=> Building biology/py-pysam
Started : Wednesday, 29 NOV 2017 at 20:59:15 UTC
Platform: 5.1-DEVELOPMENT DragonFly v5.1.0.211.g5913f-DEVELOPMENT #23: Mon Nov  6 09:10:01 PST 2017     root@pkgbox64.dragonflybsd.org:/usr/obj/usr/src/sys/X86_64_GENERIC  x86_64


--------------------------------------------------
--  Environment
--------------------------------------------------
UNAME_r=5.1-SYNTH
UNAME_m=x86_64
UNAME_p=x86_64
UNAME_v=DragonFly 5.1-SYNTH
UNAME_s=DragonFly
PATH=/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin
SSL_NO_VERIFY_PEER=1
TERM=dumb
PKG_CACHEDIR=/var/cache/pkg8
PKG_DBDIR=/var/db/pkg8
PORTSDIR=/xports
LANG=C
HOME=/root
USER=root



--------------------------------------------------
--  Options
--------------------------------------------------



--------------------------------------------------
--  CONFIGURE_ENV
--------------------------------------------------
MAKE=gmake
PYTHON="/usr/local/bin/python2.7"
XDG_DATA_HOME=/construction/biology/py-pysam
XDG_CONFIG_HOME=/construction/biology/py-pysam
HOME=/construction/biology/py-pysam
TMPDIR="/tmp"
PATH=/construction/biology/py-pysam/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin
SHELL=/bin/sh
CONFIG_SHELL=/bin/sh
CCVER=gcc50



--------------------------------------------------
--  CONFIGURE_ARGS
--------------------------------------------------




--------------------------------------------------
--  MAKE_ENV
--------------------------------------------------
XDG_DATA_HOME=/construction/biology/py-pysam
XDG_CONFIG_HOME=/construction/biology/py-pysam
HOME=/construction/biology/py-pysam
TMPDIR="/tmp"
PATH=/construction/biology/py-pysam/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin
NO_PIE=yes
MK_DEBUG_FILES=no
MK_KERNEL_SYMBOLS=no
SHELL=/bin/sh
NO_LINT=YES
CCVER=gcc50
LDSHARED="cc -shared"
PYTHONDONTWRITEBYTECODE=
PYTHONOPTIMIZE=
PREFIX=/usr/local
LOCALBASE=/usr/local
LIBDIR="/usr/lib"
NOPROFILE=1
CC="cc"
CFLAGS="-pipe -O2 -fno-strict-aliasing"
CPP="cpp"
CPPFLAGS=""
LDFLAGS=""
LIBS=""
CXX="c++"
CXXFLAGS=" -pipe -O2 -fno-strict-aliasing"
MANPREFIX="/usr/local"
BSD_INSTALL_PROGRAM="install  -s -m 555"
BSD_INSTALL_LIB="install  -s -m 0644"
BSD_INSTALL_SCRIPT="install  -m 555"
BSD_INSTALL_DATA="install  -m 0644"
BSD_INSTALL_MAN="install  -m 444"



--------------------------------------------------
--  MAKE_ARGS
--------------------------------------------------
DESTDIR=/construction/biology/py-pysam/stage



--------------------------------------------------
--  PLIST_SUB
--------------------------------------------------
PYTHON_INCLUDEDIR=include/python2.7
PYTHON_LIBDIR=lib/python2.7
PYTHON_PLATFORM=dragonfly5
PYTHON_PYOEXTENSION=pyo
PYTHON_SITELIBDIR=lib/python2.7/site-packages
PYTHON_SUFFIX=27
PYTHON_VER=2.7
PYTHON_VERSION=python2.7
PYTHON2=""
PYTHON3="@comment "
OSREL=5.1
PREFIX=%D
LOCALBASE=/usr/local
RESETPREFIX=/usr/local
PORTDOCS=""
PORTEXAMPLES=""
LIB32DIR=lib
PROFILE="@comment "
DOCSDIR="share/doc/pysam"
EXAMPLESDIR="share/examples/pysam"
DATADIR="share/pysam"
WWWDIR="www/pysam"
ETCDIR="etc/pysam"



--------------------------------------------------
--  SUB_LIST
--------------------------------------------------
PREFIX=/usr/local
LOCALBASE=/usr/local
DATADIR=/usr/local/share/pysam
DOCSDIR=/usr/local/share/doc/pysam
EXAMPLESDIR=/usr/local/share/examples/pysam
WWWDIR=/usr/local/www/pysam
ETCDIR=/usr/local/etc/pysam



--------------------------------------------------
--  /etc/make.conf
--------------------------------------------------
SYNTHPROFILE=Release-BE
USE_PACKAGE_DEPENDS_ONLY=yes
PACKAGE_BUILDING=yes
BATCH=yes
PKG_CREATE_VERBOSE=yes
PORTSDIR=/xports
DISTDIR=/distfiles
WRKDIRPREFIX=/construction
PORT_DBDIR=/options
PACKAGES=/packages
MAKE_JOBS_NUMBER_LIMIT=5
LICENSES_ACCEPTED=	NONE
HAVE_COMPAT_IA32_KERN=
CONFIGURE_MAX_CMD_LEN=262144
_SMP_CPUS=8
UID=0
ARCH=x86_64
OPSYS=DragonFly
DFLYVERSION=500103
OSVERSION=9999999
OSREL=5.1
_OSRELEASE=5.1-SYNTH



--------------------------------------------------------------------------------
--  Phase: check-sanity
--------------------------------------------------------------------------------
===>  License MIT accepted by the user



--------------------------------------------------------------------------------
--  Phase: pkg-depends
--------------------------------------------------------------------------------
===>   py27-pysam-0.13 depends on file: /usr/local/sbin/pkg - not found
===>   Installing existing package /packages/All/pkg-1.10.2.txz
Installing pkg-1.10.2...
Extracting pkg-1.10.2: .......... done
===>   py27-pysam-0.13 depends on file: /usr/local/sbin/pkg - found
===>   Returning to build of py27-pysam-0.13



--------------------------------------------------------------------------------
--  Phase: fetch-depends
--------------------------------------------------------------------------------



--------------------------------------------------------------------------------
--  Phase: fetch
--------------------------------------------------------------------------------
===>  License MIT accepted by the user
===> Fetching all distfiles required by py27-pysam-0.13 for building



--------------------------------------------------------------------------------
--  Phase: checksum
--------------------------------------------------------------------------------
===>  License MIT accepted by the user
===> Fetching all distfiles required by py27-pysam-0.13 for building
=> SHA256 Checksum OK for pysam-0.13.tar.gz.



--------------------------------------------------------------------------------
--  Phase: extract-depends
--------------------------------------------------------------------------------



--------------------------------------------------------------------------------
--  Phase: extract
--------------------------------------------------------------------------------
===>  License MIT accepted by the user
===> Fetching all distfiles required by py27-pysam-0.13 for building
===>  Extracting for py27-pysam-0.13
=> SHA256 Checksum OK for pysam-0.13.tar.gz.



--------------------------------------------------------------------------------
--  Phase: patch-depends
--------------------------------------------------------------------------------



--------------------------------------------------------------------------------
--  Phase: patch
--------------------------------------------------------------------------------
===>  Patching for py27-pysam-0.13
===>  Applying ports patches for py27-pysam-0.13



--------------------------------------------------------------------------------
--  Phase: build-depends
--------------------------------------------------------------------------------
===>   py27-pysam-0.13 depends on executable: cython - not found
===>   Installing existing package /packages/All/cython-0.26.txz
Installing cython-0.26...
`-- Installing py27-setuptools-36.5.0...
|   `-- Installing python27-2.7.14_1...
|   | `-- Installing expat-2.2.1...
|   | `-- Extracting expat-2.2.1: .......... done
|   | `-- Installing gettext-runtime-0.19.8.1_1...
|   |   `-- Installing indexinfo-0.3.1...
|   |   `-- Extracting indexinfo-0.3.1: .... done
|   | `-- Extracting gettext-runtime-0.19.8.1_1: .......... done
|   | `-- Installing libffi-3.2.1_1...
|   | `-- Extracting libffi-3.2.1_1: .......... done
|   | `-- Installing libressl-2.6.3...
|   | `-- Extracting libressl-2.6.3: .......... done
|   | `-- Installing ncurses-6.0.0s20171007_1...
|   | `-- Extracting ncurses-6.0.0s20171007_1: .......... done
|   | `-- Installing readline-7.0.3_1...
|   | `-- Extracting readline-7.0.3_1: .......... done
|   `-- Extracting python27-2.7.14_1: .......... done
`-- Extracting py27-setuptools-36.5.0: .......... done
Extracting cython-0.26: .......... done
Message from python27-2.7.14_1:

===========================================================================

Note that some standard Python modules are provided as separate ports
as they require additional dependencies. They are available as:

bsddb           databases/py-bsddb
gdbm            databases/py-gdbm
sqlite3         databases/py-sqlite3
tkinter         x11-toolkits/py-tkinter

===========================================================================
===>   py27-pysam-0.13 depends on executable: cython - found
===>   Returning to build of py27-pysam-0.13
===>   py27-pysam-0.13 depends on executable: gmake - not found
===>   Installing existing package /packages/All/gmake-4.2.1_1.txz
Installing gmake-4.2.1_1...
Extracting gmake-4.2.1_1: .......... done
===>   py27-pysam-0.13 depends on executable: gmake - found
===>   Returning to build of py27-pysam-0.13
===>   py27-pysam-0.13 depends on package: py27-setuptools>0 - found
===>   py27-pysam-0.13 depends on file: /usr/local/bin/python2.7 - found



--------------------------------------------------------------------------------
--  Phase: lib-depends
--------------------------------------------------------------------------------



--------------------------------------------------------------------------------
--  Phase: configure
--------------------------------------------------------------------------------
===>  Configuring for py27-pysam-0.13
checking for gcc... cc
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
checking for suffix of executables... 
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether cc accepts -g... yes
checking for cc option to accept ISO C89... none needed
checking for ranlib... ranlib
checking for special C compiler options needed for large files... no
checking for _FILE_OFFSET_BITS value needed for large files... no
checking for _LARGEFILE_SOURCE value needed for large files... no
checking shared library type for unknown-DragonFly... plain .so
checking how to run the C preprocessor... cpp
checking for grep that handles long lines and -e... /usr/bin/grep
checking for egrep... /usr/bin/grep -E
checking for ANSI C header files... yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking for stdlib.h... (cached) yes
checking for unistd.h... (cached) yes
checking for sys/param.h... yes
checking for getpagesize... yes
checking for working mmap... yes
checking for gmtime_r... yes
checking for fsync... yes
checking for drand48... yes
checking whether fdatasync is declared... no
checking for library containing log... -lm
checking for zlib.h... yes
checking for inflate in -lz... yes
checking for library containing recv... none required
checking for bzlib.h... yes
checking for BZ2_bzBuffToBuffCompress in -lbz2... yes
checking for lzma.h... yes
checking for lzma_easy_buffer_encode in -llzma... yes
checking for curl_easy_pause in -lcurl... no
checking for curl_easy_init in -lcurl... no
configure: error: libcurl library not found

Support for HTTPS and other SSL-based URLs requires routines from the libcurl
library <http://curl.haxx.se/libcurl/>.  Building HTSlib with libcurl enabled
requires libcurl development files to be installed on the build machine; you
may need to ensure a package such as libcurl4-{gnutls,nss,openssl}-dev (on
Debian or Ubuntu Linux) or libcurl-devel (on RPM-based Linux distributions
or Cygwin) is installed.

Either configure with --disable-libcurl or resolve this error to build HTSlib.
checking for gcc... cc
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
checking for suffix of executables... 
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether cc accepts -g... yes
checking for cc option to accept ISO C89... none needed
checking for ranlib... ranlib
checking for special C compiler options needed for large files... no
checking for _FILE_OFFSET_BITS value needed for large files... no
checking for _LARGEFILE_SOURCE value needed for large files... no
checking shared library type for unknown-DragonFly... plain .so
checking how to run the C preprocessor... cpp
checking for grep that handles long lines and -e... /usr/bin/grep
checking for egrep... /usr/bin/grep -E
checking for ANSI C header files... yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking for stdlib.h... (cached) yes
checking for unistd.h... (cached) yes
checking for sys/param.h... yes
checking for getpagesize... yes
checking for working mmap... yes
checking for gmtime_r... yes
checking for fsync... yes
checking for drand48... yes
checking whether fdatasync is declared... no
checking for library containing log... -lm
checking for zlib.h... yes
checking for inflate in -lz... yes
checking for library containing recv... none required
checking for bzlib.h... yes
checking for BZ2_bzBuffToBuffCompress in -lbz2... yes
checking for lzma.h... yes
checking for lzma_easy_buffer_encode in -llzma... yes
configure: WARNING: GCS support not enabled: requires libcurl support
configure: WARNING: S3 support not enabled: requires libcurl support
checking whether PTHREAD_MUTEX_RECURSIVE is declared... yes
configure: creating ./config.status
config.status: creating config.mk
config.status: creating htslib.pc.tmp
config.status: creating config.h
gmake[1]: ./version.sh: Command not found
gmake[1]: ./version.sh: Command not found
# pysam: cython is available - using cythonize if necessary
# pysam: htslib mode is shared
# pysam: HTSLIB_CONFIGURE_OPTIONS=None
# pysam: htslib configure options: --disable-libcurl
# pysam: htslib_config LIBS=-llzma -lbz2 -lz -lm
# pysam: htslib_config PLATFORM=default
# pysam: htslib_config LIBHTS_OBJS=kfunc.o knetfile.o kstring.o bcf_sr_sort.o bgzf.o errmod.o faidx.o hfile.o hfile_net.o hts.o hts_os.o md5.o multipart.o probaln.o realn.o regidx.o sam.o synced_bcf_reader.o vcf_sweep.o tbx.o textutils.o thread_pool.o vcf.o vcfutils.o cram/cram_codecs.o cram/cram_decode.o cram/cram_encode.o cram/cram_external.o cram/cram_index.o cram/cram_io.o cram/cram_samtools.o cram/cram_stats.o cram/files.o cram/mFILE.o cram/open_trace_file.o cram/pooled_alloc.o cram/rANS_static.o cram/sam_header.o cram/string_alloc.o
# pysam: htslib_config LDFLAGS=
# pysam: config_option: ENABLE_PLUGINS=0
# pysam: config_option: HAVE_COMMONCRYPTO=0
# pysam: config_option: HAVE_GMTIME_R=1
# pysam: config_option: HAVE_HMAC=0
# pysam: config_option: HAVE_IRODS=0
# pysam: config_option: HAVE_LIBCURL=0
# pysam: config_option: HAVE_MMAP=1
running config



--------------------------------------------------------------------------------
--  Phase: build
--------------------------------------------------------------------------------
===>  Building for py27-pysam-0.13
checking for gcc... cc
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
checking for suffix of executables... 
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether cc accepts -g... yes
checking for cc option to accept ISO C89... none needed
checking for ranlib... ranlib
checking for special C compiler options needed for large files... no
checking for _FILE_OFFSET_BITS value needed for large files... no
checking for _LARGEFILE_SOURCE value needed for large files... no
checking shared library type for unknown-DragonFly... plain .so
checking how to run the C preprocessor... cpp
checking for grep that handles long lines and -e... /usr/bin/grep
checking for egrep... /usr/bin/grep -E
checking for ANSI C header files... yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking for stdlib.h... (cached) yes
checking for unistd.h... (cached) yes
checking for sys/param.h... yes
checking for getpagesize... yes
checking for working mmap... yes
checking for gmtime_r... yes
checking for fsync... yes
checking for drand48... yes
checking whether fdatasync is declared... no
checking for library containing log... -lm
checking for zlib.h... yes
checking for inflate in -lz... yes
checking for library containing recv... none required
checking for bzlib.h... yes
checking for BZ2_bzBuffToBuffCompress in -lbz2... yes
checking for lzma.h... yes
checking for lzma_easy_buffer_encode in -llzma... yes
checking for curl_easy_pause in -lcurl... no
checking for curl_easy_init in -lcurl... no
configure: error: libcurl library not found

Support for HTTPS and other SSL-based URLs requires routines from the libcurl
library <http://curl.haxx.se/libcurl/>.  Building HTSlib with libcurl enabled
requires libcurl development files to be installed on the build machine; you
may need to ensure a package such as libcurl4-{gnutls,nss,openssl}-dev (on
Debian or Ubuntu Linux) or libcurl-devel (on RPM-based Linux distributions
or Cygwin) is installed.

Either configure with --disable-libcurl or resolve this error to build HTSlib.
checking for gcc... cc
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
checking for suffix of executables... 
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether cc accepts -g... yes
checking for cc option to accept ISO C89... none needed
checking for ranlib... ranlib
checking for special C compiler options needed for large files... no
checking for _FILE_OFFSET_BITS value needed for large files... no
checking for _LARGEFILE_SOURCE value needed for large files... no
checking shared library type for unknown-DragonFly... plain .so
checking how to run the C preprocessor... cpp
checking for grep that handles long lines and -e... /usr/bin/grep
checking for egrep... /usr/bin/grep -E
checking for ANSI C header files... yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking for stdlib.h... (cached) yes
checking for unistd.h... (cached) yes
checking for sys/param.h... yes
checking for getpagesize... yes
checking for working mmap... yes
checking for gmtime_r... yes
checking for fsync... yes
checking for drand48... yes
checking whether fdatasync is declared... no
checking for library containing log... -lm
checking for zlib.h... yes
checking for inflate in -lz... yes
checking for library containing recv... none required
checking for bzlib.h... yes
checking for BZ2_bzBuffToBuffCompress in -lbz2... yes
checking for lzma.h... yes
checking for lzma_easy_buffer_encode in -llzma... yes
configure: WARNING: GCS support not enabled: requires libcurl support
configure: WARNING: S3 support not enabled: requires libcurl support
checking whether PTHREAD_MUTEX_RECURSIVE is declared... yes
configure: creating ./config.status
config.status: creating config.mk
config.status: creating htslib.pc.tmp
config.status: creating config.h
config.status: config.h is unchanged
gmake[1]: ./version.sh: Command not found
gmake[1]: ./version.sh: Command not found
# pysam: cython is available - using cythonize if necessary
# pysam: htslib mode is shared
# pysam: HTSLIB_CONFIGURE_OPTIONS=None
# pysam: htslib configure options: --disable-libcurl
# pysam: htslib_config LIBS=-llzma -lbz2 -lz -lm
# pysam: htslib_config PLATFORM=default
# pysam: htslib_config LIBHTS_OBJS=kfunc.o knetfile.o kstring.o bcf_sr_sort.o bgzf.o errmod.o faidx.o hfile.o hfile_net.o hts.o hts_os.o md5.o multipart.o probaln.o realn.o regidx.o sam.o synced_bcf_reader.o vcf_sweep.o tbx.o textutils.o thread_pool.o vcf.o vcfutils.o cram/cram_codecs.o cram/cram_decode.o cram/cram_encode.o cram/cram_external.o cram/cram_index.o cram/cram_io.o cram/cram_samtools.o cram/cram_stats.o cram/files.o cram/mFILE.o cram/open_trace_file.o cram/pooled_alloc.o cram/rANS_static.o cram/sam_header.o cram/string_alloc.o
# pysam: htslib_config LDFLAGS=
# pysam: config_option: ENABLE_PLUGINS=0
# pysam: config_option: HAVE_COMMONCRYPTO=0
# pysam: config_option: HAVE_GMTIME_R=1
# pysam: config_option: HAVE_HMAC=0
# pysam: config_option: HAVE_IRODS=0
# pysam: config_option: HAVE_LIBCURL=0
# pysam: config_option: HAVE_MMAP=1
running build
running build_py
creating build
creating build/lib.dragonfly-5.1-SYNTH-x86_64-2.7
creating build/lib.dragonfly-5.1-SYNTH-x86_64-2.7/pysam
copying pysam/Pileup.py -> build/lib.dragonfly-5.1-SYNTH-x86_64-2.7/pysam
copying pysam/config.py -> build/lib.dragonfly-5.1-SYNTH-x86_64-2.7/pysam
copying pysam/__init__.py -> build/lib.dragonfly-5.1-SYNTH-x86_64-2.7/pysam
copying pysam/namedtuple.py -> build/lib.dragonfly-5.1-SYNTH-x86_64-2.7/pysam
copying pysam/version.py -> build/lib.dragonfly-5.1-SYNTH-x86_64-2.7/pysam
copying pysam/bcftools.py -> build/lib.dragonfly-5.1-SYNTH-x86_64-2.7/pysam
copying pysam/utils.py -> build/lib.dragonfly-5.1-SYNTH-x86_64-2.7/pysam
copying pysam/samtools.py -> build/lib.dragonfly-5.1-SYNTH-x86_64-2.7/pysam
creating build/lib.dragonfly-5.1-SYNTH-x86_64-2.7/pysam/include
copying pysam/include/__init__.py -> build/lib.dragonfly-5.1-SYNTH-x86_64-2.7/pysam/include
package init file 'samtools/__init__.py' not found (or not a regular file)
package init file 'bcftools/__init__.py' not found (or not a regular file)
package init file 'samtools/win32/__init__.py' not found (or not a regular file)
package init file 'htslib/__init__.py' not found (or not a regular file)
package init file 'htslib/htslib/__init__.py' not found (or not a regular file)
copying pysam/libcbcf.pxd -> build/lib.dragonfly-5.1-SYNTH-x86_64-2.7/pysam
copying pysam/libctabixproxies.pxd -> build/lib.dragonfly-5.1-SYNTH-x86_64-2.7/pysam
copying pysam/libcalignedsegment.pxd -> build/lib.dragonfly-5.1-SYNTH-x86_64-2.7/pysam
copying pysam/libchtslib.pxd -> build/lib.dragonfly-5.1-SYNTH-x86_64-2.7/pysam
copying pysam/libcutils.pxd -> build/lib.dragonfly-5.1-SYNTH-x86_64-2.7/pysam
copying pysam/libcfaidx.pxd -> build/lib.dragonfly-5.1-SYNTH-x86_64-2.7/pysam
copying pysam/libcsamfile.pxd -> build/lib.dragonfly-5.1-SYNTH-x86_64-2.7/pysam
copying pysam/libcvcf.pxd -> build/lib.dragonfly-5.1-SYNTH-x86_64-2.7/pysam
copying pysam/libcsamtools.pxd -> build/lib.dragonfly-5.1-SYNTH-x86_64-2.7/pysam
copying pysam/libcbcftools.pxd -> build/lib.dragonfly-5.1-SYNTH-x86_64-2.7/pysam
copying pysam/libcalignmentfile.pxd -> build/lib.dragonfly-5.1-SYNTH-x86_64-2.7/pysam
copying pysam/libctabix.pxd -> build/lib.dragonfly-5.1-SYNTH-x86_64-2.7/pysam
copying pysam/htslib_util.h -> build/lib.dragonfly-5.1-SYNTH-x86_64-2.7/pysam
copying pysam/csamtools_util.h -> build/lib.dragonfly-5.1-SYNTH-x86_64-2.7/pysam
copying pysam/samfile_util.h -> build/lib.dragonfly-5.1-SYNTH-x86_64-2.7/pysam
copying pysam/cbcftools_util.h -> build/lib.dragonfly-5.1-SYNTH-x86_64-2.7/pysam
copying pysam/tabix_util.h -> build/lib.dragonfly-5.1-SYNTH-x86_64-2.7/pysam
copying pysam/pysam_stream.h -> build/lib.dragonfly-5.1-SYNTH-x86_64-2.7/pysam
copying pysam/pysam_util.h -> build/lib.dragonfly-5.1-SYNTH-x86_64-2.7/pysam
creating build/lib.dragonfly-5.1-SYNTH-x86_64-2.7/pysam/include/samtools
copying samtools/config.h -> build/lib.dragonfly-5.1-SYNTH-x86_64-2.7/pysam/include/samtools
copying samtools/bam_endian.h -> build/lib.dragonfly-5.1-SYNTH-x86_64-2.7/pysam/include/samtools
copying samtools/version.h -> build/lib.dragonfly-5.1-SYNTH-x86_64-2.7/pysam/include/samtools
copying samtools/sam_opts.h -> build/lib.dragonfly-5.1-SYNTH-x86_64-2.7/pysam/include/samtools
copying samtools/bam_plbuf.h -> build/lib.dragonfly-5.1-SYNTH-x86_64-2.7/pysam/include/samtools
copying samtools/sam_header.h -> build/lib.dragonfly-5.1-SYNTH-x86_64-2.7/pysam/include/samtools
copying samtools/stats_isize.h -> build/lib.dragonfly-5.1-SYNTH-x86_64-2.7/pysam/include/samtools
copying samtools/bam.h -> build/lib.dragonfly-5.1-SYNTH-x86_64-2.7/pysam/include/samtools
copying samtools/samtools.h -> build/lib.dragonfly-5.1-SYNTH-x86_64-2.7/pysam/include/samtools
copying samtools/sample.h -> build/lib.dragonfly-5.1-SYNTH-x86_64-2.7/pysam/include/samtools
copying samtools/bam2bcf.h -> build/lib.dragonfly-5.1-SYNTH-x86_64-2.7/pysam/include/samtools
copying samtools/bam_lpileup.h -> build/lib.dragonfly-5.1-SYNTH-x86_64-2.7/pysam/include/samtools
copying samtools/pysam.h -> build/lib.dragonfly-5.1-SYNTH-x86_64-2.7/pysam/include/samtools
copying samtools/sam.h -> build/lib.dragonfly-5.1-SYNTH-x86_64-2.7/pysam/include/samtools
creating build/lib.dragonfly-5.1-SYNTH-x86_64-2.7/pysam/include/bcftools
copying bcftools/gvcf.h -> build/lib.dragonfly-5.1-SYNTH-x86_64-2.7/pysam/include/bcftools
copying bcftools/tsv2vcf.h -> build/lib.dragonfly-5.1-SYNTH-x86_64-2.7/pysam/include/bcftools
copying bcftools/vcmp.h -> build/lib.dragonfly-5.1-SYNTH-x86_64-2.7/pysam/include/bcftools
copying bcftools/convert.h -> build/lib.dragonfly-5.1-SYNTH-x86_64-2.7/pysam/include/bcftools
copying bcftools/HMM.h -> build/lib.dragonfly-5.1-SYNTH-x86_64-2.7/pysam/include/bcftools
copying bcftools/hclust.h -> build/lib.dragonfly-5.1-SYNTH-x86_64-2.7/pysam/include/bcftools
copying bcftools/vcfbuf.h -> build/lib.dragonfly-5.1-SYNTH-x86_64-2.7/pysam/include/bcftools
copying bcftools/smpl_ilist.h -> build/lib.dragonfly-5.1-SYNTH-x86_64-2.7/pysam/include/bcftools
copying bcftools/ploidy.h -> build/lib.dragonfly-5.1-SYNTH-x86_64-2.7/pysam/include/bcftools
copying bcftools/bin.h -> build/lib.dragonfly-5.1-SYNTH-x86_64-2.7/pysam/include/bcftools
copying bcftools/version.h -> build/lib.dragonfly-5.1-SYNTH-x86_64-2.7/pysam/include/bcftools
copying bcftools/mw.h -> build/lib.dragonfly-5.1-SYNTH-x86_64-2.7/pysam/include/bcftools
copying bcftools/filter.h -> build/lib.dragonfly-5.1-SYNTH-x86_64-2.7/pysam/include/bcftools
copying bcftools/kmin.h -> build/lib.dragonfly-5.1-SYNTH-x86_64-2.7/pysam/include/bcftools
copying bcftools/rbuf.h -> build/lib.dragonfly-5.1-SYNTH-x86_64-2.7/pysam/include/bcftools
copying bcftools/bam2bcf.h -> build/lib.dragonfly-5.1-SYNTH-x86_64-2.7/pysam/include/bcftools
copying bcftools/regidx.h -> build/lib.dragonfly-5.1-SYNTH-x86_64-2.7/pysam/include/bcftools
copying bcftools/call.h -> build/lib.dragonfly-5.1-SYNTH-x86_64-2.7/pysam/include/bcftools
copying bcftools/bcftools.h -> build/lib.dragonfly-5.1-SYNTH-x86_64-2.7/pysam/include/bcftools
copying bcftools/prob1.h -> build/lib.dragonfly-5.1-SYNTH-x86_64-2.7/pysam/include/bcftools
copying bcftools/khash_str2str.h -> build/lib.dragonfly-5.1-SYNTH-x86_64-2.7/pysam/include/bcftools
copying bcftools/pysam.h -> build/lib.dragonfly-5.1-SYNTH-x86_64-2.7/pysam/include/bcftools
copying bcftools/bam_sample.h -> build/lib.dragonfly-5.1-SYNTH-x86_64-2.7/pysam/include/bcftools
copying bcftools/kheap.h -> build/lib.dragonfly-5.1-SYNTH-x86_64-2.7/pysam/include/bcftools
copying bcftools/config.h -> build/lib.dragonfly-5.1-SYNTH-x86_64-2.7/pysam/include/bcftools
creating build/lib.dragonfly-5.1-SYNTH-x86_64-2.7/pysam/include/samtools/win32
copying samtools/win32/zconf.h -> build/lib.dragonfly-5.1-SYNTH-x86_64-2.7/pysam/include/samtools/win32
copying samtools/win32/zlib.h -> build/lib.dragonfly-5.1-SYNTH-x86_64-2.7/pysam/include/samtools/win32
copying samtools/win32/xcurses.h -> build/lib.dragonfly-5.1-SYNTH-x86_64-2.7/pysam/include/samtools/win32
creating build/lib.dragonfly-5.1-SYNTH-x86_64-2.7/pysam/include/htslib
copying htslib/config.h -> build/lib.dragonfly-5.1-SYNTH-x86_64-2.7/pysam/include/htslib
copying htslib/version.h -> build/lib.dragonfly-5.1-SYNTH-x86_64-2.7/pysam/include/htslib
copying htslib/hts_internal.h -> build/lib.dragonfly-5.1-SYNTH-x86_64-2.7/pysam/include/htslib
copying htslib/hfile_internal.h -> build/lib.dragonfly-5.1-SYNTH-x86_64-2.7/pysam/include/htslib
copying htslib/thread_pool_internal.h -> build/lib.dragonfly-5.1-SYNTH-x86_64-2.7/pysam/include/htslib
copying htslib/bcf_sr_sort.h -> build/lib.dragonfly-5.1-SYNTH-x86_64-2.7/pysam/include/htslib
creating build/lib.dragonfly-5.1-SYNTH-x86_64-2.7/pysam/include/htslib/htslib
copying htslib/htslib/vcfutils.h -> build/lib.dragonfly-5.1-SYNTH-x86_64-2.7/pysam/include/htslib/htslib
copying htslib/htslib/khash.h -> build/lib.dragonfly-5.1-SYNTH-x86_64-2.7/pysam/include/htslib/htslib
copying htslib/htslib/regidx.h -> build/lib.dragonfly-5.1-SYNTH-x86_64-2.7/pysam/include/htslib/htslib
copying htslib/htslib/hts_os.h -> build/lib.dragonfly-5.1-SYNTH-x86_64-2.7/pysam/include/htslib/htslib
copying htslib/htslib/hts.h -> build/lib.dragonfly-5.1-SYNTH-x86_64-2.7/pysam/include/htslib/htslib
copying htslib/htslib/hts_endian.h -> build/lib.dragonfly-5.1-SYNTH-x86_64-2.7/pysam/include/htslib/htslib
copying htslib/htslib/vcf_sweep.h -> build/lib.dragonfly-5.1-SYNTH-x86_64-2.7/pysam/include/htslib/htslib
copying htslib/htslib/synced_bcf_reader.h -> build/lib.dragonfly-5.1-SYNTH-x86_64-2.7/pysam/include/htslib/htslib
copying htslib/htslib/thread_pool.h -> build/lib.dragonfly-5.1-SYNTH-x86_64-2.7/pysam/include/htslib/htslib
copying htslib/htslib/sam.h -> build/lib.dragonfly-5.1-SYNTH-x86_64-2.7/pysam/include/htslib/htslib
copying htslib/htslib/hfile.h -> build/lib.dragonfly-5.1-SYNTH-x86_64-2.7/pysam/include/htslib/htslib
copying htslib/htslib/ksort.h -> build/lib.dragonfly-5.1-SYNTH-x86_64-2.7/pysam/include/htslib/htslib
copying htslib/htslib/hts_log.h -> build/lib.dragonfly-5.1-SYNTH-x86_64-2.7/pysam/include/htslib/htslib
copying htslib/htslib/bgzf.h -> build/lib.dragonfly-5.1-SYNTH-x86_64-2.7/pysam/include/htslib/htslib
copying htslib/htslib/tbx.h -> build/lib.dragonfly-5.1-SYNTH-x86_64-2.7/pysam/include/htslib/htslib
copying htslib/htslib/klist.h -> build/lib.dragonfly-5.1-SYNTH-x86_64-2.7/pysam/include/htslib/htslib
copying htslib/htslib/hts_defs.h -> build/lib.dragonfly-5.1-SYNTH-x86_64-2.7/pysam/include/htslib/htslib
copying htslib/htslib/cram.h -> build/lib.dragonfly-5.1-SYNTH-x86_64-2.7/pysam/include/htslib/htslib
copying htslib/htslib/kfunc.h -> build/lib.dragonfly-5.1-SYNTH-x86_64-2.7/pysam/include/htslib/htslib
copying htslib/htslib/faidx.h -> build/lib.dragonfly-5.1-SYNTH-x86_64-2.7/pysam/include/htslib/htslib
copying htslib/htslib/kstring.h -> build/lib.dragonfly-5.1-SYNTH-x86_64-2.7/pysam/include/htslib/htslib
copying htslib/htslib/vcf.h -> build/lib.dragonfly-5.1-SYNTH-x86_64-2.7/pysam/include/htslib/htslib
copying htslib/htslib/khash_str2int.h -> build/lib.dragonfly-5.1-SYNTH-x86_64-2.7/pysam/include/htslib/htslib
copying htslib/htslib/knetfile.h -> build/lib.dragonfly-5.1-SYNTH-x86_64-2.7/pysam/include/htslib/htslib
copying htslib/htslib/kbitset.h -> build/lib.dragonfly-5.1-SYNTH-x86_64-2.7/pysam/include/htslib/htslib
copying htslib/htslib/kseq.h -> build/lib.dragonfly-5.1-SYNTH-x86_64-2.7/pysam/include/htslib/htslib
running build_ext
skipping 'pysam/libchtslib.c' Cython extension (up-to-date)
building 'pysam.libchtslib' extension
creating build/temp.dragonfly-5.1-SYNTH-x86_64-2.7
creating build/temp.dragonfly-5.1-SYNTH-x86_64-2.7/pysam
creating build/temp.dragonfly-5.1-SYNTH-x86_64-2.7/htslib
creating build/temp.dragonfly-5.1-SYNTH-x86_64-2.7/htslib/cram
cc -DNDEBUG -pipe -O2 -fno-strict-aliasing -fPIC -Ipysam -I. -Ihtslib -I/usr/local/include/python2.7 -c pysam/libchtslib.c -o build/temp.dragonfly-5.1-SYNTH-x86_64-2.7/pysam/libchtslib.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
cc -DNDEBUG -pipe -O2 -fno-strict-aliasing -fPIC -Ipysam -I. -Ihtslib -I/usr/local/include/python2.7 -c pysam/htslib_util.c -o build/temp.dragonfly-5.1-SYNTH-x86_64-2.7/pysam/htslib_util.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
cc -DNDEBUG -pipe -O2 -fno-strict-aliasing -fPIC -Ipysam -I. -Ihtslib -I/usr/local/include/python2.7 -c htslib/kfunc.c -o build/temp.dragonfly-5.1-SYNTH-x86_64-2.7/htslib/kfunc.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
cc -DNDEBUG -pipe -O2 -fno-strict-aliasing -fPIC -Ipysam -I. -Ihtslib -I/usr/local/include/python2.7 -c htslib/knetfile.c -o build/temp.dragonfly-5.1-SYNTH-x86_64-2.7/htslib/knetfile.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
cc -DNDEBUG -pipe -O2 -fno-strict-aliasing -fPIC -Ipysam -I. -Ihtslib -I/usr/local/include/python2.7 -c htslib/kstring.c -o build/temp.dragonfly-5.1-SYNTH-x86_64-2.7/htslib/kstring.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
cc -DNDEBUG -pipe -O2 -fno-strict-aliasing -fPIC -Ipysam -I. -Ihtslib -I/usr/local/include/python2.7 -c htslib/bcf_sr_sort.c -o build/temp.dragonfly-5.1-SYNTH-x86_64-2.7/htslib/bcf_sr_sort.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
cc -DNDEBUG -pipe -O2 -fno-strict-aliasing -fPIC -Ipysam -I. -Ihtslib -I/usr/local/include/python2.7 -c htslib/bgzf.c -o build/temp.dragonfly-5.1-SYNTH-x86_64-2.7/htslib/bgzf.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
cc -DNDEBUG -pipe -O2 -fno-strict-aliasing -fPIC -Ipysam -I. -Ihtslib -I/usr/local/include/python2.7 -c htslib/errmod.c -o build/temp.dragonfly-5.1-SYNTH-x86_64-2.7/htslib/errmod.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
cc -DNDEBUG -pipe -O2 -fno-strict-aliasing -fPIC -Ipysam -I. -Ihtslib -I/usr/local/include/python2.7 -c htslib/faidx.c -o build/temp.dragonfly-5.1-SYNTH-x86_64-2.7/htslib/faidx.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
cc -DNDEBUG -pipe -O2 -fno-strict-aliasing -fPIC -Ipysam -I. -Ihtslib -I/usr/local/include/python2.7 -c htslib/hfile.c -o build/temp.dragonfly-5.1-SYNTH-x86_64-2.7/htslib/hfile.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
cc -DNDEBUG -pipe -O2 -fno-strict-aliasing -fPIC -Ipysam -I. -Ihtslib -I/usr/local/include/python2.7 -c htslib/hfile_net.c -o build/temp.dragonfly-5.1-SYNTH-x86_64-2.7/htslib/hfile_net.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
cc -DNDEBUG -pipe -O2 -fno-strict-aliasing -fPIC -Ipysam -I. -Ihtslib -I/usr/local/include/python2.7 -c htslib/hts.c -o build/temp.dragonfly-5.1-SYNTH-x86_64-2.7/htslib/hts.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
cc -DNDEBUG -pipe -O2 -fno-strict-aliasing -fPIC -Ipysam -I. -Ihtslib -I/usr/local/include/python2.7 -c htslib/hts_os.c -o build/temp.dragonfly-5.1-SYNTH-x86_64-2.7/htslib/hts_os.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
cc -DNDEBUG -pipe -O2 -fno-strict-aliasing -fPIC -Ipysam -I. -Ihtslib -I/usr/local/include/python2.7 -c htslib/md5.c -o build/temp.dragonfly-5.1-SYNTH-x86_64-2.7/htslib/md5.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
cc -DNDEBUG -pipe -O2 -fno-strict-aliasing -fPIC -Ipysam -I. -Ihtslib -I/usr/local/include/python2.7 -c htslib/multipart.c -o build/temp.dragonfly-5.1-SYNTH-x86_64-2.7/htslib/multipart.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
cc -DNDEBUG -pipe -O2 -fno-strict-aliasing -fPIC -Ipysam -I. -Ihtslib -I/usr/local/include/python2.7 -c htslib/probaln.c -o build/temp.dragonfly-5.1-SYNTH-x86_64-2.7/htslib/probaln.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
cc -DNDEBUG -pipe -O2 -fno-strict-aliasing -fPIC -Ipysam -I. -Ihtslib -I/usr/local/include/python2.7 -c htslib/realn.c -o build/temp.dragonfly-5.1-SYNTH-x86_64-2.7/htslib/realn.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
cc -DNDEBUG -pipe -O2 -fno-strict-aliasing -fPIC -Ipysam -I. -Ihtslib -I/usr/local/include/python2.7 -c htslib/regidx.c -o build/temp.dragonfly-5.1-SYNTH-x86_64-2.7/htslib/regidx.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
cc -DNDEBUG -pipe -O2 -fno-strict-aliasing -fPIC -Ipysam -I. -Ihtslib -I/usr/local/include/python2.7 -c htslib/sam.c -o build/temp.dragonfly-5.1-SYNTH-x86_64-2.7/htslib/sam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
cc -DNDEBUG -pipe -O2 -fno-strict-aliasing -fPIC -Ipysam -I. -Ihtslib -I/usr/local/include/python2.7 -c htslib/synced_bcf_reader.c -o build/temp.dragonfly-5.1-SYNTH-x86_64-2.7/htslib/synced_bcf_reader.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
cc -DNDEBUG -pipe -O2 -fno-strict-aliasing -fPIC -Ipysam -I. -Ihtslib -I/usr/local/include/python2.7 -c htslib/vcf_sweep.c -o build/temp.dragonfly-5.1-SYNTH-x86_64-2.7/htslib/vcf_sweep.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
cc -DNDEBUG -pipe -O2 -fno-strict-aliasing -fPIC -Ipysam -I. -Ihtslib -I/usr/local/include/python2.7 -c htslib/tbx.c -o build/temp.dragonfly-5.1-SYNTH-x86_64-2.7/htslib/tbx.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
cc -DNDEBUG -pipe -O2 -fno-strict-aliasing -fPIC -Ipysam -I. -Ihtslib -I/usr/local/include/python2.7 -c htslib/textutils.c -o build/temp.dragonfly-5.1-SYNTH-x86_64-2.7/htslib/textutils.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
cc -DNDEBUG -pipe -O2 -fno-strict-aliasing -fPIC -Ipysam -I. -Ihtslib -I/usr/local/include/python2.7 -c htslib/thread_pool.c -o build/temp.dragonfly-5.1-SYNTH-x86_64-2.7/htslib/thread_pool.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
cc -DNDEBUG -pipe -O2 -fno-strict-aliasing -fPIC -Ipysam -I. -Ihtslib -I/usr/local/include/python2.7 -c htslib/vcf.c -o build/temp.dragonfly-5.1-SYNTH-x86_64-2.7/htslib/vcf.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
cc -DNDEBUG -pipe -O2 -fno-strict-aliasing -fPIC -Ipysam -I. -Ihtslib -I/usr/local/include/python2.7 -c htslib/vcfutils.c -o build/temp.dragonfly-5.1-SYNTH-x86_64-2.7/htslib/vcfutils.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
cc -DNDEBUG -pipe -O2 -fno-strict-aliasing -fPIC -Ipysam -I. -Ihtslib -I/usr/local/include/python2.7 -c htslib/cram/cram_codecs.c -o build/temp.dragonfly-5.1-SYNTH-x86_64-2.7/htslib/cram/cram_codecs.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
cc -DNDEBUG -pipe -O2 -fno-strict-aliasing -fPIC -Ipysam -I. -Ihtslib -I/usr/local/include/python2.7 -c htslib/cram/cram_decode.c -o build/temp.dragonfly-5.1-SYNTH-x86_64-2.7/htslib/cram/cram_decode.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
cc -DNDEBUG -pipe -O2 -fno-strict-aliasing -fPIC -Ipysam -I. -Ihtslib -I/usr/local/include/python2.7 -c htslib/cram/cram_encode.c -o build/temp.dragonfly-5.1-SYNTH-x86_64-2.7/htslib/cram/cram_encode.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
cc -DNDEBUG -pipe -O2 -fno-strict-aliasing -fPIC -Ipysam -I. -Ihtslib -I/usr/local/include/python2.7 -c htslib/cram/cram_external.c -o build/temp.dragonfly-5.1-SYNTH-x86_64-2.7/htslib/cram/cram_external.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
cc -DNDEBUG -pipe -O2 -fno-strict-aliasing -fPIC -Ipysam -I. -Ihtslib -I/usr/local/include/python2.7 -c htslib/cram/cram_index.c -o build/temp.dragonfly-5.1-SYNTH-x86_64-2.7/htslib/cram/cram_index.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
cc -DNDEBUG -pipe -O2 -fno-strict-aliasing -fPIC -Ipysam -I. -Ihtslib -I/usr/local/include/python2.7 -c htslib/cram/cram_io.c -o build/temp.dragonfly-5.1-SYNTH-x86_64-2.7/htslib/cram/cram_io.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
cc -DNDEBUG -pipe -O2 -fno-strict-aliasing -fPIC -Ipysam -I. -Ihtslib -I/usr/local/include/python2.7 -c htslib/cram/cram_samtools.c -o build/temp.dragonfly-5.1-SYNTH-x86_64-2.7/htslib/cram/cram_samtools.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
cc -DNDEBUG -pipe -O2 -fno-strict-aliasing -fPIC -Ipysam -I. -Ihtslib -I/usr/local/include/python2.7 -c htslib/cram/cram_stats.c -o build/temp.dragonfly-5.1-SYNTH-x86_64-2.7/htslib/cram/cram_stats.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
cc -DNDEBUG -pipe -O2 -fno-strict-aliasing -fPIC -Ipysam -I. -Ihtslib -I/usr/local/include/python2.7 -c htslib/cram/files.c -o build/temp.dragonfly-5.1-SYNTH-x86_64-2.7/htslib/cram/files.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
cc -DNDEBUG -pipe -O2 -fno-strict-aliasing -fPIC -Ipysam -I. -Ihtslib -I/usr/local/include/python2.7 -c htslib/cram/mFILE.c -o build/temp.dragonfly-5.1-SYNTH-x86_64-2.7/htslib/cram/mFILE.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
cc -DNDEBUG -pipe -O2 -fno-strict-aliasing -fPIC -Ipysam -I. -Ihtslib -I/usr/local/include/python2.7 -c htslib/cram/open_trace_file.c -o build/temp.dragonfly-5.1-SYNTH-x86_64-2.7/htslib/cram/open_trace_file.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
cc -DNDEBUG -pipe -O2 -fno-strict-aliasing -fPIC -Ipysam -I. -Ihtslib -I/usr/local/include/python2.7 -c htslib/cram/pooled_alloc.c -o build/temp.dragonfly-5.1-SYNTH-x86_64-2.7/htslib/cram/pooled_alloc.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
cc -DNDEBUG -pipe -O2 -fno-strict-aliasing -fPIC -Ipysam -I. -Ihtslib -I/usr/local/include/python2.7 -c htslib/cram/rANS_static.c -o build/temp.dragonfly-5.1-SYNTH-x86_64-2.7/htslib/cram/rANS_static.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
cc -DNDEBUG -pipe -O2 -fno-strict-aliasing -fPIC -Ipysam -I. -Ihtslib -I/usr/local/include/python2.7 -c htslib/cram/sam_header.c -o build/temp.dragonfly-5.1-SYNTH-x86_64-2.7/htslib/cram/sam_header.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
cc -DNDEBUG -pipe -O2 -fno-strict-aliasing -fPIC -Ipysam -I. -Ihtslib -I/usr/local/include/python2.7 -c htslib/cram/string_alloc.c -o build/temp.dragonfly-5.1-SYNTH-x86_64-2.7/htslib/cram/string_alloc.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
cc -shared -pipe -O2 -fno-strict-aliasing build/temp.dragonfly-5.1-SYNTH-x86_64-2.7/pysam/libchtslib.o build/temp.dragonfly-5.1-SYNTH-x86_64-2.7/pysam/htslib_util.o build/temp.dragonfly-5.1-SYNTH-x86_64-2.7/htslib/kfunc.o build/temp.dragonfly-5.1-SYNTH-x86_64-2.7/htslib/knetfile.o build/temp.dragonfly-5.1-SYNTH-x86_64-2.7/htslib/kstring.o build/temp.dragonfly-5.1-SYNTH-x86_64-2.7/htslib/bcf_sr_sort.o build/temp.dragonfly-5.1-SYNTH-x86_64-2.7/htslib/bgzf.o build/temp.dragonfly-5.1-SYNTH-x86_64-2.7/htslib/errmod.o build/temp.dragonfly-5.1-SYNTH-x86_64-2.7/htslib/faidx.o build/temp.dragonfly-5.1-SYNTH-x86_64-2.7/htslib/hfile.o build/temp.dragonfly-5.1-SYNTH-x86_64-2.7/htslib/hfile_net.o build/temp.dragonfly-5.1-SYNTH-x86_64-2.7/htslib/hts.o build/temp.dragonfly-5.1-SYNTH-x86_64-2.7/htslib/hts_os.o build/temp.dragonfly-5.1-SYNTH-x86_64-2.7/htslib/md5.o build/temp.dragonfly-5.1-SYNTH-x86_64-2.7/htslib/multipart.o build/temp.dragonfly-5.1-SYNTH-x86_64-2.7/htslib/probaln.o build/temp.dragonfly-5.1-SYNTH-x86_64-2.7/htslib/realn.o build/temp.dragonfly-5.1-SYNTH-x86_64-2.7/htslib/regidx.o build/temp.dragonfly-5.1-SYNTH-x86_64-2.7/htslib/sam.o build/temp.dragonfly-5.1-SYNTH-x86_64-2.7/htslib/synced_bcf_reader.o build/temp.dragonfly-5.1-SYNTH-x86_64-2.7/htslib/vcf_sweep.o build/temp.dragonfly-5.1-SYNTH-x86_64-2.7/htslib/tbx.o build/temp.dragonfly-5.1-SYNTH-x86_64-2.7/htslib/textutils.o build/temp.dragonfly-5.1-SYNTH-x86_64-2.7/htslib/thread_pool.o build/temp.dragonfly-5.1-SYNTH-x86_64-2.7/htslib/vcf.o build/temp.dragonfly-5.1-SYNTH-x86_64-2.7/htslib/vcfutils.o build/temp.dragonfly-5.1-SYNTH-x86_64-2.7/htslib/cram/cram_codecs.o build/temp.dragonfly-5.1-SYNTH-x86_64-2.7/htslib/cram/cram_decode.o build/temp.dragonfly-5.1-SYNTH-x86_64-2.7/htslib/cram/cram_encode.o build/temp.dragonfly-5.1-SYNTH-x86_64-2.7/htslib/cram/cram_external.o build/temp.dragonfly-5.1-SYNTH-x86_64-2.7/htslib/cram/cram_index.o build/temp.dragonfly-5.1-SYNTH-x86_64-2.7/htslib/cram/cram_io.o build/temp.dragonfly-5.1-SYNTH-x86_64-2.7/htslib/cram/cram_samtools.o build/temp.dragonfly-5.1-SYNTH-x86_64-2.7/htslib/cram/cram_stats.o build/temp.dragonfly-5.1-SYNTH-x86_64-2.7/htslib/cram/files.o build/temp.dragonfly-5.1-SYNTH-x86_64-2.7/htslib/cram/mFILE.o build/temp.dragonfly-5.1-SYNTH-x86_64-2.7/htslib/cram/open_trace_file.o build/temp.dragonfly-5.1-SYNTH-x86_64-2.7/htslib/cram/pooled_alloc.o build/temp.dragonfly-5.1-SYNTH-x86_64-2.7/htslib/cram/rANS_static.o build/temp.dragonfly-5.1-SYNTH-x86_64-2.7/htslib/cram/sam_header.o build/temp.dragonfly-5.1-SYNTH-x86_64-2.7/htslib/cram/string_alloc.o -Lpysam -L. -Lbuild/lib.dragonfly-5.1-SYNTH-x86_64-2.7/pysam -Lbuild/lib.dragonfly-5.1-SYNTH-x86_64-2.7/pysam -L/usr/local/lib -lz -llzma -lbz2 -lz -lm -lpython2.7 -o build/lib.dragonfly-5.1-SYNTH-x86_64-2.7/pysam/libchtslib.so -Wl,-rpath,$ORIGIN
skipping 'pysam/libcsamfile.c' Cython extension (up-to-date)
building 'pysam.libcsamfile' extension
cc -DNDEBUG -pipe -O2 -fno-strict-aliasing -fPIC -Ipysam -I. -I/construction/biology/py-pysam/pysam-0.13/samtools -Ihtslib -I/usr/local/include/python2.7 -c pysam/libcsamfile.c -o build/temp.dragonfly-5.1-SYNTH-x86_64-2.7/pysam/libcsamfile.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
cc -DNDEBUG -pipe -O2 -fno-strict-aliasing -fPIC -Ipysam -I. -I/construction/biology/py-pysam/pysam-0.13/samtools -Ihtslib -I/usr/local/include/python2.7 -c pysam/htslib_util.c -o build/temp.dragonfly-5.1-SYNTH-x86_64-2.7/pysam/htslib_util.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
cc -DNDEBUG -pipe -O2 -fno-strict-aliasing -fPIC -Ipysam -I. -I/construction/biology/py-pysam/pysam-0.13/samtools -Ihtslib -I/usr/local/include/python2.7 -c pysam/samfile_util.c -o build/temp.dragonfly-5.1-SYNTH-x86_64-2.7/pysam/samfile_util.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
cc -shared -pipe -O2 -fno-strict-aliasing build/temp.dragonfly-5.1-SYNTH-x86_64-2.7/pysam/libcsamfile.o build/temp.dragonfly-5.1-SYNTH-x86_64-2.7/pysam/htslib_util.o build/temp.dragonfly-5.1-SYNTH-x86_64-2.7/pysam/samfile_util.o -Lpysam -L. -Lbuild/lib.dragonfly-5.1-SYNTH-x86_64-2.7/pysam -Lbuild/lib.dragonfly-5.1-SYNTH-x86_64-2.7/pysam -Lbuild/lib.dragonfly-5.1-SYNTH-x86_64-2.7/pysam -L/usr/local/lib -lz -llzma -lbz2 -lz -lm -lchtslib -lpython2.7 -o build/lib.dragonfly-5.1-SYNTH-x86_64-2.7/pysam/libcsamfile.so -Wl,-rpath,$ORIGIN
skipping 'pysam/libcalignmentfile.c' Cython extension (up-to-date)
building 'pysam.libcalignmentfile' extension
cc -DNDEBUG -pipe -O2 -fno-strict-aliasing -fPIC -Ipysam -I/construction/biology/py-pysam/pysam-0.13/samtools -Ihtslib -I/usr/local/include/python2.7 -c pysam/libcalignmentfile.c -o build/temp.dragonfly-5.1-SYNTH-x86_64-2.7/pysam/libcalignmentfile.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
pysam/libcalignmentfile.c: In function '__pyx_f_5pysam_17libcalignmentfile_14IteratorColumn_cnext':
pysam/libcalignmentfile.c:23498:21: warning: assignment discards 'const' qualifier from pointer target type [-Wdiscarded-qualifiers]
   __pyx_v_self->plp = bam_plp_auto(__pyx_v_self->pileup_iter, (&__pyx_v_self->tid), (&__pyx_v_self->pos), (&__pyx_v_self->n_plp));
                     ^
pysam/libcalignmentfile.c: In function '__pyx_f_5pysam_17libcalignmentfile_20IteratorRowSelection_cnext':
pysam/libcalignmentfile.c:22054:9: warning: ignoring return value of 'bgzf_seek', declared with attribute warn_unused_result [-Wunused-result]
         bgzf_seek(hts_get_bgzfp(__pyx_v_self->__pyx_base.htsfile), __pyx_v_pos, 0);
         ^
pysam/libcalignmentfile.c: In function '__pyx_pf_5pysam_17libcalignmentfile_13AlignmentFile_6_open':
pysam/libcalignmentfile.c:8531:13: warning: ignoring return value of 'sam_hdr_write', declared with attribute warn_unused_result [-Wunused-result]
             sam_hdr_write(__pyx_v_self->__pyx_base.htsfile, __pyx_v_self->header);
             ^
cc -DNDEBUG -pipe -O2 -fno-strict-aliasing -fPIC -Ipysam -I/construction/biology/py-pysam/pysam-0.13/samtools -Ihtslib -I/usr/local/include/python2.7 -c pysam/htslib_util.c -o build/temp.dragonfly-5.1-SYNTH-x86_64-2.7/pysam/htslib_util.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
cc -DNDEBUG -pipe -O2 -fno-strict-aliasing -fPIC -Ipysam -I/construction/biology/py-pysam/pysam-0.13/samtools -Ihtslib -I/usr/local/include/python2.7 -c pysam/samfile_util.c -o build/temp.dragonfly-5.1-SYNTH-x86_64-2.7/pysam/samfile_util.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
cc -shared -pipe -O2 -fno-strict-aliasing build/temp.dragonfly-5.1-SYNTH-x86_64-2.7/pysam/libcalignmentfile.o build/temp.dragonfly-5.1-SYNTH-x86_64-2.7/pysam/htslib_util.o build/temp.dragonfly-5.1-SYNTH-x86_64-2.7/pysam/samfile_util.o -Lpysam -L. -Lbuild/lib.dragonfly-5.1-SYNTH-x86_64-2.7/pysam -Lbuild/lib.dragonfly-5.1-SYNTH-x86_64-2.7/pysam -Lbuild/lib.dragonfly-5.1-SYNTH-x86_64-2.7/pysam -Lbuild/lib.dragonfly-5.1-SYNTH-x86_64-2.7/pysam -L/usr/local/lib -lz -llzma -lbz2 -lz -lm -lchtslib -lpython2.7 -o build/lib.dragonfly-5.1-SYNTH-x86_64-2.7/pysam/libcalignmentfile.so -Wl,-rpath,$ORIGIN
skipping 'pysam/libcalignedsegment.c' Cython extension (up-to-date)
building 'pysam.libcalignedsegment' extension
cc -DNDEBUG -pipe -O2 -fno-strict-aliasing -fPIC -Ipysam -I. -I/construction/biology/py-pysam/pysam-0.13/samtools -Ihtslib -I/usr/local/include/python2.7 -c pysam/libcalignedsegment.c -o build/temp.dragonfly-5.1-SYNTH-x86_64-2.7/pysam/libcalignedsegment.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
cc -DNDEBUG -pipe -O2 -fno-strict-aliasing -fPIC -Ipysam -I. -I/construction/biology/py-pysam/pysam-0.13/samtools -Ihtslib -I/usr/local/include/python2.7 -c pysam/htslib_util.c -o build/temp.dragonfly-5.1-SYNTH-x86_64-2.7/pysam/htslib_util.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
cc -DNDEBUG -pipe -O2 -fno-strict-aliasing -fPIC -Ipysam -I. -I/construction/biology/py-pysam/pysam-0.13/samtools -Ihtslib -I/usr/local/include/python2.7 -c pysam/samfile_util.c -o build/temp.dragonfly-5.1-SYNTH-x86_64-2.7/pysam/samfile_util.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
cc -shared -pipe -O2 -fno-strict-aliasing build/temp.dragonfly-5.1-SYNTH-x86_64-2.7/pysam/libcalignedsegment.o build/temp.dragonfly-5.1-SYNTH-x86_64-2.7/pysam/htslib_util.o build/temp.dragonfly-5.1-SYNTH-x86_64-2.7/pysam/samfile_util.o -Lpysam -L. -Lbuild/lib.dragonfly-5.1-SYNTH-x86_64-2.7/pysam -Lbuild/lib.dragonfly-5.1-SYNTH-x86_64-2.7/pysam -Lbuild/lib.dragonfly-5.1-SYNTH-x86_64-2.7/pysam -Lbuild/lib.dragonfly-5.1-SYNTH-x86_64-2.7/pysam -Lbuild/lib.dragonfly-5.1-SYNTH-x86_64-2.7/pysam -L/usr/local/lib -lz -llzma -lbz2 -lz -lm -lchtslib -lpython2.7 -o build/lib.dragonfly-5.1-SYNTH-x86_64-2.7/pysam/libcalignedsegment.so -Wl,-rpath,$ORIGIN
skipping 'pysam/libctabix.c' Cython extension (up-to-date)
building 'pysam.libctabix' extension
cc -DNDEBUG -pipe -O2 -fno-strict-aliasing -fPIC -Ipysam -I. -Ihtslib -I/usr/local/include/python2.7 -c pysam/libctabix.c -o build/temp.dragonfly-5.1-SYNTH-x86_64-2.7/pysam/libctabix.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
pysam/libctabix.c: In function '__pyx_pf_5pysam_9libctabix_9TabixFile_7contigs___get__':
pysam/libctabix.c:6542:27: warning: assignment from incompatible pointer type [-Wincompatible-pointer-types]
         __pyx_v_sequences = tbx_seqnames(__pyx_v_self->index, (&__pyx_v_nsequences));
                           ^
In file included from pysam/libctabix.c:447:0:
pysam/libctabix.c: In function '__pyx_pf_5pysam_9libctabix_4tabix_index':
htslib/htslib/tbx.h:41:21: warning: overflow in implicit constant conversion [-Woverflow]
 #define TBX_UCSC    0x10000
                     ^
pysam/libctabix.c:11139:39: note: in expansion of macro 'TBX_UCSC'
   __pyx_t_2 = __Pyx_PyInt_From_int8_t(TBX_UCSC); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 957, __pyx_L1_error)
                                       ^
htslib/htslib/tbx.h:41:21: warning: overflow in implicit constant conversion [-Woverflow]
 #define TBX_UCSC    0x10000
                     ^
pysam/libctabix.c:11171:39: note: in expansion of macro 'TBX_UCSC'
   __pyx_t_3 = __Pyx_PyInt_From_int8_t(TBX_UCSC); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 958, __pyx_L1_error)
                                       ^
htslib/htslib/tbx.h:41:21: warning: overflow in implicit constant conversion [-Woverflow]
 #define TBX_UCSC    0x10000
                     ^
pysam/libctabix.c:11472:43: note: in expansion of macro 'TBX_UCSC'
       __pyx_t_3 = __Pyx_PyInt_From_int8_t(TBX_UCSC); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 982, __pyx_L1_error)
                                           ^
cc -DNDEBUG -pipe -O2 -fno-strict-aliasing -fPIC -Ipysam -I. -Ihtslib -I/usr/local/include/python2.7 -c pysam/tabix_util.c -o build/temp.dragonfly-5.1-SYNTH-x86_64-2.7/pysam/tabix_util.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
cc -shared -pipe -O2 -fno-strict-aliasing build/temp.dragonfly-5.1-SYNTH-x86_64-2.7/pysam/libctabix.o build/temp.dragonfly-5.1-SYNTH-x86_64-2.7/pysam/tabix_util.o -Lpysam -Lpysam -L. -Lbuild/lib.dragonfly-5.1-SYNTH-x86_64-2.7/pysam -Lbuild/lib.dragonfly-5.1-SYNTH-x86_64-2.7/pysam -L/usr/local/lib -lz -llzma -lbz2 -lz -lm -lchtslib -lpython2.7 -o build/lib.dragonfly-5.1-SYNTH-x86_64-2.7/pysam/libctabix.so -Wl,-rpath,$ORIGIN
skipping 'pysam/libctabixproxies.c' Cython extension (up-to-date)
building 'pysam.libctabixproxies' extension
cc -DNDEBUG -pipe -O2 -fno-strict-aliasing -fPIC -I/usr/local/include/python2.7 -c pysam/libctabixproxies.c -o build/temp.dragonfly-5.1-SYNTH-x86_64-2.7/pysam/libctabixproxies.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
cc -shared -pipe -O2 -fno-strict-aliasing build/temp.dragonfly-5.1-SYNTH-x86_64-2.7/pysam/libctabixproxies.o -Lpysam -L. -Lbuild/lib.dragonfly-5.1-SYNTH-x86_64-2.7/pysam -Lbuild/lib.dragonfly-5.1-SYNTH-x86_64-2.7/pysam -Lbuild/lib.dragonfly-5.1-SYNTH-x86_64-2.7/pysam -Lbuild/lib.dragonfly-5.1-SYNTH-x86_64-2.7/pysam -Lbuild/lib.dragonfly-5.1-SYNTH-x86_64-2.7/pysam -Lbuild/lib.dragonfly-5.1-SYNTH-x86_64-2.7/pysam -L/usr/local/lib -lz -llzma -lbz2 -lz -lm -lchtslib -lpython2.7 -o build/lib.dragonfly-5.1-SYNTH-x86_64-2.7/pysam/libctabixproxies.so -Wl,-rpath,$ORIGIN
skipping 'pysam/libcvcf.c' Cython extension (up-to-date)
building 'pysam.libcvcf' extension
cc -DNDEBUG -pipe -O2 -fno-strict-aliasing -fPIC -Ihtslib -I. -Ihtslib -I/usr/local/include/python2.7 -c pysam/libcvcf.c -o build/temp.dragonfly-5.1-SYNTH-x86_64-2.7/pysam/libcvcf.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
cc -shared -pipe -O2 -fno-strict-aliasing build/temp.dragonfly-5.1-SYNTH-x86_64-2.7/pysam/libcvcf.o -Lpysam -L. -Lbuild/lib.dragonfly-5.1-SYNTH-x86_64-2.7/pysam -Lbuild/lib.dragonfly-5.1-SYNTH-x86_64-2.7/pysam -Lbuild/lib.dragonfly-5.1-SYNTH-x86_64-2.7/pysam -Lbuild/lib.dragonfly-5.1-SYNTH-x86_64-2.7/pysam -Lbuild/lib.dragonfly-5.1-SYNTH-x86_64-2.7/pysam -Lbuild/lib.dragonfly-5.1-SYNTH-x86_64-2.7/pysam -Lbuild/lib.dragonfly-5.1-SYNTH-x86_64-2.7/pysam -L/usr/local/lib -lz -llzma -lbz2 -lz -lm -lchtslib -lpython2.7 -o build/lib.dragonfly-5.1-SYNTH-x86_64-2.7/pysam/libcvcf.so -Wl,-rpath,$ORIGIN
skipping 'pysam/libcbcf.c' Cython extension (up-to-date)
building 'pysam.libcbcf' extension
cc -DNDEBUG -pipe -O2 -fno-strict-aliasing -fPIC -Ihtslib -I. -Ihtslib -I/usr/local/include/python2.7 -c pysam/libcbcf.c -o build/temp.dragonfly-5.1-SYNTH-x86_64-2.7/pysam/libcbcf.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
pysam/libcbcf.c: In function '__pyx_pf_5pysam_7libcbcf_13VariantHeader_12__str__':
pysam/libcbcf.c:30545:3: warning: 'bcf_hdr_fmt_text' is deprecated: use bcf_hdr_format() instead [-Wdeprecated-declarations]
   __pyx_v_hstr = bcf_hdr_fmt_text(__pyx_v_self->ptr, 0, (&__pyx_v_hlen));
   ^
In file included from pysam/htslib_util.h:5:0,
                 from pysam/libcbcf.c:439:
htslib/htslib/vcf.h:439:11: note: declared here
     char *bcf_hdr_fmt_text(const bcf_hdr_t *hdr, int is_bcf, int *len)
           ^
cc -shared -pipe -O2 -fno-strict-aliasing build/temp.dragonfly-5.1-SYNTH-x86_64-2.7/pysam/libcbcf.o -Lpysam -L. -Lbuild/lib.dragonfly-5.1-SYNTH-x86_64-2.7/pysam -Lbuild/lib.dragonfly-5.1-SYNTH-x86_64-2.7/pysam -Lbuild/lib.dragonfly-5.1-SYNTH-x86_64-2.7/pysam -Lbuild/lib.dragonfly-5.1-SYNTH-x86_64-2.7/pysam -Lbuild/lib.dragonfly-5.1-SYNTH-x86_64-2.7/pysam -Lbuild/lib.dragonfly-5.1-SYNTH-x86_64-2.7/pysam -Lbuild/lib.dragonfly-5.1-SYNTH-x86_64-2.7/pysam -Lbuild/lib.dragonfly-5.1-SYNTH-x86_64-2.7/pysam -L/usr/local/lib -lz -llzma -lbz2 -lz -lm -lchtslib -lpython2.7 -o build/lib.dragonfly-5.1-SYNTH-x86_64-2.7/pysam/libcbcf.so -Wl,-rpath,$ORIGIN
skipping 'pysam/libcbgzf.c' Cython extension (up-to-date)
building 'pysam.libcbgzf' extension
cc -DNDEBUG -pipe -O2 -fno-strict-aliasing -fPIC -Ihtslib -I. -Ihtslib -I/usr/local/include/python2.7 -c pysam/libcbgzf.c -o build/temp.dragonfly-5.1-SYNTH-x86_64-2.7/pysam/libcbgzf.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
cc -shared -pipe -O2 -fno-strict-aliasing build/temp.dragonfly-5.1-SYNTH-x86_64-2.7/pysam/libcbgzf.o -Lpysam -L. -Lbuild/lib.dragonfly-5.1-SYNTH-x86_64-2.7/pysam -Lbuild/lib.dragonfly-5.1-SYNTH-x86_64-2.7/pysam -Lbuild/lib.dragonfly-5.1-SYNTH-x86_64-2.7/pysam -Lbuild/lib.dragonfly-5.1-SYNTH-x86_64-2.7/pysam -Lbuild/lib.dragonfly-5.1-SYNTH-x86_64-2.7/pysam -Lbuild/lib.dragonfly-5.1-SYNTH-x86_64-2.7/pysam -Lbuild/lib.dragonfly-5.1-SYNTH-x86_64-2.7/pysam -Lbuild/lib.dragonfly-5.1-SYNTH-x86_64-2.7/pysam -Lbuild/lib.dragonfly-5.1-SYNTH-x86_64-2.7/pysam -L/usr/local/lib -lz -llzma -lbz2 -lz -lm -lchtslib -lpython2.7 -o build/lib.dragonfly-5.1-SYNTH-x86_64-2.7/pysam/libcbgzf.so -Wl,-rpath,$ORIGIN
skipping 'pysam/libcfaidx.c' Cython extension (up-to-date)
building 'pysam.libcfaidx' extension
cc -DNDEBUG -pipe -O2 -fno-strict-aliasing -fPIC -Ipysam -I. -Ihtslib -I/usr/local/include/python2.7 -c pysam/libcfaidx.c -o build/temp.dragonfly-5.1-SYNTH-x86_64-2.7/pysam/libcfaidx.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
cc -shared -pipe -O2 -fno-strict-aliasing build/temp.dragonfly-5.1-SYNTH-x86_64-2.7/pysam/libcfaidx.o -Lpysam -Lpysam -L. -Lbuild/lib.dragonfly-5.1-SYNTH-x86_64-2.7/pysam -Lbuild/lib.dragonfly-5.1-SYNTH-x86_64-2.7/pysam -L/usr/local/lib -lz -llzma -lbz2 -lz -lm -lchtslib -lpython2.7 -o build/lib.dragonfly-5.1-SYNTH-x86_64-2.7/pysam/libcfaidx.so -Wl,-rpath,$ORIGIN
skipping 'pysam/libcsamtools.c' Cython extension (up-to-date)
building 'pysam.libcsamtools' extension
creating build/temp.dragonfly-5.1-SYNTH-x86_64-2.7/samtools
cc -DNDEBUG -pipe -O2 -fno-strict-aliasing -fPIC -Ipysam -I. -I/construction/biology/py-pysam/pysam-0.13/samtools -Ihtslib -I/usr/local/include/python2.7 -c pysam/libcsamtools.c -o build/temp.dragonfly-5.1-SYNTH-x86_64-2.7/pysam/libcsamtools.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
cc -DNDEBUG -pipe -O2 -fno-strict-aliasing -fPIC -Ipysam -I. -I/construction/biology/py-pysam/pysam-0.13/samtools -Ihtslib -I/usr/local/include/python2.7 -c samtools/sam_opts.c.pysam.c -o build/temp.dragonfly-5.1-SYNTH-x86_64-2.7/samtools/sam_opts.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
cc -DNDEBUG -pipe -O2 -fno-strict-aliasing -fPIC -Ipysam -I. -I/construction/biology/py-pysam/pysam-0.13/samtools -Ihtslib -I/usr/local/include/python2.7 -c samtools/bam_addrprg.c.pysam.c -o build/temp.dragonfly-5.1-SYNTH-x86_64-2.7/samtools/bam_addrprg.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
cc -DNDEBUG -pipe -O2 -fno-strict-aliasing -fPIC -Ipysam -I. -I/construction/biology/py-pysam/pysam-0.13/samtools -Ihtslib -I/usr/local/include/python2.7 -c samtools/bam_stat.c.pysam.c -o build/temp.dragonfly-5.1-SYNTH-x86_64-2.7/samtools/bam_stat.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
cc -DNDEBUG -pipe -O2 -fno-strict-aliasing -fPIC -Ipysam -I. -I/construction/biology/py-pysam/pysam-0.13/samtools -Ihtslib -I/usr/local/include/python2.7 -c samtools/bam_md.c.pysam.c -o build/temp.dragonfly-5.1-SYNTH-x86_64-2.7/samtools/bam_md.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
cc -DNDEBUG -pipe -O2 -fno-strict-aliasing -fPIC -Ipysam -I. -I/construction/biology/py-pysam/pysam-0.13/samtools -Ihtslib -I/usr/local/include/python2.7 -c samtools/bam.c.pysam.c -o build/temp.dragonfly-5.1-SYNTH-x86_64-2.7/samtools/bam.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
cc -DNDEBUG -pipe -O2 -fno-strict-aliasing -fPIC -Ipysam -I. -I/construction/biology/py-pysam/pysam-0.13/samtools -Ihtslib -I/usr/local/include/python2.7 -c samtools/bam_markdup.c.pysam.c -o build/temp.dragonfly-5.1-SYNTH-x86_64-2.7/samtools/bam_markdup.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
cc -DNDEBUG -pipe -O2 -fno-strict-aliasing -fPIC -Ipysam -I. -I/construction/biology/py-pysam/pysam-0.13/samtools -Ihtslib -I/usr/local/include/python2.7 -c samtools/sam_header.c.pysam.c -o build/temp.dragonfly-5.1-SYNTH-x86_64-2.7/samtools/sam_header.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
cc -DNDEBUG -pipe -O2 -fno-strict-aliasing -fPIC -Ipysam -I. -I/construction/biology/py-pysam/pysam-0.13/samtools -Ihtslib -I/usr/local/include/python2.7 -c samtools/bam_plcmd.c.pysam.c -o build/temp.dragonfly-5.1-SYNTH-x86_64-2.7/samtools/bam_plcmd.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
cc -DNDEBUG -pipe -O2 -fno-strict-aliasing -fPIC -Ipysam -I. -I/construction/biology/py-pysam/pysam-0.13/samtools -Ihtslib -I/usr/local/include/python2.7 -c samtools/dict.c.pysam.c -o build/temp.dragonfly-5.1-SYNTH-x86_64-2.7/samtools/dict.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
cc -DNDEBUG -pipe -O2 -fno-strict-aliasing -fPIC -Ipysam -I. -I/construction/biology/py-pysam/pysam-0.13/samtools -Ihtslib -I/usr/local/include/python2.7 -c samtools/sample.c.pysam.c -o build/temp.dragonfly-5.1-SYNTH-x86_64-2.7/samtools/sample.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
cc -DNDEBUG -pipe -O2 -fno-strict-aliasing -fPIC -Ipysam -I. -I/construction/biology/py-pysam/pysam-0.13/samtools -Ihtslib -I/usr/local/include/python2.7 -c samtools/bam_rmdupse.c.pysam.c -o build/temp.dragonfly-5.1-SYNTH-x86_64-2.7/samtools/bam_rmdupse.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
cc -DNDEBUG -pipe -O2 -fno-strict-aliasing -fPIC -Ipysam -I. -I/construction/biology/py-pysam/pysam-0.13/samtools -Ihtslib -I/usr/local/include/python2.7 -c samtools/bam_quickcheck.c.pysam.c -o build/temp.dragonfly-5.1-SYNTH-x86_64-2.7/samtools/bam_quickcheck.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
cc -DNDEBUG -pipe -O2 -fno-strict-aliasing -fPIC -Ipysam -I. -I/construction/biology/py-pysam/pysam-0.13/samtools -Ihtslib -I/usr/local/include/python2.7 -c samtools/phase.c.pysam.c -o build/temp.dragonfly-5.1-SYNTH-x86_64-2.7/samtools/phase.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
cc -DNDEBUG -pipe -O2 -fno-strict-aliasing -fPIC -Ipysam -I. -I/construction/biology/py-pysam/pysam-0.13/samtools -Ihtslib -I/usr/local/include/python2.7 -c samtools/bamshuf.c.pysam.c -o build/temp.dragonfly-5.1-SYNTH-x86_64-2.7/samtools/bamshuf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
cc -DNDEBUG -pipe -O2 -fno-strict-aliasing -fPIC -Ipysam -I. -I/construction/biology/py-pysam/pysam-0.13/samtools -Ihtslib -I/usr/local/include/python2.7 -c samtools/bam_cat.c.pysam.c -o build/temp.dragonfly-5.1-SYNTH-x86_64-2.7/samtools/bam_cat.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
cc -DNDEBUG -pipe -O2 -fno-strict-aliasing -fPIC -Ipysam -I. -I/construction/biology/py-pysam/pysam-0.13/samtools -Ihtslib -I/usr/local/include/python2.7 -c samtools/bam_reheader.c.pysam.c -o build/temp.dragonfly-5.1-SYNTH-x86_64-2.7/samtools/bam_reheader.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
cc -DNDEBUG -pipe -O2 -fno-strict-aliasing -fPIC -Ipysam -I. -I/construction/biology/py-pysam/pysam-0.13/samtools -Ihtslib -I/usr/local/include/python2.7 -c samtools/padding.c.pysam.c -o build/temp.dragonfly-5.1-SYNTH-x86_64-2.7/samtools/padding.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
cc -DNDEBUG -pipe -O2 -fno-strict-aliasing -fPIC -Ipysam -I. -I/construction/biology/py-pysam/pysam-0.13/samtools -Ihtslib -I/usr/local/include/python2.7 -c samtools/bedcov.c.pysam.c -o build/temp.dragonfly-5.1-SYNTH-x86_64-2.7/samtools/bedcov.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
cc -DNDEBUG -pipe -O2 -fno-strict-aliasing -fPIC -Ipysam -I. -I/construction/biology/py-pysam/pysam-0.13/samtools -Ihtslib -I/usr/local/include/python2.7 -c samtools/bam_import.c.pysam.c -o build/temp.dragonfly-5.1-SYNTH-x86_64-2.7/samtools/bam_import.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
cc -DNDEBUG -pipe -O2 -fno-strict-aliasing -fPIC -Ipysam -I. -I/construction/biology/py-pysam/pysam-0.13/samtools -Ihtslib -I/usr/local/include/python2.7 -c samtools/bam_rmdup.c.pysam.c -o build/temp.dragonfly-5.1-SYNTH-x86_64-2.7/samtools/bam_rmdup.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
cc -DNDEBUG -pipe -O2 -fno-strict-aliasing -fPIC -Ipysam -I. -I/construction/biology/py-pysam/pysam-0.13/samtools -Ihtslib -I/usr/local/include/python2.7 -c samtools/bam_aux.c.pysam.c -o build/temp.dragonfly-5.1-SYNTH-x86_64-2.7/samtools/bam_aux.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
cc -DNDEBUG -pipe -O2 -fno-strict-aliasing -fPIC -Ipysam -I. -I/construction/biology/py-pysam/pysam-0.13/samtools -Ihtslib -I/usr/local/include/python2.7 -c samtools/stats.c.pysam.c -o build/temp.dragonfly-5.1-SYNTH-x86_64-2.7/samtools/stats.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
cc -DNDEBUG -pipe -O2 -fno-strict-aliasing -fPIC -Ipysam -I. -I/construction/biology/py-pysam/pysam-0.13/samtools -Ihtslib -I/usr/local/include/python2.7 -c samtools/bam_split.c.pysam.c -o build/temp.dragonfly-5.1-SYNTH-x86_64-2.7/samtools/bam_split.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
cc -DNDEBUG -pipe -O2 -fno-strict-aliasing -fPIC -Ipysam -I. -I/construction/biology/py-pysam/pysam-0.13/samtools -Ihtslib -I/usr/local/include/python2.7 -c samtools/bamtk.c.pysam.c -o build/temp.dragonfly-5.1-SYNTH-x86_64-2.7/samtools/bamtk.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
cc -DNDEBUG -pipe -O2 -fno-strict-aliasing -fPIC -Ipysam -I. -I/construction/biology/py-pysam/pysam-0.13/samtools -Ihtslib -I/usr/local/include/python2.7 -c samtools/bam_lpileup.c.pysam.c -o build/temp.dragonfly-5.1-SYNTH-x86_64-2.7/samtools/bam_lpileup.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
cc -DNDEBUG -pipe -O2 -fno-strict-aliasing -fPIC -Ipysam -I. -I/construction/biology/py-pysam/pysam-0.13/samtools -Ihtslib -I/usr/local/include/python2.7 -c samtools/bam2bcf_indel.c.pysam.c -o build/temp.dragonfly-5.1-SYNTH-x86_64-2.7/samtools/bam2bcf_indel.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
cc -DNDEBUG -pipe -O2 -fno-strict-aliasing -fPIC -Ipysam -I. -I/construction/biology/py-pysam/pysam-0.13/samtools -Ihtslib -I/usr/local/include/python2.7 -c samtools/faidx.c.pysam.c -o build/temp.dragonfly-5.1-SYNTH-x86_64-2.7/samtools/faidx.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
cc -DNDEBUG -pipe -O2 -fno-strict-aliasing -fPIC -Ipysam -I. -I/construction/biology/py-pysam/pysam-0.13/samtools -Ihtslib -I/usr/local/include/python2.7 -c samtools/bam_index.c.pysam.c -o build/temp.dragonfly-5.1-SYNTH-x86_64-2.7/samtools/bam_index.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
cc -DNDEBUG -pipe -O2 -fno-strict-aliasing -fPIC -Ipysam -I. -I/construction/biology/py-pysam/pysam-0.13/samtools -Ihtslib -I/usr/local/include/python2.7 -c samtools/sam.c.pysam.c -o build/temp.dragonfly-5.1-SYNTH-x86_64-2.7/samtools/sam.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
cc -DNDEBUG -pipe -O2 -fno-strict-aliasing -fPIC -Ipysam -I. -I/construction/biology/py-pysam/pysam-0.13/samtools -Ihtslib -I/usr/local/include/python2.7 -c samtools/bam_mate.c.pysam.c -o build/temp.dragonfly-5.1-SYNTH-x86_64-2.7/samtools/bam_mate.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
cc -DNDEBUG -pipe -O2 -fno-strict-aliasing -fPIC -Ipysam -I. -I/construction/biology/py-pysam/pysam-0.13/samtools -Ihtslib -I/usr/local/include/python2.7 -c samtools/bam_flags.c.pysam.c -o build/temp.dragonfly-5.1-SYNTH-x86_64-2.7/samtools/bam_flags.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
cc -DNDEBUG -pipe -O2 -fno-strict-aliasing -fPIC -Ipysam -I. -I/construction/biology/py-pysam/pysam-0.13/samtools -Ihtslib -I/usr/local/include/python2.7 -c samtools/bedidx.c.pysam.c -o build/temp.dragonfly-5.1-SYNTH-x86_64-2.7/samtools/bedidx.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
cc -DNDEBUG -pipe -O2 -fno-strict-aliasing -fPIC -Ipysam -I. -I/construction/biology/py-pysam/pysam-0.13/samtools -Ihtslib -I/usr/local/include/python2.7 -c samtools/bam_plbuf.c.pysam.c -o build/temp.dragonfly-5.1-SYNTH-x86_64-2.7/samtools/bam_plbuf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
cc -DNDEBUG -pipe -O2 -fno-strict-aliasing -fPIC -Ipysam -I. -I/construction/biology/py-pysam/pysam-0.13/samtools -Ihtslib -I/usr/local/include/python2.7 -c samtools/bam_sort.c.pysam.c -o build/temp.dragonfly-5.1-SYNTH-x86_64-2.7/samtools/bam_sort.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
cc -DNDEBUG -pipe -O2 -fno-strict-aliasing -fPIC -Ipysam -I. -I/construction/biology/py-pysam/pysam-0.13/samtools -Ihtslib -I/usr/local/include/python2.7 -c samtools/sam_utils.c.pysam.c -o build/temp.dragonfly-5.1-SYNTH-x86_64-2.7/samtools/sam_utils.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
cc -DNDEBUG -pipe -O2 -fno-strict-aliasing -fPIC -Ipysam -I. -I/construction/biology/py-pysam/pysam-0.13/samtools -Ihtslib -I/usr/local/include/python2.7 -c samtools/bam_color.c.pysam.c -o build/temp.dragonfly-5.1-SYNTH-x86_64-2.7/samtools/bam_color.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
cc -DNDEBUG -pipe -O2 -fno-strict-aliasing -fPIC -Ipysam -I. -I/construction/biology/py-pysam/pysam-0.13/samtools -Ihtslib -I/usr/local/include/python2.7 -c samtools/cut_target.c.pysam.c -o build/temp.dragonfly-5.1-SYNTH-x86_64-2.7/samtools/cut_target.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
cc -DNDEBUG -pipe -O2 -fno-strict-aliasing -fPIC -Ipysam -I. -I/construction/biology/py-pysam/pysam-0.13/samtools -Ihtslib -I/usr/local/include/python2.7 -c samtools/sam_view.c.pysam.c -o build/temp.dragonfly-5.1-SYNTH-x86_64-2.7/samtools/sam_view.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
cc -DNDEBUG -pipe -O2 -fno-strict-aliasing -fPIC -Ipysam -I. -I/construction/biology/py-pysam/pysam-0.13/samtools -Ihtslib -I/usr/local/include/python2.7 -c samtools/bam2depth.c.pysam.c -o build/temp.dragonfly-5.1-SYNTH-x86_64-2.7/samtools/bam2depth.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
cc -DNDEBUG -pipe -O2 -fno-strict-aliasing -fPIC -Ipysam -I. -I/construction/biology/py-pysam/pysam-0.13/samtools -Ihtslib -I/usr/local/include/python2.7 -c samtools/bam2bcf.c.pysam.c -o build/temp.dragonfly-5.1-SYNTH-x86_64-2.7/samtools/bam2bcf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
cc -DNDEBUG -pipe -O2 -fno-strict-aliasing -fPIC -Ipysam -I. -I/construction/biology/py-pysam/pysam-0.13/samtools -Ihtslib -I/usr/local/include/python2.7 -c samtools/stats_isize.c.pysam.c -o build/temp.dragonfly-5.1-SYNTH-x86_64-2.7/samtools/stats_isize.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
cc -shared -pipe -O2 -fno-strict-aliasing build/temp.dragonfly-5.1-SYNTH-x86_64-2.7/pysam/libcsamtools.o build/temp.dragonfly-5.1-SYNTH-x86_64-2.7/samtools/sam_opts.c.pysam.o build/temp.dragonfly-5.1-SYNTH-x86_64-2.7/samtools/bam_addrprg.c.pysam.o build/temp.dragonfly-5.1-SYNTH-x86_64-2.7/samtools/bam_stat.c.pysam.o build/temp.dragonfly-5.1-SYNTH-x86_64-2.7/samtools/bam_md.c.pysam.o build/temp.dragonfly-5.1-SYNTH-x86_64-2.7/samtools/bam.c.pysam.o build/temp.dragonfly-5.1-SYNTH-x86_64-2.7/samtools/bam_markdup.c.pysam.o build/temp.dragonfly-5.1-SYNTH-x86_64-2.7/samtools/sam_header.c.pysam.o build/temp.dragonfly-5.1-SYNTH-x86_64-2.7/samtools/bam_plcmd.c.pysam.o build/temp.dragonfly-5.1-SYNTH-x86_64-2.7/samtools/dict.c.pysam.o build/temp.dragonfly-5.1-SYNTH-x86_64-2.7/samtools/sample.c.pysam.o build/temp.dragonfly-5.1-SYNTH-x86_64-2.7/samtools/bam_rmdupse.c.pysam.o build/temp.dragonfly-5.1-SYNTH-x86_64-2.7/samtools/bam_quickcheck.c.pysam.o build/temp.dragonfly-5.1-SYNTH-x86_64-2.7/samtools/phase.c.pysam.o build/temp.dragonfly-5.1-SYNTH-x86_64-2.7/samtools/bamshuf.c.pysam.o build/temp.dragonfly-5.1-SYNTH-x86_64-2.7/samtools/bam_cat.c.pysam.o build/temp.dragonfly-5.1-SYNTH-x86_64-2.7/samtools/bam_reheader.c.pysam.o build/temp.dragonfly-5.1-SYNTH-x86_64-2.7/samtools/padding.c.pysam.o build/temp.dragonfly-5.1-SYNTH-x86_64-2.7/samtools/bedcov.c.pysam.o build/temp.dragonfly-5.1-SYNTH-x86_64-2.7/samtools/bam_import.c.pysam.o build/temp.dragonfly-5.1-SYNTH-x86_64-2.7/samtools/bam_rmdup.c.pysam.o build/temp.dragonfly-5.1-SYNTH-x86_64-2.7/samtools/bam_aux.c.pysam.o build/temp.dragonfly-5.1-SYNTH-x86_64-2.7/samtools/stats.c.pysam.o build/temp.dragonfly-5.1-SYNTH-x86_64-2.7/samtools/bam_split.c.pysam.o build/temp.dragonfly-5.1-SYNTH-x86_64-2.7/samtools/bamtk.c.pysam.o build/temp.dragonfly-5.1-SYNTH-x86_64-2.7/samtools/bam_lpileup.c.pysam.o build/temp.dragonfly-5.1-SYNTH-x86_64-2.7/samtools/bam2bcf_indel.c.pysam.o build/temp.dragonfly-5.1-SYNTH-x86_64-2.7/samtools/faidx.c.pysam.o build/temp.dragonfly-5.1-SYNTH-x86_64-2.7/samtools/bam_index.c.pysam.o build/temp.dragonfly-5.1-SYNTH-x86_64-2.7/samtools/sam.c.pysam.o build/temp.dragonfly-5.1-SYNTH-x86_64-2.7/samtools/bam_mate.c.pysam.o build/temp.dragonfly-5.1-SYNTH-x86_64-2.7/samtools/bam_flags.c.pysam.o build/temp.dragonfly-5.1-SYNTH-x86_64-2.7/samtools/bedidx.c.pysam.o build/temp.dragonfly-5.1-SYNTH-x86_64-2.7/samtools/bam_plbuf.c.pysam.o build/temp.dragonfly-5.1-SYNTH-x86_64-2.7/samtools/bam_sort.c.pysam.o build/temp.dragonfly-5.1-SYNTH-x86_64-2.7/samtools/sam_utils.c.pysam.o build/temp.dragonfly-5.1-SYNTH-x86_64-2.7/samtools/bam_color.c.pysam.o build/temp.dragonfly-5.1-SYNTH-x86_64-2.7/samtools/cut_target.c.pysam.o build/temp.dragonfly-5.1-SYNTH-x86_64-2.7/samtools/sam_view.c.pysam.o build/temp.dragonfly-5.1-SYNTH-x86_64-2.7/samtools/bam2depth.c.pysam.o build/temp.dragonfly-5.1-SYNTH-x86_64-2.7/samtools/bam2bcf.c.pysam.o build/temp.dragonfly-5.1-SYNTH-x86_64-2.7/samtools/stats_isize.c.pysam.o -Lpysam -Lpysam -L. -Lbuild/lib.dragonfly-5.1-SYNTH-x86_64-2.7/pysam -Lbuild/lib.dragonfly-5.1-SYNTH-x86_64-2.7/pysam -L/usr/local/lib -lz -llzma -lbz2 -lz -lm -lchtslib -lpython2.7 -o build/lib.dragonfly-5.1-SYNTH-x86_64-2.7/pysam/libcsamtools.so -Wl,-rpath,$ORIGIN
skipping 'pysam/libcbcftools.c' Cython extension (up-to-date)
building 'pysam.libcbcftools' extension
creating build/temp.dragonfly-5.1-SYNTH-x86_64-2.7/bcftools
cc -DNDEBUG -pipe -O2 -fno-strict-aliasing -fPIC -Ibcftools -Ipysam -I. -I/construction/biology/py-pysam/pysam-0.13/samtools -Ihtslib -I/usr/local/include/python2.7 -c pysam/libcbcftools.c -o build/temp.dragonfly-5.1-SYNTH-x86_64-2.7/pysam/libcbcftools.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
cc -DNDEBUG -pipe -O2 -fno-strict-aliasing -fPIC -Ibcftools -Ipysam -I. -I/construction/biology/py-pysam/pysam-0.13/samtools -Ihtslib -I/usr/local/include/python2.7 -c bcftools/vcfconvert.c.pysam.c -o build/temp.dragonfly-5.1-SYNTH-x86_64-2.7/bcftools/vcfconvert.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
cc -DNDEBUG -pipe -O2 -fno-strict-aliasing -fPIC -Ibcftools -Ipysam -I. -I/construction/biology/py-pysam/pysam-0.13/samtools -Ihtslib -I/usr/local/include/python2.7 -c bcftools/regidx.c.pysam.c -o build/temp.dragonfly-5.1-SYNTH-x86_64-2.7/bcftools/regidx.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
cc -DNDEBUG -pipe -O2 -fno-strict-aliasing -fPIC -Ibcftools -Ipysam -I. -I/construction/biology/py-pysam/pysam-0.13/samtools -Ihtslib -I/usr/local/include/python2.7 -c bcftools/vcfroh.c.pysam.c -o build/temp.dragonfly-5.1-SYNTH-x86_64-2.7/bcftools/vcfroh.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
cc -DNDEBUG -pipe -O2 -fno-strict-aliasing -fPIC -Ibcftools -Ipysam -I. -I/construction/biology/py-pysam/pysam-0.13/samtools -Ihtslib -I/usr/local/include/python2.7 -c bcftools/vcfnorm.c.pysam.c -o build/temp.dragonfly-5.1-SYNTH-x86_64-2.7/bcftools/vcfnorm.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
cc -DNDEBUG -pipe -O2 -fno-strict-aliasing -fPIC -Ibcftools -Ipysam -I. -I/construction/biology/py-pysam/pysam-0.13/samtools -Ihtslib -I/usr/local/include/python2.7 -c bcftools/tsv2vcf.c.pysam.c -o build/temp.dragonfly-5.1-SYNTH-x86_64-2.7/bcftools/tsv2vcf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
cc -DNDEBUG -pipe -O2 -fno-strict-aliasing -fPIC -Ibcftools -Ipysam -I. -I/construction/biology/py-pysam/pysam-0.13/samtools -Ihtslib -I/usr/local/include/python2.7 -c bcftools/kmin.c.pysam.c -o build/temp.dragonfly-5.1-SYNTH-x86_64-2.7/bcftools/kmin.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
cc -DNDEBUG -pipe -O2 -fno-strict-aliasing -fPIC -Ibcftools -Ipysam -I. -I/construction/biology/py-pysam/pysam-0.13/samtools -Ihtslib -I/usr/local/include/python2.7 -c bcftools/vcfisec.c.pysam.c -o build/temp.dragonfly-5.1-SYNTH-x86_64-2.7/bcftools/vcfisec.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
cc -DNDEBUG -pipe -O2 -fno-strict-aliasing -fPIC -Ibcftools -Ipysam -I. -I/construction/biology/py-pysam/pysam-0.13/samtools -Ihtslib -I/usr/local/include/python2.7 -c bcftools/mcall.c.pysam.c -o build/temp.dragonfly-5.1-SYNTH-x86_64-2.7/bcftools/mcall.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
cc -DNDEBUG -pipe -O2 -fno-strict-aliasing -fPIC -Ibcftools -Ipysam -I. -I/construction/biology/py-pysam/pysam-0.13/samtools -Ihtslib -I/usr/local/include/python2.7 -c bcftools/vcffilter.c.pysam.c -o build/temp.dragonfly-5.1-SYNTH-x86_64-2.7/bcftools/vcffilter.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
cc -DNDEBUG -pipe -O2 -fno-strict-aliasing -fPIC -Ibcftools -Ipysam -I. -I/construction/biology/py-pysam/pysam-0.13/samtools -Ihtslib -I/usr/local/include/python2.7 -c bcftools/prob1.c.pysam.c -o build/temp.dragonfly-5.1-SYNTH-x86_64-2.7/bcftools/prob1.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
cc -DNDEBUG -pipe -O2 -fno-strict-aliasing -fPIC -Ibcftools -Ipysam -I. -I/construction/biology/py-pysam/pysam-0.13/samtools -Ihtslib -I/usr/local/include/python2.7 -c bcftools/tabix.c.pysam.c -o build/temp.dragonfly-5.1-SYNTH-x86_64-2.7/bcftools/tabix.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
cc -DNDEBUG -pipe -O2 -fno-strict-aliasing -fPIC -Ibcftools -Ipysam -I. -I/construction/biology/py-pysam/pysam-0.13/samtools -Ihtslib -I/usr/local/include/python2.7 -c bcftools/HMM.c.pysam.c -o build/temp.dragonfly-5.1-SYNTH-x86_64-2.7/bcftools/HMM.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
cc -DNDEBUG -pipe -O2 -fno-strict-aliasing -fPIC -Ibcftools -Ipysam -I. -I/construction/biology/py-pysam/pysam-0.13/samtools -Ihtslib -I/usr/local/include/python2.7 -c bcftools/vcfannotate.c.pysam.c -o build/temp.dragonfly-5.1-SYNTH-x86_64-2.7/bcftools/vcfannotate.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
cc -DNDEBUG -pipe -O2 -fno-strict-aliasing -fPIC -Ibcftools -Ipysam -I. -I/construction/biology/py-pysam/pysam-0.13/samtools -Ihtslib -I/usr/local/include/python2.7 -c bcftools/vcfview.c.pysam.c -o build/temp.dragonfly-5.1-SYNTH-x86_64-2.7/bcftools/vcfview.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
cc -DNDEBUG -pipe -O2 -fno-strict-aliasing -fPIC -Ibcftools -Ipysam -I. -I/construction/biology/py-pysam/pysam-0.13/samtools -Ihtslib -I/usr/local/include/python2.7 -c bcftools/vcfplugin.c.pysam.c -o build/temp.dragonfly-5.1-SYNTH-x86_64-2.7/bcftools/vcfplugin.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
cc -DNDEBUG -pipe -O2 -fno-strict-aliasing -fPIC -Ibcftools -Ipysam -I. -I/construction/biology/py-pysam/pysam-0.13/samtools -Ihtslib -I/usr/local/include/python2.7 -c bcftools/main.c.pysam.c -o build/temp.dragonfly-5.1-SYNTH-x86_64-2.7/bcftools/main.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
cc -DNDEBUG -pipe -O2 -fno-strict-aliasing -fPIC -Ibcftools -Ipysam -I. -I/construction/biology/py-pysam/pysam-0.13/samtools -Ihtslib -I/usr/local/include/python2.7 -c bcftools/vcfsort.c.pysam.c -o build/temp.dragonfly-5.1-SYNTH-x86_64-2.7/bcftools/vcfsort.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
cc -DNDEBUG -pipe -O2 -fno-strict-aliasing -fPIC -Ibcftools -Ipysam -I. -I/construction/biology/py-pysam/pysam-0.13/samtools -Ihtslib -I/usr/local/include/python2.7 -c bcftools/vcfcall.c.pysam.c -o build/temp.dragonfly-5.1-SYNTH-x86_64-2.7/bcftools/vcfcall.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
cc -DNDEBUG -pipe -O2 -fno-strict-aliasing -fPIC -Ibcftools -Ipysam -I. -I/construction/biology/py-pysam/pysam-0.13/samtools -Ihtslib -I/usr/local/include/python2.7 -c bcftools/vcmp.c.pysam.c -o build/temp.dragonfly-5.1-SYNTH-x86_64-2.7/bcftools/vcmp.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
cc -DNDEBUG -pipe -O2 -fno-strict-aliasing -fPIC -Ibcftools -Ipysam -I. -I/construction/biology/py-pysam/pysam-0.13/samtools -Ihtslib -I/usr/local/include/python2.7 -c bcftools/vcfstats.c.pysam.c -o build/temp.dragonfly-5.1-SYNTH-x86_64-2.7/bcftools/vcfstats.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
cc -DNDEBUG -pipe -O2 -fno-strict-aliasing -fPIC -Ibcftools -Ipysam -I. -I/construction/biology/py-pysam/pysam-0.13/samtools -Ihtslib -I/usr/local/include/python2.7 -c bcftools/bam2bcf_indel.c.pysam.c -o build/temp.dragonfly-5.1-SYNTH-x86_64-2.7/bcftools/bam2bcf_indel.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
cc -DNDEBUG -pipe -O2 -fno-strict-aliasing -fPIC -Ibcftools -Ipysam -I. -I/construction/biology/py-pysam/pysam-0.13/samtools -Ihtslib -I/usr/local/include/python2.7 -c bcftools/vcfquery.c.pysam.c -o build/temp.dragonfly-5.1-SYNTH-x86_64-2.7/bcftools/vcfquery.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
cc -DNDEBUG -pipe -O2 -fno-strict-aliasing -fPIC -Ibcftools -Ipysam -I. -I/construction/biology/py-pysam/pysam-0.13/samtools -Ihtslib -I/usr/local/include/python2.7 -c bcftools/csq.c.pysam.c -o build/temp.dragonfly-5.1-SYNTH-x86_64-2.7/bcftools/csq.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
cc -DNDEBUG -pipe -O2 -fno-strict-aliasing -fPIC -Ibcftools -Ipysam -I. -I/construction/biology/py-pysam/pysam-0.13/samtools -Ihtslib -I/usr/local/include/python2.7 -c bcftools/ploidy.c.pysam.c -o build/temp.dragonfly-5.1-SYNTH-x86_64-2.7/bcftools/ploidy.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
cc -DNDEBUG -pipe -O2 -fno-strict-aliasing -fPIC -Ibcftools -Ipysam -I. -I/construction/biology/py-pysam/pysam-0.13/samtools -Ihtslib -I/usr/local/include/python2.7 -c bcftools/convert.c.pysam.c -o build/temp.dragonfly-5.1-SYNTH-x86_64-2.7/bcftools/convert.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
cc -DNDEBUG -pipe -O2 -fno-strict-aliasing -fPIC -Ibcftools -Ipysam -I. -I/construction/biology/py-pysam/pysam-0.13/samtools -Ihtslib -I/usr/local/include/python2.7 -c bcftools/bin.c.pysam.c -o build/temp.dragonfly-5.1-SYNTH-x86_64-2.7/bcftools/bin.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
cc -DNDEBUG -pipe -O2 -fno-strict-aliasing -fPIC -Ibcftools -Ipysam -I. -I/construction/biology/py-pysam/pysam-0.13/samtools -Ihtslib -I/usr/local/include/python2.7 -c bcftools/vcfconcat.c.pysam.c -o build/temp.dragonfly-5.1-SYNTH-x86_64-2.7/bcftools/vcfconcat.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
cc -DNDEBUG -pipe -O2 -fno-strict-aliasing -fPIC -Ibcftools -Ipysam -I. -I/construction/biology/py-pysam/pysam-0.13/samtools -Ihtslib -I/usr/local/include/python2.7 -c bcftools/hclust.c.pysam.c -o build/temp.dragonfly-5.1-SYNTH-x86_64-2.7/bcftools/hclust.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
cc -DNDEBUG -pipe -O2 -fno-strict-aliasing -fPIC -Ibcftools -Ipysam -I. -I/construction/biology/py-pysam/pysam-0.13/samtools -Ihtslib -I/usr/local/include/python2.7 -c bcftools/ccall.c.pysam.c -o build/temp.dragonfly-5.1-SYNTH-x86_64-2.7/bcftools/ccall.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
cc -DNDEBUG -pipe -O2 -fno-strict-aliasing -fPIC -Ibcftools -Ipysam -I. -I/construction/biology/py-pysam/pysam-0.13/samtools -Ihtslib -I/usr/local/include/python2.7 -c bcftools/bam_sample.c.pysam.c -o build/temp.dragonfly-5.1-SYNTH-x86_64-2.7/bcftools/bam_sample.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
cc -DNDEBUG -pipe -O2 -fno-strict-aliasing -fPIC -Ibcftools -Ipysam -I. -I/construction/biology/py-pysam/pysam-0.13/samtools -Ihtslib -I/usr/local/include/python2.7 -c bcftools/vcfcnv.c.pysam.c -o build/temp.dragonfly-5.1-SYNTH-x86_64-2.7/bcftools/vcfcnv.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
cc -DNDEBUG -pipe -O2 -fno-strict-aliasing -fPIC -Ibcftools -Ipysam -I. -I/construction/biology/py-pysam/pysam-0.13/samtools -Ihtslib -I/usr/local/include/python2.7 -c bcftools/filter.c.pysam.c -o build/temp.dragonfly-5.1-SYNTH-x86_64-2.7/bcftools/filter.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
cc -DNDEBUG -pipe -O2 -fno-strict-aliasing -fPIC -Ibcftools -Ipysam -I. -I/construction/biology/py-pysam/pysam-0.13/samtools -Ihtslib -I/usr/local/include/python2.7 -c bcftools/gvcf.c.pysam.c -o build/temp.dragonfly-5.1-SYNTH-x86_64-2.7/bcftools/gvcf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
cc -DNDEBUG -pipe -O2 -fno-strict-aliasing -fPIC -Ibcftools -Ipysam -I. -I/construction/biology/py-pysam/pysam-0.13/samtools -Ihtslib -I/usr/local/include/python2.7 -c bcftools/vcfsom.c.pysam.c -o build/temp.dragonfly-5.1-SYNTH-x86_64-2.7/bcftools/vcfsom.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
cc -DNDEBUG -pipe -O2 -fno-strict-aliasing -fPIC -Ibcftools -Ipysam -I. -I/construction/biology/py-pysam/pysam-0.13/samtools -Ihtslib -I/usr/local/include/python2.7 -c bcftools/consensus.c.pysam.c -o build/temp.dragonfly-5.1-SYNTH-x86_64-2.7/bcftools/consensus.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
cc -DNDEBUG -pipe -O2 -fno-strict-aliasing -fPIC -Ibcftools -Ipysam -I. -I/construction/biology/py-pysam/pysam-0.13/samtools -Ihtslib -I/usr/local/include/python2.7 -c bcftools/bam2bcf.c.pysam.c -o build/temp.dragonfly-5.1-SYNTH-x86_64-2.7/bcftools/bam2bcf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
cc -DNDEBUG -pipe -O2 -fno-strict-aliasing -fPIC -Ibcftools -Ipysam -I. -I/construction/biology/py-pysam/pysam-0.13/samtools -Ihtslib -I/usr/local/include/python2.7 -c bcftools/version.c.pysam.c -o build/temp.dragonfly-5.1-SYNTH-x86_64-2.7/bcftools/version.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
cc -DNDEBUG -pipe -O2 -fno-strict-aliasing -fPIC -Ibcftools -Ipysam -I. -I/construction/biology/py-pysam/pysam-0.13/samtools -Ihtslib -I/usr/local/include/python2.7 -c bcftools/vcfindex.c.pysam.c -o build/temp.dragonfly-5.1-SYNTH-x86_64-2.7/bcftools/vcfindex.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
cc -DNDEBUG -pipe -O2 -fno-strict-aliasing -fPIC -Ibcftools -Ipysam -I. -I/construction/biology/py-pysam/pysam-0.13/samtools -Ihtslib -I/usr/local/include/python2.7 -c bcftools/em.c.pysam.c -o build/temp.dragonfly-5.1-SYNTH-x86_64-2.7/bcftools/em.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
cc -DNDEBUG -pipe -O2 -fno-strict-aliasing -fPIC -Ibcftools -Ipysam -I. -I/construction/biology/py-pysam/pysam-0.13/samtools -Ihtslib -I/usr/local/include/python2.7 -c bcftools/mpileup.c.pysam.c -o build/temp.dragonfly-5.1-SYNTH-x86_64-2.7/bcftools/mpileup.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
cc -DNDEBUG -pipe -O2 -fno-strict-aliasing -fPIC -Ibcftools -Ipysam -I. -I/construction/biology/py-pysam/pysam-0.13/samtools -Ihtslib -I/usr/local/include/python2.7 -c bcftools/vcfgtcheck.c.pysam.c -o build/temp.dragonfly-5.1-SYNTH-x86_64-2.7/bcftools/vcfgtcheck.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
cc -DNDEBUG -pipe -O2 -fno-strict-aliasing -fPIC -Ibcftools -Ipysam -I. -I/construction/biology/py-pysam/pysam-0.13/samtools -Ihtslib -I/usr/local/include/python2.7 -c bcftools/smpl_ilist.c.pysam.c -o build/temp.dragonfly-5.1-SYNTH-x86_64-2.7/bcftools/smpl_ilist.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
cc -DNDEBUG -pipe -O2 -fno-strict-aliasing -fPIC -Ibcftools -Ipysam -I. -I/construction/biology/py-pysam/pysam-0.13/samtools -Ihtslib -I/usr/local/include/python2.7 -c bcftools/vcfbuf.c.pysam.c -o build/temp.dragonfly-5.1-SYNTH-x86_64-2.7/bcftools/vcfbuf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
cc -DNDEBUG -pipe -O2 -fno-strict-aliasing -fPIC -Ibcftools -Ipysam -I. -I/construction/biology/py-pysam/pysam-0.13/samtools -Ihtslib -I/usr/local/include/python2.7 -c bcftools/vcfmerge.c.pysam.c -o build/temp.dragonfly-5.1-SYNTH-x86_64-2.7/bcftools/vcfmerge.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
cc -shared -pipe -O2 -fno-strict-aliasing build/temp.dragonfly-5.1-SYNTH-x86_64-2.7/pysam/libcbcftools.o build/temp.dragonfly-5.1-SYNTH-x86_64-2.7/bcftools/vcfconvert.c.pysam.o build/temp.dragonfly-5.1-SYNTH-x86_64-2.7/bcftools/regidx.c.pysam.o build/temp.dragonfly-5.1-SYNTH-x86_64-2.7/bcftools/vcfroh.c.pysam.o build/temp.dragonfly-5.1-SYNTH-x86_64-2.7/bcftools/vcfnorm.c.pysam.o build/temp.dragonfly-5.1-SYNTH-x86_64-2.7/bcftools/tsv2vcf.c.pysam.o build/temp.dragonfly-5.1-SYNTH-x86_64-2.7/bcftools/kmin.c.pysam.o build/temp.dragonfly-5.1-SYNTH-x86_64-2.7/bcftools/vcfisec.c.pysam.o build/temp.dragonfly-5.1-SYNTH-x86_64-2.7/bcftools/mcall.c.pysam.o build/temp.dragonfly-5.1-SYNTH-x86_64-2.7/bcftools/vcffilter.c.pysam.o build/temp.dragonfly-5.1-SYNTH-x86_64-2.7/bcftools/prob1.c.pysam.o build/temp.dragonfly-5.1-SYNTH-x86_64-2.7/bcftools/tabix.c.pysam.o build/temp.dragonfly-5.1-SYNTH-x86_64-2.7/bcftools/HMM.c.pysam.o build/temp.dragonfly-5.1-SYNTH-x86_64-2.7/bcftools/vcfannotate.c.pysam.o build/temp.dragonfly-5.1-SYNTH-x86_64-2.7/bcftools/vcfview.c.pysam.o build/temp.dragonfly-5.1-SYNTH-x86_64-2.7/bcftools/vcfplugin.c.pysam.o build/temp.dragonfly-5.1-SYNTH-x86_64-2.7/bcftools/main.c.pysam.o build/temp.dragonfly-5.1-SYNTH-x86_64-2.7/bcftools/vcfsort.c.pysam.o build/temp.dragonfly-5.1-SYNTH-x86_64-2.7/bcftools/vcfcall.c.pysam.o build/temp.dragonfly-5.1-SYNTH-x86_64-2.7/bcftools/vcmp.c.pysam.o build/temp.dragonfly-5.1-SYNTH-x86_64-2.7/bcftools/vcfstats.c.pysam.o build/temp.dragonfly-5.1-SYNTH-x86_64-2.7/bcftools/bam2bcf_indel.c.pysam.o build/temp.dragonfly-5.1-SYNTH-x86_64-2.7/bcftools/vcfquery.c.pysam.o build/temp.dragonfly-5.1-SYNTH-x86_64-2.7/bcftools/csq.c.pysam.o build/temp.dragonfly-5.1-SYNTH-x86_64-2.7/bcftools/ploidy.c.pysam.o build/temp.dragonfly-5.1-SYNTH-x86_64-2.7/bcftools/convert.c.pysam.o build/temp.dragonfly-5.1-SYNTH-x86_64-2.7/bcftools/bin.c.pysam.o build/temp.dragonfly-5.1-SYNTH-x86_64-2.7/bcftools/vcfconcat.c.pysam.o build/temp.dragonfly-5.1-SYNTH-x86_64-2.7/bcftools/hclust.c.pysam.o build/temp.dragonfly-5.1-SYNTH-x86_64-2.7/bcftools/ccall.c.pysam.o build/temp.dragonfly-5.1-SYNTH-x86_64-2.7/bcftools/bam_sample.c.pysam.o build/temp.dragonfly-5.1-SYNTH-x86_64-2.7/bcftools/vcfcnv.c.pysam.o build/temp.dragonfly-5.1-SYNTH-x86_64-2.7/bcftools/filter.c.pysam.o build/temp.dragonfly-5.1-SYNTH-x86_64-2.7/bcftools/gvcf.c.pysam.o build/temp.dragonfly-5.1-SYNTH-x86_64-2.7/bcftools/vcfsom.c.pysam.o build/temp.dragonfly-5.1-SYNTH-x86_64-2.7/bcftools/consensus.c.pysam.o build/temp.dragonfly-5.1-SYNTH-x86_64-2.7/bcftools/bam2bcf.c.pysam.o build/temp.dragonfly-5.1-SYNTH-x86_64-2.7/bcftools/version.c.pysam.o build/temp.dragonfly-5.1-SYNTH-x86_64-2.7/bcftools/vcfindex.c.pysam.o build/temp.dragonfly-5.1-SYNTH-x86_64-2.7/bcftools/em.c.pysam.o build/temp.dragonfly-5.1-SYNTH-x86_64-2.7/bcftools/mpileup.c.pysam.o build/temp.dragonfly-5.1-SYNTH-x86_64-2.7/bcftools/vcfgtcheck.c.pysam.o build/temp.dragonfly-5.1-SYNTH-x86_64-2.7/bcftools/smpl_ilist.c.pysam.o build/temp.dragonfly-5.1-SYNTH-x86_64-2.7/bcftools/vcfbuf.c.pysam.o build/temp.dragonfly-5.1-SYNTH-x86_64-2.7/bcftools/vcfmerge.c.pysam.o -Lpysam -Lpysam -L. -Lbuild/lib.dragonfly-5.1-SYNTH-x86_64-2.7/pysam -Lbuild/lib.dragonfly-5.1-SYNTH-x86_64-2.7/pysam -L/usr/local/lib -lz -llzma -lbz2 -lz -lm -lchtslib -lpython2.7 -o build/lib.dragonfly-5.1-SYNTH-x86_64-2.7/pysam/libcbcftools.so -Wl,-rpath,$ORIGIN
skipping 'pysam/libcutils.c' Cython extension (up-to-date)
building 'pysam.libcutils' extension
cc -DNDEBUG -pipe -O2 -fno-strict-aliasing -fPIC -Ipysam -I. -Ihtslib -I/usr/local/include/python2.7 -c pysam/libcutils.c -o build/temp.dragonfly-5.1-SYNTH-x86_64-2.7/pysam/libcutils.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
cc -DNDEBUG -pipe -O2 -fno-strict-aliasing -fPIC -Ipysam -I. -Ihtslib -I/usr/local/include/python2.7 -c pysam/pysam_util.c -o build/temp.dragonfly-5.1-SYNTH-x86_64-2.7/pysam/pysam_util.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
cc -shared -pipe -O2 -fno-strict-aliasing build/temp.dragonfly-5.1-SYNTH-x86_64-2.7/pysam/libcutils.o build/temp.dragonfly-5.1-SYNTH-x86_64-2.7/pysam/pysam_util.o -Lpysam -Lpysam -L. -Lbuild/lib.dragonfly-5.1-SYNTH-x86_64-2.7/pysam -Lbuild/lib.dragonfly-5.1-SYNTH-x86_64-2.7/pysam -L/usr/local/lib -lz -llzma -lbz2 -lz -lm -lchtslib -lcsamtools -lcbcftools -lpython2.7 -o build/lib.dragonfly-5.1-SYNTH-x86_64-2.7/pysam/libcutils.so -Wl,-rpath,$ORIGIN



--------------------------------------------------------------------------------
--  Phase: run-depends
--------------------------------------------------------------------------------
===>   py27-pysam-0.13 depends on executable: cython - found
===>   py27-pysam-0.13 depends on package: py27-setuptools>0 - found
===>   py27-pysam-0.13 depends on file: /usr/local/bin/python2.7 - found



--------------------------------------------------------------------------------
--  Phase: stage
--------------------------------------------------------------------------------
===>  Staging for py27-pysam-0.13
===>   Generating temporary packing list
checking for gcc... cc
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
checking for suffix of executables... 
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether cc accepts -g... yes
checking for cc option to accept ISO C89... none needed
checking for ranlib... ranlib
checking for special C compiler options needed for large files... no
checking for _FILE_OFFSET_BITS value needed for large files... no
checking for _LARGEFILE_SOURCE value needed for large files... no
checking shared library type for unknown-DragonFly... plain .so
checking how to run the C preprocessor... cpp
checking for grep that handles long lines and -e... /usr/bin/grep
checking for egrep... /usr/bin/grep -E
checking for ANSI C header files... yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking for stdlib.h... (cached) yes
checking for unistd.h... (cached) yes
checking for sys/param.h... yes
checking for getpagesize... yes
checking for working mmap... yes
checking for gmtime_r... yes
checking for fsync... yes
checking for drand48... yes
checking whether fdatasync is declared... no
checking for library containing log... -lm
checking for zlib.h... yes
checking for inflate in -lz... yes
checking for library containing recv... none required
checking for bzlib.h... yes
checking for BZ2_bzBuffToBuffCompress in -lbz2... yes
checking for lzma.h... yes
checking for lzma_easy_buffer_encode in -llzma... yes
checking for curl_easy_pause in -lcurl... no
checking for curl_easy_init in -lcurl... no
configure: error: libcurl library not found

Support for HTTPS and other SSL-based URLs requires routines from the libcurl
library <http://curl.haxx.se/libcurl/>.  Building HTSlib with libcurl enabled
requires libcurl development files to be installed on the build machine; you
may need to ensure a package such as libcurl4-{gnutls,nss,openssl}-dev (on
Debian or Ubuntu Linux) or libcurl-devel (on RPM-based Linux distributions
or Cygwin) is installed.

Either configure with --disable-libcurl or resolve this error to build HTSlib.
checking for gcc... cc
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
checking for suffix of executables... 
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether cc accepts -g... yes
checking for cc option to accept ISO C89... none needed
checking for ranlib... ranlib
checking for special C compiler options needed for large files... no
checking for _FILE_OFFSET_BITS value needed for large files... no
checking for _LARGEFILE_SOURCE value needed for large files... no
checking shared library type for unknown-DragonFly... plain .so
checking how to run the C preprocessor... cpp
checking for grep that handles long lines and -e... /usr/bin/grep
checking for egrep... /usr/bin/grep -E
checking for ANSI C header files... yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking for stdlib.h... (cached) yes
checking for unistd.h... (cached) yes
checking for sys/param.h... yes
checking for getpagesize... yes
checking for working mmap... yes
checking for gmtime_r... yes
checking for fsync... yes
checking for drand48... yes
checking whether fdatasync is declared... no
checking for library containing log... -lm
checking for zlib.h... yes
checking for inflate in -lz... yes
checking for library containing recv... none required
checking for bzlib.h... yes
checking for BZ2_bzBuffToBuffCompress in -lbz2... yes
checking for lzma.h... yes
checking for lzma_easy_buffer_encode in -llzma... yes
configure: WARNING: GCS support not enabled: requires libcurl support
configure: WARNING: S3 support not enabled: requires libcurl support
checking whether PTHREAD_MUTEX_RECURSIVE is declared... yes
configure: creating ./config.status
config.status: creating config.mk
config.status: creating htslib.pc.tmp
config.status: creating config.h
config.status: config.h is unchanged
gmake[1]: ./version.sh: Command not found
gmake[1]: ./version.sh: Command not found
# pysam: cython is available - using cythonize if necessary
# pysam: htslib mode is shared
# pysam: HTSLIB_CONFIGURE_OPTIONS=None
# pysam: htslib configure options: --disable-libcurl
# pysam: htslib_config LIBS=-llzma -lbz2 -lz -lm
# pysam: htslib_config PLATFORM=default
# pysam: htslib_config LIBHTS_OBJS=kfunc.o knetfile.o kstring.o bcf_sr_sort.o bgzf.o errmod.o faidx.o hfile.o hfile_net.o hts.o hts_os.o md5.o multipart.o probaln.o realn.o regidx.o sam.o synced_bcf_reader.o vcf_sweep.o tbx.o textutils.o thread_pool.o vcf.o vcfutils.o cram/cram_codecs.o cram/cram_decode.o cram/cram_encode.o cram/cram_external.o cram/cram_index.o cram/cram_io.o cram/cram_samtools.o cram/cram_stats.o cram/files.o cram/mFILE.o cram/open_trace_file.o cram/pooled_alloc.o cram/rANS_static.o cram/sam_header.o cram/string_alloc.o
# pysam: htslib_config LDFLAGS=
# pysam: config_option: ENABLE_PLUGINS=0
# pysam: config_option: HAVE_COMMONCRYPTO=0
# pysam: config_option: HAVE_GMTIME_R=1
# pysam: config_option: HAVE_HMAC=0
# pysam: config_option: HAVE_IRODS=0
# pysam: config_option: HAVE_LIBCURL=0
# pysam: config_option: HAVE_MMAP=1
running install
running build
running build_py
copying pysam/config.py -> build/lib.dragonfly-5.1-SYNTH-x86_64-2.7/pysam
package init file 'samtools/__init__.py' not found (or not a regular file)
package init file 'bcftools/__init__.py' not found (or not a regular file)
package init file 'samtools/win32/__init__.py' not found (or not a regular file)
package init file 'htslib/__init__.py' not found (or not a regular file)
package init file 'htslib/htslib/__init__.py' not found (or not a regular file)
running build_ext
skipping 'pysam/libchtslib.c' Cython extension (up-to-date)
skipping 'pysam/libcsamfile.c' Cython extension (up-to-date)
skipping 'pysam/libcalignmentfile.c' Cython extension (up-to-date)
skipping 'pysam/libcalignedsegment.c' Cython extension (up-to-date)
skipping 'pysam/libctabix.c' Cython extension (up-to-date)
skipping 'pysam/libctabixproxies.c' Cython extension (up-to-date)
skipping 'pysam/libcvcf.c' Cython extension (up-to-date)
skipping 'pysam/libcbcf.c' Cython extension (up-to-date)
skipping 'pysam/libcbgzf.c' Cython extension (up-to-date)
skipping 'pysam/libcfaidx.c' Cython extension (up-to-date)
skipping 'pysam/libcsamtools.c' Cython extension (up-to-date)
skipping 'pysam/libcbcftools.c' Cython extension (up-to-date)
skipping 'pysam/libcutils.c' Cython extension (up-to-date)
running install_lib
creating /construction/biology/py-pysam/stage/usr/local/lib/python2.7
creating /construction/biology/py-pysam/stage/usr/local/lib/python2.7/site-packages
creating /construction/biology/py-pysam/stage/usr/local/lib/python2.7/site-packages/pysam
copying build/lib.dragonfly-5.1-SYNTH-x86_64-2.7/pysam/libcfaidx.so -> /construction/biology/py-pysam/stage/usr/local/lib/python2.7/site-packages/pysam
copying build/lib.dragonfly-5.1-SYNTH-x86_64-2.7/pysam/libcvcf.so -> /construction/biology/py-pysam/stage/usr/local/lib/python2.7/site-packages/pysam
copying build/lib.dragonfly-5.1-SYNTH-x86_64-2.7/pysam/libcalignedsegment.so -> /construction/biology/py-pysam/stage/usr/local/lib/python2.7/site-packages/pysam
copying build/lib.dragonfly-5.1-SYNTH-x86_64-2.7/pysam/libcutils.so -> /construction/biology/py-pysam/stage/usr/local/lib/python2.7/site-packages/pysam
copying build/lib.dragonfly-5.1-SYNTH-x86_64-2.7/pysam/libchtslib.so -> /construction/biology/py-pysam/stage/usr/local/lib/python2.7/site-packages/pysam
copying build/lib.dragonfly-5.1-SYNTH-x86_64-2.7/pysam/libcbcf.so -> /construction/biology/py-pysam/stage/usr/local/lib/python2.7/site-packages/pysam
copying build/lib.dragonfly-5.1-SYNTH-x86_64-2.7/pysam/libctabixproxies.so -> /construction/biology/py-pysam/stage/usr/local/lib/python2.7/site-packages/pysam
copying build/lib.dragonfly-5.1-SYNTH-x86_64-2.7/pysam/libctabix.so -> /construction/biology/py-pysam/stage/usr/local/lib/python2.7/site-packages/pysam
copying build/lib.dragonfly-5.1-SYNTH-x86_64-2.7/pysam/libcsamtools.so -> /construction/biology/py-pysam/stage/usr/local/lib/python2.7/site-packages/pysam
copying build/lib.dragonfly-5.1-SYNTH-x86_64-2.7/pysam/libcbcftools.so -> /construction/biology/py-pysam/stage/usr/local/lib/python2.7/site-packages/pysam
copying build/lib.dragonfly-5.1-SYNTH-x86_64-2.7/pysam/libcsamfile.so -> /construction/biology/py-pysam/stage/usr/local/lib/python2.7/site-packages/pysam
copying build/lib.dragonfly-5.1-SYNTH-x86_64-2.7/pysam/libcalignmentfile.so -> /construction/biology/py-pysam/stage/usr/local/lib/python2.7/site-packages/pysam
copying build/lib.dragonfly-5.1-SYNTH-x86_64-2.7/pysam/Pileup.py -> /construction/biology/py-pysam/stage/usr/local/lib/python2.7/site-packages/pysam
copying build/lib.dragonfly-5.1-SYNTH-x86_64-2.7/pysam/libcsamtools.pxd -> /construction/biology/py-pysam/stage/usr/local/lib/python2.7/site-packages/pysam
copying build/lib.dragonfly-5.1-SYNTH-x86_64-2.7/pysam/utils.py -> /construction/biology/py-pysam/stage/usr/local/lib/python2.7/site-packages/pysam
copying build/lib.dragonfly-5.1-SYNTH-x86_64-2.7/pysam/libcsamfile.pxd -> /construction/biology/py-pysam/stage/usr/local/lib/python2.7/site-packages/pysam
copying build/lib.dragonfly-5.1-SYNTH-x86_64-2.7/pysam/cbcftools_util.h -> /construction/biology/py-pysam/stage/usr/local/lib/python2.7/site-packages/pysam
copying build/lib.dragonfly-5.1-SYNTH-x86_64-2.7/pysam/htslib_util.h -> /construction/biology/py-pysam/stage/usr/local/lib/python2.7/site-packages/pysam
copying build/lib.dragonfly-5.1-SYNTH-x86_64-2.7/pysam/libcbcftools.pxd -> /construction/biology/py-pysam/stage/usr/local/lib/python2.7/site-packages/pysam
copying build/lib.dragonfly-5.1-SYNTH-x86_64-2.7/pysam/config.py -> /construction/biology/py-pysam/stage/usr/local/lib/python2.7/site-packages/pysam
copying build/lib.dragonfly-5.1-SYNTH-x86_64-2.7/pysam/version.py -> /construction/biology/py-pysam/stage/usr/local/lib/python2.7/site-packages/pysam
copying build/lib.dragonfly-5.1-SYNTH-x86_64-2.7/pysam/csamtools_util.h -> /construction/biology/py-pysam/stage/usr/local/lib/python2.7/site-packages/pysam
copying build/lib.dragonfly-5.1-SYNTH-x86_64-2.7/pysam/samtools.py -> /construction/biology/py-pysam/stage/usr/local/lib/python2.7/site-packages/pysam
creating /construction/biology/py-pysam/stage/usr/local/lib/python2.7/site-packages/pysam/include
creating /construction/biology/py-pysam/stage/usr/local/lib/python2.7/site-packages/pysam/include/htslib
copying build/lib.dragonfly-5.1-SYNTH-x86_64-2.7/pysam/include/htslib/version.h -> /construction/biology/py-pysam/stage/usr/local/lib/python2.7/site-packages/pysam/include/htslib
creating /construction/biology/py-pysam/stage/usr/local/lib/python2.7/site-packages/pysam/include/htslib/htslib
copying build/lib.dragonfly-5.1-SYNTH-x86_64-2.7/pysam/include/htslib/htslib/khash_str2int.h -> /construction/biology/py-pysam/stage/usr/local/lib/python2.7/site-packages/pysam/include/htslib/htslib
copying build/lib.dragonfly-5.1-SYNTH-x86_64-2.7/pysam/include/htslib/htslib/knetfile.h -> /construction/biology/py-pysam/stage/usr/local/lib/python2.7/site-packages/pysam/include/htslib/htslib
copying build/lib.dragonfly-5.1-SYNTH-x86_64-2.7/pysam/include/htslib/htslib/hfile.h -> /construction/biology/py-pysam/stage/usr/local/lib/python2.7/site-packages/pysam/include/htslib/htslib
copying build/lib.dragonfly-5.1-SYNTH-x86_64-2.7/pysam/include/htslib/htslib/hts.h -> /construction/biology/py-pysam/stage/usr/local/lib/python2.7/site-packages/pysam/include/htslib/htslib
copying build/lib.dragonfly-5.1-SYNTH-x86_64-2.7/pysam/include/htslib/htslib/cram.h -> /construction/biology/py-pysam/stage/usr/local/lib/python2.7/site-packages/pysam/include/htslib/htslib
copying build/lib.dragonfly-5.1-SYNTH-x86_64-2.7/pysam/include/htslib/htslib/sam.h -> /construction/biology/py-pysam/stage/usr/local/lib/python2.7/site-packages/pysam/include/htslib/htslib
copying build/lib.dragonfly-5.1-SYNTH-x86_64-2.7/pysam/include/htslib/htslib/kseq.h -> /construction/biology/py-pysam/stage/usr/local/lib/python2.7/site-packages/pysam/include/htslib/htslib
copying build/lib.dragonfly-5.1-SYNTH-x86_64-2.7/pysam/include/htslib/htslib/thread_pool.h -> /construction/biology/py-pysam/stage/usr/local/lib/python2.7/site-packages/pysam/include/htslib/htslib
copying build/lib.dragonfly-5.1-SYNTH-x86_64-2.7/pysam/include/htslib/htslib/hts_log.h -> /construction/biology/py-pysam/stage/usr/local/lib/python2.7/site-packages/pysam/include/htslib/htslib
copying build/lib.dragonfly-5.1-SYNTH-x86_64-2.7/pysam/include/htslib/htslib/faidx.h -> /construction/biology/py-pysam/stage/usr/local/lib/python2.7/site-packages/pysam/include/htslib/htslib
copying build/lib.dragonfly-5.1-SYNTH-x86_64-2.7/pysam/include/htslib/htslib/klist.h -> /construction/biology/py-pysam/stage/usr/local/lib/python2.7/site-packages/pysam/include/htslib/htslib
copying build/lib.dragonfly-5.1-SYNTH-x86_64-2.7/pysam/include/htslib/htslib/vcf_sweep.h -> /construction/biology/py-pysam/stage/usr/local/lib/python2.7/site-packages/pysam/include/htslib/htslib
copying build/lib.dragonfly-5.1-SYNTH-x86_64-2.7/pysam/include/htslib/htslib/kfunc.h -> /construction/biology/py-pysam/stage/usr/local/lib/python2.7/site-packages/pysam/include/htslib/htslib
copying build/lib.dragonfly-5.1-SYNTH-x86_64-2.7/pysam/include/htslib/htslib/synced_bcf_reader.h -> /construction/biology/py-pysam/stage/usr/local/lib/python2.7/site-packages/pysam/include/htslib/htslib
copying build/lib.dragonfly-5.1-SYNTH-x86_64-2.7/pysam/include/htslib/htslib/hts_endian.h -> /construction/biology/py-pysam/stage/usr/local/lib/python2.7/site-packages/pysam/include/htslib/htslib
copying build/lib.dragonfly-5.1-SYNTH-x86_64-2.7/pysam/include/htslib/htslib/vcfutils.h -> /construction/biology/py-pysam/stage/usr/local/lib/python2.7/site-packages/pysam/include/htslib/htslib
copying build/lib.dragonfly-5.1-SYNTH-x86_64-2.7/pysam/include/htslib/htslib/kbitset.h -> /construction/biology/py-pysam/stage/usr/local/lib/python2.7/site-packages/pysam/include/htslib/htslib
copying build/lib.dragonfly-5.1-SYNTH-x86_64-2.7/pysam/include/htslib/htslib/regidx.h -> /construction/biology/py-pysam/stage/usr/local/lib/python2.7/site-packages/pysam/include/htslib/htslib
copying build/lib.dragonfly-5.1-SYNTH-x86_64-2.7/pysam/include/htslib/htslib/bgzf.h -> /construction/biology/py-pysam/stage/usr/local/lib/python2.7/site-packages/pysam/include/htslib/htslib
copying build/lib.dragonfly-5.1-SYNTH-x86_64-2.7/pysam/include/htslib/htslib/ksort.h -> /construction/biology/py-pysam/stage/usr/local/lib/python2.7/site-packages/pysam/include/htslib/htslib
copying build/lib.dragonfly-5.1-SYNTH-x86_64-2.7/pysam/include/htslib/htslib/hts_defs.h -> /construction/biology/py-pysam/stage/usr/local/lib/python2.7/site-packages/pysam/include/htslib/htslib
copying build/lib.dragonfly-5.1-SYNTH-x86_64-2.7/pysam/include/htslib/htslib/vcf.h -> /construction/biology/py-pysam/stage/usr/local/lib/python2.7/site-packages/pysam/include/htslib/htslib
copying build/lib.dragonfly-5.1-SYNTH-x86_64-2.7/pysam/include/htslib/htslib/tbx.h -> /construction/biology/py-pysam/stage/usr/local/lib/python2.7/site-packages/pysam/include/htslib/htslib
copying build/lib.dragonfly-5.1-SYNTH-x86_64-2.7/pysam/include/htslib/htslib/hts_os.h -> /construction/biology/py-pysam/stage/usr/local/lib/python2.7/site-packages/pysam/include/htslib/htslib
copying build/lib.dragonfly-5.1-SYNTH-x86_64-2.7/pysam/include/htslib/htslib/khash.h -> /construction/biology/py-pysam/stage/usr/local/lib/python2.7/site-packages/pysam/include/htslib/htslib
copying build/lib.dragonfly-5.1-SYNTH-x86_64-2.7/pysam/include/htslib/htslib/kstring.h -> /construction/biology/py-pysam/stage/usr/local/lib/python2.7/site-packages/pysam/include/htslib/htslib
copying build/lib.dragonfly-5.1-SYNTH-x86_64-2.7/pysam/include/htslib/hts_internal.h -> /construction/biology/py-pysam/stage/usr/local/lib/python2.7/site-packages/pysam/include/htslib
copying build/lib.dragonfly-5.1-SYNTH-x86_64-2.7/pysam/include/htslib/hfile_internal.h -> /construction/biology/py-pysam/stage/usr/local/lib/python2.7/site-packages/pysam/include/htslib
copying build/lib.dragonfly-5.1-SYNTH-x86_64-2.7/pysam/include/htslib/thread_pool_internal.h -> /construction/biology/py-pysam/stage/usr/local/lib/python2.7/site-packages/pysam/include/htslib
copying build/lib.dragonfly-5.1-SYNTH-x86_64-2.7/pysam/include/htslib/bcf_sr_sort.h -> /construction/biology/py-pysam/stage/usr/local/lib/python2.7/site-packages/pysam/include/htslib
copying build/lib.dragonfly-5.1-SYNTH-x86_64-2.7/pysam/include/htslib/config.h -> /construction/biology/py-pysam/stage/usr/local/lib/python2.7/site-packages/pysam/include/htslib
creating /construction/biology/py-pysam/stage/usr/local/lib/python2.7/site-packages/pysam/include/samtools
copying build/lib.dragonfly-5.1-SYNTH-x86_64-2.7/pysam/include/samtools/stats_isize.h -> /construction/biology/py-pysam/stage/usr/local/lib/python2.7/site-packages/pysam/include/samtools
copying build/lib.dragonfly-5.1-SYNTH-x86_64-2.7/pysam/include/samtools/bam_lpileup.h -> /construction/biology/py-pysam/stage/usr/local/lib/python2.7/site-packages/pysam/include/samtools
copying build/lib.dragonfly-5.1-SYNTH-x86_64-2.7/pysam/include/samtools/sample.h -> /construction/biology/py-pysam/stage/usr/local/lib/python2.7/site-packages/pysam/include/samtools
copying build/lib.dragonfly-5.1-SYNTH-x86_64-2.7/pysam/include/samtools/bam2bcf.h -> /construction/biology/py-pysam/stage/usr/local/lib/python2.7/site-packages/pysam/include/samtools
copying build/lib.dragonfly-5.1-SYNTH-x86_64-2.7/pysam/include/samtools/sam.h -> /construction/biology/py-pysam/stage/usr/local/lib/python2.7/site-packages/pysam/include/samtools
copying build/lib.dragonfly-5.1-SYNTH-x86_64-2.7/pysam/include/samtools/bam.h -> /construction/biology/py-pysam/stage/usr/local/lib/python2.7/site-packages/pysam/include/samtools
copying build/lib.dragonfly-5.1-SYNTH-x86_64-2.7/pysam/include/samtools/config.h -> /construction/biology/py-pysam/stage/usr/local/lib/python2.7/site-packages/pysam/include/samtools
copying build/lib.dragonfly-5.1-SYNTH-x86_64-2.7/pysam/include/samtools/version.h -> /construction/biology/py-pysam/stage/usr/local/lib/python2.7/site-packages/pysam/include/samtools
copying build/lib.dragonfly-5.1-SYNTH-x86_64-2.7/pysam/include/samtools/bam_plbuf.h -> /construction/biology/py-pysam/stage/usr/local/lib/python2.7/site-packages/pysam/include/samtools
copying build/lib.dragonfly-5.1-SYNTH-x86_64-2.7/pysam/include/samtools/samtools.h -> /construction/biology/py-pysam/stage/usr/local/lib/python2.7/site-packages/pysam/include/samtools
copying build/lib.dragonfly-5.1-SYNTH-x86_64-2.7/pysam/include/samtools/pysam.h -> /construction/biology/py-pysam/stage/usr/local/lib/python2.7/site-packages/pysam/include/samtools
creating /construction/biology/py-pysam/stage/usr/local/lib/python2.7/site-packages/pysam/include/samtools/win32
copying build/lib.dragonfly-5.1-SYNTH-x86_64-2.7/pysam/include/samtools/win32/xcurses.h -> /construction/biology/py-pysam/stage/usr/local/lib/python2.7/site-packages/pysam/include/samtools/win32
copying build/lib.dragonfly-5.1-SYNTH-x86_64-2.7/pysam/include/samtools/win32/zlib.h -> /construction/biology/py-pysam/stage/usr/local/lib/python2.7/site-packages/pysam/include/samtools/win32
copying build/lib.dragonfly-5.1-SYNTH-x86_64-2.7/pysam/include/samtools/win32/zconf.h -> /construction/biology/py-pysam/stage/usr/local/lib/python2.7/site-packages/pysam/include/samtools/win32
copying build/lib.dragonfly-5.1-SYNTH-x86_64-2.7/pysam/include/samtools/bam_endian.h -> /construction/biology/py-pysam/stage/usr/local/lib/python2.7/site-packages/pysam/include/samtools
copying build/lib.dragonfly-5.1-SYNTH-x86_64-2.7/pysam/include/samtools/sam_opts.h -> /construction/biology/py-pysam/stage/usr/local/lib/python2.7/site-packages/pysam/include/samtools
copying build/lib.dragonfly-5.1-SYNTH-x86_64-2.7/pysam/include/samtools/sam_header.h -> /construction/biology/py-pysam/stage/usr/local/lib/python2.7/site-packages/pysam/include/samtools
copying build/lib.dragonfly-5.1-SYNTH-x86_64-2.7/pysam/include/__init__.py -> /construction/biology/py-pysam/stage/usr/local/lib/python2.7/site-packages/pysam/include
creating /construction/biology/py-pysam/stage/usr/local/lib/python2.7/site-packages/pysam/include/bcftools
copying build/lib.dragonfly-5.1-SYNTH-x86_64-2.7/pysam/include/bcftools/kmin.h -> /construction/biology/py-pysam/stage/usr/local/lib/python2.7/site-packages/pysam/include/bcftools
copying build/lib.dragonfly-5.1-SYNTH-x86_64-2.7/pysam/include/bcftools/pysam.h -> /construction/biology/py-pysam/stage/usr/local/lib/python2.7/site-packages/pysam/include/bcftools
copying build/lib.dragonfly-5.1-SYNTH-x86_64-2.7/pysam/include/bcftools/HMM.h -> /construction/biology/py-pysam/stage/usr/local/lib/python2.7/site-packages/pysam/include/bcftools
copying build/lib.dragonfly-5.1-SYNTH-x86_64-2.7/pysam/include/bcftools/filter.h -> /construction/biology/py-pysam/stage/usr/local/lib/python2.7/site-packages/pysam/include/bcftools
copying build/lib.dragonfly-5.1-SYNTH-x86_64-2.7/pysam/include/bcftools/gvcf.h -> /construction/biology/py-pysam/stage/usr/local/lib/python2.7/site-packages/pysam/include/bcftools
copying build/lib.dragonfly-5.1-SYNTH-x86_64-2.7/pysam/include/bcftools/bin.h -> /construction/biology/py-pysam/stage/usr/local/lib/python2.7/site-packages/pysam/include/bcftools
copying build/lib.dragonfly-5.1-SYNTH-x86_64-2.7/pysam/include/bcftools/version.h -> /construction/biology/py-pysam/stage/usr/local/lib/python2.7/site-packages/pysam/include/bcftools
copying build/lib.dragonfly-5.1-SYNTH-x86_64-2.7/pysam/include/bcftools/mw.h -> /construction/biology/py-pysam/stage/usr/local/lib/python2.7/site-packages/pysam/include/bcftools
copying build/lib.dragonfly-5.1-SYNTH-x86_64-2.7/pysam/include/bcftools/convert.h -> /construction/biology/py-pysam/stage/usr/local/lib/python2.7/site-packages/pysam/include/bcftools
copying build/lib.dragonfly-5.1-SYNTH-x86_64-2.7/pysam/include/bcftools/khash_str2str.h -> /construction/biology/py-pysam/stage/usr/local/lib/python2.7/site-packages/pysam/include/bcftools
copying build/lib.dragonfly-5.1-SYNTH-x86_64-2.7/pysam/include/bcftools/rbuf.h -> /construction/biology/py-pysam/stage/usr/local/lib/python2.7/site-packages/pysam/include/bcftools
copying build/lib.dragonfly-5.1-SYNTH-x86_64-2.7/pysam/include/bcftools/hclust.h -> /construction/biology/py-pysam/stage/usr/local/lib/python2.7/site-packages/pysam/include/bcftools
copying build/lib.dragonfly-5.1-SYNTH-x86_64-2.7/pysam/include/bcftools/tsv2vcf.h -> /construction/biology/py-pysam/stage/usr/local/lib/python2.7/site-packages/pysam/include/bcftools
copying build/lib.dragonfly-5.1-SYNTH-x86_64-2.7/pysam/include/bcftools/kheap.h -> /construction/biology/py-pysam/stage/usr/local/lib/python2.7/site-packages/pysam/include/bcftools
copying build/lib.dragonfly-5.1-SYNTH-x86_64-2.7/pysam/include/bcftools/bam_sample.h -> /construction/biology/py-pysam/stage/usr/local/lib/python2.7/site-packages/pysam/include/bcftools
copying build/lib.dragonfly-5.1-SYNTH-x86_64-2.7/pysam/include/bcftools/vcfbuf.h -> /construction/biology/py-pysam/stage/usr/local/lib/python2.7/site-packages/pysam/include/bcftools
copying build/lib.dragonfly-5.1-SYNTH-x86_64-2.7/pysam/include/bcftools/config.h -> /construction/biology/py-pysam/stage/usr/local/lib/python2.7/site-packages/pysam/include/bcftools
copying build/lib.dragonfly-5.1-SYNTH-x86_64-2.7/pysam/include/bcftools/bam2bcf.h -> /construction/biology/py-pysam/stage/usr/local/lib/python2.7/site-packages/pysam/include/bcftools
copying build/lib.dragonfly-5.1-SYNTH-x86_64-2.7/pysam/include/bcftools/call.h -> /construction/biology/py-pysam/stage/usr/local/lib/python2.7/site-packages/pysam/include/bcftools
copying build/lib.dragonfly-5.1-SYNTH-x86_64-2.7/pysam/include/bcftools/smpl_ilist.h -> /construction/biology/py-pysam/stage/usr/local/lib/python2.7/site-packages/pysam/include/bcftools
copying build/lib.dragonfly-5.1-SYNTH-x86_64-2.7/pysam/include/bcftools/regidx.h -> /construction/biology/py-pysam/stage/usr/local/lib/python2.7/site-packages/pysam/include/bcftools
copying build/lib.dragonfly-5.1-SYNTH-x86_64-2.7/pysam/include/bcftools/ploidy.h -> /construction/biology/py-pysam/stage/usr/local/lib/python2.7/site-packages/pysam/include/bcftools
copying build/lib.dragonfly-5.1-SYNTH-x86_64-2.7/pysam/include/bcftools/vcmp.h -> /construction/biology/py-pysam/stage/usr/local/lib/python2.7/site-packages/pysam/include/bcftools
copying build/lib.dragonfly-5.1-SYNTH-x86_64-2.7/pysam/include/bcftools/prob1.h -> /construction/biology/py-pysam/stage/usr/local/lib/python2.7/site-packages/pysam/include/bcftools
copying build/lib.dragonfly-5.1-SYNTH-x86_64-2.7/pysam/include/bcftools/bcftools.h -> /construction/biology/py-pysam/stage/usr/local/lib/python2.7/site-packages/pysam/include/bcftools
copying build/lib.dragonfly-5.1-SYNTH-x86_64-2.7/pysam/__init__.py -> /construction/biology/py-pysam/stage/usr/local/lib/python2.7/site-packages/pysam
copying build/lib.dragonfly-5.1-SYNTH-x86_64-2.7/pysam/libcutils.pxd -> /construction/biology/py-pysam/stage/usr/local/lib/python2.7/site-packages/pysam
copying build/lib.dragonfly-5.1-SYNTH-x86_64-2.7/pysam/pysam_stream.h -> /construction/biology/py-pysam/stage/usr/local/lib/python2.7/site-packages/pysam
copying build/lib.dragonfly-5.1-SYNTH-x86_64-2.7/pysam/libcfaidx.pxd -> /construction/biology/py-pysam/stage/usr/local/lib/python2.7/site-packages/pysam
copying build/lib.dragonfly-5.1-SYNTH-x86_64-2.7/pysam/libcvcf.pxd -> /construction/biology/py-pysam/stage/usr/local/lib/python2.7/site-packages/pysam
copying build/lib.dragonfly-5.1-SYNTH-x86_64-2.7/pysam/namedtuple.py -> /construction/biology/py-pysam/stage/usr/local/lib/python2.7/site-packages/pysam
copying build/lib.dragonfly-5.1-SYNTH-x86_64-2.7/pysam/libcalignmentfile.pxd -> /construction/biology/py-pysam/stage/usr/local/lib/python2.7/site-packages/pysam
copying build/lib.dragonfly-5.1-SYNTH-x86_64-2.7/pysam/libchtslib.pxd -> /construction/biology/py-pysam/stage/usr/local/lib/python2.7/site-packages/pysam
copying build/lib.dragonfly-5.1-SYNTH-x86_64-2.7/pysam/bcftools.py -> /construction/biology/py-pysam/stage/usr/local/lib/python2.7/site-packages/pysam
copying build/lib.dragonfly-5.1-SYNTH-x86_64-2.7/pysam/libctabixproxies.pxd -> /construction/biology/py-pysam/stage/usr/local/lib/python2.7/site-packages/pysam
copying build/lib.dragonfly-5.1-SYNTH-x86_64-2.7/pysam/samfile_util.h -> /construction/biology/py-pysam/stage/usr/local/lib/python2.7/site-packages/pysam
copying build/lib.dragonfly-5.1-SYNTH-x86_64-2.7/pysam/pysam_util.h -> /construction/biology/py-pysam/stage/usr/local/lib/python2.7/site-packages/pysam
copying build/lib.dragonfly-5.1-SYNTH-x86_64-2.7/pysam/libctabix.pxd -> /construction/biology/py-pysam/stage/usr/local/lib/python2.7/site-packages/pysam
copying build/lib.dragonfly-5.1-SYNTH-x86_64-2.7/pysam/libcalignedsegment.pxd -> /construction/biology/py-pysam/stage/usr/local/lib/python2.7/site-packages/pysam
copying build/lib.dragonfly-5.1-SYNTH-x86_64-2.7/pysam/libcbcf.pxd -> /construction/biology/py-pysam/stage/usr/local/lib/python2.7/site-packages/pysam
copying build/lib.dragonfly-5.1-SYNTH-x86_64-2.7/pysam/tabix_util.h -> /construction/biology/py-pysam/stage/usr/local/lib/python2.7/site-packages/pysam
copying build/lib.dragonfly-5.1-SYNTH-x86_64-2.7/pysam/libcbgzf.so -> /construction/biology/py-pysam/stage/usr/local/lib/python2.7/site-packages/pysam
byte-compiling /construction/biology/py-pysam/stage/usr/local/lib/python2.7/site-packages/pysam/Pileup.py to Pileup.pyc
byte-compiling /construction/biology/py-pysam/stage/usr/local/lib/python2.7/site-packages/pysam/utils.py to utils.pyc
byte-compiling /construction/biology/py-pysam/stage/usr/local/lib/python2.7/site-packages/pysam/config.py to config.pyc
byte-compiling /construction/biology/py-pysam/stage/usr/local/lib/python2.7/site-packages/pysam/version.py to version.pyc
byte-compiling /construction/biology/py-pysam/stage/usr/local/lib/python2.7/site-packages/pysam/samtools.py to samtools.pyc
byte-compiling /construction/biology/py-pysam/stage/usr/local/lib/python2.7/site-packages/pysam/include/__init__.py to __init__.pyc
byte-compiling /construction/biology/py-pysam/stage/usr/local/lib/python2.7/site-packages/pysam/__init__.py to __init__.pyc
byte-compiling /construction/biology/py-pysam/stage/usr/local/lib/python2.7/site-packages/pysam/namedtuple.py to namedtuple.pyc
byte-compiling /construction/biology/py-pysam/stage/usr/local/lib/python2.7/site-packages/pysam/bcftools.py to bcftools.pyc
writing byte-compilation script '/tmp/tmpumnOK4.py'
/usr/local/bin/python2.7 -O /tmp/tmpumnOK4.py
removing /tmp/tmpumnOK4.py
running install_egg_info
running egg_info
writing pysam.egg-info/PKG-INFO
writing top-level names to pysam.egg-info/top_level.txt
writing dependency_links to pysam.egg-info/dependency_links.txt
reading manifest file 'pysam.egg-info/SOURCES.txt'
reading manifest template 'MANIFEST.in'
warning: no files found matching 'KNOWN_BUGS'
warning: no files found matching 'THANKS'
warning: no files found matching 'samtools/configure'
warning: no files found matching 'samtools/config.mk.in'
warning: no files found matching 'samtools/config.h.in'
warning: no files found matching 'tests/pysam_data'
warning: no files found matching 'tests/tabix_data'
writing manifest file 'pysam.egg-info/SOURCES.txt'
Copying pysam.egg-info to /construction/biology/py-pysam/stage/usr/local/lib/python2.7/site-packages/pysam-0.13-py2.7.egg-info
running install_scripts
writing list of installed files to '/construction/biology/py-pysam/.PLIST.pymodtmp'
/usr/bin/strip /construction/biology/py-pysam/stage/usr/local/lib/python2.7/site-packages/pysam/*.so
====> Compressing man pages (compress-man)



--------------------------------------------------------------------------------
--  Phase: package
--------------------------------------------------------------------------------
===>  Building package for py27-pysam-0.13
file sizes/checksums   [141]: .. done
packing files          [141]: .. done
packing directories      [0]: . done



--------------------------------------------------
--  Termination
--------------------------------------------------
Finished: Wednesday, 29 NOV 2017 at 21:05:05 UTC
Duration: 00:05:50