Reading package lists... Building dependency tree... Reading state information... NOTICE: 'blasr' packaging is maintained in the 'Git' version control system at: git://anonscm.debian.org/debian-med/blasr.git Need to get 1,050 kB of source archives. Get:1 http://urika:3142/ftp.debian.org/debian/ sid/main blasr 0~20150724+git3ca7fe8-1 (dsc) [2,033 B] Get:2 http://urika:3142/ftp.debian.org/debian/ sid/main blasr 0~20150724+git3ca7fe8-1 (tar) [1,035 kB] Get:3 http://urika:3142/ftp.debian.org/debian/ sid/main blasr 0~20150724+git3ca7fe8-1 (diff) [13.5 kB] gpgv: keyblock resource `/tmp/.gnupg/trustedkeys.gpg': file open error gpgv: Signature made Fri 31 Jul 2015 07:56:38 AM 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 Fetched 1,050 kB in 0s (40.6 MB/s) Reading package lists... Building dependency tree... Reading state information... The following NEW packages will be installed: bsdmainutils debhelper file gettext gettext-base groff-base hdf5-helpers intltool-debian libasprintf0v5 libcroco3 libexpat1 libffi6 libgfortran3 libglib2.0-0 libhdf5-8 libhdf5-cpp-8 libhdf5-dev libicu55 libjpeg-dev libjpeg62-turbo libjpeg62-turbo-dev libmagic1 libpipeline1 libpython-stdlib libpython2.7-minimal libpython2.7-stdlib libsqlite3-0 libunistring0 libxml2 man-db mime-support po-debconf python python-minimal python2.7 python2.7-minimal zlib1g-dev 0 upgraded, 37 newly installed, 0 to remove and 0 not upgraded. Need to get 29.2 MB of archives. After this operation, 119 MB of additional disk space will be used. Get:1 http://urika:3142/ftp.debian.org/debian/ sid/main libasprintf0v5 amd64 0.19.5.1-1 [32.2 kB] Get:2 http://urika:3142/ftp.debian.org/debian/ sid/main libmagic1 amd64 1:5.22+15-2 [249 kB] Get:3 http://urika:3142/ftp.debian.org/debian/ sid/main groff-base amd64 1.22.3-1 [1,205 kB] Get:4 http://urika:3142/ftp.debian.org/debian/ sid/main bsdmainutils amd64 9.0.6 [183 kB] Get:5 http://urika:3142/ftp.debian.org/debian/ sid/main libpipeline1 amd64 1.4.1-1 [27.8 kB] Get:6 http://urika:3142/ftp.debian.org/debian/ sid/main man-db amd64 2.7.2-1 [1,000 kB] Get:7 http://urika:3142/ftp.debian.org/debian/ sid/main libpython2.7-minimal amd64 2.7.10-3 [382 kB] Get:8 http://urika:3142/ftp.debian.org/debian/ sid/main python2.7-minimal amd64 2.7.10-3 [1,418 kB] Get:9 http://urika:3142/ftp.debian.org/debian/ sid/main python-minimal amd64 2.7.9-1 [40.3 kB] Get:10 http://urika:3142/ftp.debian.org/debian/ sid/main mime-support all 3.59 [36.4 kB] Get:11 http://urika:3142/ftp.debian.org/debian/ sid/main libexpat1 amd64 2.1.0-7 [80.0 kB] Get:12 http://urika:3142/ftp.debian.org/debian/ sid/main libffi6 amd64 3.2.1-3 [20.1 kB] Get:13 http://urika:3142/ftp.debian.org/debian/ sid/main libsqlite3-0 amd64 3.8.11.1-1 [454 kB] Get:14 http://urika:3142/ftp.debian.org/debian/ sid/main libpython2.7-stdlib amd64 2.7.10-3 [1,854 kB] Get:15 http://urika:3142/ftp.debian.org/debian/ sid/main python2.7 amd64 2.7.10-3 [258 kB] Get:16 http://urika:3142/ftp.debian.org/debian/ sid/main libpython-stdlib amd64 2.7.9-1 [19.5 kB] Get:17 http://urika:3142/ftp.debian.org/debian/ sid/main python amd64 2.7.9-1 [151 kB] Get:18 http://urika:3142/ftp.debian.org/debian/ sid/main libglib2.0-0 amd64 2.44.1-1.1 [2,461 kB] Get:19 http://urika:3142/ftp.debian.org/debian/ sid/main libicu55 amd64 55.1-4 [7,655 kB] Get:20 http://urika:3142/ftp.debian.org/debian/ sid/main libxml2 amd64 2.9.2+really2.9.1+dfsg1-0.1 [905 kB] Get:21 http://urika:3142/ftp.debian.org/debian/ sid/main libcroco3 amd64 0.6.8-3+b1 [135 kB] Get:22 http://urika:3142/ftp.debian.org/debian/ sid/main libgfortran3 amd64 5.2.1-15 [253 kB] Get:23 http://urika:3142/ftp.debian.org/debian/ sid/main libunistring0 amd64 0.9.3-5.2+b1 [288 kB] Get:24 http://urika:3142/ftp.debian.org/debian/ sid/main file amd64 1:5.22+15-2 [60.1 kB] Get:25 http://urika:3142/ftp.debian.org/debian/ sid/main gettext-base amd64 0.19.5.1-1 [122 kB] Get:26 http://urika:3142/ftp.debian.org/debian/ sid/main gettext amd64 0.19.5.1-1 [1,459 kB] Get:27 http://urika:3142/ftp.debian.org/debian/ sid/main intltool-debian all 0.35.0+20060710.2 [25.9 kB] Get:28 http://urika:3142/ftp.debian.org/debian/ sid/main po-debconf all 1.0.18 [248 kB] Get:29 http://urika:3142/ftp.debian.org/debian/ sid/main debhelper all 9.20150811 [817 kB] Get:30 http://urika:3142/ftp.debian.org/debian/ sid/main hdf5-helpers amd64 1.8.13+docs-15.1 [36.5 kB] Get:31 http://urika:3142/ftp.debian.org/debian/ sid/main libhdf5-8 amd64 1.8.13+docs-15.1 [1,060 kB] Get:32 http://urika:3142/ftp.debian.org/debian/ sid/main libhdf5-cpp-8 amd64 1.8.13+docs-15.1 [118 kB] Get:33 http://urika:3142/ftp.debian.org/debian/ sid/main zlib1g-dev amd64 1:1.2.8.dfsg-2+b1 [206 kB] Get:34 http://urika:3142/ftp.debian.org/debian/ sid/main libjpeg62-turbo amd64 1:1.4.1-2 [126 kB] Get:35 http://urika:3142/ftp.debian.org/debian/ sid/main libjpeg62-turbo-dev amd64 1:1.4.1-2 [481 kB] Get:36 http://urika:3142/ftp.debian.org/debian/ sid/main libjpeg-dev all 1:1.4.1-2 [51.9 kB] Get:37 http://urika:3142/ftp.debian.org/debian/ sid/main libhdf5-dev amd64 1.8.13+docs-15.1 [5,281 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 29.2 MB in 0s (50.5 MB/s) Selecting previously unselected package libasprintf0v5:amd64. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 15325 files and directories currently installed.) Preparing to unpack .../libasprintf0v5_0.19.5.1-1_amd64.deb ... Unpacking libasprintf0v5:amd64 (0.19.5.1-1) ... Selecting previously unselected package libmagic1:amd64. Preparing to unpack .../libmagic1_1%3a5.22+15-2_amd64.deb ... Unpacking libmagic1:amd64 (1:5.22+15-2) ... Selecting previously unselected package groff-base. Preparing to unpack .../groff-base_1.22.3-1_amd64.deb ... Unpacking groff-base (1.22.3-1) ... Selecting previously unselected package bsdmainutils. Preparing to unpack .../bsdmainutils_9.0.6_amd64.deb ... Unpacking bsdmainutils (9.0.6) ... Selecting previously unselected package libpipeline1:amd64. Preparing to unpack .../libpipeline1_1.4.1-1_amd64.deb ... Unpacking libpipeline1:amd64 (1.4.1-1) ... Selecting previously unselected package man-db. Preparing to unpack .../man-db_2.7.2-1_amd64.deb ... Unpacking man-db (2.7.2-1) ... Selecting previously unselected package libpython2.7-minimal:amd64. Preparing to unpack .../libpython2.7-minimal_2.7.10-3_amd64.deb ... Unpacking libpython2.7-minimal:amd64 (2.7.10-3) ... Selecting previously unselected package python2.7-minimal. Preparing to unpack .../python2.7-minimal_2.7.10-3_amd64.deb ... Unpacking python2.7-minimal (2.7.10-3) ... Selecting previously unselected package python-minimal. Preparing to unpack .../python-minimal_2.7.9-1_amd64.deb ... Unpacking python-minimal (2.7.9-1) ... Selecting previously unselected package mime-support. Preparing to unpack .../mime-support_3.59_all.deb ... Unpacking mime-support (3.59) ... Selecting previously unselected package libexpat1:amd64. Preparing to unpack .../libexpat1_2.1.0-7_amd64.deb ... Unpacking libexpat1:amd64 (2.1.0-7) ... Selecting previously unselected package libffi6:amd64. Preparing to unpack .../libffi6_3.2.1-3_amd64.deb ... Unpacking libffi6:amd64 (3.2.1-3) ... Selecting previously unselected package libsqlite3-0:amd64. Preparing to unpack .../libsqlite3-0_3.8.11.1-1_amd64.deb ... Unpacking libsqlite3-0:amd64 (3.8.11.1-1) ... Selecting previously unselected package libpython2.7-stdlib:amd64. Preparing to unpack .../libpython2.7-stdlib_2.7.10-3_amd64.deb ... Unpacking libpython2.7-stdlib:amd64 (2.7.10-3) ... Selecting previously unselected package python2.7. Preparing to unpack .../python2.7_2.7.10-3_amd64.deb ... Unpacking python2.7 (2.7.10-3) ... Selecting previously unselected package libpython-stdlib:amd64. Preparing to unpack .../libpython-stdlib_2.7.9-1_amd64.deb ... Unpacking libpython-stdlib:amd64 (2.7.9-1) ... Setting up libpython2.7-minimal:amd64 (2.7.10-3) ... Setting up python2.7-minimal (2.7.10-3) ... Setting up python-minimal (2.7.9-1) ... Selecting previously unselected package python. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 16691 files and directories currently installed.) Preparing to unpack .../python_2.7.9-1_amd64.deb ... Unpacking python (2.7.9-1) ... Selecting previously unselected package libglib2.0-0:amd64. Preparing to unpack .../libglib2.0-0_2.44.1-1.1_amd64.deb ... Unpacking libglib2.0-0:amd64 (2.44.1-1.1) ... Selecting previously unselected package libicu55:amd64. Preparing to unpack .../libicu55_55.1-4_amd64.deb ... Unpacking libicu55:amd64 (55.1-4) ... Selecting previously unselected package libxml2:amd64. Preparing to unpack .../libxml2_2.9.2+really2.9.1+dfsg1-0.1_amd64.deb ... Unpacking libxml2:amd64 (2.9.2+really2.9.1+dfsg1-0.1) ... Selecting previously unselected package libcroco3:amd64. Preparing to unpack .../libcroco3_0.6.8-3+b1_amd64.deb ... Unpacking libcroco3:amd64 (0.6.8-3+b1) ... Selecting previously unselected package libgfortran3:amd64. Preparing to unpack .../libgfortran3_5.2.1-15_amd64.deb ... Unpacking libgfortran3:amd64 (5.2.1-15) ... Selecting previously unselected package libunistring0:amd64. Preparing to unpack .../libunistring0_0.9.3-5.2+b1_amd64.deb ... Unpacking libunistring0:amd64 (0.9.3-5.2+b1) ... Selecting previously unselected package file. Preparing to unpack .../file_1%3a5.22+15-2_amd64.deb ... Unpacking file (1:5.22+15-2) ... Selecting previously unselected package gettext-base. Preparing to unpack .../gettext-base_0.19.5.1-1_amd64.deb ... Unpacking gettext-base (0.19.5.1-1) ... Selecting previously unselected package gettext. Preparing to unpack .../gettext_0.19.5.1-1_amd64.deb ... Unpacking gettext (0.19.5.1-1) ... Selecting previously unselected package intltool-debian. Preparing to unpack .../intltool-debian_0.35.0+20060710.2_all.deb ... Unpacking intltool-debian (0.35.0+20060710.2) ... Selecting previously unselected package po-debconf. Preparing to unpack .../po-debconf_1.0.18_all.deb ... Unpacking po-debconf (1.0.18) ... Selecting previously unselected package debhelper. Preparing to unpack .../debhelper_9.20150811_all.deb ... Unpacking debhelper (9.20150811) ... Selecting previously unselected package hdf5-helpers. Preparing to unpack .../hdf5-helpers_1.8.13+docs-15.1_amd64.deb ... Unpacking hdf5-helpers (1.8.13+docs-15.1) ... Selecting previously unselected package libhdf5-8:amd64. Preparing to unpack .../libhdf5-8_1.8.13+docs-15.1_amd64.deb ... Unpacking libhdf5-8:amd64 (1.8.13+docs-15.1) ... Selecting previously unselected package libhdf5-cpp-8:amd64. Preparing to unpack .../libhdf5-cpp-8_1.8.13+docs-15.1_amd64.deb ... Unpacking libhdf5-cpp-8:amd64 (1.8.13+docs-15.1) ... Selecting previously unselected package zlib1g-dev:amd64. Preparing to unpack .../zlib1g-dev_1%3a1.2.8.dfsg-2+b1_amd64.deb ... Unpacking zlib1g-dev:amd64 (1:1.2.8.dfsg-2+b1) ... Selecting previously unselected package libjpeg62-turbo:amd64. Preparing to unpack .../libjpeg62-turbo_1%3a1.4.1-2_amd64.deb ... Unpacking libjpeg62-turbo:amd64 (1:1.4.1-2) ... Selecting previously unselected package libjpeg62-turbo-dev:amd64. Preparing to unpack .../libjpeg62-turbo-dev_1%3a1.4.1-2_amd64.deb ... Unpacking libjpeg62-turbo-dev:amd64 (1:1.4.1-2) ... Selecting previously unselected package libjpeg-dev. Preparing to unpack .../libjpeg-dev_1%3a1.4.1-2_all.deb ... Unpacking libjpeg-dev (1:1.4.1-2) ... Selecting previously unselected package libhdf5-dev. Preparing to unpack .../libhdf5-dev_1.8.13+docs-15.1_amd64.deb ... Unpacking libhdf5-dev (1.8.13+docs-15.1) ... Setting up libasprintf0v5:amd64 (0.19.5.1-1) ... Setting up libmagic1:amd64 (1:5.22+15-2) ... Setting up groff-base (1.22.3-1) ... Setting up bsdmainutils (9.0.6) ... update-alternatives: using /usr/bin/bsd-write to provide /usr/bin/write (write) in auto mode update-alternatives: using /usr/bin/bsd-from to provide /usr/bin/from (from) in auto mode Setting up libpipeline1:amd64 (1.4.1-1) ... Setting up man-db (2.7.2-1) ... Building database of manual pages ... Setting up mime-support (3.59) ... Setting up libexpat1:amd64 (2.1.0-7) ... Setting up libffi6:amd64 (3.2.1-3) ... Setting up libsqlite3-0:amd64 (3.8.11.1-1) ... Setting up libpython2.7-stdlib:amd64 (2.7.10-3) ... Setting up python2.7 (2.7.10-3) ... Setting up libpython-stdlib:amd64 (2.7.9-1) ... Setting up python (2.7.9-1) ... Setting up libglib2.0-0:amd64 (2.44.1-1.1) ... No schema files found: doing nothing. Setting up libicu55:amd64 (55.1-4) ... Setting up libxml2:amd64 (2.9.2+really2.9.1+dfsg1-0.1) ... Setting up libcroco3:amd64 (0.6.8-3+b1) ... Setting up libgfortran3:amd64 (5.2.1-15) ... Setting up libunistring0:amd64 (0.9.3-5.2+b1) ... Setting up file (1:5.22+15-2) ... Setting up gettext-base (0.19.5.1-1) ... Setting up gettext (0.19.5.1-1) ... Setting up intltool-debian (0.35.0+20060710.2) ... Setting up po-debconf (1.0.18) ... Setting up debhelper (9.20150811) ... Setting up hdf5-helpers (1.8.13+docs-15.1) ... Setting up libhdf5-8:amd64 (1.8.13+docs-15.1) ... Setting up libhdf5-cpp-8:amd64 (1.8.13+docs-15.1) ... Setting up zlib1g-dev:amd64 (1:1.2.8.dfsg-2+b1) ... Setting up libjpeg62-turbo:amd64 (1:1.4.1-2) ... Setting up libjpeg62-turbo-dev:amd64 (1:1.4.1-2) ... Setting up libjpeg-dev (1:1.4.1-2) ... Setting up libhdf5-dev (1.8.13+docs-15.1) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/pkgconfig/hdf5-serial.pc to provide /usr/lib/x86_64-linux-gnu/pkgconfig/hdf5.pc (hdf5.pc) in auto mode Processing triggers for libc-bin (2.19-19) ... Killed old client process Internet Systems Consortium DHCP Client 4.3.2 Copyright 2004-2015 Internet Systems Consortium. All rights reserved. For info, please visit https://www.isc.org/software/dhcp/ Listening on LPF/eth0/06:3d:32:6c:8d:fe Sending on LPF/eth0/06:3d:32:6c:8d:fe Sending on Socket/fallback DHCPRELEASE on eth0 to 10.0.3.1 port 67 dpkg-buildpackage: source package blasr dpkg-buildpackage: source version 0~20150724+git3ca7fe8-1 dpkg-buildpackage: source distribution unstable dpkg-buildpackage: source changed by Afif Elghraoui dpkg-source --before-build blasr-0~20150724+git3ca7fe8 dpkg-buildpackage: host architecture amd64 debian/rules clean dh clean dh_testdir debian/rules override_dh_auto_clean make[1]: Entering directory '/blasr-0~20150724+git3ca7fe8' ./configure.py --no-pbbam --submodules writing to '/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/x86_64-linux-gnu/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 '/blasr-0~20150724+git3ca7fe8/libcpp/defines.mk' """ HDF5_INCLUDE:=/usr/include/hdf5/serial HDF5_LIB:=/usr/lib/x86_64-linux-gnu/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 '/blasr-0~20150724+git3ca7fe8/libcpp/pbdata/libconfig.h' """ """ NOT2 /usr/bin/make cleanall make[2]: Entering directory '/blasr-0~20150724+git3ca7fe8' /usr/bin/make -C libcpp clean make[3]: Entering directory '/blasr-0~20150724+git3ca7fe8/libcpp' /usr/bin/make -C pbdata clean make[4]: Entering directory '/blasr-0~20150724+git3ca7fe8/libcpp/pbdata' make[4]: Leaving directory '/blasr-0~20150724+git3ca7fe8/libcpp/pbdata' /usr/bin/make -C hdf clean make[4]: Entering directory '/blasr-0~20150724+git3ca7fe8/libcpp/hdf' make[4]: Leaving directory '/blasr-0~20150724+git3ca7fe8/libcpp/hdf' /usr/bin/make -C alignment clean make[4]: Entering directory '/blasr-0~20150724+git3ca7fe8/libcpp/alignment' make[4]: Leaving directory '/blasr-0~20150724+git3ca7fe8/libcpp/alignment' #@/usr/bin/make -C unittest clean make[3]: Leaving directory '/blasr-0~20150724+git3ca7fe8/libcpp' rm -f blasr Blasr.o Blasr.d blasr.d /usr/bin/make -C utils clean make[3]: Entering directory '/blasr-0~20150724+git3ca7fe8/utils' make[3]: Leaving directory '/blasr-0~20150724+git3ca7fe8/utils' /usr/bin/make -C extrautils clean make[3]: Entering directory '/blasr-0~20150724+git3ca7fe8/extrautils' make[3]: Leaving directory '/blasr-0~20150724+git3ca7fe8/extrautils' make[2]: Leaving directory '/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 '/blasr-0~20150724+git3ca7fe8' dh_clean dpkg-source -b blasr-0~20150724+git3ca7fe8 dpkg-source: info: using source format '3.0 (quilt)' dpkg-source: info: building blasr using existing ./blasr_0~20150724+git3ca7fe8.orig.tar.xz dpkg-source: info: building blasr in blasr_0~20150724+git3ca7fe8-1.debian.tar.xz dpkg-source: info: building blasr in blasr_0~20150724+git3ca7fe8-1.dsc debian/rules build dh build dh_testdir debian/rules override_dh_auto_configure make[1]: Entering directory '/blasr-0~20150724+git3ca7fe8' ./configure.py --no-pbbam --submodules writing to '/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/x86_64-linux-gnu/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 '/blasr-0~20150724+git3ca7fe8/libcpp/defines.mk' """ HDF5_INCLUDE:=/usr/include/hdf5/serial HDF5_LIB:=/usr/lib/x86_64-linux-gnu/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 '/blasr-0~20150724+git3ca7fe8/libcpp/pbdata/libconfig.h' """ """ NOT2 make[1]: Leaving directory '/blasr-0~20150724+git3ca7fe8' debian/rules override_dh_auto_build make[1]: Entering directory '/blasr-0~20150724+git3ca7fe8' /usr/bin/make build-submodule make[2]: Entering directory '/blasr-0~20150724+git3ca7fe8' # DON'T use pbbam which is not on github. cd libcpp && NOPBBAM=true HDF5_LIB=/usr/lib/x86_64-linux-gnu/hdf5/serial/libhdf5.so HDF5_INCLUDE=/usr/include/hdf5/serial ./configure.py writing to '/blasr-0~20150724+git3ca7fe8/libcpp/defines.mk' """ HDF5_INCLUDE:=/usr/include/hdf5/serial HDF5_LIB:=/usr/lib/x86_64-linux-gnu/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 '/blasr-0~20150724+git3ca7fe8/libcpp' /usr/bin/make -C pbdata all make[4]: Entering directory '/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 '/blasr-0~20150724+git3ca7fe8/libcpp/pbdata' /usr/bin/make -C hdf all make[4]: Entering directory '/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/x86_64-linux-gnu/hdf5/serial/libhdf5.so make[4]: Leaving directory '/blasr-0~20150724+git3ca7fe8/libcpp/hdf' /usr/bin/make -C alignment all make[4]: Entering directory '/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/x86_64-linux-gnu/hdf5/serial/libhdf5.so make[4]: Leaving directory '/blasr-0~20150724+git3ca7fe8/libcpp/alignment' make[3]: Leaving directory '/blasr-0~20150724+git3ca7fe8/libcpp' make[2]: Leaving directory '/blasr-0~20150724+git3ca7fe8' /usr/bin/make make[2]: Entering directory '/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/x86_64-linux-gnu/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/x86_64-linux-gnu/hdf5/serial:./libcpp/alignment:./libcpp/hdf:./libcpp/pbdata /usr/bin/make -C utils make[3]: Entering directory '/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/x86_64-linux-gnu/hdf5/serial -static -L../libcpp/alignment -L../libcpp/pbdata -L../libcpp/hdf -L/usr/lib/x86_64-linux-gnu/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/x86_64-linux-gnu/hdf5/serial -static -L../libcpp/alignment -L../libcpp/pbdata -L../libcpp/hdf -L/usr/lib/x86_64-linux-gnu/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/x86_64-linux-gnu/hdf5/serial -static -L../libcpp/alignment -L../libcpp/pbdata -L../libcpp/hdf -L/usr/lib/x86_64-linux-gnu/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/x86_64-linux-gnu/hdf5/serial -static -L../libcpp/alignment -L../libcpp/pbdata -L../libcpp/hdf -L/usr/lib/x86_64-linux-gnu/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/x86_64-linux-gnu/hdf5/serial -static -L../libcpp/alignment -L../libcpp/pbdata -L../libcpp/hdf -L/usr/lib/x86_64-linux-gnu/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/x86_64-linux-gnu/hdf5/serial -static -L../libcpp/alignment -L../libcpp/pbdata -L../libcpp/hdf -L/usr/lib/x86_64-linux-gnu/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/x86_64-linux-gnu/hdf5/serial -static -L../libcpp/alignment -L../libcpp/pbdata -L../libcpp/hdf -L/usr/lib/x86_64-linux-gnu/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/x86_64-linux-gnu/hdf5/serial -static -L../libcpp/alignment -L../libcpp/pbdata -L../libcpp/hdf -L/usr/lib/x86_64-linux-gnu/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 '/blasr-0~20150724+git3ca7fe8/utils' make[2]: Leaving directory '/blasr-0~20150724+git3ca7fe8' make[1]: Leaving directory '/blasr-0~20150724+git3ca7fe8' debian/rules binary dh binary dh_testroot dh_prep dh_auto_install dh_install dh_installdocs dh_installchangelogs dh_installman dh_perl dh_link dh_compress dh_fixperms dh_strip dh_makeshlibs dh_shlibdeps dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/blasr/usr/bin/sdpMatcher debian/blasr/usr/bin/loadPulses debian/blasr/usr/bin/toAfg debian/blasr/usr/bin/samtoh5 debian/blasr/usr/bin/pls2fasta debian/blasr/usr/bin/samtom4 debian/blasr/usr/bin/sawriter debian/blasr/usr/bin/samFilter debian/blasr/usr/bin/blasr were not linked against libz.so.1 (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/loadPulses debian/blasr/usr/bin/toAfg debian/blasr/usr/bin/samtoh5 debian/blasr/usr/bin/pls2fasta debian/blasr/usr/bin/samtom4 debian/blasr/usr/bin/sawriter debian/blasr/usr/bin/samFilter debian/blasr/usr/bin/blasr were not linked against libdl.so.2 (they use none of the library's symbols) dh_installdeb dh_gencontrol dh_md5sums dh_builddeb dpkg-deb: building package 'blasr' in '../blasr_0~20150724+git3ca7fe8-1_amd64.deb'. dpkg-genchanges >../blasr_0~20150724+git3ca7fe8-1_amd64.changes dpkg-genchanges: including full source code in upload dpkg-source --after-build blasr-0~20150724+git3ca7fe8 dpkg-buildpackage: full upload (original source is included)