_armhf.deb'.
dpkg-deb: building package 'libblasr' in '../libblasr_0~20151014+gitbe5d1bf-2_armhf.deb'.
 dpkg-genchanges -B -mRaspbian wandboard test autobuilder <root@raspbian.org> >../pbseqlib_0~20151014+gitbe5d1bf-2_armhf.changes
dpkg-genchanges: binary-only arch-specific upload (source code and arch-indep packages not included)
 dpkg-source --after-build pbseqlib-0~20151014+gitbe5d1bf
dpkg-buildpackage: binary-only upload (no source included)
────────────────────────────────────────────────────────────────────────────────
Build finished at 20151219-2115

Finished
────────

I: Built successfully

┌──────────────────────────────────────────────────────────────────────────────┐
│ Post Build Chroot                                                            │
└──────────────────────────────────────────────────────────────────────────────┘


┌──────────────────────────────────────────────────────────────────────────────┐
│ Changes                                                                      │
└──────────────────────────────────────────────────────────────────────────────┘


pbseqlib_0~20151014+gitbe5d1bf-2_armhf.changes:
───────────────────────────────────────────────

Format: 1.8
Date: Sun, 13 Dec 2015 19:37:03 -0800
Source: pbseqlib
Binary: libpbseq libpbseq-dev libpbdata-dev libpbdata libpbihdf-dev libpbihdf libblasr-dev libblasr
Architecture: armhf
Version: 0~20151014+gitbe5d1bf-2
Distribution: stretch-staging
Urgency: medium
Maintainer: Raspbian wandboard test autobuilder <root@raspbian.org>
Changed-By: Afif Elghraoui <afif@ghraoui.name>
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)
Closes: 807583
Changes:
 pbseqlib (0~20151014+gitbe5d1bf-2) unstable; urgency=medium
 .
   * Add package interdependencies.
   * Correct the dependencies of libpbseq-dev
   * Set up some build-time tests
   * Fix build on 32-bit architectures (Closes: #807583)
   * Drop symlinks from -dev packages
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 187af4abaf17cd2cd0c80a3cfc735842 101828 libs optional libpbihdf_0~20151014+gitbe5d1bf-2_armhf.deb

┌──────────────────────────────────────────────────────────────────────────────┐
│ Package contents                                                             │
└──────────────────────────────────────────────────────────────────────────────┘


libblasr-dev_0~20151014+gitbe5d1bf-2_armhf.deb
──────────────────────────────────────────────

 new debian package, version 2.0.
 size 1613526 bytes: control archive=5642 bytes.
     742 bytes,    18 lines      control              
   14438 bytes,   166 lines      md5sums              
 Package: libblasr-dev
 Source: pbseqlib
 Version: 0~20151014+gitbe5d1bf-2
 Architecture: armhf
 Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
 Installed-Size: 6136
 Depends: libblasr (= 0~20151014+gitbe5d1bf-2)
 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.

drwxr-xr-x root/root         0 2015-12-19 21:14 ./
drwxr-xr-x root/root         0 2015-12-19 21:14 ./usr/
drwxr-xr-x root/root         0 2015-12-19 21:14 ./usr/include/
drwxr-xr-x root/root         0 2015-12-19 21:14 ./usr/include/blasr/
-rw-r--r-- root/root      2785 2015-12-19 21:14 ./usr/include/blasr/MappingMetrics.hpp
drwxr-xr-x root/root         0 2015-12-19 21:14 ./usr/include/blasr/algorithms/
drwxr-xr-x root/root         0 2015-12-19 21:14 ./usr/include/blasr/algorithms/alignment/
-rw-r--r-- root/root     21177 2015-12-19 21:14 ./usr/include/blasr/algorithms/alignment/AffineGuidedAlign.hpp
-rw-r--r-- root/root     14134 2015-12-19 21:14 ./usr/include/blasr/algorithms/alignment/AffineKBandAlign.hpp
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libblasr_0~20151014+gitbe5d1bf-2_armhf.deb
──────────────────────────────────────────

 new debian package, version 2.0.
 size 786466 bytes: control archive=790 bytes.
     771 bytes,    17 lines      control              
     295 bytes,     4 lines      md5sums              
 Package: libblasr
 Source: pbseqlib
 Version: 0~20151014+gitbe5d1bf-2
 Architecture: armhf
 Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
 Installed-Size: 2139
 Depends: libc6 (>= 2.17), libgcc1 (>= 1:3.5), libstdc++6 (>= 5.2), libpbdata (= 0~20151014+gitbe5d1bf-2), libpbihdf (= 0~20151014+gitbe5d1bf-2)
 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 2015-12-19 21:14 ./
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drwxr-xr-x root/root         0 2015-12-19 21:14 ./usr/lib/
drwxr-xr-x root/root         0 2015-12-19 21:14 ./usr/lib/arm-linux-gnueabihf/
drwxr-xr-x root/root         0 2015-12-19 21:14 ./usr/lib/arm-linux-gnueabihf/blasr/
-rw-r--r-- root/root   2171596 2015-12-19 21:14 ./usr/lib/arm-linux-gnueabihf/blasr/libblasr.so
drwxr-xr-x root/root         0 2015-12-19 21:14 ./usr/share/
drwxr-xr-x root/root         0 2015-12-19 21:14 ./usr/share/doc/
drwxr-xr-x root/root         0 2015-12-19 21:14 ./usr/share/doc/libblasr/
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-rw-r--r-- root/root      4676 2015-10-25 21:02 ./usr/share/doc/libblasr/copyright
drwxr-xr-x root/root         0 2015-12-19 21:14 ./usr/share/lintian/
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-rw-r--r-- root/root        59 2015-11-17 05:45 ./usr/share/lintian/overrides/libblasr


libpbdata-dev_0~20151014+gitbe5d1bf-2_armhf.deb
───────────────────────────────────────────────

 new debian package, version 2.0.
 size 150928 bytes: control archive=3115 bytes.
     724 bytes,    18 lines      control              
    6234 bytes,    84 lines      md5sums              
 Package: libpbdata-dev
 Source: pbseqlib
 Version: 0~20151014+gitbe5d1bf-2
 Architecture: armhf
 Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
 Installed-Size: 936
 Depends: libpbdata (= 0~20151014+gitbe5d1bf-2)
 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
  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 pbdata
  sublibrary.

drwxr-xr-x root/root         0 2015-12-19 21:14 ./
drwxr-xr-x root/root         0 2015-12-19 21:14 ./usr/
drwxr-xr-x root/root         0 2015-12-19 21:14 ./usr/include/
drwxr-xr-x root/root         0 2015-12-19 21:14 ./usr/include/pbdata/
-rw-r--r-- root/root      1383 2015-12-19 21:14 ./usr/include/pbdata/CCSSequence.hpp
-rw-r--r-- root/root       863 2015-12-19 21:14 ./usr/include/pbdata/ChangeListID.hpp
-rw-r--r-- root/root      5127 2015-12-19 21:14 ./usr/include/pbdata/CommandLineParser.hpp
-rw-r--r-- root/root      2066 2015-12-19 21:14 ./usr/include/pbdata/Compare4BitCompressed.hpp
-rw-r--r-- root/root      2096 2015-12-19 21:14 ./usr/include/pbdata/CompressedDNASequence.hpp
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-rw-r--r-- root/root      2611 2015-12-19 21:14 ./usr/include/pbdata/Enumerations.h
-rw-r--r-- root/root      1796 2015-12-19 21:14 ./usr/include/pbdata/FASTAReader.hpp
-rw-r--r-- root/root      1823 2015-12-19 21:14 ./usr/include/pbdata/FASTASequence.hpp
-rw-r--r-- root/root       465 2015-12-19 21:14 ./usr/include/pbdata/FASTQReader.hpp
-rw-r--r-- root/root      4891 2015-12-19 21:14 ./usr/include/pbdata/FASTQSequence.hpp
-rw-r--r-- root/root       706 2015-12-19 21:14 ./usr/include/pbdata/GFFFile.hpp
-rw-r--r-- root/root      4504 2015-12-19 21:14 ./usr/include/pbdata/MD5Utils.hpp
-rw-r--r-- root/root      1378 2015-12-19 21:14 ./usr/include/pbdata/MD5UtilsImpl.hpp
-rw-r--r-- root/root       977 2015-12-19 21:14 ./usr/include/pbdata/NucConversion.hpp
-rw-r--r-- root/root      6946 2015-12-19 21:14 ./usr/include/pbdata/PacBioDefs.h
-rw-r--r-- root/root      1791 2015-12-19 21:14 ./usr/include/pbdata/PackedDNASequence.hpp
-rw-r--r-- root/root       484 2015-12-19 21:14 ./usr/include/pbdata/ReverseCompressIndex.hpp
-rw-r--r-- root/root      6827 2015-12-19 21:14 ./usr/include/pbdata/SMRTSequence.hpp
-rw-r--r-- root/root       357 2015-12-19 21:14 ./usr/include/pbdata/SeqUtils.hpp
-rw-r--r-- root/root      1047 2015-12-19 21:14 ./usr/include/pbdata/SeqUtilsImpl.hpp
-rw-r--r-- root/root      1908 2015-12-19 21:14 ./usr/include/pbdata/StringUtils.hpp
-rw-r--r-- root/root       453 2015-12-19 21:14 ./usr/include/pbdata/Types.h
-rw-r--r-- root/root       409 2015-12-19 21:14 ./usr/include/pbdata/VectorUtils.hpp
drwxr-xr-x root/root         0 2015-12-19 21:14 ./usr/include/pbdata/alignment/
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drwxr-xr-x root/root         0 2015-12-19 21:14 ./usr/include/pbdata/amos/
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-rw-r--r-- root/root         1 2015-12-19 21:14 ./usr/include/pbdata/libconfig.h
drwxr-xr-x root/root         0 2015-12-19 21:14 ./usr/include/pbdata/loadpulses/
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-rw-r--r-- root/root      4762 2015-12-19 21:14 ./usr/include/pbdata/loadpulses/MovieAlnIndexLookupTable.hpp
drwxr-xr-x root/root         0 2015-12-19 21:14 ./usr/include/pbdata/matrix/
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drwxr-xr-x root/root         0 2015-12-19 21:14 ./usr/include/pbdata/reads/
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-rw-r--r-- root/root      5378 2015-12-19 21:14 ./usr/include/pbdata/reads/RegionTable.hpp
-rw-r--r-- root/root      3444 2015-12-19 21:14 ./usr/include/pbdata/reads/RegionTypeMap.hpp
-rw-r--r-- root/root      3954 2015-12-19 21:14 ./usr/include/pbdata/reads/ScanData.hpp
-rw-r--r-- root/root       272 2015-12-19 21:14 ./usr/include/pbdata/reads/ZMWGroupEntry.hpp
drwxr-xr-x root/root         0 2015-12-19 21:14 ./usr/include/pbdata/saf/
-rw-r--r-- root/root       269 2015-12-19 21:14 ./usr/include/pbdata/saf/AlnGroup.hpp
-rw-r--r-- root/root       296 2015-12-19 21:14 ./usr/include/pbdata/saf/AlnInfo.hpp
-rw-r--r-- root/root       342 2015-12-19 21:14 ./usr/include/pbdata/saf/MovieInfo.hpp
-rw-r--r-- root/root       391 2015-12-19 21:14 ./usr/include/pbdata/saf/RefGroup.hpp
-rw-r--r-- root/root       471 2015-12-19 21:14 ./usr/include/pbdata/saf/RefInfo.hpp
drwxr-xr-x root/root         0 2015-12-19 21:14 ./usr/include/pbdata/sam/
-rw-r--r-- root/root       818 2015-12-19 21:14 ./usr/include/pbdata/sam/AlignmentSet.hpp
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-rw-r--r-- root/root       516 2015-12-19 21:14 ./usr/include/pbdata/sam/CigarString.h
-rw-r--r-- root/root       888 2015-12-19 21:14 ./usr/include/pbdata/sam/ReadGroup.hpp
-rw-r--r-- root/root      1588 2015-12-19 21:14 ./usr/include/pbdata/sam/ReferenceSequence.hpp
-rw-r--r-- root/root      2170 2015-12-19 21:14 ./usr/include/pbdata/sam/SAMAlignment.hpp
-rw-r--r-- root/root       877 2015-12-19 21:14 ./usr/include/pbdata/sam/SAMFlag.h
-rw-r--r-- root/root       361 2015-12-19 21:14 ./usr/include/pbdata/sam/SAMHeader.hpp
-rw-r--r-- root/root      1153 2015-12-19 21:14 ./usr/include/pbdata/sam/SAMKeywordValuePair.hpp
-rw-r--r-- root/root       802 2015-12-19 21:14 ./usr/include/pbdata/sam/SAMKeywordValuePairImpl.hpp
-rw-r--r-- root/root      2117 2015-12-19 21:14 ./usr/include/pbdata/sam/SAMReader.hpp
-rw-r--r-- root/root      7473 2015-12-19 21:14 ./usr/include/pbdata/sam/SAMReaderImpl.hpp
-rw-r--r-- root/root       521 2015-12-19 21:14 ./usr/include/pbdata/utils.hpp
drwxr-xr-x root/root         0 2015-12-19 21:14 ./usr/include/pbdata/utils/
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-rw-r--r-- root/root      1074 2015-12-19 21:14 ./usr/include/pbdata/utils/SMRTTitle.hpp
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drwxr-xr-x root/root         0 2015-12-19 21:14 ./usr/lib/
drwxr-xr-x root/root         0 2015-12-19 21:14 ./usr/lib/arm-linux-gnueabihf/
drwxr-xr-x root/root         0 2015-12-19 21:14 ./usr/lib/arm-linux-gnueabihf/pbdata/
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drwxr-xr-x root/root         0 2015-12-19 21:14 ./usr/share/
drwxr-xr-x root/root         0 2015-12-19 21:14 ./usr/share/doc/
drwxr-xr-x root/root         0 2015-12-19 21:14 ./usr/share/doc/libpbdata-dev/
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-rw-r--r-- root/root      4676 2015-10-25 21:02 ./usr/share/doc/libpbdata-dev/copyright


libpbdata_0~20151014+gitbe5d1bf-2_armhf.deb
───────────────────────────────────────────

 new debian package, version 2.0.
 size 91108 bytes: control archive=724 bytes.
     673 bytes,    17 lines      control              
     228 bytes,     3 lines      md5sums              
 Package: libpbdata
 Source: pbseqlib
 Version: 0~20151014+gitbe5d1bf-2
 Architecture: armhf
 Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
 Installed-Size: 295
 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 2015-12-19 21:14 ./
drwxr-xr-x root/root         0 2015-12-19 21:14 ./usr/
drwxr-xr-x root/root         0 2015-12-19 21:14 ./usr/lib/
drwxr-xr-x root/root         0 2015-12-19 21:14 ./usr/lib/arm-linux-gnueabihf/
drwxr-xr-x root/root         0 2015-12-19 21:14 ./usr/lib/arm-linux-gnueabihf/pbdata/
-rw-r--r-- root/root    285876 2015-12-19 21:14 ./usr/lib/arm-linux-gnueabihf/pbdata/libpbdata.so
drwxr-xr-x root/root         0 2015-12-19 21:14 ./usr/share/
drwxr-xr-x root/root         0 2015-12-19 21:14 ./usr/share/doc/
drwxr-xr-x root/root         0 2015-12-19 21:14 ./usr/share/doc/libpbdata/
-rw-r--r-- root/root       316 2015-12-14 03:37 ./usr/share/doc/libpbdata/changelog.Debian.gz
-rw-r--r-- root/root      4676 2015-10-25 21:02 ./usr/share/doc/libpbdata/copyright


libpbihdf-dev_0~20151014+gitbe5d1bf-2_armhf.deb
───────────────────────────────────────────────

 new debian package, version 2.0.
 size 194090 bytes: control archive=2174 bytes.
     723 bytes,    18 lines      control              
    3931 bytes,    54 lines      md5sums              
 Package: libpbihdf-dev
 Source: pbseqlib
 Version: 0~20151014+gitbe5d1bf-2
 Architecture: armhf
 Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
 Installed-Size: 1594
 Depends: libpbihdf (= 0~20151014+gitbe5d1bf-2)
 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 2015-12-19 21:14 ./
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drwxr-xr-x root/root         0 2015-12-19 21:14 ./usr/include/pbihdf/
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-rw-r--r-- root/root      3421 2015-12-19 21:14 ./usr/include/pbihdf/HDFCmpRefAlignmentGroup.hpp
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-rw-r--r-- root/root       228 2015-12-19 21:14 ./usr/include/pbihdf/HDFCmpSupportedFields.hpp
-rw-r--r-- root/root       153 2015-12-19 21:14 ./usr/include/pbihdf/HDFCommonFG.hpp
-rw-r--r-- root/root        92 2015-12-19 21:14 ./usr/include/pbihdf/HDFConfig.hpp
-rw-r--r-- root/root      1479 2015-12-19 21:14 ./usr/include/pbihdf/HDFData.hpp
-rw-r--r-- root/root       715 2015-12-19 21:14 ./usr/include/pbihdf/HDFFile.hpp
-rw-r--r-- root/root      1614 2015-12-19 21:14 ./usr/include/pbihdf/HDFFileLogGroup.hpp
-rw-r--r-- root/root       701 2015-12-19 21:14 ./usr/include/pbihdf/HDFGroup.hpp
-rw-r--r-- root/root      1921 2015-12-19 21:14 ./usr/include/pbihdf/HDFMovieInfoGroup.hpp
-rw-r--r-- root/root       839 2015-12-19 21:14 ./usr/include/pbihdf/HDFNewBasReader.hpp
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-rw-r--r-- root/root      5783 2015-12-19 21:14 ./usr/include/pbihdf/HDFPlsWriter.hpp
-rw-r--r-- root/root      1651 2015-12-19 21:14 ./usr/include/pbihdf/HDFPulseDataFile.hpp
-rw-r--r-- root/root      1673 2015-12-19 21:14 ./usr/include/pbihdf/HDFRefGroupGroup.hpp
-rw-r--r-- root/root      2634 2015-12-19 21:14 ./usr/include/pbihdf/HDFRefInfoGroup.hpp
-rw-r--r-- root/root      1307 2015-12-19 21:14 ./usr/include/pbihdf/HDFRegionTableReader.hpp
-rw-r--r-- root/root      3848 2015-12-19 21:14 ./usr/include/pbihdf/HDFRegionTableWriter.hpp
-rw-r--r-- root/root      3682 2015-12-19 21:14 ./usr/include/pbihdf/HDFRegionsWriter.hpp
-rw-r--r-- root/root      1824 2015-12-19 21:14 ./usr/include/pbihdf/HDFSMRTSequenceReader.hpp
-rw-r--r-- root/root      3308 2015-12-19 21:14 ./usr/include/pbihdf/HDFScanDataReader.hpp
-rw-r--r-- root/root      3546 2015-12-19 21:14 ./usr/include/pbihdf/HDFScanDataWriter.hpp
-rw-r--r-- root/root       452 2015-12-19 21:14 ./usr/include/pbihdf/HDFSentinalFile.hpp
-rw-r--r-- root/root      1625 2015-12-19 21:14 ./usr/include/pbihdf/HDFUtils.hpp
-rw-r--r-- root/root       970 2015-12-19 21:14 ./usr/include/pbihdf/HDFWriteBuffer.hpp
-rw-r--r-- root/root      3169 2015-12-19 21:14 ./usr/include/pbihdf/HDFWriterBase.hpp
-rw-r--r-- root/root      3821 2015-12-19 21:14 ./usr/include/pbihdf/HDFZMWMetricsWriter.hpp
-rw-r--r-- root/root       984 2015-12-19 21:14 ./usr/include/pbihdf/HDFZMWReader.hpp
-rw-r--r-- root/root      3898 2015-12-19 21:14 ./usr/include/pbihdf/HDFZMWWriter.hpp
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drwxr-xr-x root/root         0 2015-12-19 21:14 ./usr/share/
drwxr-xr-x root/root         0 2015-12-19 21:14 ./usr/share/doc/
drwxr-xr-x root/root         0 2015-12-19 21:14 ./usr/share/doc/libpbihdf-dev/
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-rw-r--r-- root/root      4676 2015-10-25 21:02 ./usr/share/doc/libpbihdf-dev/copyright


libpbihdf_0~20151014+gitbe5d1bf-2_armhf.deb
───────────────────────────────────────────

 new debian package, version 2.0.
 size 101828 bytes: control archive=760 bytes.
     750 bytes,    17 lines      control              
     228 bytes,     3 lines      md5sums              
 Package: libpbihdf
 Source: pbseqlib
 Version: 0~20151014+gitbe5d1bf-2
 Architecture: armhf
 Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
 Installed-Size: 399
 Depends: libc6 (>= 2.4), libgcc1 (>= 1:3.5), libhdf5-10, libhdf5-cpp-11 (>= 1.8.16), libstdc++6 (>= 5.2), libpbdata (= 0~20151014+gitbe5d1bf-2)
 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 2015-12-19 21:14 ./
drwxr-xr-x root/root         0 2015-12-19 21:14 ./usr/
drwxr-xr-x root/root         0 2015-12-19 21:14 ./usr/lib/
drwxr-xr-x root/root         0 2015-12-19 21:14 ./usr/lib/arm-linux-gnueabihf/
drwxr-xr-x root/root         0 2015-12-19 21:14 ./usr/lib/arm-linux-gnueabihf/pbihdf/
-rw-r--r-- root/root    392760 2015-12-19 21:14 ./usr/lib/arm-linux-gnueabihf/pbihdf/libpbihdf.so
drwxr-xr-x root/root         0 2015-12-19 21:14 ./usr/share/
drwxr-xr-x root/root         0 2015-12-19 21:14 ./usr/share/doc/
drwxr-xr-x root/root         0 2015-12-19 21:14 ./usr/share/doc/libpbihdf/
-rw-r--r-- root/root       316 2015-12-14 03:37 ./usr/share/doc/libpbihdf/changelog.Debian.gz
-rw-r--r-- root/root      4676 2015-10-25 21:02 ./usr/share/doc/libpbihdf/copyright


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Build Architecture: armhf
Build-Space: 166232
Build-Time: 1505
Distribution: stretch-staging
Host Architecture: armhf
Install-Time: 266
Job: pbseqlib_0~20151014+gitbe5d1bf-2
Machine Architecture: armhf
Package: pbseqlib
Package-Time: 1820
Source-Version: 0~20151014+gitbe5d1bf-2
Space: 166232
Status: successful
Version: 0~20151014+gitbe5d1bf-2
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Finished at 20151219-2115
Build needed 00:30:20, 166232k disc space
Raspbian Package Auto-Building

Build log for pbseqlib (0~20151014+gitbe5d1bf-2) on armhf
