blasr →
0~20150724+git3ca7fe8-1+b2 →
armhf → 2015-12-19 04:12:21
sbuild (Debian sbuild) 0.65.2 (24 Mar 2015) on testbuildd.raspbian.org
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║ blasr 0~20150724+git3ca7fe8-1+b2 (armhf) 19 Dec 2015 03:19 ║
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Package: blasr
Version: 0~20150724+git3ca7fe8-1+b2
Source Version: 0~20150724+git3ca7fe8-1
Distribution: stretch-staging
Machine Architecture: armhf
Host Architecture: armhf
Build Architecture: armhf
I: NOTICE: Log filtering will replace 'build/blasr-XMOEiH/blasr-0~20150724+git3ca7fe8' with '«PKGBUILDDIR»'
I: NOTICE: Log filtering will replace 'build/blasr-XMOEiH' with '«BUILDDIR»'
I: NOTICE: Log filtering will replace 'var/lib/schroot/mount/stretch-staging-armhf-sbuild-1d4b4300-74d1-4006-95f1-4236a267f4c3' with '«CHROOT»'
┌──────────────────────────────────────────────────────────────────────────────┐
│ Update chroot │
└──────────────────────────────────────────────────────────────────────────────┘
Get:1 http://172.17.0.1 stretch-staging InRelease [11.3 kB]
Get:2 http://172.17.0.1 stretch-staging/main Sources [8538 kB]
Get:3 http://172.17.0.1 stretch-staging/main armhf Packages [10.5 MB]
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┌──────────────────────────────────────────────────────────────────────────────┐
│ Fetch source files │
└──────────────────────────────────────────────────────────────────────────────┘
Check APT
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Checking available source versions...
Download source files with APT
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NOTICE: 'blasr' packaging is maintained in the 'Git' version control system at:
git://anonscm.debian.org/debian-med/blasr.git
Need to get 1050 kB of source archives.
Get:1 http://172.17.0.1/private/ stretch-staging/main blasr 0~20150724+git3ca7fe8-1 (dsc) [2033 B]
Get:2 http://172.17.0.1/private/ stretch-staging/main blasr 0~20150724+git3ca7fe8-1 (tar) [1035 kB]
Get:3 http://172.17.0.1/private/ stretch-staging/main blasr 0~20150724+git3ca7fe8-1 (diff) [13.5 kB]
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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-oKK7ce/apt_archive/sbuild-build-depends-core-dummy.deb'.
OK
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┌──────────────────────────────────────────────────────────────────────────────┐
│ Install core build dependencies (apt-based resolver) │
└──────────────────────────────────────────────────────────────────────────────┘
Installing build dependencies
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The following NEW packages will be installed:
sbuild-build-depends-core-dummy
debconf: delaying package configuration, since apt-utils is not installed
0 upgraded, 1 newly installed, 0 to remove and 35 not upgraded.
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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, libhdf5-dev, zlib1g-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, libhdf5-dev, zlib1g-dev
dpkg-deb: building package 'sbuild-build-depends-blasr-dummy' in '/«BUILDDIR»/resolver-ptqIEB/apt_archive/sbuild-build-depends-blasr-dummy.deb'.
OK
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┌──────────────────────────────────────────────────────────────────────────────┐
│ Install blasr build dependencies (apt-based resolver) │
└──────────────────────────────────────────────────────────────────────────────┘
Installing build dependencies
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Building dependency tree...
Reading state information...
The following extra packages will be installed:
binutils bsdmainutils cpp-5 debhelper dh-strip-nondeterminism file g++-5
gcc-5 gcc-5-base gettext gettext-base groff-base hdf5-helpers
intltool-debian libarchive-zip-perl libasan2 libatomic1 libcc1-0 libcroco3
libexpat1 libffi6 libfile-stripnondeterminism-perl libgcc-5-dev libgcc1
libgfortran3 libglib2.0-0 libgomp1 libhdf5-10 libhdf5-cpp-11 libhdf5-dev
libicu55 libisl15 libjpeg-dev libjpeg62-turbo libjpeg62-turbo-dev libmagic1
libpipeline1 libpython-stdlib libpython2.7-minimal libpython2.7-stdlib
libsqlite3-0 libssl1.0.2 libstdc++-5-dev libstdc++6 libtimedate-perl
libubsan0 libunistring0 libxml2 man-db mime-support po-debconf python
python-minimal python2.7 python2.7-minimal zlib1g-dev
Suggested packages:
binutils-doc wamerican wordlist whois vacation gcc-5-locales dh-make
gcc-5-doc libstdc++6-5-dbg libgcc1-dbg libgomp1-dbg libitm1-dbg
libatomic1-dbg libasan2-dbg liblsan0-dbg libtsan0-dbg libubsan0-dbg
libcilkrts5-dbg libmpx0-dbg libquadmath-dbg gettext-doc autopoint
libasprintf-dev libgettextpo-dev groff libhdf5-doc libstdc++-5-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 libcroco3
libexpat1 libffi6 libfile-stripnondeterminism-perl libgfortran3 libglib2.0-0
libhdf5-10 libhdf5-cpp-11 libhdf5-dev libicu55 libisl15 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-blasr-dummy
zlib1g-dev
The following packages will be upgraded:
binutils cpp-5 g++-5 gcc-5 gcc-5-base libasan2 libatomic1 libcc1-0
libgcc-5-dev libgcc1 libgomp1 libstdc++-5-dev libstdc++6 libubsan0
14 upgraded, 43 newly installed, 0 to remove and 21 not upgraded.
Need to get 106 MB/106 MB of archives.
After this operation, 99.1 MB of additional disk space will be used.
Get:1 http://172.17.0.1/private/ stretch-staging/main libgomp1 armhf 5.3.1-3+rpi1 [47.5 kB]
Get:2 http://172.17.0.1/private/ stretch-staging/main libatomic1 armhf 5.3.1-3+rpi1 [6590 B]
Get:3 http://172.17.0.1/private/ stretch-staging/main gcc-5-base armhf 5.3.1-3+rpi1 [168 kB]
Get:4 http://172.17.0.1/private/ stretch-staging/main libgcc1 armhf 1:5.3.1-3+rpi1 [38.4 kB]
Get:5 http://172.17.0.1/private/ stretch-staging/main libasan2 armhf 5.3.1-3+rpi1 [227 kB]
Get:6 http://172.17.0.1/private/ stretch-staging/main libubsan0 armhf 5.3.1-3+rpi1 [84.2 kB]
Get:7 http://172.17.0.1/private/ stretch-staging/main libisl15 armhf 0.15-3 [397 kB]
Get:8 http://172.17.0.1/private/ stretch-staging/main cpp-5 armhf 5.3.1-3+rpi1 [22.9 MB]
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Get:10 http://172.17.0.1/private/ stretch-staging/main binutils armhf 2.25.90.20151209-1 [3588 kB]
Get:11 http://172.17.0.1/private/ stretch-staging/main g++-5 armhf 5.3.1-3+rpi1 [24.5 MB]
Get:12 http://172.17.0.1/private/ stretch-staging/main gcc-5 armhf 5.3.1-3+rpi1 [22.9 MB]
Get:13 http://172.17.0.1/private/ stretch-staging/main libgcc-5-dev armhf 5.3.1-3+rpi1 [450 kB]
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Get:16 http://172.17.0.1/private/ stretch-staging/main groff-base armhf 1.22.3-4 [1084 kB]
Get:17 http://172.17.0.1/private/ stretch-staging/main bsdmainutils armhf 9.0.6 [177 kB]
Get:18 http://172.17.0.1/private/ stretch-staging/main libpipeline1 armhf 1.4.1-1 [23.9 kB]
Get:19 http://172.17.0.1/private/ stretch-staging/main man-db armhf 2.7.5-1 [975 kB]
Get:20 http://172.17.0.1/private/ stretch-staging/main libpython2.7-minimal armhf 2.7.11-2 [380 kB]
Get:21 http://172.17.0.1/private/ stretch-staging/main python2.7-minimal armhf 2.7.11-2 [1081 kB]
Get:22 http://172.17.0.1/private/ stretch-staging/main python-minimal armhf 2.7.11-1 [40.0 kB]
Get:23 http://172.17.0.1/private/ stretch-staging/main mime-support all 3.59 [36.4 kB]
Get:24 http://172.17.0.1/private/ stretch-staging/main libexpat1 armhf 2.1.0-7 [59.8 kB]
Get:25 http://172.17.0.1/private/ stretch-staging/main libffi6 armhf 3.2.1-3 [18.5 kB]
Get:26 http://172.17.0.1/private/ stretch-staging/main libsqlite3-0 armhf 3.9.2-1 [404 kB]
Get:27 http://172.17.0.1/private/ stretch-staging/main libssl1.0.2 armhf 1.0.2e-1 [883 kB]
Get:28 http://172.17.0.1/private/ stretch-staging/main libpython2.7-stdlib armhf 2.7.11-2 [1836 kB]
Get:29 http://172.17.0.1/private/ stretch-staging/main python2.7 armhf 2.7.11-2 [266 kB]
Get:30 http://172.17.0.1/private/ stretch-staging/main libpython-stdlib armhf 2.7.11-1 [19.5 kB]
Get:31 http://172.17.0.1/private/ stretch-staging/main python armhf 2.7.11-1 [150 kB]
Get:32 http://172.17.0.1/private/ stretch-staging/main libunistring0 armhf 0.9.3-5.2 [253 kB]
Get:33 http://172.17.0.1/private/ stretch-staging/main libmagic1 armhf 1:5.25-2 [250 kB]
Get:34 http://172.17.0.1/private/ stretch-staging/main file armhf 1:5.25-2 [61.2 kB]
Get:35 http://172.17.0.1/private/ stretch-staging/main gettext-base armhf 0.19.6-1 [119 kB]
Get:36 http://172.17.0.1/private/ stretch-staging/main libicu55 armhf 55.1-6 [7379 kB]
Get:37 http://172.17.0.1/private/ stretch-staging/main libxml2 armhf 2.9.2+zdfsg1-4 [797 kB]
Get:38 http://172.17.0.1/private/ stretch-staging/main libglib2.0-0 armhf 2.46.2-1 [2482 kB]
Get:39 http://172.17.0.1/private/ stretch-staging/main libcroco3 armhf 0.6.9-1 [129 kB]
Get:40 http://172.17.0.1/private/ stretch-staging/main gettext armhf 0.19.6-1 [1393 kB]
Get:41 http://172.17.0.1/private/ stretch-staging/main intltool-debian all 0.35.0+20060710.4 [26.3 kB]
Get:42 http://172.17.0.1/private/ stretch-staging/main po-debconf all 1.0.18 [248 kB]
Get:43 http://172.17.0.1/private/ stretch-staging/main libarchive-zip-perl all 1.55-1 [97.4 kB]
Get:44 http://172.17.0.1/private/ stretch-staging/main libfile-stripnondeterminism-perl all 0.014-1 [10.6 kB]
Get:45 http://172.17.0.1/private/ stretch-staging/main libtimedate-perl all 2.3000-2 [42.2 kB]
Get:46 http://172.17.0.1/private/ stretch-staging/main dh-strip-nondeterminism all 0.014-1 [7472 B]
Get:47 http://172.17.0.1/private/ stretch-staging/main debhelper all 9.20151126 [830 kB]
Get:48 http://172.17.0.1/private/ stretch-staging/main hdf5-helpers armhf 1.8.16+docs-1 [35.0 kB]
Get:49 http://172.17.0.1/private/ stretch-staging/main libgfortran3 armhf 5.3.1-3+rpi1 [154 kB]
Get:50 http://172.17.0.1/private/ stretch-staging/main libhdf5-10 armhf 1.8.16+docs-1 [977 kB]
Get:51 http://172.17.0.1/private/ stretch-staging/main libhdf5-cpp-11 armhf 1.8.16+docs-1 [115 kB]
Get:52 http://172.17.0.1/private/ stretch-staging/main zlib1g-dev armhf 1:1.2.8.dfsg-2+b1 [197 kB]
Get:53 http://172.17.0.1/private/ stretch-staging/main libjpeg62-turbo armhf 1:1.4.1-2 [103 kB]
Get:54 http://172.17.0.1/private/ stretch-staging/main libjpeg62-turbo-dev armhf 1:1.4.1-2 [415 kB]
Get:55 http://172.17.0.1/private/ stretch-staging/main libjpeg-dev all 1:1.4.1-2 [51.9 kB]
Get:56 http://172.17.0.1/private/ stretch-staging/main libhdf5-dev armhf 1.8.16+docs-1 [4912 kB]
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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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┌──────────────────────────────────────────────────────────────────────────────┐
│ 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_2.19-22 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_1.0.10.2 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+rpi2 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_2:1.02.110-1+rpi1 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+rpi2 g++-5_5.3.1-3+rpi1 gcc_4:5.2.1-4+rpi2 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 gcc-4.9-base_4.9.3-5 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_2.0.4-2+rpi1 kmod_21-1 libacl1_2.2.52-2 libapparmor1_2.10-2+b2 libapt-pkg4.16_1.0.10.2 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 libbz2-1.0_1.0.6-8 libc-bin_2.19-22 libc-dev-bin_2.19-22 libc6_2.19-22 libc6-dev_2.19-22 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_1.10.4-1 libdebconfclient0_0.197 libdevmapper1.02.1_2:1.02.110-1+rpi1 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 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 libhdf5-10_1.8.16+docs-1 libhdf5-cpp-11_1.8.16+docs-1 libhdf5-dev_1.8.16+docs-1 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_2.0.4-2+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 libnih-dbus1_1.0.3-4.3 libnih1_1.0.3-4.3 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_2:8.35-7.4 libpipeline1_1.4.1-1 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 mawk_1.3.3-17 mime-support_3.59 mount_2.27.1-1 multiarch-support_2.19-22 nano_2.4.2-1 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 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-blasr-dummy_0.invalid.0 sbuild-build-depends-core-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 Fri Jul 31 07:56:38 2015 UTC using RSA key ID D1C646D1
gpgv: Can't check signature: public key not found
dpkg-source: warning: failed to verify signature on ./blasr_0~20150724+git3ca7fe8-1.dsc
dpkg-source: info: extracting blasr in blasr-0~20150724+git3ca7fe8
dpkg-source: info: unpacking blasr_0~20150724+git3ca7fe8.orig.tar.xz
dpkg-source: info: unpacking blasr_0~20150724+git3ca7fe8-1.debian.tar.xz
dpkg-source: info: applying selective-static-linking
Check disc space
────────────────
Sufficient free space for build
Hack binNMU version
───────────────────
Created changelog entry for binNMU version 0~20150724+git3ca7fe8-1+b2
User Environment
────────────────
DEB_BUILD_OPTIONS=parallel=4
HOME=/sbuild-nonexistent
LOGNAME=buildd
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=111
SCHROOT_GROUP=buildd
SCHROOT_SESSION_ID=stretch-staging-armhf-sbuild-1d4b4300-74d1-4006-95f1-4236a267f4c3
SCHROOT_UID=106
SCHROOT_USER=buildd
SHELL=/bin/sh
TERM=linux
USER=buildd
dpkg-buildpackage
─────────────────
dpkg-buildpackage: source package blasr
dpkg-buildpackage: source version 0~20150724+git3ca7fe8-1+b2
dpkg-buildpackage: source distribution stretch-staging
dpkg-source --before-build blasr-0~20150724+git3ca7fe8
dpkg-buildpackage: host architecture armhf
fakeroot debian/rules clean
dh clean
dh_testdir
debian/rules override_dh_auto_clean
make[1]: Entering directory '/«BUILDDIR»/blasr-0~20150724+git3ca7fe8'
./configure.py --no-pbbam --submodules
writing to '/«BUILDDIR»/blasr-0~20150724+git3ca7fe8/defines.mk'
"""
LIBBLASR_LIBFLAGS ?= -Wl,-Bstatic -lblasr
SHELL ?= bash
LIBPBIHDF_INCLUDE ?= ${ROOT}/libcpp/hdf
DL_LIBFLAGS ?= -Wl,-Bdynamic -ldl
LIBPBDATA_INCLUDE ?= ${ROOT}/libcpp/pbdata
LIBPBIHDF_LIBFLAGS ?= -Wl,-Bstatic -lpbihdf
LIBPBDATA_LIB ?= ${ROOT}/libcpp/pbdata
LIBBLASR_INCLUDE ?= ${ROOT}/libcpp/alignment
LIBBLASR_LIB ?= ${ROOT}/libcpp/alignment
HDF5_LIB ?= /usr/lib/arm-linux-gnueabihf/hdf5/serial
HDF5_LIBFLAGS ?= -Wl,-Bdynamic -lhdf5_cpp -lhdf5
LIBPBDATA_LIBFLAGS ?= -Wl,-Bstatic -lpbdata
ZLIB_LIBFLAGS ?= -Wl,-Bdynamic -lz
HDF5_INCLUDE ?= /usr/include/hdf5/serial
PTHREAD_LIBFLAGS ?= -Wl,-Bdynamic -lpthread
LIBPBIHDF_LIB ?= ${ROOT}/libcpp/hdf
LDFLAGS+=-static
SUB_CONF_FLAGS+=--shared
"""
libcpp/configure.py
writing to '/«BUILDDIR»/blasr-0~20150724+git3ca7fe8/libcpp/defines.mk'
"""
HDF5_INCLUDE:=/usr/include/hdf5/serial
HDF5_LIB:=/usr/lib/arm-linux-gnueabihf/hdf5/serial
#CPPFLAGS+=-I../pbdata -I../hdf -I../alignment
LIBPBDATA_INCLUDE ?=../pbdata
LIBPBIHDF_INCLUDE ?=../hdf
LIBBLASR_INCLUDE ?=../alignment
LIBPBDATA_LIB ?=../pbdata/libpbdata.so
LIBPBIHDF_LIB ?=../hdf/libpbihdf.so
LIBBLASR_LIB ?=../alignment/libblasr.so
"""
writing to '/«BUILDDIR»/blasr-0~20150724+git3ca7fe8/libcpp/pbdata/libconfig.h'
"""
"""
NOT2
/usr/bin/make cleanall
make[2]: Entering directory '/«BUILDDIR»/blasr-0~20150724+git3ca7fe8'
/usr/bin/make -C libcpp clean
ERROR: ld.so: object 'libfakeroot-sysv.so' from LD_PRELOAD cannot be preloaded (cannot open shared object file): ignored.
make[3]: Entering directory '/«BUILDDIR»/blasr-0~20150724+git3ca7fe8/libcpp'
/usr/bin/make -C pbdata clean
ERROR: ld.so: object 'libfakeroot-sysv.so' from LD_PRELOAD cannot be preloaded (cannot open shared object file): ignored.
ERROR: ld.so: object 'libfakeroot-sysv.so' from LD_PRELOAD cannot be preloaded (cannot open shared object file): ignored.
make[4]: Entering directory '/«BUILDDIR»/blasr-0~20150724+git3ca7fe8/libcpp/pbdata'
ERROR: ld.so: object 'libfakeroot-sysv.so' from LD_PRELOAD cannot be preloaded (cannot open shared object file): ignored.
ERROR: ld.so: object 'libfakeroot-sysv.so' from LD_PRELOAD cannot be preloaded (cannot open shared object file): ignored.
make[4]: Leaving directory '/«BUILDDIR»/blasr-0~20150724+git3ca7fe8/libcpp/pbdata'
/usr/bin/make -C hdf clean
ERROR: ld.so: object 'libfakeroot-sysv.so' from LD_PRELOAD cannot be preloaded (cannot open shared object file): ignored.
ERROR: ld.so: object 'libfakeroot-sysv.so' from LD_PRELOAD cannot be preloaded (cannot open shared object file): ignored.
make[4]: Entering directory '/«BUILDDIR»/blasr-0~20150724+git3ca7fe8/libcpp/hdf'
ERROR: ld.so: object 'libfakeroot-sysv.so' from LD_PRELOAD cannot be preloaded (cannot open shared object file): ignored.
ERROR: ld.so: object 'libfakeroot-sysv.so' from LD_PRELOAD cannot be preloaded (cannot open shared object file): ignored.
make[4]: Leaving directory '/«BUILDDIR»/blasr-0~20150724+git3ca7fe8/libcpp/hdf'
/usr/bin/make -C alignment clean
ERROR: ld.so: object 'libfakeroot-sysv.so' from LD_PRELOAD cannot be preloaded (cannot open shared object file): ignored.
ERROR: ld.so: object 'libfakeroot-sysv.so' from LD_PRELOAD cannot be preloaded (cannot open shared object file): ignored.
make[4]: Entering directory '/«BUILDDIR»/blasr-0~20150724+git3ca7fe8/libcpp/alignment'
ERROR: ld.so: object 'libfakeroot-sysv.so' from LD_PRELOAD cannot be preloaded (cannot open shared object file): ignored.
ERROR: ld.so: object 'libfakeroot-sysv.so' from LD_PRELOAD cannot be preloaded (cannot open shared object file): ignored.
ERROR: ld.so: object 'libfakeroot-sysv.so' from LD_PRELOAD cannot be preloaded (cannot open shared object file): ignored.
ERROR: ld.so: object 'libfakeroot-sysv.so' from LD_PRELOAD cannot be preloaded (cannot open shared object file): ignored.
make[4]: Leaving directory '/«BUILDDIR»/blasr-0~20150724+git3ca7fe8/libcpp/alignment'
#@/usr/bin/make -C unittest clean
ERROR: ld.so: object 'libfakeroot-sysv.so' from LD_PRELOAD cannot be preloaded (cannot open shared object file): ignored.
make[3]: Leaving directory '/«BUILDDIR»/blasr-0~20150724+git3ca7fe8/libcpp'
rm -f blasr Blasr.o Blasr.d blasr.d
ERROR: ld.so: object 'libfakeroot-sysv.so' from LD_PRELOAD cannot be preloaded (cannot open shared object file): ignored.
/usr/bin/make -C utils clean
ERROR: ld.so: object 'libfakeroot-sysv.so' from LD_PRELOAD cannot be preloaded (cannot open shared object file): ignored.
make[3]: Entering directory '/«BUILDDIR»/blasr-0~20150724+git3ca7fe8/utils'
ERROR: ld.so: object 'libfakeroot-sysv.so' from LD_PRELOAD cannot be preloaded (cannot open shared object file): ignored.
ERROR: ld.so: object 'libfakeroot-sysv.so' from LD_PRELOAD cannot be preloaded (cannot open shared object file): ignored.
ERROR: ld.so: object 'libfakeroot-sysv.so' from LD_PRELOAD cannot be preloaded (cannot open shared object file): ignored.
make[3]: Leaving directory '/«BUILDDIR»/blasr-0~20150724+git3ca7fe8/utils'
/usr/bin/make -C extrautils clean
ERROR: ld.so: object 'libfakeroot-sysv.so' from LD_PRELOAD cannot be preloaded (cannot open shared object file): ignored.
make[3]: Entering directory '/«BUILDDIR»/blasr-0~20150724+git3ca7fe8/extrautils'
ERROR: ld.so: object 'libfakeroot-sysv.so' from LD_PRELOAD cannot be preloaded (cannot open shared object file): ignored.
ERROR: ld.so: object 'libfakeroot-sysv.so' from LD_PRELOAD cannot be preloaded (cannot open shared object file): ignored.
ERROR: ld.so: object 'libfakeroot-sysv.so' from LD_PRELOAD cannot be preloaded (cannot open shared object file): ignored.
make[3]: Leaving directory '/«BUILDDIR»/blasr-0~20150724+git3ca7fe8/extrautils'
make[2]: Leaving directory '/«BUILDDIR»/blasr-0~20150724+git3ca7fe8'
# This is created by configure.py
rm -f defines.mk
# These are created by libcpp/configure.py
rm -f libcpp/defines.mk libcpp/pbdata/libconfig.h
make[1]: Leaving directory '/«BUILDDIR»/blasr-0~20150724+git3ca7fe8'
dh_clean
debian/rules build-arch
dh build-arch
dh_testdir -a
debian/rules override_dh_auto_configure
make[1]: Entering directory '/«BUILDDIR»/blasr-0~20150724+git3ca7fe8'
./configure.py --no-pbbam --submodules
writing to '/«BUILDDIR»/blasr-0~20150724+git3ca7fe8/defines.mk'
"""
LIBBLASR_LIBFLAGS ?= -Wl,-Bstatic -lblasr
SHELL ?= bash
LIBPBIHDF_INCLUDE ?= ${ROOT}/libcpp/hdf
DL_LIBFLAGS ?= -Wl,-Bdynamic -ldl
LIBPBDATA_INCLUDE ?= ${ROOT}/libcpp/pbdata
LIBPBIHDF_LIBFLAGS ?= -Wl,-Bstatic -lpbihdf
LIBPBDATA_LIB ?= ${ROOT}/libcpp/pbdata
LIBBLASR_INCLUDE ?= ${ROOT}/libcpp/alignment
LIBBLASR_LIB ?= ${ROOT}/libcpp/alignment
HDF5_LIB ?= /usr/lib/arm-linux-gnueabihf/hdf5/serial
HDF5_LIBFLAGS ?= -Wl,-Bdynamic -lhdf5_cpp -lhdf5
LIBPBDATA_LIBFLAGS ?= -Wl,-Bstatic -lpbdata
ZLIB_LIBFLAGS ?= -Wl,-Bdynamic -lz
HDF5_INCLUDE ?= /usr/include/hdf5/serial
PTHREAD_LIBFLAGS ?= -Wl,-Bdynamic -lpthread
LIBPBIHDF_LIB ?= ${ROOT}/libcpp/hdf
LDFLAGS+=-static
SUB_CONF_FLAGS+=--shared
"""
libcpp/configure.py
writing to '/«BUILDDIR»/blasr-0~20150724+git3ca7fe8/libcpp/defines.mk'
"""
HDF5_INCLUDE:=/usr/include/hdf5/serial
HDF5_LIB:=/usr/lib/arm-linux-gnueabihf/hdf5/serial
#CPPFLAGS+=-I../pbdata -I../hdf -I../alignment
LIBPBDATA_INCLUDE ?=../pbdata
LIBPBIHDF_INCLUDE ?=../hdf
LIBBLASR_INCLUDE ?=../alignment
LIBPBDATA_LIB ?=../pbdata/libpbdata.so
LIBPBIHDF_LIB ?=../hdf/libpbihdf.so
LIBBLASR_LIB ?=../alignment/libblasr.so
"""
writing to '/«BUILDDIR»/blasr-0~20150724+git3ca7fe8/libcpp/pbdata/libconfig.h'
"""
"""
NOT2
make[1]: Leaving directory '/«BUILDDIR»/blasr-0~20150724+git3ca7fe8'
debian/rules override_dh_auto_build
make[1]: Entering directory '/«BUILDDIR»/blasr-0~20150724+git3ca7fe8'
/usr/bin/make build-submodule
make[2]: Entering directory '/«BUILDDIR»/blasr-0~20150724+git3ca7fe8'
# DON'T use pbbam which is not on github.
cd libcpp && NOPBBAM=true HDF5_LIB=/usr/lib/arm-linux-gnueabihf/hdf5/serial/libhdf5.so HDF5_INCLUDE=/usr/include/hdf5/serial ./configure.py
writing to '/«BUILDDIR»/blasr-0~20150724+git3ca7fe8/libcpp/defines.mk'
"""
HDF5_INCLUDE:=/usr/include/hdf5/serial
HDF5_LIB:=/usr/lib/arm-linux-gnueabihf/hdf5/serial/libhdf5.so
#CPPFLAGS+=-I../pbdata -I../hdf -I../alignment
LIBPBDATA_INCLUDE ?=../pbdata
LIBPBIHDF_INCLUDE ?=../hdf
LIBBLASR_INCLUDE ?=../alignment
LIBPBDATA_LIB ?=../pbdata/libpbdata.so
LIBPBIHDF_LIB ?=../hdf/libpbihdf.so
LIBBLASR_LIB ?=../alignment/libblasr.so
"""
/usr/bin/make -C libcpp
make[3]: Entering directory '/«BUILDDIR»/blasr-0~20150724+git3ca7fe8/libcpp'
/usr/bin/make -C pbdata all
make[4]: Entering directory '/«BUILDDIR»/blasr-0~20150724+git3ca7fe8/libcpp/pbdata'
g++ -std=c++11 -pedantic -MMD -MP -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -I. -Imatrix -Ireads -Iqvs -Imetagenome -Isaf -Iutils -Ialignment -MF"GFFFile.d" -MT"GFFFile.o GFFFile.d" -c GFFFile.cpp -o GFFFile.o
g++ -std=c++11 -pedantic -MMD -MP -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -I. -Imatrix -Ireads -Iqvs -Imetagenome -Isaf -Iutils -Ialignment -MF"ChangeListID.d" -MT"ChangeListID.o ChangeListID.d" -c ChangeListID.cpp -o ChangeListID.o
g++ -std=c++11 -pedantic -MMD -MP -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -I. -Imatrix -Ireads -Iqvs -Imetagenome -Isaf -Iutils -Ialignment -MF"StringUtils.d" -MT"StringUtils.o StringUtils.d" -c StringUtils.cpp -o StringUtils.o
g++ -std=c++11 -pedantic -MMD -MP -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -I. -Imatrix -Ireads -Iqvs -Imetagenome -Isaf -Iutils -Ialignment -MF"SMRTSequence.d" -MT"SMRTSequence.o SMRTSequence.d" -c SMRTSequence.cpp -o SMRTSequence.o
g++ -std=c++11 -pedantic -MMD -MP -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -I. -Imatrix -Ireads -Iqvs -Imetagenome -Isaf -Iutils -Ialignment -MF"MD5Utils.d" -MT"MD5Utils.o MD5Utils.d" -c MD5Utils.cpp -o MD5Utils.o
g++ -std=c++11 -pedantic -MMD -MP -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -I. -Imatrix -Ireads -Iqvs -Imetagenome -Isaf -Iutils -Ialignment -MF"ReverseCompressIndex.d" -MT"ReverseCompressIndex.o ReverseCompressIndex.d" -c ReverseCompressIndex.cpp -o ReverseCompressIndex.o
g++ -std=c++11 -pedantic -MMD -MP -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -I. -Imatrix -Ireads -Iqvs -Imetagenome -Isaf -Iutils -Ialignment -MF"FASTAReader.d" -MT"FASTAReader.o FASTAReader.d" -c FASTAReader.cpp -o FASTAReader.o
g++ -std=c++11 -pedantic -MMD -MP -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -I. -Imatrix -Ireads -Iqvs -Imetagenome -Isaf -Iutils -Ialignment -MF"FASTQSequence.d" -MT"FASTQSequence.o FASTQSequence.d" -c FASTQSequence.cpp -o FASTQSequence.o
g++ -std=c++11 -pedantic -MMD -MP -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -I. -Imatrix -Ireads -Iqvs -Imetagenome -Isaf -Iutils -Ialignment -MF"CommandLineParser.d" -MT"CommandLineParser.o CommandLineParser.d" -c CommandLineParser.cpp -o CommandLineParser.o
g++ -std=c++11 -pedantic -MMD -MP -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -I. -Imatrix -Ireads -Iqvs -Imetagenome -Isaf -Iutils -Ialignment -MF"CCSSequence.d" -MT"CCSSequence.o CCSSequence.d" -c CCSSequence.cpp -o CCSSequence.o
g++ -std=c++11 -pedantic -MMD -MP -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -I. -Imatrix -Ireads -Iqvs -Imetagenome -Isaf -Iutils -Ialignment -MF"PackedDNASequence.d" -MT"PackedDNASequence.o PackedDNASequence.d" -c PackedDNASequence.cpp -o PackedDNASequence.o
g++ -std=c++11 -pedantic -MMD -MP -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -I. -Imatrix -Ireads -Iqvs -Imetagenome -Isaf -Iutils -Ialignment -MF"DNASequence.d" -MT"DNASequence.o DNASequence.d" -c DNASequence.cpp -o DNASequence.o
g++ -std=c++11 -pedantic -MMD -MP -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -I. -Imatrix -Ireads -Iqvs -Imetagenome -Isaf -Iutils -Ialignment -MF"NucConversion.d" -MT"NucConversion.o NucConversion.d" -c NucConversion.cpp -o NucConversion.o
g++ -std=c++11 -pedantic -MMD -MP -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -I. -Imatrix -Ireads -Iqvs -Imetagenome -Isaf -Iutils -Ialignment -MF"FASTQReader.d" -MT"FASTQReader.o FASTQReader.d" -c FASTQReader.cpp -o FASTQReader.o
g++ -std=c++11 -pedantic -MMD -MP -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -I. -Imatrix -Ireads -Iqvs -Imetagenome -Isaf -Iutils -Ialignment -MF"FASTASequence.d" -MT"FASTASequence.o FASTASequence.d" -c FASTASequence.cpp -o FASTASequence.o
g++ -std=c++11 -pedantic -MMD -MP -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -I. -Imatrix -Ireads -Iqvs -Imetagenome -Isaf -Iutils -Ialignment -MF"reads/RegionTable.d" -MT"reads/RegionTable.o reads/RegionTable.d" -c reads/RegionTable.cpp -o reads/RegionTable.o
g++ -std=c++11 -pedantic -MMD -MP -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -I. -Imatrix -Ireads -Iqvs -Imetagenome -Isaf -Iutils -Ialignment -MF"reads/ScanData.d" -MT"reads/ScanData.o reads/ScanData.d" -c reads/ScanData.cpp -o reads/ScanData.o
g++ -std=c++11 -pedantic -MMD -MP -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -I. -Imatrix -Ireads -Iqvs -Imetagenome -Isaf -Iutils -Ialignment -MF"reads/BaseFile.d" -MT"reads/BaseFile.o reads/BaseFile.d" -c reads/BaseFile.cpp -o reads/BaseFile.o
g++ -std=c++11 -pedantic -MMD -MP -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -I. -Imatrix -Ireads -Iqvs -Imetagenome -Isaf -Iutils -Ialignment -MF"reads/ZMWGroupEntry.d" -MT"reads/ZMWGroupEntry.o reads/ZMWGroupEntry.d" -c reads/ZMWGroupEntry.cpp -o reads/ZMWGroupEntry.o
g++ -std=c++11 -pedantic -MMD -MP -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -I. -Imatrix -Ireads -Iqvs -Imetagenome -Isaf -Iutils -Ialignment -MF"reads/PulseBaseCommon.d" -MT"reads/PulseBaseCommon.o reads/PulseBaseCommon.d" -c reads/PulseBaseCommon.cpp -o reads/PulseBaseCommon.o
g++ -std=c++11 -pedantic -MMD -MP -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -I. -Imatrix -Ireads -Iqvs -Imetagenome -Isaf -Iutils -Ialignment -MF"reads/PulseFile.d" -MT"reads/PulseFile.o reads/PulseFile.d" -c reads/PulseFile.cpp -o reads/PulseFile.o
g++ -std=c++11 -pedantic -MMD -MP -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -I. -Imatrix -Ireads -Iqvs -Imetagenome -Isaf -Iutils -Ialignment -MF"reads/HoleXY.d" -MT"reads/HoleXY.o reads/HoleXY.d" -c reads/HoleXY.cpp -o reads/HoleXY.o
g++ -std=c++11 -pedantic -MMD -MP -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -I. -Imatrix -Ireads -Iqvs -Imetagenome -Isaf -Iutils -Ialignment -MF"reads/ReadType.d" -MT"reads/ReadType.o reads/ReadType.d" -c reads/ReadType.cpp -o reads/ReadType.o
g++ -std=c++11 -pedantic -MMD -MP -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -I. -Imatrix -Ireads -Iqvs -Imetagenome -Isaf -Iutils -Ialignment -MF"metagenome/TitleTable.d" -MT"metagenome/TitleTable.o metagenome/TitleTable.d" -c metagenome/TitleTable.cpp -o metagenome/TitleTable.o
g++ -std=c++11 -pedantic -MMD -MP -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -I. -Imatrix -Ireads -Iqvs -Imetagenome -Isaf -Iutils -Ialignment -MF"qvs/QualityTransform.d" -MT"qvs/QualityTransform.o qvs/QualityTransform.d" -c qvs/QualityTransform.cpp -o qvs/QualityTransform.o
g++ -std=c++11 -pedantic -MMD -MP -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -I. -Imatrix -Ireads -Iqvs -Imetagenome -Isaf -Iutils -Ialignment -MF"qvs/QualityValue.d" -MT"qvs/QualityValue.o qvs/QualityValue.d" -c qvs/QualityValue.cpp -o qvs/QualityValue.o
g++ -std=c++11 -pedantic -MMD -MP -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -I. -Imatrix -Ireads -Iqvs -Imetagenome -Isaf -Iutils -Ialignment -MF"saf/RefGroup.d" -MT"saf/RefGroup.o saf/RefGroup.d" -c saf/RefGroup.cpp -o saf/RefGroup.o
g++ -std=c++11 -pedantic -MMD -MP -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -I. -Imatrix -Ireads -Iqvs -Imetagenome -Isaf -Iutils -Ialignment -MF"saf/RefInfo.d" -MT"saf/RefInfo.o saf/RefInfo.d" -c saf/RefInfo.cpp -o saf/RefInfo.o
g++ -std=c++11 -pedantic -MMD -MP -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -I. -Imatrix -Ireads -Iqvs -Imetagenome -Isaf -Iutils -Ialignment -MF"saf/AlnGroup.d" -MT"saf/AlnGroup.o saf/AlnGroup.d" -c saf/AlnGroup.cpp -o saf/AlnGroup.o
g++ -std=c++11 -pedantic -MMD -MP -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -I. -Imatrix -Ireads -Iqvs -Imetagenome -Isaf -Iutils -Ialignment -MF"saf/MovieInfo.d" -MT"saf/MovieInfo.o saf/MovieInfo.d" -c saf/MovieInfo.cpp -o saf/MovieInfo.o
g++ -std=c++11 -pedantic -MMD -MP -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -I. -Imatrix -Ireads -Iqvs -Imetagenome -Isaf -Iutils -Ialignment -MF"utils/BitUtils.d" -MT"utils/BitUtils.o utils/BitUtils.d" -c utils/BitUtils.cpp -o utils/BitUtils.o
g++ -std=c++11 -pedantic -MMD -MP -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -I. -Imatrix -Ireads -Iqvs -Imetagenome -Isaf -Iutils -Ialignment -MF"utils/SMRTTitle.d" -MT"utils/SMRTTitle.o utils/SMRTTitle.d" -c utils/SMRTTitle.cpp -o utils/SMRTTitle.o
g++ -std=c++11 -pedantic -MMD -MP -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -I. -Imatrix -Ireads -Iqvs -Imetagenome -Isaf -Iutils -Ialignment -MF"utils/SMRTReadUtils.d" -MT"utils/SMRTReadUtils.o utils/SMRTReadUtils.d" -c utils/SMRTReadUtils.cpp -o utils/SMRTReadUtils.o
g++ -std=c++11 -pedantic -MMD -MP -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -I. -Imatrix -Ireads -Iqvs -Imetagenome -Isaf -Iutils -Ialignment -MF"loadpulses/MetricField.d" -MT"loadpulses/MetricField.o loadpulses/MetricField.d" -c loadpulses/MetricField.cpp -o loadpulses/MetricField.o
g++ -std=c++11 -pedantic -MMD -MP -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -I. -Imatrix -Ireads -Iqvs -Imetagenome -Isaf -Iutils -Ialignment -MF"loadpulses/MovieAlnIndexLookupTable.d" -MT"loadpulses/MovieAlnIndexLookupTable.o loadpulses/MovieAlnIndexLookupTable.d" -c loadpulses/MovieAlnIndexLookupTable.cpp -o loadpulses/MovieAlnIndexLookupTable.o
g++ -std=c++11 -pedantic -MMD -MP -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -I. -Imatrix -Ireads -Iqvs -Imetagenome -Isaf -Iutils -Ialignment -MF"alignment/CmpAlignment.d" -MT"alignment/CmpAlignment.o alignment/CmpAlignment.d" -c alignment/CmpAlignment.cpp -o alignment/CmpAlignment.o
g++ -std=c++11 -pedantic -MMD -MP -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -I. -Imatrix -Ireads -Iqvs -Imetagenome -Isaf -Iutils -Ialignment -MF"amos/AfgBasWriter.d" -MT"amos/AfgBasWriter.o amos/AfgBasWriter.d" -c amos/AfgBasWriter.cpp -o amos/AfgBasWriter.o
g++ -std=c++11 -pedantic -MMD -MP -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -I. -Imatrix -Ireads -Iqvs -Imetagenome -Isaf -Iutils -Ialignment -MF"sam/ReferenceSequence.d" -MT"sam/ReferenceSequence.o sam/ReferenceSequence.d" -c sam/ReferenceSequence.cpp -o sam/ReferenceSequence.o
g++ -std=c++11 -pedantic -MMD -MP -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -I. -Imatrix -Ireads -Iqvs -Imetagenome -Isaf -Iutils -Ialignment -MF"sam/SAMAlignment.d" -MT"sam/SAMAlignment.o sam/SAMAlignment.d" -c sam/SAMAlignment.cpp -o sam/SAMAlignment.o
g++ -std=c++11 -pedantic -MMD -MP -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -I. -Imatrix -Ireads -Iqvs -Imetagenome -Isaf -Iutils -Ialignment -MF"sam/SAMHeader.d" -MT"sam/SAMHeader.o sam/SAMHeader.d" -c sam/SAMHeader.cpp -o sam/SAMHeader.o
g++ -std=c++11 -pedantic -MMD -MP -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -I. -Imatrix -Ireads -Iqvs -Imetagenome -Isaf -Iutils -Ialignment -MF"sam/ReadGroup.d" -MT"sam/ReadGroup.o sam/ReadGroup.d" -c sam/ReadGroup.cpp -o sam/ReadGroup.o
g++ -std=c++11 -pedantic -MMD -MP -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -I. -Imatrix -Ireads -Iqvs -Imetagenome -Isaf -Iutils -Ialignment -MF"sam/SAMKeywordValuePair.d" -MT"sam/SAMKeywordValuePair.o sam/SAMKeywordValuePair.d" -c sam/SAMKeywordValuePair.cpp -o sam/SAMKeywordValuePair.o
ar rc libpbdata.a GFFFile.o ChangeListID.o StringUtils.o SMRTSequence.o MD5Utils.o ReverseCompressIndex.o FASTAReader.o FASTQSequence.o CommandLineParser.o CCSSequence.o PackedDNASequence.o DNASequence.o NucConversion.o FASTQReader.o FASTASequence.o reads/RegionTable.o reads/ScanData.o reads/BaseFile.o reads/ZMWGroupEntry.o reads/PulseBaseCommon.o reads/PulseFile.o reads/HoleXY.o reads/ReadType.o metagenome/TitleTable.o qvs/QualityTransform.o qvs/QualityValue.o saf/RefGroup.o saf/RefInfo.o saf/AlnGroup.o saf/MovieInfo.o utils/BitUtils.o utils/SMRTTitle.o utils/SMRTReadUtils.o loadpulses/MetricField.o loadpulses/MovieAlnIndexLookupTable.o alignment/CmpAlignment.o amos/AfgBasWriter.o sam/ReferenceSequence.o sam/SAMAlignment.o sam/SAMHeader.o sam/ReadGroup.o sam/SAMKeywordValuePair.o
g++ -std=c++11 -pedantic -MMD -MP -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -I. -Imatrix -Ireads -Iqvs -Imetagenome -Isaf -Iutils -Ialignment -fPIC -MF"GFFFile.shared.d" -MT"GFFFile.shared.o GFFFile.shared.d" -c GFFFile.cpp -o GFFFile.shared.o
g++ -std=c++11 -pedantic -MMD -MP -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -I. -Imatrix -Ireads -Iqvs -Imetagenome -Isaf -Iutils -Ialignment -fPIC -MF"ChangeListID.shared.d" -MT"ChangeListID.shared.o ChangeListID.shared.d" -c ChangeListID.cpp -o ChangeListID.shared.o
g++ -std=c++11 -pedantic -MMD -MP -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -I. -Imatrix -Ireads -Iqvs -Imetagenome -Isaf -Iutils -Ialignment -fPIC -MF"StringUtils.shared.d" -MT"StringUtils.shared.o StringUtils.shared.d" -c StringUtils.cpp -o StringUtils.shared.o
g++ -std=c++11 -pedantic -MMD -MP -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -I. -Imatrix -Ireads -Iqvs -Imetagenome -Isaf -Iutils -Ialignment -fPIC -MF"SMRTSequence.shared.d" -MT"SMRTSequence.shared.o SMRTSequence.shared.d" -c SMRTSequence.cpp -o SMRTSequence.shared.o
g++ -std=c++11 -pedantic -MMD -MP -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -I. -Imatrix -Ireads -Iqvs -Imetagenome -Isaf -Iutils -Ialignment -fPIC -MF"MD5Utils.shared.d" -MT"MD5Utils.shared.o MD5Utils.shared.d" -c MD5Utils.cpp -o MD5Utils.shared.o
g++ -std=c++11 -pedantic -MMD -MP -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -I. -Imatrix -Ireads -Iqvs -Imetagenome -Isaf -Iutils -Ialignment -fPIC -MF"ReverseCompressIndex.shared.d" -MT"ReverseCompressIndex.shared.o ReverseCompressIndex.shared.d" -c ReverseCompressIndex.cpp -o ReverseCompressIndex.shared.o
g++ -std=c++11 -pedantic -MMD -MP -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -I. -Imatrix -Ireads -Iqvs -Imetagenome -Isaf -Iutils -Ialignment -fPIC -MF"FASTAReader.shared.d" -MT"FASTAReader.shared.o FASTAReader.shared.d" -c FASTAReader.cpp -o FASTAReader.shared.o
g++ -std=c++11 -pedantic -MMD -MP -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -I. -Imatrix -Ireads -Iqvs -Imetagenome -Isaf -Iutils -Ialignment -fPIC -MF"FASTQSequence.shared.d" -MT"FASTQSequence.shared.o FASTQSequence.shared.d" -c FASTQSequence.cpp -o FASTQSequence.shared.o
g++ -std=c++11 -pedantic -MMD -MP -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -I. -Imatrix -Ireads -Iqvs -Imetagenome -Isaf -Iutils -Ialignment -fPIC -MF"CommandLineParser.shared.d" -MT"CommandLineParser.shared.o CommandLineParser.shared.d" -c CommandLineParser.cpp -o CommandLineParser.shared.o
g++ -std=c++11 -pedantic -MMD -MP -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -I. -Imatrix -Ireads -Iqvs -Imetagenome -Isaf -Iutils -Ialignment -fPIC -MF"CCSSequence.shared.d" -MT"CCSSequence.shared.o CCSSequence.shared.d" -c CCSSequence.cpp -o CCSSequence.shared.o
g++ -std=c++11 -pedantic -MMD -MP -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -I. -Imatrix -Ireads -Iqvs -Imetagenome -Isaf -Iutils -Ialignment -fPIC -MF"PackedDNASequence.shared.d" -MT"PackedDNASequence.shared.o PackedDNASequence.shared.d" -c PackedDNASequence.cpp -o PackedDNASequence.shared.o
g++ -std=c++11 -pedantic -MMD -MP -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -I. -Imatrix -Ireads -Iqvs -Imetagenome -Isaf -Iutils -Ialignment -fPIC -MF"DNASequence.shared.d" -MT"DNASequence.shared.o DNASequence.shared.d" -c DNASequence.cpp -o DNASequence.shared.o
g++ -std=c++11 -pedantic -MMD -MP -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -I. -Imatrix -Ireads -Iqvs -Imetagenome -Isaf -Iutils -Ialignment -fPIC -MF"NucConversion.shared.d" -MT"NucConversion.shared.o NucConversion.shared.d" -c NucConversion.cpp -o NucConversion.shared.o
g++ -std=c++11 -pedantic -MMD -MP -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -I. -Imatrix -Ireads -Iqvs -Imetagenome -Isaf -Iutils -Ialignment -fPIC -MF"FASTQReader.shared.d" -MT"FASTQReader.shared.o FASTQReader.shared.d" -c FASTQReader.cpp -o FASTQReader.shared.o
g++ -std=c++11 -pedantic -MMD -MP -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -I. -Imatrix -Ireads -Iqvs -Imetagenome -Isaf -Iutils -Ialignment -fPIC -MF"FASTASequence.shared.d" -MT"FASTASequence.shared.o FASTASequence.shared.d" -c FASTASequence.cpp -o FASTASequence.shared.o
g++ -std=c++11 -pedantic -MMD -MP -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -I. -Imatrix -Ireads -Iqvs -Imetagenome -Isaf -Iutils -Ialignment -fPIC -MF"reads/RegionTable.shared.d" -MT"reads/RegionTable.shared.o reads/RegionTable.shared.d" -c reads/RegionTable.cpp -o reads/RegionTable.shared.o
g++ -std=c++11 -pedantic -MMD -MP -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -I. -Imatrix -Ireads -Iqvs -Imetagenome -Isaf -Iutils -Ialignment -fPIC -MF"reads/ScanData.shared.d" -MT"reads/ScanData.shared.o reads/ScanData.shared.d" -c reads/ScanData.cpp -o reads/ScanData.shared.o
g++ -std=c++11 -pedantic -MMD -MP -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -I. -Imatrix -Ireads -Iqvs -Imetagenome -Isaf -Iutils -Ialignment -fPIC -MF"reads/BaseFile.shared.d" -MT"reads/BaseFile.shared.o reads/BaseFile.shared.d" -c reads/BaseFile.cpp -o reads/BaseFile.shared.o
g++ -std=c++11 -pedantic -MMD -MP -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -I. -Imatrix -Ireads -Iqvs -Imetagenome -Isaf -Iutils -Ialignment -fPIC -MF"reads/ZMWGroupEntry.shared.d" -MT"reads/ZMWGroupEntry.shared.o reads/ZMWGroupEntry.shared.d" -c reads/ZMWGroupEntry.cpp -o reads/ZMWGroupEntry.shared.o
g++ -std=c++11 -pedantic -MMD -MP -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -I. -Imatrix -Ireads -Iqvs -Imetagenome -Isaf -Iutils -Ialignment -fPIC -MF"reads/PulseBaseCommon.shared.d" -MT"reads/PulseBaseCommon.shared.o reads/PulseBaseCommon.shared.d" -c reads/PulseBaseCommon.cpp -o reads/PulseBaseCommon.shared.o
g++ -std=c++11 -pedantic -MMD -MP -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -I. -Imatrix -Ireads -Iqvs -Imetagenome -Isaf -Iutils -Ialignment -fPIC -MF"reads/PulseFile.shared.d" -MT"reads/PulseFile.shared.o reads/PulseFile.shared.d" -c reads/PulseFile.cpp -o reads/PulseFile.shared.o
g++ -std=c++11 -pedantic -MMD -MP -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -I. -Imatrix -Ireads -Iqvs -Imetagenome -Isaf -Iutils -Ialignment -fPIC -MF"reads/HoleXY.shared.d" -MT"reads/HoleXY.shared.o reads/HoleXY.shared.d" -c reads/HoleXY.cpp -o reads/HoleXY.shared.o
g++ -std=c++11 -pedantic -MMD -MP -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -I. -Imatrix -Ireads -Iqvs -Imetagenome -Isaf -Iutils -Ialignment -fPIC -MF"reads/ReadType.shared.d" -MT"reads/ReadType.shared.o reads/ReadType.shared.d" -c reads/ReadType.cpp -o reads/ReadType.shared.o
g++ -std=c++11 -pedantic -MMD -MP -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -I. -Imatrix -Ireads -Iqvs -Imetagenome -Isaf -Iutils -Ialignment -fPIC -MF"metagenome/TitleTable.shared.d" -MT"metagenome/TitleTable.shared.o metagenome/TitleTable.shared.d" -c metagenome/TitleTable.cpp -o metagenome/TitleTable.shared.o
g++ -std=c++11 -pedantic -MMD -MP -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -I. -Imatrix -Ireads -Iqvs -Imetagenome -Isaf -Iutils -Ialignment -fPIC -MF"qvs/QualityTransform.shared.d" -MT"qvs/QualityTransform.shared.o qvs/QualityTransform.shared.d" -c qvs/QualityTransform.cpp -o qvs/QualityTransform.shared.o
g++ -std=c++11 -pedantic -MMD -MP -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -I. -Imatrix -Ireads -Iqvs -Imetagenome -Isaf -Iutils -Ialignment -fPIC -MF"qvs/QualityValue.shared.d" -MT"qvs/QualityValue.shared.o qvs/QualityValue.shared.d" -c qvs/QualityValue.cpp -o qvs/QualityValue.shared.o
g++ -std=c++11 -pedantic -MMD -MP -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -I. -Imatrix -Ireads -Iqvs -Imetagenome -Isaf -Iutils -Ialignment -fPIC -MF"saf/RefGroup.shared.d" -MT"saf/RefGroup.shared.o saf/RefGroup.shared.d" -c saf/RefGroup.cpp -o saf/RefGroup.shared.o
g++ -std=c++11 -pedantic -MMD -MP -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -I. -Imatrix -Ireads -Iqvs -Imetagenome -Isaf -Iutils -Ialignment -fPIC -MF"saf/RefInfo.shared.d" -MT"saf/RefInfo.shared.o saf/RefInfo.shared.d" -c saf/RefInfo.cpp -o saf/RefInfo.shared.o
g++ -std=c++11 -pedantic -MMD -MP -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -I. -Imatrix -Ireads -Iqvs -Imetagenome -Isaf -Iutils -Ialignment -fPIC -MF"saf/AlnGroup.shared.d" -MT"saf/AlnGroup.shared.o saf/AlnGroup.shared.d" -c saf/AlnGroup.cpp -o saf/AlnGroup.shared.o
g++ -std=c++11 -pedantic -MMD -MP -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -I. -Imatrix -Ireads -Iqvs -Imetagenome -Isaf -Iutils -Ialignment -fPIC -MF"saf/MovieInfo.shared.d" -MT"saf/MovieInfo.shared.o saf/MovieInfo.shared.d" -c saf/MovieInfo.cpp -o saf/MovieInfo.shared.o
g++ -std=c++11 -pedantic -MMD -MP -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -I. -Imatrix -Ireads -Iqvs -Imetagenome -Isaf -Iutils -Ialignment -fPIC -MF"utils/BitUtils.shared.d" -MT"utils/BitUtils.shared.o utils/BitUtils.shared.d" -c utils/BitUtils.cpp -o utils/BitUtils.shared.o
g++ -std=c++11 -pedantic -MMD -MP -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -I. -Imatrix -Ireads -Iqvs -Imetagenome -Isaf -Iutils -Ialignment -fPIC -MF"utils/SMRTTitle.shared.d" -MT"utils/SMRTTitle.shared.o utils/SMRTTitle.shared.d" -c utils/SMRTTitle.cpp -o utils/SMRTTitle.shared.o
g++ -std=c++11 -pedantic -MMD -MP -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -I. -Imatrix -Ireads -Iqvs -Imetagenome -Isaf -Iutils -Ialignment -fPIC -MF"utils/SMRTReadUtils.shared.d" -MT"utils/SMRTReadUtils.shared.o utils/SMRTReadUtils.shared.d" -c utils/SMRTReadUtils.cpp -o utils/SMRTReadUtils.shared.o
g++ -std=c++11 -pedantic -MMD -MP -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -I. -Imatrix -Ireads -Iqvs -Imetagenome -Isaf -Iutils -Ialignment -fPIC -MF"loadpulses/MetricField.shared.d" -MT"loadpulses/MetricField.shared.o loadpulses/MetricField.shared.d" -c loadpulses/MetricField.cpp -o loadpulses/MetricField.shared.o
g++ -std=c++11 -pedantic -MMD -MP -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -I. -Imatrix -Ireads -Iqvs -Imetagenome -Isaf -Iutils -Ialignment -fPIC -MF"loadpulses/MovieAlnIndexLookupTable.shared.d" -MT"loadpulses/MovieAlnIndexLookupTable.shared.o loadpulses/MovieAlnIndexLookupTable.shared.d" -c loadpulses/MovieAlnIndexLookupTable.cpp -o loadpulses/MovieAlnIndexLookupTable.shared.o
g++ -std=c++11 -pedantic -MMD -MP -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -I. -Imatrix -Ireads -Iqvs -Imetagenome -Isaf -Iutils -Ialignment -fPIC -MF"alignment/CmpAlignment.shared.d" -MT"alignment/CmpAlignment.shared.o alignment/CmpAlignment.shared.d" -c alignment/CmpAlignment.cpp -o alignment/CmpAlignment.shared.o
g++ -std=c++11 -pedantic -MMD -MP -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -I. -Imatrix -Ireads -Iqvs -Imetagenome -Isaf -Iutils -Ialignment -fPIC -MF"amos/AfgBasWriter.shared.d" -MT"amos/AfgBasWriter.shared.o amos/AfgBasWriter.shared.d" -c amos/AfgBasWriter.cpp -o amos/AfgBasWriter.shared.o
g++ -std=c++11 -pedantic -MMD -MP -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -I. -Imatrix -Ireads -Iqvs -Imetagenome -Isaf -Iutils -Ialignment -fPIC -MF"sam/ReferenceSequence.shared.d" -MT"sam/ReferenceSequence.shared.o sam/ReferenceSequence.shared.d" -c sam/ReferenceSequence.cpp -o sam/ReferenceSequence.shared.o
g++ -std=c++11 -pedantic -MMD -MP -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -I. -Imatrix -Ireads -Iqvs -Imetagenome -Isaf -Iutils -Ialignment -fPIC -MF"sam/SAMAlignment.shared.d" -MT"sam/SAMAlignment.shared.o sam/SAMAlignment.shared.d" -c sam/SAMAlignment.cpp -o sam/SAMAlignment.shared.o
g++ -std=c++11 -pedantic -MMD -MP -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -I. -Imatrix -Ireads -Iqvs -Imetagenome -Isaf -Iutils -Ialignment -fPIC -MF"sam/SAMHeader.shared.d" -MT"sam/SAMHeader.shared.o sam/SAMHeader.shared.d" -c sam/SAMHeader.cpp -o sam/SAMHeader.shared.o
g++ -std=c++11 -pedantic -MMD -MP -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -I. -Imatrix -Ireads -Iqvs -Imetagenome -Isaf -Iutils -Ialignment -fPIC -MF"sam/ReadGroup.shared.d" -MT"sam/ReadGroup.shared.o sam/ReadGroup.shared.d" -c sam/ReadGroup.cpp -o sam/ReadGroup.shared.o
g++ -std=c++11 -pedantic -MMD -MP -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -I. -Imatrix -Ireads -Iqvs -Imetagenome -Isaf -Iutils -Ialignment -fPIC -MF"sam/SAMKeywordValuePair.shared.d" -MT"sam/SAMKeywordValuePair.shared.o sam/SAMKeywordValuePair.shared.d" -c sam/SAMKeywordValuePair.cpp -o sam/SAMKeywordValuePair.shared.o
g++ -shared -fPIC -o libpbdata.so -Wl,-soname,libpbdata.so GFFFile.shared.o ChangeListID.shared.o StringUtils.shared.o SMRTSequence.shared.o MD5Utils.shared.o ReverseCompressIndex.shared.o FASTAReader.shared.o FASTQSequence.shared.o CommandLineParser.shared.o CCSSequence.shared.o PackedDNASequence.shared.o DNASequence.shared.o NucConversion.shared.o FASTQReader.shared.o FASTASequence.shared.o reads/RegionTable.shared.o reads/ScanData.shared.o reads/BaseFile.shared.o reads/ZMWGroupEntry.shared.o reads/PulseBaseCommon.shared.o reads/PulseFile.shared.o reads/HoleXY.shared.o reads/ReadType.shared.o metagenome/TitleTable.shared.o qvs/QualityTransform.shared.o qvs/QualityValue.shared.o saf/RefGroup.shared.o saf/RefInfo.shared.o saf/AlnGroup.shared.o saf/MovieInfo.shared.o utils/BitUtils.shared.o utils/SMRTTitle.shared.o utils/SMRTReadUtils.shared.o loadpulses/MetricField.shared.o loadpulses/MovieAlnIndexLookupTable.shared.o alignment/CmpAlignment.shared.o amos/AfgBasWriter.shared.o sam/ReferenceSequence.shared.o sam/SAMAlignment.shared.o sam/SAMHeader.shared.o sam/ReadGroup.shared.o sam/SAMKeywordValuePair.shared.o
make[4]: Leaving directory '/«BUILDDIR»/blasr-0~20150724+git3ca7fe8/libcpp/pbdata'
/usr/bin/make -C hdf all
make[4]: Entering directory '/«BUILDDIR»/blasr-0~20150724+git3ca7fe8/libcpp/hdf'
g++ -std=c++11 -pedantic -MMD -MP -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -I../pbdata -I/usr/include/hdf5/serial -MF"HDFAttributable.d" -MT"HDFAttributable.o HDFAttributable.d" -c HDFAttributable.cpp -o HDFAttributable.o
g++ -std=c++11 -pedantic -MMD -MP -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -I../pbdata -I/usr/include/hdf5/serial -MF"HDFScanDataReader.d" -MT"HDFScanDataReader.o HDFScanDataReader.d" -c HDFScanDataReader.cpp -o HDFScanDataReader.o
g++ -std=c++11 -pedantic -MMD -MP -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -I../pbdata -I/usr/include/hdf5/serial -MF"DatasetCollection.d" -MT"DatasetCollection.o DatasetCollection.d" -c DatasetCollection.cpp -o DatasetCollection.o
g++ -std=c++11 -pedantic -MMD -MP -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -I../pbdata -I/usr/include/hdf5/serial -MF"HDFRegionTableReader.d" -MT"HDFRegionTableReader.o HDFRegionTableReader.d" -c HDFRegionTableReader.cpp -o HDFRegionTableReader.o
g++ -std=c++11 -pedantic -MMD -MP -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -I../pbdata -I/usr/include/hdf5/serial -MF"HDFBasReader.d" -MT"HDFBasReader.o HDFBasReader.d" -c HDFBasReader.cpp -o HDFBasReader.o
g++ -std=c++11 -pedantic -MMD -MP -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -I../pbdata -I/usr/include/hdf5/serial -MF"HDFAtom.d" -MT"HDFAtom.o HDFAtom.d" -c HDFAtom.cpp -o HDFAtom.o
g++ -std=c++11 -pedantic -MMD -MP -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -I../pbdata -I/usr/include/hdf5/serial -MF"HDFCmpExperimentGroup.d" -MT"HDFCmpExperimentGroup.o HDFCmpExperimentGroup.d" -c HDFCmpExperimentGroup.cpp -o HDFCmpExperimentGroup.o
g++ -std=c++11 -pedantic -MMD -MP -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -I../pbdata -I/usr/include/hdf5/serial -MF"HDFPulseDataFile.d" -MT"HDFPulseDataFile.o HDFPulseDataFile.d" -c HDFPulseDataFile.cpp -o HDFPulseDataFile.o
g++ -std=c++11 -pedantic -MMD -MP -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -I../pbdata -I/usr/include/hdf5/serial -MF"HDFCmpSupportedFields.d" -MT"HDFCmpSupportedFields.o HDFCmpSupportedFields.d" -c HDFCmpSupportedFields.cpp -o HDFCmpSupportedFields.o
g++ -std=c++11 -pedantic -MMD -MP -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -I../pbdata -I/usr/include/hdf5/serial -MF"HDFZMWReader.d" -MT"HDFZMWReader.o HDFZMWReader.d" -c HDFZMWReader.cpp -o HDFZMWReader.o
g++ -std=c++11 -pedantic -MMD -MP -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -I../pbdata -I/usr/include/hdf5/serial -MF"HDFAlnGroupGroup.d" -MT"HDFAlnGroupGroup.o HDFAlnGroupGroup.d" -c HDFAlnGroupGroup.cpp -o HDFAlnGroupGroup.o
g++ -std=c++11 -pedantic -MMD -MP -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -I../pbdata -I/usr/include/hdf5/serial -MF"HDFFile.d" -MT"HDFFile.o HDFFile.d" -c HDFFile.cpp -o HDFFile.o
g++ -std=c++11 -pedantic -MMD -MP -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -I../pbdata -I/usr/include/hdf5/serial -MF"HDFAlnInfoGroup.d" -MT"HDFAlnInfoGroup.o HDFAlnInfoGroup.d" -c HDFAlnInfoGroup.cpp -o HDFAlnInfoGroup.o
g++ -std=c++11 -pedantic -MMD -MP -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -I../pbdata -I/usr/include/hdf5/serial -MF"HDFNewBasReader.d" -MT"HDFNewBasReader.o HDFNewBasReader.d" -c HDFNewBasReader.cpp -o HDFNewBasReader.o
g++ -std=c++11 -pedantic -MMD -MP -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -I../pbdata -I/usr/include/hdf5/serial -MF"HDFGroup.d" -MT"HDFGroup.o HDFGroup.d" -c HDFGroup.cpp -o HDFGroup.o
g++ -std=c++11 -pedantic -MMD -MP -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -I../pbdata -I/usr/include/hdf5/serial -MF"HDFUtils.d" -MT"HDFUtils.o HDFUtils.d" -c HDFUtils.cpp -o HDFUtils.o
g++ -std=c++11 -pedantic -MMD -MP -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -I../pbdata -I/usr/include/hdf5/serial -MF"HDFScanDataWriter.d" -MT"HDFScanDataWriter.o HDFScanDataWriter.d" -c HDFScanDataWriter.cpp -o HDFScanDataWriter.o
g++ -std=c++11 -pedantic -MMD -MP -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -I../pbdata -I/usr/include/hdf5/serial -MF"HDFData.d" -MT"HDFData.o HDFData.d" -c HDFData.cpp -o HDFData.o
g++ -std=c++11 -pedantic -MMD -MP -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -I../pbdata -I/usr/include/hdf5/serial -MF"BufferedHDFArray.d" -MT"BufferedHDFArray.o BufferedHDFArray.d" -c BufferedHDFArray.cpp -o BufferedHDFArray.o
g++ -std=c++11 -pedantic -MMD -MP -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -I../pbdata -I/usr/include/hdf5/serial -MF"BufferedHDF2DArray.d" -MT"BufferedHDF2DArray.o BufferedHDF2DArray.d" -c BufferedHDF2DArray.cpp -o BufferedHDF2DArray.o
ar rc libpbihdf.a HDFAttributable.o HDFScanDataReader.o DatasetCollection.o HDFRegionTableReader.o HDFBasReader.o HDFAtom.o HDFCmpExperimentGroup.o HDFPulseDataFile.o HDFCmpSupportedFields.o HDFZMWReader.o HDFAlnGroupGroup.o HDFFile.o HDFAlnInfoGroup.o HDFNewBasReader.o HDFGroup.o HDFUtils.o HDFScanDataWriter.o HDFData.o BufferedHDFArray.o BufferedHDF2DArray.o
g++ -std=c++11 -pedantic -MMD -MP -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -I../pbdata -I/usr/include/hdf5/serial -fPIC -MF"HDFAttributable.shared.d" -MT"HDFAttributable.shared.o HDFAttributable.shared.d" -c HDFAttributable.cpp -o HDFAttributable.shared.o
g++ -std=c++11 -pedantic -MMD -MP -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -I../pbdata -I/usr/include/hdf5/serial -fPIC -MF"HDFScanDataReader.shared.d" -MT"HDFScanDataReader.shared.o HDFScanDataReader.shared.d" -c HDFScanDataReader.cpp -o HDFScanDataReader.shared.o
g++ -std=c++11 -pedantic -MMD -MP -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -I../pbdata -I/usr/include/hdf5/serial -fPIC -MF"DatasetCollection.shared.d" -MT"DatasetCollection.shared.o DatasetCollection.shared.d" -c DatasetCollection.cpp -o DatasetCollection.shared.o
g++ -std=c++11 -pedantic -MMD -MP -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -I../pbdata -I/usr/include/hdf5/serial -fPIC -MF"HDFRegionTableReader.shared.d" -MT"HDFRegionTableReader.shared.o HDFRegionTableReader.shared.d" -c HDFRegionTableReader.cpp -o HDFRegionTableReader.shared.o
g++ -std=c++11 -pedantic -MMD -MP -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -I../pbdata -I/usr/include/hdf5/serial -fPIC -MF"HDFBasReader.shared.d" -MT"HDFBasReader.shared.o HDFBasReader.shared.d" -c HDFBasReader.cpp -o HDFBasReader.shared.o
g++ -std=c++11 -pedantic -MMD -MP -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -I../pbdata -I/usr/include/hdf5/serial -fPIC -MF"HDFAtom.shared.d" -MT"HDFAtom.shared.o HDFAtom.shared.d" -c HDFAtom.cpp -o HDFAtom.shared.o
g++ -std=c++11 -pedantic -MMD -MP -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -I../pbdata -I/usr/include/hdf5/serial -fPIC -MF"HDFCmpExperimentGroup.shared.d" -MT"HDFCmpExperimentGroup.shared.o HDFCmpExperimentGroup.shared.d" -c HDFCmpExperimentGroup.cpp -o HDFCmpExperimentGroup.shared.o
g++ -std=c++11 -pedantic -MMD -MP -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -I../pbdata -I/usr/include/hdf5/serial -fPIC -MF"HDFPulseDataFile.shared.d" -MT"HDFPulseDataFile.shared.o HDFPulseDataFile.shared.d" -c HDFPulseDataFile.cpp -o HDFPulseDataFile.shared.o
g++ -std=c++11 -pedantic -MMD -MP -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -I../pbdata -I/usr/include/hdf5/serial -fPIC -MF"HDFCmpSupportedFields.shared.d" -MT"HDFCmpSupportedFields.shared.o HDFCmpSupportedFields.shared.d" -c HDFCmpSupportedFields.cpp -o HDFCmpSupportedFields.shared.o
g++ -std=c++11 -pedantic -MMD -MP -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -I../pbdata -I/usr/include/hdf5/serial -fPIC -MF"HDFZMWReader.shared.d" -MT"HDFZMWReader.shared.o HDFZMWReader.shared.d" -c HDFZMWReader.cpp -o HDFZMWReader.shared.o
g++ -std=c++11 -pedantic -MMD -MP -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -I../pbdata -I/usr/include/hdf5/serial -fPIC -MF"HDFAlnGroupGroup.shared.d" -MT"HDFAlnGroupGroup.shared.o HDFAlnGroupGroup.shared.d" -c HDFAlnGroupGroup.cpp -o HDFAlnGroupGroup.shared.o
g++ -std=c++11 -pedantic -MMD -MP -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -I../pbdata -I/usr/include/hdf5/serial -fPIC -MF"HDFFile.shared.d" -MT"HDFFile.shared.o HDFFile.shared.d" -c HDFFile.cpp -o HDFFile.shared.o
g++ -std=c++11 -pedantic -MMD -MP -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -I../pbdata -I/usr/include/hdf5/serial -fPIC -MF"HDFAlnInfoGroup.shared.d" -MT"HDFAlnInfoGroup.shared.o HDFAlnInfoGroup.shared.d" -c HDFAlnInfoGroup.cpp -o HDFAlnInfoGroup.shared.o
g++ -std=c++11 -pedantic -MMD -MP -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -I../pbdata -I/usr/include/hdf5/serial -fPIC -MF"HDFNewBasReader.shared.d" -MT"HDFNewBasReader.shared.o HDFNewBasReader.shared.d" -c HDFNewBasReader.cpp -o HDFNewBasReader.shared.o
g++ -std=c++11 -pedantic -MMD -MP -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -I../pbdata -I/usr/include/hdf5/serial -fPIC -MF"HDFGroup.shared.d" -MT"HDFGroup.shared.o HDFGroup.shared.d" -c HDFGroup.cpp -o HDFGroup.shared.o
g++ -std=c++11 -pedantic -MMD -MP -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -I../pbdata -I/usr/include/hdf5/serial -fPIC -MF"HDFUtils.shared.d" -MT"HDFUtils.shared.o HDFUtils.shared.d" -c HDFUtils.cpp -o HDFUtils.shared.o
g++ -std=c++11 -pedantic -MMD -MP -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -I../pbdata -I/usr/include/hdf5/serial -fPIC -MF"HDFScanDataWriter.shared.d" -MT"HDFScanDataWriter.shared.o HDFScanDataWriter.shared.d" -c HDFScanDataWriter.cpp -o HDFScanDataWriter.shared.o
g++ -std=c++11 -pedantic -MMD -MP -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -I../pbdata -I/usr/include/hdf5/serial -fPIC -MF"HDFData.shared.d" -MT"HDFData.shared.o HDFData.shared.d" -c HDFData.cpp -o HDFData.shared.o
g++ -std=c++11 -pedantic -MMD -MP -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -I../pbdata -I/usr/include/hdf5/serial -fPIC -MF"BufferedHDFArray.shared.d" -MT"BufferedHDFArray.shared.o BufferedHDFArray.shared.d" -c BufferedHDFArray.cpp -o BufferedHDFArray.shared.o
g++ -std=c++11 -pedantic -MMD -MP -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -I../pbdata -I/usr/include/hdf5/serial -fPIC -MF"BufferedHDF2DArray.shared.d" -MT"BufferedHDF2DArray.shared.o BufferedHDF2DArray.shared.d" -c BufferedHDF2DArray.cpp -o BufferedHDF2DArray.shared.o
g++ -shared -fPIC -o libpbihdf.so -Wl,-soname,libpbihdf.so HDFAttributable.shared.o HDFScanDataReader.shared.o DatasetCollection.shared.o HDFRegionTableReader.shared.o HDFBasReader.shared.o HDFAtom.shared.o HDFCmpExperimentGroup.shared.o HDFPulseDataFile.shared.o HDFCmpSupportedFields.shared.o HDFZMWReader.shared.o HDFAlnGroupGroup.shared.o HDFFile.shared.o HDFAlnInfoGroup.shared.o HDFNewBasReader.shared.o HDFGroup.shared.o HDFUtils.shared.o HDFScanDataWriter.shared.o HDFData.shared.o BufferedHDFArray.shared.o BufferedHDF2DArray.shared.o ../pbdata/libpbdata.so /usr/lib/arm-linux-gnueabihf/hdf5/serial/libhdf5.so
make[4]: Leaving directory '/«BUILDDIR»/blasr-0~20150724+git3ca7fe8/libcpp/hdf'
/usr/bin/make -C alignment all
make[4]: Entering directory '/«BUILDDIR»/blasr-0~20150724+git3ca7fe8/libcpp/alignment'
g++ -std=c++11 -pedantic -MMD -MP -Wno-long-long -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -I. -I../pbdata -I../hdf -I/usr/include/hdf5/serial -MF"algorithms/alignment/BaseScoreFunction.d" -MT"algorithms/alignment/BaseScoreFunction.o algorithms/alignment/BaseScoreFunction.d" -c algorithms/alignment/BaseScoreFunction.cpp -o algorithms/alignment/BaseScoreFunction.o
g++ -std=c++11 -pedantic -MMD -MP -Wno-long-long -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -I. -I../pbdata -I../hdf -I/usr/include/hdf5/serial -MF"algorithms/alignment/AlignmentUtils.d" -MT"algorithms/alignment/AlignmentUtils.o algorithms/alignment/AlignmentUtils.d" -c algorithms/alignment/AlignmentUtils.cpp -o algorithms/alignment/AlignmentUtils.o
g++ -std=c++11 -pedantic -MMD -MP -Wno-long-long -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -I. -I../pbdata -I../hdf -I/usr/include/hdf5/serial -MF"algorithms/alignment/ExtendAlign.d" -MT"algorithms/alignment/ExtendAlign.o algorithms/alignment/ExtendAlign.d" -c algorithms/alignment/ExtendAlign.cpp -o algorithms/alignment/ExtendAlign.o
g++ -std=c++11 -pedantic -MMD -MP -Wno-long-long -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -I. -I../pbdata -I../hdf -I/usr/include/hdf5/serial -MF"algorithms/alignment/GuidedAlign.d" -MT"algorithms/alignment/GuidedAlign.o algorithms/alignment/GuidedAlign.d" -c algorithms/alignment/GuidedAlign.cpp -o algorithms/alignment/GuidedAlign.o
g++ -std=c++11 -pedantic -MMD -MP -Wno-long-long -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -I. -I../pbdata -I../hdf -I/usr/include/hdf5/serial -MF"algorithms/alignment/QualityValueScoreFunction.d" -MT"algorithms/alignment/QualityValueScoreFunction.o algorithms/alignment/QualityValueScoreFunction.d" -c algorithms/alignment/QualityValueScoreFunction.cpp -o algorithms/alignment/QualityValueScoreFunction.o
g++ -std=c++11 -pedantic -MMD -MP -Wno-long-long -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -I. -I../pbdata -I../hdf -I/usr/include/hdf5/serial -MF"algorithms/alignment/IDSScoreFunction.d" -MT"algorithms/alignment/IDSScoreFunction.o algorithms/alignment/IDSScoreFunction.d" -c algorithms/alignment/IDSScoreFunction.cpp -o algorithms/alignment/IDSScoreFunction.o
g++ -std=c++11 -pedantic -MMD -MP -Wno-long-long -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -I. -I../pbdata -I../hdf -I/usr/include/hdf5/serial -MF"algorithms/alignment/StringToScoreMatrix.d" -MT"algorithms/alignment/StringToScoreMatrix.o algorithms/alignment/StringToScoreMatrix.d" -c algorithms/alignment/StringToScoreMatrix.cpp -o algorithms/alignment/StringToScoreMatrix.o
g++ -std=c++11 -pedantic -MMD -MP -Wno-long-long -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -I. -I../pbdata -I../hdf -I/usr/include/hdf5/serial -MF"algorithms/alignment/ScoreMatrices.d" -MT"algorithms/alignment/ScoreMatrices.o algorithms/alignment/ScoreMatrices.d" -c algorithms/alignment/ScoreMatrices.cpp -o algorithms/alignment/ScoreMatrices.o
g++ -std=c++11 -pedantic -MMD -MP -Wno-long-long -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -I. -I../pbdata -I../hdf -I/usr/include/hdf5/serial -MF"algorithms/alignment/KBandAlign.d" -MT"algorithms/alignment/KBandAlign.o algorithms/alignment/KBandAlign.d" -c algorithms/alignment/KBandAlign.cpp -o algorithms/alignment/KBandAlign.o
g++ -std=c++11 -pedantic -MMD -MP -Wno-long-long -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -I. -I../pbdata -I../hdf -I/usr/include/hdf5/serial -MF"algorithms/alignment/sdp/SparseDynamicProgramming.d" -MT"algorithms/alignment/sdp/SparseDynamicProgramming.o algorithms/alignment/sdp/SparseDynamicProgramming.d" -c algorithms/alignment/sdp/SparseDynamicProgramming.cpp -o algorithms/alignment/sdp/SparseDynamicProgramming.o
g++ -std=c++11 -pedantic -MMD -MP -Wno-long-long -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -I. -I../pbdata -I../hdf -I/usr/include/hdf5/serial -MF"algorithms/alignment/sdp/SDPFragment.d" -MT"algorithms/alignment/sdp/SDPFragment.o algorithms/alignment/sdp/SDPFragment.d" -c algorithms/alignment/sdp/SDPFragment.cpp -o algorithms/alignment/sdp/SDPFragment.o
g++ -std=c++11 -pedantic -MMD -MP -Wno-long-long -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -I. -I../pbdata -I../hdf -I/usr/include/hdf5/serial -MF"algorithms/anchoring/Coordinate.d" -MT"algorithms/anchoring/Coordinate.o algorithms/anchoring/Coordinate.d" -c algorithms/anchoring/Coordinate.cpp -o algorithms/anchoring/Coordinate.o
g++ -std=c++11 -pedantic -MMD -MP -Wno-long-long -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -I. -I../pbdata -I../hdf -I/usr/include/hdf5/serial -MF"algorithms/anchoring/ClusterProbability.d" -MT"algorithms/anchoring/ClusterProbability.o algorithms/anchoring/ClusterProbability.d" -c algorithms/anchoring/ClusterProbability.cpp -o algorithms/anchoring/ClusterProbability.o
g++ -std=c++11 -pedantic -MMD -MP -Wno-long-long -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -I. -I../pbdata -I../hdf -I/usr/include/hdf5/serial -MF"algorithms/anchoring/FindMaxInterval.d" -MT"algorithms/anchoring/FindMaxInterval.o algorithms/anchoring/FindMaxInterval.d" -c algorithms/anchoring/FindMaxInterval.cpp -o algorithms/anchoring/FindMaxInterval.o
g++ -std=c++11 -pedantic -MMD -MP -Wno-long-long -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -I. -I../pbdata -I../hdf -I/usr/include/hdf5/serial -MF"algorithms/anchoring/BWTSearch.d" -MT"algorithms/anchoring/BWTSearch.o algorithms/anchoring/BWTSearch.d" -c algorithms/anchoring/BWTSearch.cpp -o algorithms/anchoring/BWTSearch.o
g++ -std=c++11 -pedantic -MMD -MP -Wno-long-long -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -I. -I../pbdata -I../hdf -I/usr/include/hdf5/serial -MF"algorithms/sorting/LightweightSuffixArray.d" -MT"algorithms/sorting/LightweightSuffixArray.o algorithms/sorting/LightweightSuffixArray.d" -c algorithms/sorting/LightweightSuffixArray.cpp -o algorithms/sorting/LightweightSuffixArray.o
g++ -std=c++11 -pedantic -MMD -MP -Wno-long-long -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -I. -I../pbdata -I../hdf -I/usr/include/hdf5/serial -MF"algorithms/sorting/qsufsort.d" -MT"algorithms/sorting/qsufsort.o algorithms/sorting/qsufsort.d" -c algorithms/sorting/qsufsort.cpp -o algorithms/sorting/qsufsort.o
g++ -std=c++11 -pedantic -MMD -MP -Wno-long-long -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -I. -I../pbdata -I../hdf -I/usr/include/hdf5/serial -MF"algorithms/sorting/DifferenceCovers.d" -MT"algorithms/sorting/DifferenceCovers.o algorithms/sorting/DifferenceCovers.d" -c algorithms/sorting/DifferenceCovers.cpp -o algorithms/sorting/DifferenceCovers.o
g++ -std=c++11 -pedantic -MMD -MP -Wno-long-long -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -I. -I../pbdata -I../hdf -I/usr/include/hdf5/serial -MF"algorithms/sorting/MultikeyQuicksort.d" -MT"algorithms/sorting/MultikeyQuicksort.o algorithms/sorting/MultikeyQuicksort.d" -c algorithms/sorting/MultikeyQuicksort.cpp -o algorithms/sorting/MultikeyQuicksort.o
g++ -std=c++11 -pedantic -MMD -MP -Wno-long-long -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -I. -I../pbdata -I../hdf -I/usr/include/hdf5/serial -MF"datastructures/alignment/AlignmentContext.d" -MT"datastructures/alignment/AlignmentContext.o datastructures/alignment/AlignmentContext.d" -c datastructures/alignment/AlignmentContext.cpp -o datastructures/alignment/AlignmentContext.o
g++ -std=c++11 -pedantic -MMD -MP -Wno-long-long -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -I. -I../pbdata -I../hdf -I/usr/include/hdf5/serial -MF"datastructures/alignment/AlignmentCandidate.d" -MT"datastructures/alignment/AlignmentCandidate.o datastructures/alignment/AlignmentCandidate.d" -c datastructures/alignment/AlignmentCandidate.cpp -o datastructures/alignment/AlignmentCandidate.o
g++ -std=c++11 -pedantic -MMD -MP -Wno-long-long -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -I. -I../pbdata -I../hdf -I/usr/include/hdf5/serial -MF"datastructures/alignment/CmpFile.d" -MT"datastructures/alignment/CmpFile.o datastructures/alignment/CmpFile.d" -c datastructures/alignment/CmpFile.cpp -o datastructures/alignment/CmpFile.o
g++ -std=c++11 -pedantic -MMD -MP -Wno-long-long -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -I. -I../pbdata -I../hdf -I/usr/include/hdf5/serial -MF"datastructures/alignment/AlignmentStats.d" -MT"datastructures/alignment/AlignmentStats.o datastructures/alignment/AlignmentStats.d" -c datastructures/alignment/AlignmentStats.cpp -o datastructures/alignment/AlignmentStats.o
g++ -std=c++11 -pedantic -MMD -MP -Wno-long-long -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -I. -I../pbdata -I../hdf -I/usr/include/hdf5/serial -MF"datastructures/alignment/FilterCriteria.d" -MT"datastructures/alignment/FilterCriteria.o datastructures/alignment/FilterCriteria.d" -c datastructures/alignment/FilterCriteria.cpp -o datastructures/alignment/FilterCriteria.o
g++ -std=c++11 -pedantic -MMD -MP -Wno-long-long -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -I. -I../pbdata -I../hdf -I/usr/include/hdf5/serial -MF"datastructures/alignment/Alignment.d" -MT"datastructures/alignment/Alignment.o datastructures/alignment/Alignment.d" -c datastructures/alignment/Alignment.cpp -o datastructures/alignment/Alignment.o
g++ -std=c++11 -pedantic -MMD -MP -Wno-long-long -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -I. -I../pbdata -I../hdf -I/usr/include/hdf5/serial -MF"datastructures/alignment/SAMToAlignmentCandidateAdapter.d" -MT"datastructures/alignment/SAMToAlignmentCandidateAdapter.o datastructures/alignment/SAMToAlignmentCandidateAdapter.d" -c datastructures/alignment/SAMToAlignmentCandidateAdapter.cpp -o datastructures/alignment/SAMToAlignmentCandidateAdapter.o
g++ -std=c++11 -pedantic -MMD -MP -Wno-long-long -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -I. -I../pbdata -I../hdf -I/usr/include/hdf5/serial -MF"datastructures/alignment/AlignmentMap.d" -MT"datastructures/alignment/AlignmentMap.o datastructures/alignment/AlignmentMap.d" -c datastructures/alignment/AlignmentMap.cpp -o datastructures/alignment/AlignmentMap.o
g++ -std=c++11 -pedantic -MMD -MP -Wno-long-long -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -I. -I../pbdata -I../hdf -I/usr/include/hdf5/serial -MF"datastructures/alignmentset/SAMSupplementalQVList.d" -MT"datastructures/alignmentset/SAMSupplementalQVList.o datastructures/alignmentset/SAMSupplementalQVList.d" -c datastructures/alignmentset/SAMSupplementalQVList.cpp -o datastructures/alignmentset/SAMSupplementalQVList.o
g++ -std=c++11 -pedantic -MMD -MP -Wno-long-long -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -I. -I../pbdata -I../hdf -I/usr/include/hdf5/serial -MF"datastructures/alignmentset/SAMQVConversion.d" -MT"datastructures/alignmentset/SAMQVConversion.o datastructures/alignmentset/SAMQVConversion.d" -c datastructures/alignmentset/SAMQVConversion.cpp -o datastructures/alignmentset/SAMQVConversion.o
g++ -std=c++11 -pedantic -MMD -MP -Wno-long-long -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -I. -I../pbdata -I../hdf -I/usr/include/hdf5/serial -MF"datastructures/anchoring/AnchorParameters.d" -MT"datastructures/anchoring/AnchorParameters.o datastructures/anchoring/AnchorParameters.d" -c datastructures/anchoring/AnchorParameters.cpp -o datastructures/anchoring/AnchorParameters.o
g++ -std=c++11 -pedantic -MMD -MP -Wno-long-long -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -I. -I../pbdata -I../hdf -I/usr/include/hdf5/serial -MF"datastructures/anchoring/MatchPos.d" -MT"datastructures/anchoring/MatchPos.o datastructures/anchoring/MatchPos.d" -c datastructures/anchoring/MatchPos.cpp -o datastructures/anchoring/MatchPos.o
g++ -std=c++11 -pedantic -MMD -MP -Wno-long-long -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -I. -I../pbdata -I../hdf -I/usr/include/hdf5/serial -MF"datastructures/anchoring/WeightedInterval.d" -MT"datastructures/anchoring/WeightedInterval.o datastructures/anchoring/WeightedInterval.d" -c datastructures/anchoring/WeightedInterval.cpp -o datastructures/anchoring/WeightedInterval.o
g++ -std=c++11 -pedantic -MMD -MP -Wno-long-long -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -I. -I../pbdata -I../hdf -I/usr/include/hdf5/serial -MF"datastructures/anchoring/ClusterList.d" -MT"datastructures/anchoring/ClusterList.o datastructures/anchoring/ClusterList.d" -c datastructures/anchoring/ClusterList.cpp -o datastructures/anchoring/ClusterList.o
g++ -std=c++11 -pedantic -MMD -MP -Wno-long-long -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -I. -I../pbdata -I../hdf -I/usr/include/hdf5/serial -MF"qvs/QualityValueProfile.d" -MT"qvs/QualityValueProfile.o qvs/QualityValueProfile.d" -c qvs/QualityValueProfile.cpp -o qvs/QualityValueProfile.o
g++ -std=c++11 -pedantic -MMD -MP -Wno-long-long -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -I. -I../pbdata -I../hdf -I/usr/include/hdf5/serial -MF"statistics/pdfs.d" -MT"statistics/pdfs.o statistics/pdfs.d" -c statistics/pdfs.cpp -o statistics/pdfs.o
g++ -std=c++11 -pedantic -MMD -MP -Wno-long-long -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -I. -I../pbdata -I../hdf -I/usr/include/hdf5/serial -MF"statistics/LookupAnchorDistribution.d" -MT"statistics/LookupAnchorDistribution.o statistics/LookupAnchorDistribution.d" -c statistics/LookupAnchorDistribution.cpp -o statistics/LookupAnchorDistribution.o
g++ -std=c++11 -pedantic -MMD -MP -Wno-long-long -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -I. -I../pbdata -I../hdf -I/usr/include/hdf5/serial -MF"statistics/cdfs.d" -MT"statistics/cdfs.o statistics/cdfs.d" -c statistics/cdfs.cpp -o statistics/cdfs.o
g++ -std=c++11 -pedantic -MMD -MP -Wno-long-long -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -I. -I../pbdata -I../hdf -I/usr/include/hdf5/serial -MF"statistics/StatUtils.d" -MT"statistics/StatUtils.o statistics/StatUtils.d" -c statistics/StatUtils.cpp -o statistics/StatUtils.o
g++ -std=c++11 -pedantic -MMD -MP -Wno-long-long -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -I. -I../pbdata -I../hdf -I/usr/include/hdf5/serial -MF"tuples/BaseTuple.d" -MT"tuples/BaseTuple.o tuples/BaseTuple.d" -c tuples/BaseTuple.cpp -o tuples/BaseTuple.o
g++ -std=c++11 -pedantic -MMD -MP -Wno-long-long -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -I. -I../pbdata -I../hdf -I/usr/include/hdf5/serial -MF"tuples/DNATuple.d" -MT"tuples/DNATuple.o tuples/DNATuple.d" -c tuples/DNATuple.cpp -o tuples/DNATuple.o
g++ -std=c++11 -pedantic -MMD -MP -Wno-long-long -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -I. -I../pbdata -I../hdf -I/usr/include/hdf5/serial -MF"tuples/TupleMetrics.d" -MT"tuples/TupleMetrics.o tuples/TupleMetrics.d" -c tuples/TupleMetrics.cpp -o tuples/TupleMetrics.o
g++ -std=c++11 -pedantic -MMD -MP -Wno-long-long -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -I. -I../pbdata -I../hdf -I/usr/include/hdf5/serial -MF"utils/RegionUtils.d" -MT"utils/RegionUtils.o utils/RegionUtils.d" -c utils/RegionUtils.cpp -o utils/RegionUtils.o
g++ -std=c++11 -pedantic -MMD -MP -Wno-long-long -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -I. -I../pbdata -I../hdf -I/usr/include/hdf5/serial -MF"utils/FileOfFileNames.d" -MT"utils/FileOfFileNames.o utils/FileOfFileNames.d" -c utils/FileOfFileNames.cpp -o utils/FileOfFileNames.o
g++ -std=c++11 -pedantic -MMD -MP -Wno-long-long -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -I. -I../pbdata -I../hdf -I/usr/include/hdf5/serial -MF"utils/LogUtils.d" -MT"utils/LogUtils.o utils/LogUtils.d" -c utils/LogUtils.cpp -o utils/LogUtils.o
g++ -std=c++11 -pedantic -MMD -MP -Wno-long-long -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -I. -I../pbdata -I../hdf -I/usr/include/hdf5/serial -MF"utils/TimeUtils.d" -MT"utils/TimeUtils.o utils/TimeUtils.d" -c utils/TimeUtils.cpp -o utils/TimeUtils.o
g++ -std=c++11 -pedantic -MMD -MP -Wno-long-long -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -I. -I../pbdata -I../hdf -I/usr/include/hdf5/serial -MF"utils/PhredUtils.d" -MT"utils/PhredUtils.o utils/PhredUtils.d" -c utils/PhredUtils.cpp -o utils/PhredUtils.o
g++ -std=c++11 -pedantic -MMD -MP -Wno-long-long -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -I. -I../pbdata -I../hdf -I/usr/include/hdf5/serial -MF"utils/RangeUtils.d" -MT"utils/RangeUtils.o utils/RangeUtils.d" -c utils/RangeUtils.cpp -o utils/RangeUtils.o
g++ -std=c++11 -pedantic -MMD -MP -Wno-long-long -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -I. -I../pbdata -I../hdf -I/usr/include/hdf5/serial -MF"utils/FileUtils.d" -MT"utils/FileUtils.o utils/FileUtils.d" -c utils/FileUtils.cpp -o utils/FileUtils.o
g++ -std=c++11 -pedantic -MMD -MP -Wno-long-long -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -I. -I../pbdata -I../hdf -I/usr/include/hdf5/serial -MF"files/ReaderAgglomerate.d" -MT"files/ReaderAgglomerate.o files/ReaderAgglomerate.d" -c files/ReaderAgglomerate.cpp -o files/ReaderAgglomerate.o
g++ -std=c++11 -pedantic -MMD -MP -Wno-long-long -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -I. -I../pbdata -I../hdf -I/usr/include/hdf5/serial -MF"files/FragmentCCSIterator.d" -MT"files/FragmentCCSIterator.o files/FragmentCCSIterator.d" -c files/FragmentCCSIterator.cpp -o files/FragmentCCSIterator.o
g++ -std=c++11 -pedantic -MMD -MP -Wno-long-long -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -I. -I../pbdata -I../hdf -I/usr/include/hdf5/serial -MF"files/CCSIterator.d" -MT"files/CCSIterator.o files/CCSIterator.d" -c files/CCSIterator.cpp -o files/CCSIterator.o
g++ -std=c++11 -pedantic -MMD -MP -Wno-long-long -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -I. -I../pbdata -I../hdf -I/usr/include/hdf5/serial -MF"files/BaseSequenceIO.d" -MT"files/BaseSequenceIO.o files/BaseSequenceIO.d" -c files/BaseSequenceIO.cpp -o files/BaseSequenceIO.o
g++ -std=c++11 -pedantic -MMD -MP -Wno-long-long -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -I. -I../pbdata -I../hdf -I/usr/include/hdf5/serial -MF"format/SAMPrinter.d" -MT"format/SAMPrinter.o format/SAMPrinter.d" -c format/SAMPrinter.cpp -o format/SAMPrinter.o
g++ -std=c++11 -pedantic -MMD -MP -Wno-long-long -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -I. -I../pbdata -I../hdf -I/usr/include/hdf5/serial -MF"format/CompareSequencesPrinter.d" -MT"format/CompareSequencesPrinter.o format/CompareSequencesPrinter.d" -c format/CompareSequencesPrinter.cpp -o format/CompareSequencesPrinter.o
g++ -std=c++11 -pedantic -MMD -MP -Wno-long-long -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -I. -I../pbdata -I../hdf -I/usr/include/hdf5/serial -MF"format/SAMHeaderPrinter.d" -MT"format/SAMHeaderPrinter.o format/SAMHeaderPrinter.d" -c format/SAMHeaderPrinter.cpp -o format/SAMHeaderPrinter.o
g++ -std=c++11 -pedantic -MMD -MP -Wno-long-long -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -I. -I../pbdata -I../hdf -I/usr/include/hdf5/serial -MF"format/IntervalPrinter.d" -MT"format/IntervalPrinter.o format/IntervalPrinter.d" -c format/IntervalPrinter.cpp -o format/IntervalPrinter.o
g++ -std=c++11 -pedantic -MMD -MP -Wno-long-long -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -I. -I../pbdata -I../hdf -I/usr/include/hdf5/serial -MF"format/SummaryPrinter.d" -MT"format/SummaryPrinter.o format/SummaryPrinter.d" -c format/SummaryPrinter.cpp -o format/SummaryPrinter.o
g++ -std=c++11 -pedantic -MMD -MP -Wno-long-long -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -I. -I../pbdata -I../hdf -I/usr/include/hdf5/serial -MF"simulator/ContextSet.d" -MT"simulator/ContextSet.o simulator/ContextSet.d" -c simulator/ContextSet.cpp -o simulator/ContextSet.o
g++ -std=c++11 -pedantic -MMD -MP -Wno-long-long -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -I. -I../pbdata -I../hdf -I/usr/include/hdf5/serial -MF"simulator/ContextSample.d" -MT"simulator/ContextSample.o simulator/ContextSample.d" -c simulator/ContextSample.cpp -o simulator/ContextSample.o
g++ -std=c++11 -pedantic -MMD -MP -Wno-long-long -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -I. -I../pbdata -I../hdf -I/usr/include/hdf5/serial -MF"simulator/QualitySample.d" -MT"simulator/QualitySample.o simulator/QualitySample.d" -c simulator/QualitySample.cpp -o simulator/QualitySample.o
g++ -std=c++11 -pedantic -MMD -MP -Wno-long-long -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -I. -I../pbdata -I../hdf -I/usr/include/hdf5/serial -MF"simulator/LengthHistogram.d" -MT"simulator/LengthHistogram.o simulator/LengthHistogram.d" -c simulator/LengthHistogram.cpp -o simulator/LengthHistogram.o
g++ -std=c++11 -pedantic -MMD -MP -Wno-long-long -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -I. -I../pbdata -I../hdf -I/usr/include/hdf5/serial -MF"MappingMetrics.d" -MT"MappingMetrics.o MappingMetrics.d" -c MappingMetrics.cpp -o MappingMetrics.o
ar rc libblasr.a algorithms/alignment/BaseScoreFunction.o algorithms/alignment/AlignmentUtils.o algorithms/alignment/ExtendAlign.o algorithms/alignment/GuidedAlign.o algorithms/alignment/QualityValueScoreFunction.o algorithms/alignment/IDSScoreFunction.o algorithms/alignment/StringToScoreMatrix.o algorithms/alignment/ScoreMatrices.o algorithms/alignment/KBandAlign.o algorithms/alignment/sdp/SparseDynamicProgramming.o algorithms/alignment/sdp/SDPFragment.o algorithms/anchoring/Coordinate.o algorithms/anchoring/ClusterProbability.o algorithms/anchoring/FindMaxInterval.o algorithms/anchoring/BWTSearch.o algorithms/sorting/LightweightSuffixArray.o algorithms/sorting/qsufsort.o algorithms/sorting/DifferenceCovers.o algorithms/sorting/MultikeyQuicksort.o datastructures/alignment/AlignmentContext.o datastructures/alignment/AlignmentCandidate.o datastructures/alignment/CmpFile.o datastructures/alignment/AlignmentStats.o datastructures/alignment/FilterCriteria.o datastructures/alignment/Alignment.o datastructures/alignment/SAMToAlignmentCandidateAdapter.o datastructures/alignment/AlignmentMap.o datastructures/alignmentset/SAMSupplementalQVList.o datastructures/alignmentset/SAMQVConversion.o datastructures/anchoring/AnchorParameters.o datastructures/anchoring/MatchPos.o datastructures/anchoring/WeightedInterval.o datastructures/anchoring/ClusterList.o qvs/QualityValueProfile.o statistics/pdfs.o statistics/LookupAnchorDistribution.o statistics/cdfs.o statistics/StatUtils.o tuples/BaseTuple.o tuples/DNATuple.o tuples/TupleMetrics.o utils/RegionUtils.o utils/FileOfFileNames.o utils/LogUtils.o utils/TimeUtils.o utils/PhredUtils.o utils/RangeUtils.o utils/FileUtils.o files/ReaderAgglomerate.o files/FragmentCCSIterator.o files/CCSIterator.o files/BaseSequenceIO.o format/SAMPrinter.o format/CompareSequencesPrinter.o format/SAMHeaderPrinter.o format/IntervalPrinter.o format/SummaryPrinter.o simulator/ContextSet.o simulator/ContextSample.o simulator/QualitySample.o simulator/LengthHistogram.o MappingMetrics.o
g++ -std=c++11 -pedantic -MMD -MP -Wno-long-long -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -I. -I../pbdata -I../hdf -I/usr/include/hdf5/serial -fPIC -MF"algorithms/alignment/BaseScoreFunction.shared.d" -MT"algorithms/alignment/BaseScoreFunction.shared.o algorithms/alignment/BaseScoreFunction.shared.d" -c algorithms/alignment/BaseScoreFunction.cpp -o algorithms/alignment/BaseScoreFunction.shared.o
g++ -std=c++11 -pedantic -MMD -MP -Wno-long-long -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -I. -I../pbdata -I../hdf -I/usr/include/hdf5/serial -fPIC -MF"algorithms/alignment/AlignmentUtils.shared.d" -MT"algorithms/alignment/AlignmentUtils.shared.o algorithms/alignment/AlignmentUtils.shared.d" -c algorithms/alignment/AlignmentUtils.cpp -o algorithms/alignment/AlignmentUtils.shared.o
g++ -std=c++11 -pedantic -MMD -MP -Wno-long-long -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -I. -I../pbdata -I../hdf -I/usr/include/hdf5/serial -fPIC -MF"algorithms/alignment/ExtendAlign.shared.d" -MT"algorithms/alignment/ExtendAlign.shared.o algorithms/alignment/ExtendAlign.shared.d" -c algorithms/alignment/ExtendAlign.cpp -o algorithms/alignment/ExtendAlign.shared.o
g++ -std=c++11 -pedantic -MMD -MP -Wno-long-long -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -I. -I../pbdata -I../hdf -I/usr/include/hdf5/serial -fPIC -MF"algorithms/alignment/GuidedAlign.shared.d" -MT"algorithms/alignment/GuidedAlign.shared.o algorithms/alignment/GuidedAlign.shared.d" -c algorithms/alignment/GuidedAlign.cpp -o algorithms/alignment/GuidedAlign.shared.o
g++ -std=c++11 -pedantic -MMD -MP -Wno-long-long -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -I. -I../pbdata -I../hdf -I/usr/include/hdf5/serial -fPIC -MF"algorithms/alignment/QualityValueScoreFunction.shared.d" -MT"algorithms/alignment/QualityValueScoreFunction.shared.o algorithms/alignment/QualityValueScoreFunction.shared.d" -c algorithms/alignment/QualityValueScoreFunction.cpp -o algorithms/alignment/QualityValueScoreFunction.shared.o
g++ -std=c++11 -pedantic -MMD -MP -Wno-long-long -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -I. -I../pbdata -I../hdf -I/usr/include/hdf5/serial -fPIC -MF"algorithms/alignment/IDSScoreFunction.shared.d" -MT"algorithms/alignment/IDSScoreFunction.shared.o algorithms/alignment/IDSScoreFunction.shared.d" -c algorithms/alignment/IDSScoreFunction.cpp -o algorithms/alignment/IDSScoreFunction.shared.o
g++ -std=c++11 -pedantic -MMD -MP -Wno-long-long -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -I. -I../pbdata -I../hdf -I/usr/include/hdf5/serial -fPIC -MF"algorithms/alignment/StringToScoreMatrix.shared.d" -MT"algorithms/alignment/StringToScoreMatrix.shared.o algorithms/alignment/StringToScoreMatrix.shared.d" -c algorithms/alignment/StringToScoreMatrix.cpp -o algorithms/alignment/StringToScoreMatrix.shared.o
g++ -std=c++11 -pedantic -MMD -MP -Wno-long-long -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -I. -I../pbdata -I../hdf -I/usr/include/hdf5/serial -fPIC -MF"algorithms/alignment/ScoreMatrices.shared.d" -MT"algorithms/alignment/ScoreMatrices.shared.o algorithms/alignment/ScoreMatrices.shared.d" -c algorithms/alignment/ScoreMatrices.cpp -o algorithms/alignment/ScoreMatrices.shared.o
g++ -std=c++11 -pedantic -MMD -MP -Wno-long-long -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -I. -I../pbdata -I../hdf -I/usr/include/hdf5/serial -fPIC -MF"algorithms/alignment/KBandAlign.shared.d" -MT"algorithms/alignment/KBandAlign.shared.o algorithms/alignment/KBandAlign.shared.d" -c algorithms/alignment/KBandAlign.cpp -o algorithms/alignment/KBandAlign.shared.o
g++ -std=c++11 -pedantic -MMD -MP -Wno-long-long -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -I. -I../pbdata -I../hdf -I/usr/include/hdf5/serial -fPIC -MF"algorithms/alignment/sdp/SparseDynamicProgramming.shared.d" -MT"algorithms/alignment/sdp/SparseDynamicProgramming.shared.o algorithms/alignment/sdp/SparseDynamicProgramming.shared.d" -c algorithms/alignment/sdp/SparseDynamicProgramming.cpp -o algorithms/alignment/sdp/SparseDynamicProgramming.shared.o
g++ -std=c++11 -pedantic -MMD -MP -Wno-long-long -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -I. -I../pbdata -I../hdf -I/usr/include/hdf5/serial -fPIC -MF"algorithms/alignment/sdp/SDPFragment.shared.d" -MT"algorithms/alignment/sdp/SDPFragment.shared.o algorithms/alignment/sdp/SDPFragment.shared.d" -c algorithms/alignment/sdp/SDPFragment.cpp -o algorithms/alignment/sdp/SDPFragment.shared.o
g++ -std=c++11 -pedantic -MMD -MP -Wno-long-long -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -I. -I../pbdata -I../hdf -I/usr/include/hdf5/serial -fPIC -MF"algorithms/anchoring/Coordinate.shared.d" -MT"algorithms/anchoring/Coordinate.shared.o algorithms/anchoring/Coordinate.shared.d" -c algorithms/anchoring/Coordinate.cpp -o algorithms/anchoring/Coordinate.shared.o
g++ -std=c++11 -pedantic -MMD -MP -Wno-long-long -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -I. -I../pbdata -I../hdf -I/usr/include/hdf5/serial -fPIC -MF"algorithms/anchoring/ClusterProbability.shared.d" -MT"algorithms/anchoring/ClusterProbability.shared.o algorithms/anchoring/ClusterProbability.shared.d" -c algorithms/anchoring/ClusterProbability.cpp -o algorithms/anchoring/ClusterProbability.shared.o
g++ -std=c++11 -pedantic -MMD -MP -Wno-long-long -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -I. -I../pbdata -I../hdf -I/usr/include/hdf5/serial -fPIC -MF"algorithms/anchoring/FindMaxInterval.shared.d" -MT"algorithms/anchoring/FindMaxInterval.shared.o algorithms/anchoring/FindMaxInterval.shared.d" -c algorithms/anchoring/FindMaxInterval.cpp -o algorithms/anchoring/FindMaxInterval.shared.o
g++ -std=c++11 -pedantic -MMD -MP -Wno-long-long -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -I. -I../pbdata -I../hdf -I/usr/include/hdf5/serial -fPIC -MF"algorithms/anchoring/BWTSearch.shared.d" -MT"algorithms/anchoring/BWTSearch.shared.o algorithms/anchoring/BWTSearch.shared.d" -c algorithms/anchoring/BWTSearch.cpp -o algorithms/anchoring/BWTSearch.shared.o
g++ -std=c++11 -pedantic -MMD -MP -Wno-long-long -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -I. -I../pbdata -I../hdf -I/usr/include/hdf5/serial -fPIC -MF"algorithms/sorting/LightweightSuffixArray.shared.d" -MT"algorithms/sorting/LightweightSuffixArray.shared.o algorithms/sorting/LightweightSuffixArray.shared.d" -c algorithms/sorting/LightweightSuffixArray.cpp -o algorithms/sorting/LightweightSuffixArray.shared.o
g++ -std=c++11 -pedantic -MMD -MP -Wno-long-long -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -I. -I../pbdata -I../hdf -I/usr/include/hdf5/serial -fPIC -MF"algorithms/sorting/qsufsort.shared.d" -MT"algorithms/sorting/qsufsort.shared.o algorithms/sorting/qsufsort.shared.d" -c algorithms/sorting/qsufsort.cpp -o algorithms/sorting/qsufsort.shared.o
g++ -std=c++11 -pedantic -MMD -MP -Wno-long-long -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -I. -I../pbdata -I../hdf -I/usr/include/hdf5/serial -fPIC -MF"algorithms/sorting/DifferenceCovers.shared.d" -MT"algorithms/sorting/DifferenceCovers.shared.o algorithms/sorting/DifferenceCovers.shared.d" -c algorithms/sorting/DifferenceCovers.cpp -o algorithms/sorting/DifferenceCovers.shared.o
g++ -std=c++11 -pedantic -MMD -MP -Wno-long-long -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -I. -I../pbdata -I../hdf -I/usr/include/hdf5/serial -fPIC -MF"algorithms/sorting/MultikeyQuicksort.shared.d" -MT"algorithms/sorting/MultikeyQuicksort.shared.o algorithms/sorting/MultikeyQuicksort.shared.d" -c algorithms/sorting/MultikeyQuicksort.cpp -o algorithms/sorting/MultikeyQuicksort.shared.o
g++ -std=c++11 -pedantic -MMD -MP -Wno-long-long -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -I. -I../pbdata -I../hdf -I/usr/include/hdf5/serial -fPIC -MF"datastructures/alignment/AlignmentContext.shared.d" -MT"datastructures/alignment/AlignmentContext.shared.o datastructures/alignment/AlignmentContext.shared.d" -c datastructures/alignment/AlignmentContext.cpp -o datastructures/alignment/AlignmentContext.shared.o
g++ -std=c++11 -pedantic -MMD -MP -Wno-long-long -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -I. -I../pbdata -I../hdf -I/usr/include/hdf5/serial -fPIC -MF"datastructures/alignment/AlignmentCandidate.shared.d" -MT"datastructures/alignment/AlignmentCandidate.shared.o datastructures/alignment/AlignmentCandidate.shared.d" -c datastructures/alignment/AlignmentCandidate.cpp -o datastructures/alignment/AlignmentCandidate.shared.o
g++ -std=c++11 -pedantic -MMD -MP -Wno-long-long -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -I. -I../pbdata -I../hdf -I/usr/include/hdf5/serial -fPIC -MF"datastructures/alignment/CmpFile.shared.d" -MT"datastructures/alignment/CmpFile.shared.o datastructures/alignment/CmpFile.shared.d" -c datastructures/alignment/CmpFile.cpp -o datastructures/alignment/CmpFile.shared.o
g++ -std=c++11 -pedantic -MMD -MP -Wno-long-long -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -I. -I../pbdata -I../hdf -I/usr/include/hdf5/serial -fPIC -MF"datastructures/alignment/AlignmentStats.shared.d" -MT"datastructures/alignment/AlignmentStats.shared.o datastructures/alignment/AlignmentStats.shared.d" -c datastructures/alignment/AlignmentStats.cpp -o datastructures/alignment/AlignmentStats.shared.o
g++ -std=c++11 -pedantic -MMD -MP -Wno-long-long -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -I. -I../pbdata -I../hdf -I/usr/include/hdf5/serial -fPIC -MF"datastructures/alignment/FilterCriteria.shared.d" -MT"datastructures/alignment/FilterCriteria.shared.o datastructures/alignment/FilterCriteria.shared.d" -c datastructures/alignment/FilterCriteria.cpp -o datastructures/alignment/FilterCriteria.shared.o
g++ -std=c++11 -pedantic -MMD -MP -Wno-long-long -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -I. -I../pbdata -I../hdf -I/usr/include/hdf5/serial -fPIC -MF"datastructures/alignment/Alignment.shared.d" -MT"datastructures/alignment/Alignment.shared.o datastructures/alignment/Alignment.shared.d" -c datastructures/alignment/Alignment.cpp -o datastructures/alignment/Alignment.shared.o
g++ -std=c++11 -pedantic -MMD -MP -Wno-long-long -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -I. -I../pbdata -I../hdf -I/usr/include/hdf5/serial -fPIC -MF"datastructures/alignment/SAMToAlignmentCandidateAdapter.shared.d" -MT"datastructures/alignment/SAMToAlignmentCandidateAdapter.shared.o datastructures/alignment/SAMToAlignmentCandidateAdapter.shared.d" -c datastructures/alignment/SAMToAlignmentCandidateAdapter.cpp -o datastructures/alignment/SAMToAlignmentCandidateAdapter.shared.o
g++ -std=c++11 -pedantic -MMD -MP -Wno-long-long -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -I. -I../pbdata -I../hdf -I/usr/include/hdf5/serial -fPIC -MF"datastructures/alignment/AlignmentMap.shared.d" -MT"datastructures/alignment/AlignmentMap.shared.o datastructures/alignment/AlignmentMap.shared.d" -c datastructures/alignment/AlignmentMap.cpp -o datastructures/alignment/AlignmentMap.shared.o
g++ -std=c++11 -pedantic -MMD -MP -Wno-long-long -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -I. -I../pbdata -I../hdf -I/usr/include/hdf5/serial -fPIC -MF"datastructures/alignmentset/SAMSupplementalQVList.shared.d" -MT"datastructures/alignmentset/SAMSupplementalQVList.shared.o datastructures/alignmentset/SAMSupplementalQVList.shared.d" -c datastructures/alignmentset/SAMSupplementalQVList.cpp -o datastructures/alignmentset/SAMSupplementalQVList.shared.o
g++ -std=c++11 -pedantic -MMD -MP -Wno-long-long -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -I. -I../pbdata -I../hdf -I/usr/include/hdf5/serial -fPIC -MF"datastructures/alignmentset/SAMQVConversion.shared.d" -MT"datastructures/alignmentset/SAMQVConversion.shared.o datastructures/alignmentset/SAMQVConversion.shared.d" -c datastructures/alignmentset/SAMQVConversion.cpp -o datastructures/alignmentset/SAMQVConversion.shared.o
g++ -std=c++11 -pedantic -MMD -MP -Wno-long-long -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -I. -I../pbdata -I../hdf -I/usr/include/hdf5/serial -fPIC -MF"datastructures/anchoring/AnchorParameters.shared.d" -MT"datastructures/anchoring/AnchorParameters.shared.o datastructures/anchoring/AnchorParameters.shared.d" -c datastructures/anchoring/AnchorParameters.cpp -o datastructures/anchoring/AnchorParameters.shared.o
g++ -std=c++11 -pedantic -MMD -MP -Wno-long-long -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -I. -I../pbdata -I../hdf -I/usr/include/hdf5/serial -fPIC -MF"datastructures/anchoring/MatchPos.shared.d" -MT"datastructures/anchoring/MatchPos.shared.o datastructures/anchoring/MatchPos.shared.d" -c datastructures/anchoring/MatchPos.cpp -o datastructures/anchoring/MatchPos.shared.o
g++ -std=c++11 -pedantic -MMD -MP -Wno-long-long -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -I. -I../pbdata -I../hdf -I/usr/include/hdf5/serial -fPIC -MF"datastructures/anchoring/WeightedInterval.shared.d" -MT"datastructures/anchoring/WeightedInterval.shared.o datastructures/anchoring/WeightedInterval.shared.d" -c datastructures/anchoring/WeightedInterval.cpp -o datastructures/anchoring/WeightedInterval.shared.o
g++ -std=c++11 -pedantic -MMD -MP -Wno-long-long -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -I. -I../pbdata -I../hdf -I/usr/include/hdf5/serial -fPIC -MF"datastructures/anchoring/ClusterList.shared.d" -MT"datastructures/anchoring/ClusterList.shared.o datastructures/anchoring/ClusterList.shared.d" -c datastructures/anchoring/ClusterList.cpp -o datastructures/anchoring/ClusterList.shared.o
g++ -std=c++11 -pedantic -MMD -MP -Wno-long-long -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -I. -I../pbdata -I../hdf -I/usr/include/hdf5/serial -fPIC -MF"qvs/QualityValueProfile.shared.d" -MT"qvs/QualityValueProfile.shared.o qvs/QualityValueProfile.shared.d" -c qvs/QualityValueProfile.cpp -o qvs/QualityValueProfile.shared.o
g++ -std=c++11 -pedantic -MMD -MP -Wno-long-long -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -I. -I../pbdata -I../hdf -I/usr/include/hdf5/serial -fPIC -MF"statistics/pdfs.shared.d" -MT"statistics/pdfs.shared.o statistics/pdfs.shared.d" -c statistics/pdfs.cpp -o statistics/pdfs.shared.o
g++ -std=c++11 -pedantic -MMD -MP -Wno-long-long -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -I. -I../pbdata -I../hdf -I/usr/include/hdf5/serial -fPIC -MF"statistics/LookupAnchorDistribution.shared.d" -MT"statistics/LookupAnchorDistribution.shared.o statistics/LookupAnchorDistribution.shared.d" -c statistics/LookupAnchorDistribution.cpp -o statistics/LookupAnchorDistribution.shared.o
g++ -std=c++11 -pedantic -MMD -MP -Wno-long-long -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -I. -I../pbdata -I../hdf -I/usr/include/hdf5/serial -fPIC -MF"statistics/cdfs.shared.d" -MT"statistics/cdfs.shared.o statistics/cdfs.shared.d" -c statistics/cdfs.cpp -o statistics/cdfs.shared.o
g++ -std=c++11 -pedantic -MMD -MP -Wno-long-long -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -I. -I../pbdata -I../hdf -I/usr/include/hdf5/serial -fPIC -MF"statistics/StatUtils.shared.d" -MT"statistics/StatUtils.shared.o statistics/StatUtils.shared.d" -c statistics/StatUtils.cpp -o statistics/StatUtils.shared.o
g++ -std=c++11 -pedantic -MMD -MP -Wno-long-long -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -I. -I../pbdata -I../hdf -I/usr/include/hdf5/serial -fPIC -MF"tuples/BaseTuple.shared.d" -MT"tuples/BaseTuple.shared.o tuples/BaseTuple.shared.d" -c tuples/BaseTuple.cpp -o tuples/BaseTuple.shared.o
g++ -std=c++11 -pedantic -MMD -MP -Wno-long-long -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -I. -I../pbdata -I../hdf -I/usr/include/hdf5/serial -fPIC -MF"tuples/DNATuple.shared.d" -MT"tuples/DNATuple.shared.o tuples/DNATuple.shared.d" -c tuples/DNATuple.cpp -o tuples/DNATuple.shared.o
g++ -std=c++11 -pedantic -MMD -MP -Wno-long-long -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -I. -I../pbdata -I../hdf -I/usr/include/hdf5/serial -fPIC -MF"tuples/TupleMetrics.shared.d" -MT"tuples/TupleMetrics.shared.o tuples/TupleMetrics.shared.d" -c tuples/TupleMetrics.cpp -o tuples/TupleMetrics.shared.o
g++ -std=c++11 -pedantic -MMD -MP -Wno-long-long -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -I. -I../pbdata -I../hdf -I/usr/include/hdf5/serial -fPIC -MF"utils/RegionUtils.shared.d" -MT"utils/RegionUtils.shared.o utils/RegionUtils.shared.d" -c utils/RegionUtils.cpp -o utils/RegionUtils.shared.o
g++ -std=c++11 -pedantic -MMD -MP -Wno-long-long -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -I. -I../pbdata -I../hdf -I/usr/include/hdf5/serial -fPIC -MF"utils/FileOfFileNames.shared.d" -MT"utils/FileOfFileNames.shared.o utils/FileOfFileNames.shared.d" -c utils/FileOfFileNames.cpp -o utils/FileOfFileNames.shared.o
g++ -std=c++11 -pedantic -MMD -MP -Wno-long-long -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -I. -I../pbdata -I../hdf -I/usr/include/hdf5/serial -fPIC -MF"utils/LogUtils.shared.d" -MT"utils/LogUtils.shared.o utils/LogUtils.shared.d" -c utils/LogUtils.cpp -o utils/LogUtils.shared.o
g++ -std=c++11 -pedantic -MMD -MP -Wno-long-long -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -I. -I../pbdata -I../hdf -I/usr/include/hdf5/serial -fPIC -MF"utils/TimeUtils.shared.d" -MT"utils/TimeUtils.shared.o utils/TimeUtils.shared.d" -c utils/TimeUtils.cpp -o utils/TimeUtils.shared.o
g++ -std=c++11 -pedantic -MMD -MP -Wno-long-long -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -I. -I../pbdata -I../hdf -I/usr/include/hdf5/serial -fPIC -MF"utils/PhredUtils.shared.d" -MT"utils/PhredUtils.shared.o utils/PhredUtils.shared.d" -c utils/PhredUtils.cpp -o utils/PhredUtils.shared.o
g++ -std=c++11 -pedantic -MMD -MP -Wno-long-long -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -I. -I../pbdata -I../hdf -I/usr/include/hdf5/serial -fPIC -MF"utils/RangeUtils.shared.d" -MT"utils/RangeUtils.shared.o utils/RangeUtils.shared.d" -c utils/RangeUtils.cpp -o utils/RangeUtils.shared.o
g++ -std=c++11 -pedantic -MMD -MP -Wno-long-long -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -I. -I../pbdata -I../hdf -I/usr/include/hdf5/serial -fPIC -MF"utils/FileUtils.shared.d" -MT"utils/FileUtils.shared.o utils/FileUtils.shared.d" -c utils/FileUtils.cpp -o utils/FileUtils.shared.o
g++ -std=c++11 -pedantic -MMD -MP -Wno-long-long -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -I. -I../pbdata -I../hdf -I/usr/include/hdf5/serial -fPIC -MF"files/ReaderAgglomerate.shared.d" -MT"files/ReaderAgglomerate.shared.o files/ReaderAgglomerate.shared.d" -c files/ReaderAgglomerate.cpp -o files/ReaderAgglomerate.shared.o
g++ -std=c++11 -pedantic -MMD -MP -Wno-long-long -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -I. -I../pbdata -I../hdf -I/usr/include/hdf5/serial -fPIC -MF"files/FragmentCCSIterator.shared.d" -MT"files/FragmentCCSIterator.shared.o files/FragmentCCSIterator.shared.d" -c files/FragmentCCSIterator.cpp -o files/FragmentCCSIterator.shared.o
g++ -std=c++11 -pedantic -MMD -MP -Wno-long-long -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -I. -I../pbdata -I../hdf -I/usr/include/hdf5/serial -fPIC -MF"files/CCSIterator.shared.d" -MT"files/CCSIterator.shared.o files/CCSIterator.shared.d" -c files/CCSIterator.cpp -o files/CCSIterator.shared.o
g++ -std=c++11 -pedantic -MMD -MP -Wno-long-long -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -I. -I../pbdata -I../hdf -I/usr/include/hdf5/serial -fPIC -MF"files/BaseSequenceIO.shared.d" -MT"files/BaseSequenceIO.shared.o files/BaseSequenceIO.shared.d" -c files/BaseSequenceIO.cpp -o files/BaseSequenceIO.shared.o
g++ -std=c++11 -pedantic -MMD -MP -Wno-long-long -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -I. -I../pbdata -I../hdf -I/usr/include/hdf5/serial -fPIC -MF"format/SAMPrinter.shared.d" -MT"format/SAMPrinter.shared.o format/SAMPrinter.shared.d" -c format/SAMPrinter.cpp -o format/SAMPrinter.shared.o
g++ -std=c++11 -pedantic -MMD -MP -Wno-long-long -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -I. -I../pbdata -I../hdf -I/usr/include/hdf5/serial -fPIC -MF"format/CompareSequencesPrinter.shared.d" -MT"format/CompareSequencesPrinter.shared.o format/CompareSequencesPrinter.shared.d" -c format/CompareSequencesPrinter.cpp -o format/CompareSequencesPrinter.shared.o
g++ -std=c++11 -pedantic -MMD -MP -Wno-long-long -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -I. -I../pbdata -I../hdf -I/usr/include/hdf5/serial -fPIC -MF"format/SAMHeaderPrinter.shared.d" -MT"format/SAMHeaderPrinter.shared.o format/SAMHeaderPrinter.shared.d" -c format/SAMHeaderPrinter.cpp -o format/SAMHeaderPrinter.shared.o
g++ -std=c++11 -pedantic -MMD -MP -Wno-long-long -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -I. -I../pbdata -I../hdf -I/usr/include/hdf5/serial -fPIC -MF"format/IntervalPrinter.shared.d" -MT"format/IntervalPrinter.shared.o format/IntervalPrinter.shared.d" -c format/IntervalPrinter.cpp -o format/IntervalPrinter.shared.o
g++ -std=c++11 -pedantic -MMD -MP -Wno-long-long -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -I. -I../pbdata -I../hdf -I/usr/include/hdf5/serial -fPIC -MF"format/SummaryPrinter.shared.d" -MT"format/SummaryPrinter.shared.o format/SummaryPrinter.shared.d" -c format/SummaryPrinter.cpp -o format/SummaryPrinter.shared.o
g++ -std=c++11 -pedantic -MMD -MP -Wno-long-long -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -I. -I../pbdata -I../hdf -I/usr/include/hdf5/serial -fPIC -MF"simulator/ContextSet.shared.d" -MT"simulator/ContextSet.shared.o simulator/ContextSet.shared.d" -c simulator/ContextSet.cpp -o simulator/ContextSet.shared.o
g++ -std=c++11 -pedantic -MMD -MP -Wno-long-long -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -I. -I../pbdata -I../hdf -I/usr/include/hdf5/serial -fPIC -MF"simulator/ContextSample.shared.d" -MT"simulator/ContextSample.shared.o simulator/ContextSample.shared.d" -c simulator/ContextSample.cpp -o simulator/ContextSample.shared.o
g++ -std=c++11 -pedantic -MMD -MP -Wno-long-long -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -I. -I../pbdata -I../hdf -I/usr/include/hdf5/serial -fPIC -MF"simulator/QualitySample.shared.d" -MT"simulator/QualitySample.shared.o simulator/QualitySample.shared.d" -c simulator/QualitySample.cpp -o simulator/QualitySample.shared.o
g++ -std=c++11 -pedantic -MMD -MP -Wno-long-long -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -I. -I../pbdata -I../hdf -I/usr/include/hdf5/serial -fPIC -MF"simulator/LengthHistogram.shared.d" -MT"simulator/LengthHistogram.shared.o simulator/LengthHistogram.shared.d" -c simulator/LengthHistogram.cpp -o simulator/LengthHistogram.shared.o
g++ -std=c++11 -pedantic -MMD -MP -Wno-long-long -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -I. -I../pbdata -I../hdf -I/usr/include/hdf5/serial -fPIC -MF"MappingMetrics.shared.d" -MT"MappingMetrics.shared.o MappingMetrics.shared.d" -c MappingMetrics.cpp -o MappingMetrics.shared.o
g++ -shared -fPIC -o libblasr.so -Wl,-soname,libblasr.so algorithms/alignment/BaseScoreFunction.shared.o algorithms/alignment/AlignmentUtils.shared.o algorithms/alignment/ExtendAlign.shared.o algorithms/alignment/GuidedAlign.shared.o algorithms/alignment/QualityValueScoreFunction.shared.o algorithms/alignment/IDSScoreFunction.shared.o algorithms/alignment/StringToScoreMatrix.shared.o algorithms/alignment/ScoreMatrices.shared.o algorithms/alignment/KBandAlign.shared.o algorithms/alignment/sdp/SparseDynamicProgramming.shared.o algorithms/alignment/sdp/SDPFragment.shared.o algorithms/anchoring/Coordinate.shared.o algorithms/anchoring/ClusterProbability.shared.o algorithms/anchoring/FindMaxInterval.shared.o algorithms/anchoring/BWTSearch.shared.o algorithms/sorting/LightweightSuffixArray.shared.o algorithms/sorting/qsufsort.shared.o algorithms/sorting/DifferenceCovers.shared.o algorithms/sorting/MultikeyQuicksort.shared.o datastructures/alignment/AlignmentContext.shared.o datastructures/alignment/AlignmentCandidate.shared.o datastructures/alignment/CmpFile.shared.o datastructures/alignment/AlignmentStats.shared.o datastructures/alignment/FilterCriteria.shared.o datastructures/alignment/Alignment.shared.o datastructures/alignment/SAMToAlignmentCandidateAdapter.shared.o datastructures/alignment/AlignmentMap.shared.o datastructures/alignmentset/SAMSupplementalQVList.shared.o datastructures/alignmentset/SAMQVConversion.shared.o datastructures/anchoring/AnchorParameters.shared.o datastructures/anchoring/MatchPos.shared.o datastructures/anchoring/WeightedInterval.shared.o datastructures/anchoring/ClusterList.shared.o qvs/QualityValueProfile.shared.o statistics/pdfs.shared.o statistics/LookupAnchorDistribution.shared.o statistics/cdfs.shared.o statistics/StatUtils.shared.o tuples/BaseTuple.shared.o tuples/DNATuple.shared.o tuples/TupleMetrics.shared.o utils/RegionUtils.shared.o utils/FileOfFileNames.shared.o utils/LogUtils.shared.o utils/TimeUtils.shared.o utils/PhredUtils.shared.o utils/RangeUtils.shared.o utils/FileUtils.shared.o files/ReaderAgglomerate.shared.o files/FragmentCCSIterator.shared.o files/CCSIterator.shared.o files/BaseSequenceIO.shared.o format/SAMPrinter.shared.o format/CompareSequencesPrinter.shared.o format/SAMHeaderPrinter.shared.o format/IntervalPrinter.shared.o format/SummaryPrinter.shared.o simulator/ContextSet.shared.o simulator/ContextSample.shared.o simulator/QualitySample.shared.o simulator/LengthHistogram.shared.o MappingMetrics.shared.o ../pbdata/libpbdata.so /usr/lib/arm-linux-gnueabihf/hdf5/serial/libhdf5.so
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make[2]: Entering directory '/«BUILDDIR»/blasr-0~20150724+git3ca7fe8'
g++ -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -c -o Blasr.o Blasr.cpp
g++ -o blasr -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -MF"blasr.d" Blasr.o -Wl,-z,relro -static -L./libcpp/alignment -L./libcpp/pbdata -L./libcpp/hdf -L/usr/lib/arm-linux-gnueabihf/hdf5/serial -Wl,-Bstatic -lpbihdf -Wl,-Bstatic -lblasr -Wl,-Bstatic -lpbdata -Wl,-Bstatic -lpbihdf -Wl,-Bdynamic -lhdf5_cpp -lhdf5 -Wl,-Bdynamic -lz -Wl,-Bdynamic -lpthread -Wl,-Bdynamic -ldl
LD_LIBRARY_PATH=/usr/lib/arm-linux-gnueabihf/hdf5/serial:./libcpp/alignment:./libcpp/hdf:./libcpp/pbdata
/usr/bin/make -C utils
make[3]: Entering directory '/«BUILDDIR»/blasr-0~20150724+git3ca7fe8/utils'
g++ -o loadPulses LoadPulses.cpp -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -I../libcpp/alignment -I../libcpp/pbdata -I../libcpp/hdf -I/usr/include/hdf5/serial -MF"loadPulses.d" -Wl,-z,relro -static -L./libcpp/alignment -L./libcpp/pbdata -L./libcpp/hdf -L/usr/lib/arm-linux-gnueabihf/hdf5/serial -static -L../libcpp/alignment -L../libcpp/pbdata -L../libcpp/hdf -L/usr/lib/arm-linux-gnueabihf/hdf5/serial -Wl,-Bstatic -lpbihdf -Wl,-Bstatic -lblasr -Wl,-Bstatic -lpbdata -Wl,-Bstatic -lpbihdf -Wl,-Bdynamic -lhdf5_cpp -lhdf5 -Wl,-Bdynamic -lz -Wl,-Bdynamic -lpthread -Wl,-Bdynamic -ldl
g++ -o pls2fasta PulseToFasta.cpp -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -I../libcpp/alignment -I../libcpp/pbdata -I../libcpp/hdf -I/usr/include/hdf5/serial -MF"pls2fasta.d" -Wl,-z,relro -static -L./libcpp/alignment -L./libcpp/pbdata -L./libcpp/hdf -L/usr/lib/arm-linux-gnueabihf/hdf5/serial -static -L../libcpp/alignment -L../libcpp/pbdata -L../libcpp/hdf -L/usr/lib/arm-linux-gnueabihf/hdf5/serial -Wl,-Bstatic -lpbihdf -Wl,-Bstatic -lblasr -Wl,-Bstatic -lpbdata -Wl,-Bstatic -lpbihdf -Wl,-Bdynamic -lhdf5_cpp -lhdf5 -Wl,-Bdynamic -lz -Wl,-Bdynamic -lpthread -Wl,-Bdynamic -ldl
g++ -o samtoh5 SamToCmpH5.cpp -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -I../libcpp/alignment -I../libcpp/pbdata -I../libcpp/hdf -I/usr/include/hdf5/serial -MF"samtoh5.d" -Wl,-z,relro -static -L./libcpp/alignment -L./libcpp/pbdata -L./libcpp/hdf -L/usr/lib/arm-linux-gnueabihf/hdf5/serial -static -L../libcpp/alignment -L../libcpp/pbdata -L../libcpp/hdf -L/usr/lib/arm-linux-gnueabihf/hdf5/serial -Wl,-Bstatic -lpbihdf -Wl,-Bstatic -lblasr -Wl,-Bstatic -lpbdata -Wl,-Bstatic -lpbihdf -Wl,-Bdynamic -lhdf5_cpp -lhdf5 -Wl,-Bdynamic -lz -Wl,-Bdynamic -lpthread -Wl,-Bdynamic -ldl
g++ -o samtom4 SamToM4.cpp -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -I../libcpp/alignment -I../libcpp/pbdata -I../libcpp/hdf -I/usr/include/hdf5/serial -MF"samtom4.d" -Wl,-z,relro -static -L./libcpp/alignment -L./libcpp/pbdata -L./libcpp/hdf -L/usr/lib/arm-linux-gnueabihf/hdf5/serial -static -L../libcpp/alignment -L../libcpp/pbdata -L../libcpp/hdf -L/usr/lib/arm-linux-gnueabihf/hdf5/serial -Wl,-Bstatic -lpbihdf -Wl,-Bstatic -lblasr -Wl,-Bstatic -lpbdata -Wl,-Bstatic -lpbihdf -Wl,-Bdynamic -lhdf5_cpp -lhdf5 -Wl,-Bdynamic -lz -Wl,-Bdynamic -lpthread -Wl,-Bdynamic -ldl
g++ -o samFilter SamFilter.cpp -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -I../libcpp/alignment -I../libcpp/pbdata -I../libcpp/hdf -I/usr/include/hdf5/serial -MF"samFilter.d" -Wl,-z,relro -static -L./libcpp/alignment -L./libcpp/pbdata -L./libcpp/hdf -L/usr/lib/arm-linux-gnueabihf/hdf5/serial -static -L../libcpp/alignment -L../libcpp/pbdata -L../libcpp/hdf -L/usr/lib/arm-linux-gnueabihf/hdf5/serial -Wl,-Bstatic -lpbihdf -Wl,-Bstatic -lblasr -Wl,-Bstatic -lpbdata -Wl,-Bstatic -lpbihdf -Wl,-Bdynamic -lhdf5_cpp -lhdf5 -Wl,-Bdynamic -lz -Wl,-Bdynamic -lpthread -Wl,-Bdynamic -ldl
g++ -o toAfg ToAfg.cpp -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -I../libcpp/alignment -I../libcpp/pbdata -I../libcpp/hdf -I/usr/include/hdf5/serial -MF"toAfg.d" -Wl,-z,relro -static -L./libcpp/alignment -L./libcpp/pbdata -L./libcpp/hdf -L/usr/lib/arm-linux-gnueabihf/hdf5/serial -static -L../libcpp/alignment -L../libcpp/pbdata -L../libcpp/hdf -L/usr/lib/arm-linux-gnueabihf/hdf5/serial -Wl,-Bstatic -lpbihdf -Wl,-Bstatic -lblasr -Wl,-Bstatic -lpbdata -Wl,-Bstatic -lpbihdf -Wl,-Bdynamic -lhdf5_cpp -lhdf5 -Wl,-Bdynamic -lz -Wl,-Bdynamic -lpthread -Wl,-Bdynamic -ldl
g++ -o sawriter SAWriter.cpp -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -I../libcpp/alignment -I../libcpp/pbdata -I../libcpp/hdf -I/usr/include/hdf5/serial -MF"sawriter.d" -Wl,-z,relro -static -L./libcpp/alignment -L./libcpp/pbdata -L./libcpp/hdf -L/usr/lib/arm-linux-gnueabihf/hdf5/serial -static -L../libcpp/alignment -L../libcpp/pbdata -L../libcpp/hdf -L/usr/lib/arm-linux-gnueabihf/hdf5/serial -Wl,-Bstatic -lpbihdf -Wl,-Bstatic -lblasr -Wl,-Bstatic -lpbdata -Wl,-Bstatic -lpbihdf -Wl,-Bdynamic -lhdf5_cpp -lhdf5 -Wl,-Bdynamic -lz -Wl,-Bdynamic -lpthread -Wl,-Bdynamic -ldl
g++ -o sdpMatcher SDPMatcher.cpp -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -I../libcpp/alignment -I../libcpp/pbdata -I../libcpp/hdf -I/usr/include/hdf5/serial -MF"sdpMatcher.d" -Wl,-z,relro -static -L./libcpp/alignment -L./libcpp/pbdata -L./libcpp/hdf -L/usr/lib/arm-linux-gnueabihf/hdf5/serial -static -L../libcpp/alignment -L../libcpp/pbdata -L../libcpp/hdf -L/usr/lib/arm-linux-gnueabihf/hdf5/serial -Wl,-Bstatic -lpbihdf -Wl,-Bstatic -lblasr -Wl,-Bstatic -lpbdata -Wl,-Bstatic -lpbihdf -Wl,-Bdynamic -lhdf5_cpp -lhdf5 -Wl,-Bdynamic -lz -Wl,-Bdynamic -lpthread -Wl,-Bdynamic -ldl
make[3]: Leaving directory '/«BUILDDIR»/blasr-0~20150724+git3ca7fe8/utils'
make[2]: Leaving directory '/«BUILDDIR»/blasr-0~20150724+git3ca7fe8'
make[1]: Leaving directory '/«BUILDDIR»/blasr-0~20150724+git3ca7fe8'
fakeroot debian/rules binary-arch
dh binary-arch
dh_testroot -a
dh_prep -a
dh_auto_install -a
dh_install -a
dh_installdocs -a
dh_installchangelogs -a
dh_installman -a
dh_perl -a
dh_link -a
dh_strip_nondeterminism -a
dh_compress -a
dh_fixperms -a
dh_strip -a
dh_makeshlibs -a
dh_shlibdeps -a
dpkg-shlibdeps: warning: debian/blasr/usr/bin/sdpMatcher contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/blasr/usr/bin/blasr contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/blasr/usr/bin/loadPulses contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/blasr/usr/bin/toAfg contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/blasr/usr/bin/sawriter contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/blasr/usr/bin/samtom4 contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/blasr/usr/bin/samFilter contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/blasr/usr/bin/samtoh5 contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/blasr/usr/bin/pls2fasta contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/blasr/usr/bin/sdpMatcher debian/blasr/usr/bin/blasr debian/blasr/usr/bin/loadPulses debian/blasr/usr/bin/toAfg debian/blasr/usr/bin/sawriter debian/blasr/usr/bin/samtom4 debian/blasr/usr/bin/samFilter debian/blasr/usr/bin/samtoh5 debian/blasr/usr/bin/pls2fasta were not linked against ld-linux-armhf.so.3 (they use none of the library's symbols)
dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/blasr/usr/bin/sdpMatcher debian/blasr/usr/bin/blasr debian/blasr/usr/bin/loadPulses debian/blasr/usr/bin/toAfg debian/blasr/usr/bin/sawriter debian/blasr/usr/bin/samtom4 debian/blasr/usr/bin/samFilter debian/blasr/usr/bin/samtoh5 debian/blasr/usr/bin/pls2fasta were not linked against libdl.so.2 (they use none of the library's symbols)
dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/blasr/usr/bin/sdpMatcher debian/blasr/usr/bin/blasr debian/blasr/usr/bin/loadPulses debian/blasr/usr/bin/toAfg debian/blasr/usr/bin/sawriter debian/blasr/usr/bin/samtom4 debian/blasr/usr/bin/samFilter debian/blasr/usr/bin/samtoh5 debian/blasr/usr/bin/pls2fasta were not linked against libz.so.1 (they use none of the library's symbols)
dh_installdeb -a
dh_gencontrol -a
dpkg-gencontrol: warning: File::FcntlLock not available; using flock which is not NFS-safe
dh_md5sums -a
dh_builddeb -a
dpkg-deb: building package 'blasr' in '../blasr_0~20150724+git3ca7fe8-1+b2_armhf.deb'.
dpkg-genchanges -B -mRaspbian nitrogen6x test autobuilder <root@raspbian.org> >../blasr_0~20150724+git3ca7fe8-1+b2_armhf.changes
dpkg-genchanges: binary-only arch-specific upload (source code and arch-indep packages not included)
dpkg-source --after-build blasr-0~20150724+git3ca7fe8
dpkg-buildpackage: binary-only upload (no source included)
────────────────────────────────────────────────────────────────────────────────
Build finished at 20151219-0409
Finished
────────
I: Built successfully
┌──────────────────────────────────────────────────────────────────────────────┐
│ Post Build Chroot │
└──────────────────────────────────────────────────────────────────────────────┘
┌──────────────────────────────────────────────────────────────────────────────┐
│ Changes │
└──────────────────────────────────────────────────────────────────────────────┘
blasr_0~20150724+git3ca7fe8-1+b2_armhf.changes:
───────────────────────────────────────────────
Format: 1.8
Date: Sun, 26 Jul 2015 22:19:06 -0700
Source: blasr (0~20150724+git3ca7fe8-1)
Binary: blasr
Binary-Only: yes
Architecture: armhf
Version: 0~20150724+git3ca7fe8-1+b2
Distribution: stretch-staging
Urgency: low
Maintainer: Raspbian nitrogen6x test autobuilder <root@raspbian.org>
Changed-By: Raspbian nitrogen6x test autobuilder <root@raspbian.org>
Description:
blasr - mapping single-molecule sequencing reads
Changes:
blasr (0~20150724+git3ca7fe8-1+b2) stretch-staging; urgency=low, binary-only=yes
.
* Binary-only non-maintainer upload for armhf; no source changes.
* rebuild due to debcheck failure
Checksums-Sha1:
46ca9f7907d98c74b32984668a2451ee3577cd44 1285170 blasr_0~20150724+git3ca7fe8-1+b2_armhf.deb
Checksums-Sha256:
a66b09a4ca84515350b580a858079c7854dd1ff659481212f55ea73000bbf332 1285170 blasr_0~20150724+git3ca7fe8-1+b2_armhf.deb
Files:
58764146cd556e9550fb9c3685b2ba56 1285170 science optional blasr_0~20150724+git3ca7fe8-1+b2_armhf.deb
┌──────────────────────────────────────────────────────────────────────────────┐
│ Package contents │
└──────────────────────────────────────────────────────────────────────────────┘
blasr_0~20150724+git3ca7fe8-1+b2_armhf.deb
──────────────────────────────────────────
new debian package, version 2.0.
size 1285170 bytes: control archive=1366 bytes.
747 bytes, 15 lines control
1537 bytes, 25 lines md5sums
Package: blasr
Source: blasr (0~20150724+git3ca7fe8-1)
Version: 0~20150724+git3ca7fe8-1+b2
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 4994
Depends: libc6 (>= 2.17), libhdf5-10, libhdf5-cpp-11 (>= 1.8.16), libstdc++6 (>= 5.2), zlib1g (>= 1:1.1.4)
Section: science
Priority: optional
Homepage: https://github.com/PacificBiosciences/blasr
Description: mapping single-molecule sequencing reads
Basic local alignment with successive refinement (BLASR) is a method
for mapping single-molecule sequencing reads against a reference genome.
Such reads are thousands of bases long, with divergence between them
and the genome being dominated by insertion and deletion error.
drwxr-xr-x root/root 0 2015-12-19 04:08 ./
drwxr-xr-x root/root 0 2015-12-19 04:08 ./usr/
drwxr-xr-x root/root 0 2015-12-19 04:08 ./usr/bin/
-rwxr-xr-x root/root 2637016 2015-12-19 04:08 ./usr/bin/blasr
-rwxr-xr-x root/root 530792 2015-12-19 04:08 ./usr/bin/loadPulses
-rwxr-xr-x root/root 420132 2015-12-19 04:08 ./usr/bin/pls2fasta
-rwxr-xr-x root/root 256172 2015-12-19 04:08 ./usr/bin/samFilter
-rwxr-xr-x root/root 383464 2015-12-19 04:08 ./usr/bin/samtoh5
-rwxr-xr-x root/root 198728 2015-12-19 04:08 ./usr/bin/samtom4
-rwxr-xr-x root/root 116592 2015-12-19 04:08 ./usr/bin/sawriter
-rwxr-xr-x root/root 141888 2015-12-19 04:08 ./usr/bin/sdpMatcher
-rwxr-xr-x root/root 383224 2015-12-19 04:08 ./usr/bin/toAfg
drwxr-xr-x root/root 0 2015-12-19 04:08 ./usr/share/
drwxr-xr-x root/root 0 2015-12-19 04:08 ./usr/share/doc/
drwxr-xr-x root/root 0 2015-12-19 04:08 ./usr/share/doc/blasr/
-rw-r--r-- root/root 1617 2015-07-27 04:52 ./usr/share/doc/blasr/LICENSES.txt
-rw-r--r-- root/root 2596 2015-07-27 04:52 ./usr/share/doc/blasr/MANUAL.md
-rw-r--r-- root/root 1136 2015-07-27 04:52 ./usr/share/doc/blasr/README.md
-rw-r--r-- root/root 111 2015-07-31 07:51 ./usr/share/doc/blasr/TODO.Debian
-rw-r--r-- root/root 232 2015-12-19 03:26 ./usr/share/doc/blasr/changelog.Debian.armhf.gz
-rw-r--r-- root/root 219 2015-12-19 03:26 ./usr/share/doc/blasr/changelog.Debian.gz
-rw-r--r-- root/root 4613 2015-07-31 07:51 ./usr/share/doc/blasr/copyright
drwxr-xr-x root/root 0 2015-12-19 04:08 ./usr/share/man/
drwxr-xr-x root/root 0 2015-12-19 04:08 ./usr/share/man/man1/
-rw-r--r-- root/root 5732 2015-12-19 04:08 ./usr/share/man/man1/blasr.1.gz
-rw-r--r-- root/root 936 2015-12-19 04:08 ./usr/share/man/man1/loadPulses.1.gz
-rw-r--r-- root/root 925 2015-12-19 04:08 ./usr/share/man/man1/pls2fasta.1.gz
-rw-r--r-- root/root 1397 2015-12-19 04:08 ./usr/share/man/man1/samFilter.1.gz
-rw-r--r-- root/root 925 2015-12-19 04:08 ./usr/share/man/man1/samtoh5.1.gz
-rw-r--r-- root/root 401 2015-12-19 04:08 ./usr/share/man/man1/samtom4.1.gz
-rw-r--r-- root/root 841 2015-12-19 04:08 ./usr/share/man/man1/sawriter.1.gz
-rw-r--r-- root/root 440 2015-12-19 04:08 ./usr/share/man/man1/sdpMatcher.1.gz
-rw-r--r-- root/root 311 2015-12-19 04:08 ./usr/share/man/man1/toAfg.1.gz
┌──────────────────────────────────────────────────────────────────────────────┐
│ Post Build │
└──────────────────────────────────────────────────────────────────────────────┘
┌──────────────────────────────────────────────────────────────────────────────┐
│ Cleanup │
└──────────────────────────────────────────────────────────────────────────────┘
Purging /«BUILDDIR»
Not cleaning session: cloned chroot in use
┌──────────────────────────────────────────────────────────────────────────────┐
│ Summary │
└──────────────────────────────────────────────────────────────────────────────┘
Build Architecture: armhf
Build-Space: 173332
Build-Time: 2591
Distribution: stretch-staging
Host Architecture: armhf
Install-Time: 374
Job: blasr_0~20150724+git3ca7fe8-1
Machine Architecture: armhf
Package: blasr
Package-Time: 3027
Source-Version: 0~20150724+git3ca7fe8-1
Space: 173332
Status: successful
Version: 0~20150724+git3ca7fe8-1+b2
────────────────────────────────────────────────────────────────────────────────
Finished at 20151219-0409
Build needed 00:50:27, 173332k disc space