=> Building biology/py-pysam@py27 Started : Friday, 20 JUL 2018 at 23:29:24 UTC Platform: 5.3-DEVELOPMENT DragonFly v5.3.0.242.g757c0-DEVELOPMENT #30: Tue May 8 14:06:27 PDT 2018 root@pkgbox64.dragonflybsd.org:/usr/obj/usr/src/sys/X86_64_GENERIC x86_64 -------------------------------------------------- -- Environment -------------------------------------------------- UNAME_r=5.2-SYNTH UNAME_m=x86_64 UNAME_p=x86_64 UNAME_v=DragonFly 5.2-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 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 -------------------------------------------------- PORTDOCS="" PORTEXAMPLES="" 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=5.2 PREFIX=%D LOCALBASE=/usr/local RESETPREFIX=/usr/local 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-5.2 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 _PERL5_FROM_BIN=5.26.1 _ALTCCVERSION_921dbbb2=none _OBJC_ALTCCVERSION_921dbbb2=none _SMP_CPUS=8 UID=0 ARCH=x86_64 OPSYS=DragonFly DFLYVERSION=500200 OSVERSION=9999999 OSREL=5.2 _OSRELEASE=5.2-SYNTH PYTHONBASE=/usr/local _PKG_CHECKED=1 -------------------------------------------------------------------------------- -- Phase: check-sanity -------------------------------------------------------------------------------- ===> License MIT accepted by the user -------------------------------------------------------------------------------- -- Phase: pkg-depends -------------------------------------------------------------------------------- ===> py27-pysam-0.14.1 depends on file: /usr/local/sbin/pkg - not found ===> Installing existing package /packages/All/pkg-1.10.5_1.txz Installing pkg-1.10.5_1... Extracting pkg-1.10.5_1: .......... done ===> py27-pysam-0.14.1 depends on file: /usr/local/sbin/pkg - found ===> Returning to build of py27-pysam-0.14.1 -------------------------------------------------------------------------------- -- Phase: fetch-depends -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- -- Phase: fetch -------------------------------------------------------------------------------- ===> License MIT accepted by the user ===> Fetching all distfiles required by py27-pysam-0.14.1 for building -------------------------------------------------------------------------------- -- Phase: checksum -------------------------------------------------------------------------------- ===> License MIT accepted by the user ===> Fetching all distfiles required by py27-pysam-0.14.1 for building => SHA256 Checksum OK for pysam-0.14.1.tar.gz. -------------------------------------------------------------------------------- -- Phase: extract-depends -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- -- Phase: extract -------------------------------------------------------------------------------- ===> License MIT accepted by the user ===> Fetching all distfiles required by py27-pysam-0.14.1 for building ===> Extracting for py27-pysam-0.14.1 => SHA256 Checksum OK for pysam-0.14.1.tar.gz. -------------------------------------------------------------------------------- -- Phase: patch-depends -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- -- Phase: patch -------------------------------------------------------------------------------- ===> Patching for py27-pysam-0.14.1 ===> Applying ports patches for py27-pysam-0.14.1 -------------------------------------------------------------------------------- -- Phase: build-depends -------------------------------------------------------------------------------- ===> py27-pysam-0.14.1 depends on executable: gmake - not found ===> Installing existing package /packages/All/gmake-4.2.1_2.txz Installing gmake-4.2.1_2... `-- 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 Extracting gmake-4.2.1_2: .......... done ===> py27-pysam-0.14.1 depends on executable: gmake - found ===> Returning to build of py27-pysam-0.14.1 ===> py27-pysam-0.14.1 depends on executable: cython-2.7 - not found ===> Installing existing package /packages/All/py27-cython-0.28.2.txz Installing py27-cython-0.28.2... `-- Installing py27-setuptools-39.2.0... | `-- Installing python27-2.7.15... | | `-- Installing expat-2.2.5... | | `-- Extracting expat-2.2.5: .......... done | | `-- Installing libffi-3.2.1_2... | | `-- Extracting libffi-3.2.1_2: .......... done | | `-- Installing libressl-2.7.4... | | `-- Extracting libressl-2.7.4: .......... done | | `-- Installing ncurses-6.0.0s20171223_1... | | `-- Extracting ncurses-6.0.0s20171223_1: .......... done | | `-- Installing readline-7.0.3_1... | | `-- Extracting readline-7.0.3_1: .......... done | `-- Extracting python27-2.7.15: .......... done `-- Extracting py27-setuptools-39.2.0: .......... done Extracting py27-cython-0.28.2: .......... done Message from python27-2.7.15: =========================================================================== 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-0.14.1 depends on executable: cython-2.7 - found ===> Returning to build of py27-pysam-0.14.1 ===> py27-pysam-0.14.1 depends on package: py27-setuptools>0 - found ===> py27-pysam-0.14.1 depends on file: /usr/local/bin/python2.7 - found -------------------------------------------------------------------------------- -- Phase: lib-depends -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- -- Phase: configure -------------------------------------------------------------------------------- ===> Configuring for py27-pysam-0.14.1 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 grep that handles long lines and -e... /usr/bin/grep checking for C compiler warning flags... -Wall 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 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 . 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 grep that handles long lines and -e... /usr/bin/grep checking for C compiler warning flags... -Wall 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 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-0.14.1 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 grep that handles long lines and -e... /usr/bin/grep checking for C compiler warning flags... -Wall 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 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 . 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 grep that handles long lines and -e... /usr/bin/grep checking for C compiler warning flags... -Wall 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 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-5.2-SYNTH-x86_64-2.7 creating build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/pysam copying pysam/bcftools.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/pysam copying pysam/__init__.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/pysam copying pysam/utils.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/pysam copying pysam/config.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/pysam copying pysam/version.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/pysam copying pysam/Pileup.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/pysam copying pysam/samtools.py -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/pysam creating build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/pysam/include copying pysam/include/__init__.py -> build/lib.dragonfly-5.2-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/libcfaidx.pxd -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/pysam copying pysam/libcbcftools.pxd -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/pysam copying pysam/libctabixproxies.pxd -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/pysam copying pysam/libctabix.pxd -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/pysam copying pysam/libcsamfile.pxd -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/pysam copying pysam/libcbcf.pxd -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/pysam copying pysam/libcalignmentfile.pxd -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/pysam copying pysam/libcalignedsegment.pxd -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/pysam copying pysam/libcutils.pxd -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/pysam copying pysam/libcsamtools.pxd -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/pysam copying pysam/libchtslib.pxd -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/pysam copying pysam/libcvcf.pxd -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/pysam copying pysam/cbcftools_util.h -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/pysam copying pysam/pysam_stream.h -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/pysam copying pysam/csamtools_util.h -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/pysam copying pysam/pysam_util.h -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/pysam copying pysam/htslib_util.h -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/pysam creating build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/pysam/include/samtools copying samtools/config.h -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/pysam/include/samtools copying samtools/tmp_file.h -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/pysam/include/samtools copying samtools/bam2bcf.h -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/pysam/include/samtools copying samtools/bam_lpileup.h -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/pysam/include/samtools copying samtools/sam_opts.h -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/pysam/include/samtools copying samtools/bam_plbuf.h -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/pysam/include/samtools copying samtools/samtools.h -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/pysam/include/samtools copying samtools/sam.h -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/pysam/include/samtools copying samtools/bedidx.h -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/pysam/include/samtools copying samtools/bam_endian.h -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/pysam/include/samtools copying samtools/stats_isize.h -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/pysam/include/samtools copying samtools/version.h -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/pysam/include/samtools copying samtools/sample.h -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/pysam/include/samtools copying samtools/samtools.pysam.h -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/pysam/include/samtools copying samtools/sam_header.h -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/pysam/include/samtools copying samtools/bam.h -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/pysam/include/samtools creating build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/pysam/include/bcftools copying bcftools/config.h -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/pysam/include/bcftools copying bcftools/kmin.h -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/pysam/include/bcftools copying bcftools/gvcf.h -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/pysam/include/bcftools copying bcftools/hclust.h -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/pysam/include/bcftools copying bcftools/version.h -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/pysam/include/bcftools copying bcftools/bcftools.h -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/pysam/include/bcftools copying bcftools/filter.h -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/pysam/include/bcftools copying bcftools/tsv2vcf.h -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/pysam/include/bcftools copying bcftools/ploidy.h -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/pysam/include/bcftools copying bcftools/smpl_ilist.h -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/pysam/include/bcftools copying bcftools/regidx.h -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/pysam/include/bcftools copying bcftools/khash_str2str.h -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/pysam/include/bcftools copying bcftools/bam_sample.h -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/pysam/include/bcftools copying bcftools/vcmp.h -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/pysam/include/bcftools copying bcftools/bam2bcf.h -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/pysam/include/bcftools copying bcftools/convert.h -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/pysam/include/bcftools copying bcftools/prob1.h -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/pysam/include/bcftools copying bcftools/HMM.h -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/pysam/include/bcftools copying bcftools/bin.h -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/pysam/include/bcftools copying bcftools/rbuf.h -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/pysam/include/bcftools copying bcftools/bcftools.pysam.h -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/pysam/include/bcftools copying bcftools/mw.h -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/pysam/include/bcftools copying bcftools/kheap.h -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/pysam/include/bcftools copying bcftools/vcfbuf.h -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/pysam/include/bcftools copying bcftools/call.h -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/pysam/include/bcftools creating build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/pysam/include/samtools/win32 copying samtools/win32/xcurses.h -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/pysam/include/samtools/win32 copying samtools/win32/zlib.h -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/pysam/include/samtools/win32 copying samtools/win32/zconf.h -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/pysam/include/samtools/win32 creating build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/pysam/include/htslib copying htslib/config.h -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/pysam/include/htslib copying htslib/version.h -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/pysam/include/htslib copying htslib/textutils_internal.h -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/pysam/include/htslib copying htslib/hts_internal.h -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/pysam/include/htslib copying htslib/bcf_sr_sort.h -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/pysam/include/htslib copying htslib/thread_pool_internal.h -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/pysam/include/htslib copying htslib/hfile_internal.h -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/pysam/include/htslib creating build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/pysam/include/htslib/htslib copying htslib/htslib/faidx.h -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/pysam/include/htslib/htslib copying htslib/htslib/vcfutils.h -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/pysam/include/htslib/htslib copying htslib/htslib/kfunc.h -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/pysam/include/htslib/htslib copying htslib/htslib/hts_os.h -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/pysam/include/htslib/htslib copying htslib/htslib/vcf.h -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/pysam/include/htslib/htslib copying htslib/htslib/hts_log.h -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/pysam/include/htslib/htslib copying htslib/htslib/khash.h -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/pysam/include/htslib/htslib copying htslib/htslib/khash_str2int.h -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/pysam/include/htslib/htslib copying htslib/htslib/ksort.h -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/pysam/include/htslib/htslib copying htslib/htslib/synced_bcf_reader.h -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/pysam/include/htslib/htslib copying htslib/htslib/thread_pool.h -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/pysam/include/htslib/htslib copying htslib/htslib/hfile.h -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/pysam/include/htslib/htslib copying htslib/htslib/sam.h -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/pysam/include/htslib/htslib copying htslib/htslib/cram.h -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/pysam/include/htslib/htslib copying htslib/htslib/regidx.h -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/pysam/include/htslib/htslib copying htslib/htslib/hts_endian.h -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/pysam/include/htslib/htslib copying htslib/htslib/kstring.h -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/pysam/include/htslib/htslib copying htslib/htslib/kbitset.h -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/pysam/include/htslib/htslib copying htslib/htslib/vcf_sweep.h -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/pysam/include/htslib/htslib copying htslib/htslib/kseq.h -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/pysam/include/htslib/htslib copying htslib/htslib/hts_defs.h -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/pysam/include/htslib/htslib copying htslib/htslib/tbx.h -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/pysam/include/htslib/htslib copying htslib/htslib/bgzf.h -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/pysam/include/htslib/htslib copying htslib/htslib/knetfile.h -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/pysam/include/htslib/htslib copying htslib/htslib/hts.h -> build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/pysam/include/htslib/htslib copying htslib/htslib/klist.h -> build/lib.dragonfly-5.2-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-5.2-SYNTH-x86_64-2.7 creating build/temp.dragonfly-5.2-SYNTH-x86_64-2.7/pysam creating build/temp.dragonfly-5.2-SYNTH-x86_64-2.7/htslib creating build/temp.dragonfly-5.2-SYNTH-x86_64-2.7/htslib/cram cc -DNDEBUG -pipe -O2 -fno-strict-aliasing -fPIC -I/construction/biology/py-pysam/pysam-0.14.1/htslib -I/construction/biology/py-pysam/pysam-0.14.1/samtools -I/construction/biology/py-pysam/pysam-0.14.1/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.14.1/bcftools -I/construction/biology/py-pysam/pysam-0.14.1/pysam -I/construction/biology/py-pysam/pysam-0.14.1 -I/usr/local/include/python2.7 -c pysam/libchtslib.c -o build/temp.dragonfly-5.2-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 -I/construction/biology/py-pysam/pysam-0.14.1/htslib -I/construction/biology/py-pysam/pysam-0.14.1/samtools -I/construction/biology/py-pysam/pysam-0.14.1/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.14.1/bcftools -I/construction/biology/py-pysam/pysam-0.14.1/pysam -I/construction/biology/py-pysam/pysam-0.14.1 -I/usr/local/include/python2.7 -c pysam/htslib_util.c -o build/temp.dragonfly-5.2-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 -I/construction/biology/py-pysam/pysam-0.14.1/htslib -I/construction/biology/py-pysam/pysam-0.14.1/samtools -I/construction/biology/py-pysam/pysam-0.14.1/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.14.1/bcftools -I/construction/biology/py-pysam/pysam-0.14.1/pysam -I/construction/biology/py-pysam/pysam-0.14.1 -I/usr/local/include/python2.7 -c htslib/kfunc.c -o build/temp.dragonfly-5.2-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 -I/construction/biology/py-pysam/pysam-0.14.1/htslib -I/construction/biology/py-pysam/pysam-0.14.1/samtools -I/construction/biology/py-pysam/pysam-0.14.1/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.14.1/bcftools -I/construction/biology/py-pysam/pysam-0.14.1/pysam -I/construction/biology/py-pysam/pysam-0.14.1 -I/usr/local/include/python2.7 -c htslib/knetfile.c -o build/temp.dragonfly-5.2-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 -I/construction/biology/py-pysam/pysam-0.14.1/htslib -I/construction/biology/py-pysam/pysam-0.14.1/samtools -I/construction/biology/py-pysam/pysam-0.14.1/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.14.1/bcftools -I/construction/biology/py-pysam/pysam-0.14.1/pysam -I/construction/biology/py-pysam/pysam-0.14.1 -I/usr/local/include/python2.7 -c htslib/kstring.c -o build/temp.dragonfly-5.2-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 -I/construction/biology/py-pysam/pysam-0.14.1/htslib -I/construction/biology/py-pysam/pysam-0.14.1/samtools -I/construction/biology/py-pysam/pysam-0.14.1/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.14.1/bcftools -I/construction/biology/py-pysam/pysam-0.14.1/pysam -I/construction/biology/py-pysam/pysam-0.14.1 -I/usr/local/include/python2.7 -c htslib/bcf_sr_sort.c -o build/temp.dragonfly-5.2-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 -I/construction/biology/py-pysam/pysam-0.14.1/htslib -I/construction/biology/py-pysam/pysam-0.14.1/samtools -I/construction/biology/py-pysam/pysam-0.14.1/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.14.1/bcftools -I/construction/biology/py-pysam/pysam-0.14.1/pysam -I/construction/biology/py-pysam/pysam-0.14.1 -I/usr/local/include/python2.7 -c htslib/bgzf.c -o build/temp.dragonfly-5.2-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 -I/construction/biology/py-pysam/pysam-0.14.1/htslib -I/construction/biology/py-pysam/pysam-0.14.1/samtools -I/construction/biology/py-pysam/pysam-0.14.1/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.14.1/bcftools -I/construction/biology/py-pysam/pysam-0.14.1/pysam -I/construction/biology/py-pysam/pysam-0.14.1 -I/usr/local/include/python2.7 -c htslib/errmod.c -o build/temp.dragonfly-5.2-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 -I/construction/biology/py-pysam/pysam-0.14.1/htslib -I/construction/biology/py-pysam/pysam-0.14.1/samtools -I/construction/biology/py-pysam/pysam-0.14.1/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.14.1/bcftools -I/construction/biology/py-pysam/pysam-0.14.1/pysam -I/construction/biology/py-pysam/pysam-0.14.1 -I/usr/local/include/python2.7 -c htslib/faidx.c -o build/temp.dragonfly-5.2-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 -I/construction/biology/py-pysam/pysam-0.14.1/htslib -I/construction/biology/py-pysam/pysam-0.14.1/samtools -I/construction/biology/py-pysam/pysam-0.14.1/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.14.1/bcftools -I/construction/biology/py-pysam/pysam-0.14.1/pysam -I/construction/biology/py-pysam/pysam-0.14.1 -I/usr/local/include/python2.7 -c htslib/hfile.c -o build/temp.dragonfly-5.2-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 -I/construction/biology/py-pysam/pysam-0.14.1/htslib -I/construction/biology/py-pysam/pysam-0.14.1/samtools -I/construction/biology/py-pysam/pysam-0.14.1/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.14.1/bcftools -I/construction/biology/py-pysam/pysam-0.14.1/pysam -I/construction/biology/py-pysam/pysam-0.14.1 -I/usr/local/include/python2.7 -c htslib/hfile_net.c -o build/temp.dragonfly-5.2-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 -I/construction/biology/py-pysam/pysam-0.14.1/htslib -I/construction/biology/py-pysam/pysam-0.14.1/samtools -I/construction/biology/py-pysam/pysam-0.14.1/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.14.1/bcftools -I/construction/biology/py-pysam/pysam-0.14.1/pysam -I/construction/biology/py-pysam/pysam-0.14.1 -I/usr/local/include/python2.7 -c htslib/hts.c -o build/temp.dragonfly-5.2-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 -I/construction/biology/py-pysam/pysam-0.14.1/htslib -I/construction/biology/py-pysam/pysam-0.14.1/samtools -I/construction/biology/py-pysam/pysam-0.14.1/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.14.1/bcftools -I/construction/biology/py-pysam/pysam-0.14.1/pysam -I/construction/biology/py-pysam/pysam-0.14.1 -I/usr/local/include/python2.7 -c htslib/hts_os.c -o build/temp.dragonfly-5.2-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 -I/construction/biology/py-pysam/pysam-0.14.1/htslib -I/construction/biology/py-pysam/pysam-0.14.1/samtools -I/construction/biology/py-pysam/pysam-0.14.1/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.14.1/bcftools -I/construction/biology/py-pysam/pysam-0.14.1/pysam -I/construction/biology/py-pysam/pysam-0.14.1 -I/usr/local/include/python2.7 -c htslib/md5.c -o build/temp.dragonfly-5.2-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 -I/construction/biology/py-pysam/pysam-0.14.1/htslib -I/construction/biology/py-pysam/pysam-0.14.1/samtools -I/construction/biology/py-pysam/pysam-0.14.1/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.14.1/bcftools -I/construction/biology/py-pysam/pysam-0.14.1/pysam -I/construction/biology/py-pysam/pysam-0.14.1 -I/usr/local/include/python2.7 -c htslib/multipart.c -o build/temp.dragonfly-5.2-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 -I/construction/biology/py-pysam/pysam-0.14.1/htslib -I/construction/biology/py-pysam/pysam-0.14.1/samtools -I/construction/biology/py-pysam/pysam-0.14.1/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.14.1/bcftools -I/construction/biology/py-pysam/pysam-0.14.1/pysam -I/construction/biology/py-pysam/pysam-0.14.1 -I/usr/local/include/python2.7 -c htslib/probaln.c -o build/temp.dragonfly-5.2-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 -I/construction/biology/py-pysam/pysam-0.14.1/htslib -I/construction/biology/py-pysam/pysam-0.14.1/samtools -I/construction/biology/py-pysam/pysam-0.14.1/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.14.1/bcftools -I/construction/biology/py-pysam/pysam-0.14.1/pysam -I/construction/biology/py-pysam/pysam-0.14.1 -I/usr/local/include/python2.7 -c htslib/realn.c -o build/temp.dragonfly-5.2-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 -I/construction/biology/py-pysam/pysam-0.14.1/htslib -I/construction/biology/py-pysam/pysam-0.14.1/samtools -I/construction/biology/py-pysam/pysam-0.14.1/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.14.1/bcftools -I/construction/biology/py-pysam/pysam-0.14.1/pysam -I/construction/biology/py-pysam/pysam-0.14.1 -I/usr/local/include/python2.7 -c htslib/regidx.c -o build/temp.dragonfly-5.2-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 -I/construction/biology/py-pysam/pysam-0.14.1/htslib -I/construction/biology/py-pysam/pysam-0.14.1/samtools -I/construction/biology/py-pysam/pysam-0.14.1/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.14.1/bcftools -I/construction/biology/py-pysam/pysam-0.14.1/pysam -I/construction/biology/py-pysam/pysam-0.14.1 -I/usr/local/include/python2.7 -c htslib/sam.c -o build/temp.dragonfly-5.2-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 -I/construction/biology/py-pysam/pysam-0.14.1/htslib -I/construction/biology/py-pysam/pysam-0.14.1/samtools -I/construction/biology/py-pysam/pysam-0.14.1/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.14.1/bcftools -I/construction/biology/py-pysam/pysam-0.14.1/pysam -I/construction/biology/py-pysam/pysam-0.14.1 -I/usr/local/include/python2.7 -c htslib/synced_bcf_reader.c -o build/temp.dragonfly-5.2-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 -I/construction/biology/py-pysam/pysam-0.14.1/htslib -I/construction/biology/py-pysam/pysam-0.14.1/samtools -I/construction/biology/py-pysam/pysam-0.14.1/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.14.1/bcftools -I/construction/biology/py-pysam/pysam-0.14.1/pysam -I/construction/biology/py-pysam/pysam-0.14.1 -I/usr/local/include/python2.7 -c htslib/vcf_sweep.c -o build/temp.dragonfly-5.2-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 -I/construction/biology/py-pysam/pysam-0.14.1/htslib -I/construction/biology/py-pysam/pysam-0.14.1/samtools -I/construction/biology/py-pysam/pysam-0.14.1/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.14.1/bcftools -I/construction/biology/py-pysam/pysam-0.14.1/pysam -I/construction/biology/py-pysam/pysam-0.14.1 -I/usr/local/include/python2.7 -c htslib/tbx.c -o build/temp.dragonfly-5.2-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 -I/construction/biology/py-pysam/pysam-0.14.1/htslib -I/construction/biology/py-pysam/pysam-0.14.1/samtools -I/construction/biology/py-pysam/pysam-0.14.1/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.14.1/bcftools -I/construction/biology/py-pysam/pysam-0.14.1/pysam -I/construction/biology/py-pysam/pysam-0.14.1 -I/usr/local/include/python2.7 -c htslib/textutils.c -o build/temp.dragonfly-5.2-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 -I/construction/biology/py-pysam/pysam-0.14.1/htslib -I/construction/biology/py-pysam/pysam-0.14.1/samtools -I/construction/biology/py-pysam/pysam-0.14.1/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.14.1/bcftools -I/construction/biology/py-pysam/pysam-0.14.1/pysam -I/construction/biology/py-pysam/pysam-0.14.1 -I/usr/local/include/python2.7 -c htslib/thread_pool.c -o build/temp.dragonfly-5.2-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 -I/construction/biology/py-pysam/pysam-0.14.1/htslib -I/construction/biology/py-pysam/pysam-0.14.1/samtools -I/construction/biology/py-pysam/pysam-0.14.1/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.14.1/bcftools -I/construction/biology/py-pysam/pysam-0.14.1/pysam -I/construction/biology/py-pysam/pysam-0.14.1 -I/usr/local/include/python2.7 -c htslib/vcf.c -o build/temp.dragonfly-5.2-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 -I/construction/biology/py-pysam/pysam-0.14.1/htslib -I/construction/biology/py-pysam/pysam-0.14.1/samtools -I/construction/biology/py-pysam/pysam-0.14.1/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.14.1/bcftools -I/construction/biology/py-pysam/pysam-0.14.1/pysam -I/construction/biology/py-pysam/pysam-0.14.1 -I/usr/local/include/python2.7 -c htslib/vcfutils.c -o build/temp.dragonfly-5.2-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 -I/construction/biology/py-pysam/pysam-0.14.1/htslib -I/construction/biology/py-pysam/pysam-0.14.1/samtools -I/construction/biology/py-pysam/pysam-0.14.1/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.14.1/bcftools -I/construction/biology/py-pysam/pysam-0.14.1/pysam -I/construction/biology/py-pysam/pysam-0.14.1 -I/usr/local/include/python2.7 -c htslib/cram/cram_codecs.c -o build/temp.dragonfly-5.2-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 -I/construction/biology/py-pysam/pysam-0.14.1/htslib -I/construction/biology/py-pysam/pysam-0.14.1/samtools -I/construction/biology/py-pysam/pysam-0.14.1/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.14.1/bcftools -I/construction/biology/py-pysam/pysam-0.14.1/pysam -I/construction/biology/py-pysam/pysam-0.14.1 -I/usr/local/include/python2.7 -c htslib/cram/cram_decode.c -o build/temp.dragonfly-5.2-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 -I/construction/biology/py-pysam/pysam-0.14.1/htslib -I/construction/biology/py-pysam/pysam-0.14.1/samtools -I/construction/biology/py-pysam/pysam-0.14.1/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.14.1/bcftools -I/construction/biology/py-pysam/pysam-0.14.1/pysam -I/construction/biology/py-pysam/pysam-0.14.1 -I/usr/local/include/python2.7 -c htslib/cram/cram_encode.c -o build/temp.dragonfly-5.2-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 -I/construction/biology/py-pysam/pysam-0.14.1/htslib -I/construction/biology/py-pysam/pysam-0.14.1/samtools -I/construction/biology/py-pysam/pysam-0.14.1/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.14.1/bcftools -I/construction/biology/py-pysam/pysam-0.14.1/pysam -I/construction/biology/py-pysam/pysam-0.14.1 -I/usr/local/include/python2.7 -c htslib/cram/cram_external.c -o build/temp.dragonfly-5.2-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 -I/construction/biology/py-pysam/pysam-0.14.1/htslib -I/construction/biology/py-pysam/pysam-0.14.1/samtools -I/construction/biology/py-pysam/pysam-0.14.1/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.14.1/bcftools -I/construction/biology/py-pysam/pysam-0.14.1/pysam -I/construction/biology/py-pysam/pysam-0.14.1 -I/usr/local/include/python2.7 -c htslib/cram/cram_index.c -o build/temp.dragonfly-5.2-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 -I/construction/biology/py-pysam/pysam-0.14.1/htslib -I/construction/biology/py-pysam/pysam-0.14.1/samtools -I/construction/biology/py-pysam/pysam-0.14.1/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.14.1/bcftools -I/construction/biology/py-pysam/pysam-0.14.1/pysam -I/construction/biology/py-pysam/pysam-0.14.1 -I/usr/local/include/python2.7 -c htslib/cram/cram_io.c -o build/temp.dragonfly-5.2-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 -I/construction/biology/py-pysam/pysam-0.14.1/htslib -I/construction/biology/py-pysam/pysam-0.14.1/samtools -I/construction/biology/py-pysam/pysam-0.14.1/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.14.1/bcftools -I/construction/biology/py-pysam/pysam-0.14.1/pysam -I/construction/biology/py-pysam/pysam-0.14.1 -I/usr/local/include/python2.7 -c htslib/cram/cram_samtools.c -o build/temp.dragonfly-5.2-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 -I/construction/biology/py-pysam/pysam-0.14.1/htslib -I/construction/biology/py-pysam/pysam-0.14.1/samtools -I/construction/biology/py-pysam/pysam-0.14.1/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.14.1/bcftools -I/construction/biology/py-pysam/pysam-0.14.1/pysam -I/construction/biology/py-pysam/pysam-0.14.1 -I/usr/local/include/python2.7 -c htslib/cram/cram_stats.c -o build/temp.dragonfly-5.2-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 -I/construction/biology/py-pysam/pysam-0.14.1/htslib -I/construction/biology/py-pysam/pysam-0.14.1/samtools -I/construction/biology/py-pysam/pysam-0.14.1/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.14.1/bcftools -I/construction/biology/py-pysam/pysam-0.14.1/pysam -I/construction/biology/py-pysam/pysam-0.14.1 -I/usr/local/include/python2.7 -c htslib/cram/files.c -o build/temp.dragonfly-5.2-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 -I/construction/biology/py-pysam/pysam-0.14.1/htslib -I/construction/biology/py-pysam/pysam-0.14.1/samtools -I/construction/biology/py-pysam/pysam-0.14.1/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.14.1/bcftools -I/construction/biology/py-pysam/pysam-0.14.1/pysam -I/construction/biology/py-pysam/pysam-0.14.1 -I/usr/local/include/python2.7 -c htslib/cram/mFILE.c -o build/temp.dragonfly-5.2-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 -I/construction/biology/py-pysam/pysam-0.14.1/htslib -I/construction/biology/py-pysam/pysam-0.14.1/samtools -I/construction/biology/py-pysam/pysam-0.14.1/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.14.1/bcftools -I/construction/biology/py-pysam/pysam-0.14.1/pysam -I/construction/biology/py-pysam/pysam-0.14.1 -I/usr/local/include/python2.7 -c htslib/cram/open_trace_file.c -o build/temp.dragonfly-5.2-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 -I/construction/biology/py-pysam/pysam-0.14.1/htslib -I/construction/biology/py-pysam/pysam-0.14.1/samtools -I/construction/biology/py-pysam/pysam-0.14.1/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.14.1/bcftools -I/construction/biology/py-pysam/pysam-0.14.1/pysam -I/construction/biology/py-pysam/pysam-0.14.1 -I/usr/local/include/python2.7 -c htslib/cram/pooled_alloc.c -o build/temp.dragonfly-5.2-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 -I/construction/biology/py-pysam/pysam-0.14.1/htslib -I/construction/biology/py-pysam/pysam-0.14.1/samtools -I/construction/biology/py-pysam/pysam-0.14.1/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.14.1/bcftools -I/construction/biology/py-pysam/pysam-0.14.1/pysam -I/construction/biology/py-pysam/pysam-0.14.1 -I/usr/local/include/python2.7 -c htslib/cram/rANS_static.c -o build/temp.dragonfly-5.2-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 -I/construction/biology/py-pysam/pysam-0.14.1/htslib -I/construction/biology/py-pysam/pysam-0.14.1/samtools -I/construction/biology/py-pysam/pysam-0.14.1/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.14.1/bcftools -I/construction/biology/py-pysam/pysam-0.14.1/pysam -I/construction/biology/py-pysam/pysam-0.14.1 -I/usr/local/include/python2.7 -c htslib/cram/sam_header.c -o build/temp.dragonfly-5.2-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 -I/construction/biology/py-pysam/pysam-0.14.1/htslib -I/construction/biology/py-pysam/pysam-0.14.1/samtools -I/construction/biology/py-pysam/pysam-0.14.1/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.14.1/bcftools -I/construction/biology/py-pysam/pysam-0.14.1/pysam -I/construction/biology/py-pysam/pysam-0.14.1 -I/usr/local/include/python2.7 -c htslib/cram/string_alloc.c -o build/temp.dragonfly-5.2-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-5.2-SYNTH-x86_64-2.7/pysam/libchtslib.o build/temp.dragonfly-5.2-SYNTH-x86_64-2.7/pysam/htslib_util.o build/temp.dragonfly-5.2-SYNTH-x86_64-2.7/htslib/kfunc.o build/temp.dragonfly-5.2-SYNTH-x86_64-2.7/htslib/knetfile.o build/temp.dragonfly-5.2-SYNTH-x86_64-2.7/htslib/kstring.o build/temp.dragonfly-5.2-SYNTH-x86_64-2.7/htslib/bcf_sr_sort.o build/temp.dragonfly-5.2-SYNTH-x86_64-2.7/htslib/bgzf.o build/temp.dragonfly-5.2-SYNTH-x86_64-2.7/htslib/errmod.o build/temp.dragonfly-5.2-SYNTH-x86_64-2.7/htslib/faidx.o build/temp.dragonfly-5.2-SYNTH-x86_64-2.7/htslib/hfile.o build/temp.dragonfly-5.2-SYNTH-x86_64-2.7/htslib/hfile_net.o build/temp.dragonfly-5.2-SYNTH-x86_64-2.7/htslib/hts.o build/temp.dragonfly-5.2-SYNTH-x86_64-2.7/htslib/hts_os.o build/temp.dragonfly-5.2-SYNTH-x86_64-2.7/htslib/md5.o build/temp.dragonfly-5.2-SYNTH-x86_64-2.7/htslib/multipart.o build/temp.dragonfly-5.2-SYNTH-x86_64-2.7/htslib/probaln.o build/temp.dragonfly-5.2-SYNTH-x86_64-2.7/htslib/realn.o build/temp.dragonfly-5.2-SYNTH-x86_64-2.7/htslib/regidx.o build/temp.dragonfly-5.2-SYNTH-x86_64-2.7/htslib/sam.o build/temp.dragonfly-5.2-SYNTH-x86_64-2.7/htslib/synced_bcf_reader.o build/temp.dragonfly-5.2-SYNTH-x86_64-2.7/htslib/vcf_sweep.o build/temp.dragonfly-5.2-SYNTH-x86_64-2.7/htslib/tbx.o build/temp.dragonfly-5.2-SYNTH-x86_64-2.7/htslib/textutils.o build/temp.dragonfly-5.2-SYNTH-x86_64-2.7/htslib/thread_pool.o build/temp.dragonfly-5.2-SYNTH-x86_64-2.7/htslib/vcf.o build/temp.dragonfly-5.2-SYNTH-x86_64-2.7/htslib/vcfutils.o build/temp.dragonfly-5.2-SYNTH-x86_64-2.7/htslib/cram/cram_codecs.o build/temp.dragonfly-5.2-SYNTH-x86_64-2.7/htslib/cram/cram_decode.o build/temp.dragonfly-5.2-SYNTH-x86_64-2.7/htslib/cram/cram_encode.o build/temp.dragonfly-5.2-SYNTH-x86_64-2.7/htslib/cram/cram_external.o build/temp.dragonfly-5.2-SYNTH-x86_64-2.7/htslib/cram/cram_index.o build/temp.dragonfly-5.2-SYNTH-x86_64-2.7/htslib/cram/cram_io.o build/temp.dragonfly-5.2-SYNTH-x86_64-2.7/htslib/cram/cram_samtools.o build/temp.dragonfly-5.2-SYNTH-x86_64-2.7/htslib/cram/cram_stats.o build/temp.dragonfly-5.2-SYNTH-x86_64-2.7/htslib/cram/files.o build/temp.dragonfly-5.2-SYNTH-x86_64-2.7/htslib/cram/mFILE.o build/temp.dragonfly-5.2-SYNTH-x86_64-2.7/htslib/cram/open_trace_file.o build/temp.dragonfly-5.2-SYNTH-x86_64-2.7/htslib/cram/pooled_alloc.o build/temp.dragonfly-5.2-SYNTH-x86_64-2.7/htslib/cram/rANS_static.o build/temp.dragonfly-5.2-SYNTH-x86_64-2.7/htslib/cram/sam_header.o build/temp.dragonfly-5.2-SYNTH-x86_64-2.7/htslib/cram/string_alloc.o -L/construction/biology/py-pysam/pysam-0.14.1/pysam -L/construction/biology/py-pysam/pysam-0.14.1/pysam -L/construction/biology/py-pysam/pysam-0.14.1 -L/construction/biology/py-pysam/pysam-0.14.1/build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/pysam -Lbuild/lib.dragonfly-5.2-SYNTH-x86_64-2.7/pysam -L/usr/local/lib -lz -llzma -lbz2 -lz -lm -lpython2.7 -o build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/pysam/libchtslib.so -Wl,-rpath,$ORIGIN skipping 'pysam/libcsamtools.c' Cython extension (up-to-date) building 'pysam.libcsamtools' extension creating build/temp.dragonfly-5.2-SYNTH-x86_64-2.7/samtools creating build/temp.dragonfly-5.2-SYNTH-x86_64-2.7/samtools/lz4 cc -DNDEBUG -pipe -O2 -fno-strict-aliasing -fPIC -I/construction/biology/py-pysam/pysam-0.14.1/htslib -I/construction/biology/py-pysam/pysam-0.14.1/samtools -I/construction/biology/py-pysam/pysam-0.14.1/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.14.1/bcftools -I/construction/biology/py-pysam/pysam-0.14.1/pysam -I/construction/biology/py-pysam/pysam-0.14.1 -I/usr/local/include/python2.7 -c pysam/libcsamtools.c -o build/temp.dragonfly-5.2-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 -I/construction/biology/py-pysam/pysam-0.14.1/htslib -I/construction/biology/py-pysam/pysam-0.14.1/samtools -I/construction/biology/py-pysam/pysam-0.14.1/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.14.1/bcftools -I/construction/biology/py-pysam/pysam-0.14.1/pysam -I/construction/biology/py-pysam/pysam-0.14.1 -I/usr/local/include/python2.7 -c samtools/bam_sort.c.pysam.c -o build/temp.dragonfly-5.2-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 -I/construction/biology/py-pysam/pysam-0.14.1/htslib -I/construction/biology/py-pysam/pysam-0.14.1/samtools -I/construction/biology/py-pysam/pysam-0.14.1/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.14.1/bcftools -I/construction/biology/py-pysam/pysam-0.14.1/pysam -I/construction/biology/py-pysam/pysam-0.14.1 -I/usr/local/include/python2.7 -c samtools/bam_aux.c.pysam.c -o build/temp.dragonfly-5.2-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 -I/construction/biology/py-pysam/pysam-0.14.1/htslib -I/construction/biology/py-pysam/pysam-0.14.1/samtools -I/construction/biology/py-pysam/pysam-0.14.1/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.14.1/bcftools -I/construction/biology/py-pysam/pysam-0.14.1/pysam -I/construction/biology/py-pysam/pysam-0.14.1 -I/usr/local/include/python2.7 -c samtools/tmp_file.c.pysam.c -o build/temp.dragonfly-5.2-SYNTH-x86_64-2.7/samtools/tmp_file.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -DNDEBUG -pipe -O2 -fno-strict-aliasing -fPIC -I/construction/biology/py-pysam/pysam-0.14.1/htslib -I/construction/biology/py-pysam/pysam-0.14.1/samtools -I/construction/biology/py-pysam/pysam-0.14.1/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.14.1/bcftools -I/construction/biology/py-pysam/pysam-0.14.1/pysam -I/construction/biology/py-pysam/pysam-0.14.1 -I/usr/local/include/python2.7 -c samtools/bam_split.c.pysam.c -o build/temp.dragonfly-5.2-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 -I/construction/biology/py-pysam/pysam-0.14.1/htslib -I/construction/biology/py-pysam/pysam-0.14.1/samtools -I/construction/biology/py-pysam/pysam-0.14.1/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.14.1/bcftools -I/construction/biology/py-pysam/pysam-0.14.1/pysam -I/construction/biology/py-pysam/pysam-0.14.1 -I/usr/local/include/python2.7 -c samtools/sam_opts.c.pysam.c -o build/temp.dragonfly-5.2-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 -I/construction/biology/py-pysam/pysam-0.14.1/htslib -I/construction/biology/py-pysam/pysam-0.14.1/samtools -I/construction/biology/py-pysam/pysam-0.14.1/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.14.1/bcftools -I/construction/biology/py-pysam/pysam-0.14.1/pysam -I/construction/biology/py-pysam/pysam-0.14.1 -I/usr/local/include/python2.7 -c samtools/bam2bcf.c.pysam.c -o build/temp.dragonfly-5.2-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 -I/construction/biology/py-pysam/pysam-0.14.1/htslib -I/construction/biology/py-pysam/pysam-0.14.1/samtools -I/construction/biology/py-pysam/pysam-0.14.1/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.14.1/bcftools -I/construction/biology/py-pysam/pysam-0.14.1/pysam -I/construction/biology/py-pysam/pysam-0.14.1 -I/usr/local/include/python2.7 -c samtools/sam_view.c.pysam.c -o build/temp.dragonfly-5.2-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 -I/construction/biology/py-pysam/pysam-0.14.1/htslib -I/construction/biology/py-pysam/pysam-0.14.1/samtools -I/construction/biology/py-pysam/pysam-0.14.1/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.14.1/bcftools -I/construction/biology/py-pysam/pysam-0.14.1/pysam -I/construction/biology/py-pysam/pysam-0.14.1 -I/usr/local/include/python2.7 -c samtools/cut_target.c.pysam.c -o build/temp.dragonfly-5.2-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 -I/construction/biology/py-pysam/pysam-0.14.1/htslib -I/construction/biology/py-pysam/pysam-0.14.1/samtools -I/construction/biology/py-pysam/pysam-0.14.1/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.14.1/bcftools -I/construction/biology/py-pysam/pysam-0.14.1/pysam -I/construction/biology/py-pysam/pysam-0.14.1 -I/usr/local/include/python2.7 -c samtools/sam_header.c.pysam.c -o build/temp.dragonfly-5.2-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 -I/construction/biology/py-pysam/pysam-0.14.1/htslib -I/construction/biology/py-pysam/pysam-0.14.1/samtools -I/construction/biology/py-pysam/pysam-0.14.1/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.14.1/bcftools -I/construction/biology/py-pysam/pysam-0.14.1/pysam -I/construction/biology/py-pysam/pysam-0.14.1 -I/usr/local/include/python2.7 -c samtools/bam_markdup.c.pysam.c -o build/temp.dragonfly-5.2-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 -I/construction/biology/py-pysam/pysam-0.14.1/htslib -I/construction/biology/py-pysam/pysam-0.14.1/samtools -I/construction/biology/py-pysam/pysam-0.14.1/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.14.1/bcftools -I/construction/biology/py-pysam/pysam-0.14.1/pysam -I/construction/biology/py-pysam/pysam-0.14.1 -I/usr/local/include/python2.7 -c samtools/bam_index.c.pysam.c -o build/temp.dragonfly-5.2-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 -I/construction/biology/py-pysam/pysam-0.14.1/htslib -I/construction/biology/py-pysam/pysam-0.14.1/samtools -I/construction/biology/py-pysam/pysam-0.14.1/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.14.1/bcftools -I/construction/biology/py-pysam/pysam-0.14.1/pysam -I/construction/biology/py-pysam/pysam-0.14.1 -I/usr/local/include/python2.7 -c samtools/bam.c.pysam.c -o build/temp.dragonfly-5.2-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 -I/construction/biology/py-pysam/pysam-0.14.1/htslib -I/construction/biology/py-pysam/pysam-0.14.1/samtools -I/construction/biology/py-pysam/pysam-0.14.1/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.14.1/bcftools -I/construction/biology/py-pysam/pysam-0.14.1/pysam -I/construction/biology/py-pysam/pysam-0.14.1 -I/usr/local/include/python2.7 -c samtools/bam_mate.c.pysam.c -o build/temp.dragonfly-5.2-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 -I/construction/biology/py-pysam/pysam-0.14.1/htslib -I/construction/biology/py-pysam/pysam-0.14.1/samtools -I/construction/biology/py-pysam/pysam-0.14.1/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.14.1/bcftools -I/construction/biology/py-pysam/pysam-0.14.1/pysam -I/construction/biology/py-pysam/pysam-0.14.1 -I/usr/local/include/python2.7 -c samtools/bam_plbuf.c.pysam.c -o build/temp.dragonfly-5.2-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 -I/construction/biology/py-pysam/pysam-0.14.1/htslib -I/construction/biology/py-pysam/pysam-0.14.1/samtools -I/construction/biology/py-pysam/pysam-0.14.1/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.14.1/bcftools -I/construction/biology/py-pysam/pysam-0.14.1/pysam -I/construction/biology/py-pysam/pysam-0.14.1 -I/usr/local/include/python2.7 -c samtools/bedidx.c.pysam.c -o build/temp.dragonfly-5.2-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 -I/construction/biology/py-pysam/pysam-0.14.1/htslib -I/construction/biology/py-pysam/pysam-0.14.1/samtools -I/construction/biology/py-pysam/pysam-0.14.1/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.14.1/bcftools -I/construction/biology/py-pysam/pysam-0.14.1/pysam -I/construction/biology/py-pysam/pysam-0.14.1 -I/usr/local/include/python2.7 -c samtools/bam_reheader.c.pysam.c -o build/temp.dragonfly-5.2-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 -I/construction/biology/py-pysam/pysam-0.14.1/htslib -I/construction/biology/py-pysam/pysam-0.14.1/samtools -I/construction/biology/py-pysam/pysam-0.14.1/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.14.1/bcftools -I/construction/biology/py-pysam/pysam-0.14.1/pysam -I/construction/biology/py-pysam/pysam-0.14.1 -I/usr/local/include/python2.7 -c samtools/faidx.c.pysam.c -o build/temp.dragonfly-5.2-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 -I/construction/biology/py-pysam/pysam-0.14.1/htslib -I/construction/biology/py-pysam/pysam-0.14.1/samtools -I/construction/biology/py-pysam/pysam-0.14.1/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.14.1/bcftools -I/construction/biology/py-pysam/pysam-0.14.1/pysam -I/construction/biology/py-pysam/pysam-0.14.1 -I/usr/local/include/python2.7 -c samtools/bam_plcmd.c.pysam.c -o build/temp.dragonfly-5.2-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 -I/construction/biology/py-pysam/pysam-0.14.1/htslib -I/construction/biology/py-pysam/pysam-0.14.1/samtools -I/construction/biology/py-pysam/pysam-0.14.1/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.14.1/bcftools -I/construction/biology/py-pysam/pysam-0.14.1/pysam -I/construction/biology/py-pysam/pysam-0.14.1 -I/usr/local/include/python2.7 -c samtools/bam_addrprg.c.pysam.c -o build/temp.dragonfly-5.2-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 -I/construction/biology/py-pysam/pysam-0.14.1/htslib -I/construction/biology/py-pysam/pysam-0.14.1/samtools -I/construction/biology/py-pysam/pysam-0.14.1/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.14.1/bcftools -I/construction/biology/py-pysam/pysam-0.14.1/pysam -I/construction/biology/py-pysam/pysam-0.14.1 -I/usr/local/include/python2.7 -c samtools/bam_flags.c.pysam.c -o build/temp.dragonfly-5.2-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 -I/construction/biology/py-pysam/pysam-0.14.1/htslib -I/construction/biology/py-pysam/pysam-0.14.1/samtools -I/construction/biology/py-pysam/pysam-0.14.1/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.14.1/bcftools -I/construction/biology/py-pysam/pysam-0.14.1/pysam -I/construction/biology/py-pysam/pysam-0.14.1 -I/usr/local/include/python2.7 -c samtools/sam_utils.c.pysam.c -o build/temp.dragonfly-5.2-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 -I/construction/biology/py-pysam/pysam-0.14.1/htslib -I/construction/biology/py-pysam/pysam-0.14.1/samtools -I/construction/biology/py-pysam/pysam-0.14.1/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.14.1/bcftools -I/construction/biology/py-pysam/pysam-0.14.1/pysam -I/construction/biology/py-pysam/pysam-0.14.1 -I/usr/local/include/python2.7 -c samtools/samtools.pysam.c -o build/temp.dragonfly-5.2-SYNTH-x86_64-2.7/samtools/samtools.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -DNDEBUG -pipe -O2 -fno-strict-aliasing -fPIC -I/construction/biology/py-pysam/pysam-0.14.1/htslib -I/construction/biology/py-pysam/pysam-0.14.1/samtools -I/construction/biology/py-pysam/pysam-0.14.1/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.14.1/bcftools -I/construction/biology/py-pysam/pysam-0.14.1/pysam -I/construction/biology/py-pysam/pysam-0.14.1 -I/usr/local/include/python2.7 -c samtools/bam_stat.c.pysam.c -o build/temp.dragonfly-5.2-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 -I/construction/biology/py-pysam/pysam-0.14.1/htslib -I/construction/biology/py-pysam/pysam-0.14.1/samtools -I/construction/biology/py-pysam/pysam-0.14.1/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.14.1/bcftools -I/construction/biology/py-pysam/pysam-0.14.1/pysam -I/construction/biology/py-pysam/pysam-0.14.1 -I/usr/local/include/python2.7 -c samtools/bam_rmdup.c.pysam.c -o build/temp.dragonfly-5.2-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 -I/construction/biology/py-pysam/pysam-0.14.1/htslib -I/construction/biology/py-pysam/pysam-0.14.1/samtools -I/construction/biology/py-pysam/pysam-0.14.1/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.14.1/bcftools -I/construction/biology/py-pysam/pysam-0.14.1/pysam -I/construction/biology/py-pysam/pysam-0.14.1 -I/usr/local/include/python2.7 -c samtools/bamtk.c.pysam.c -o build/temp.dragonfly-5.2-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 -I/construction/biology/py-pysam/pysam-0.14.1/htslib -I/construction/biology/py-pysam/pysam-0.14.1/samtools -I/construction/biology/py-pysam/pysam-0.14.1/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.14.1/bcftools -I/construction/biology/py-pysam/pysam-0.14.1/pysam -I/construction/biology/py-pysam/pysam-0.14.1 -I/usr/local/include/python2.7 -c samtools/bam_quickcheck.c.pysam.c -o build/temp.dragonfly-5.2-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 -I/construction/biology/py-pysam/pysam-0.14.1/htslib -I/construction/biology/py-pysam/pysam-0.14.1/samtools -I/construction/biology/py-pysam/pysam-0.14.1/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.14.1/bcftools -I/construction/biology/py-pysam/pysam-0.14.1/pysam -I/construction/biology/py-pysam/pysam-0.14.1 -I/usr/local/include/python2.7 -c samtools/phase.c.pysam.c -o build/temp.dragonfly-5.2-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 -I/construction/biology/py-pysam/pysam-0.14.1/htslib -I/construction/biology/py-pysam/pysam-0.14.1/samtools -I/construction/biology/py-pysam/pysam-0.14.1/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.14.1/bcftools -I/construction/biology/py-pysam/pysam-0.14.1/pysam -I/construction/biology/py-pysam/pysam-0.14.1 -I/usr/local/include/python2.7 -c samtools/bam_cat.c.pysam.c -o build/temp.dragonfly-5.2-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 -I/construction/biology/py-pysam/pysam-0.14.1/htslib -I/construction/biology/py-pysam/pysam-0.14.1/samtools -I/construction/biology/py-pysam/pysam-0.14.1/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.14.1/bcftools -I/construction/biology/py-pysam/pysam-0.14.1/pysam -I/construction/biology/py-pysam/pysam-0.14.1 -I/usr/local/include/python2.7 -c samtools/bam2depth.c.pysam.c -o build/temp.dragonfly-5.2-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 -I/construction/biology/py-pysam/pysam-0.14.1/htslib -I/construction/biology/py-pysam/pysam-0.14.1/samtools -I/construction/biology/py-pysam/pysam-0.14.1/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.14.1/bcftools -I/construction/biology/py-pysam/pysam-0.14.1/pysam -I/construction/biology/py-pysam/pysam-0.14.1 -I/usr/local/include/python2.7 -c samtools/sample.c.pysam.c -o build/temp.dragonfly-5.2-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 -I/construction/biology/py-pysam/pysam-0.14.1/htslib -I/construction/biology/py-pysam/pysam-0.14.1/samtools -I/construction/biology/py-pysam/pysam-0.14.1/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.14.1/bcftools -I/construction/biology/py-pysam/pysam-0.14.1/pysam -I/construction/biology/py-pysam/pysam-0.14.1 -I/usr/local/include/python2.7 -c samtools/bam_md.c.pysam.c -o build/temp.dragonfly-5.2-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 -I/construction/biology/py-pysam/pysam-0.14.1/htslib -I/construction/biology/py-pysam/pysam-0.14.1/samtools -I/construction/biology/py-pysam/pysam-0.14.1/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.14.1/bcftools -I/construction/biology/py-pysam/pysam-0.14.1/pysam -I/construction/biology/py-pysam/pysam-0.14.1 -I/usr/local/include/python2.7 -c samtools/bedcov.c.pysam.c -o build/temp.dragonfly-5.2-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 -I/construction/biology/py-pysam/pysam-0.14.1/htslib -I/construction/biology/py-pysam/pysam-0.14.1/samtools -I/construction/biology/py-pysam/pysam-0.14.1/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.14.1/bcftools -I/construction/biology/py-pysam/pysam-0.14.1/pysam -I/construction/biology/py-pysam/pysam-0.14.1 -I/usr/local/include/python2.7 -c samtools/bam_rmdupse.c.pysam.c -o build/temp.dragonfly-5.2-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 -I/construction/biology/py-pysam/pysam-0.14.1/htslib -I/construction/biology/py-pysam/pysam-0.14.1/samtools -I/construction/biology/py-pysam/pysam-0.14.1/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.14.1/bcftools -I/construction/biology/py-pysam/pysam-0.14.1/pysam -I/construction/biology/py-pysam/pysam-0.14.1 -I/usr/local/include/python2.7 -c samtools/bam_lpileup.c.pysam.c -o build/temp.dragonfly-5.2-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 -I/construction/biology/py-pysam/pysam-0.14.1/htslib -I/construction/biology/py-pysam/pysam-0.14.1/samtools -I/construction/biology/py-pysam/pysam-0.14.1/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.14.1/bcftools -I/construction/biology/py-pysam/pysam-0.14.1/pysam -I/construction/biology/py-pysam/pysam-0.14.1 -I/usr/local/include/python2.7 -c samtools/stats_isize.c.pysam.c -o build/temp.dragonfly-5.2-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 -DNDEBUG -pipe -O2 -fno-strict-aliasing -fPIC -I/construction/biology/py-pysam/pysam-0.14.1/htslib -I/construction/biology/py-pysam/pysam-0.14.1/samtools -I/construction/biology/py-pysam/pysam-0.14.1/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.14.1/bcftools -I/construction/biology/py-pysam/pysam-0.14.1/pysam -I/construction/biology/py-pysam/pysam-0.14.1 -I/usr/local/include/python2.7 -c samtools/bamshuf.c.pysam.c -o build/temp.dragonfly-5.2-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 -I/construction/biology/py-pysam/pysam-0.14.1/htslib -I/construction/biology/py-pysam/pysam-0.14.1/samtools -I/construction/biology/py-pysam/pysam-0.14.1/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.14.1/bcftools -I/construction/biology/py-pysam/pysam-0.14.1/pysam -I/construction/biology/py-pysam/pysam-0.14.1 -I/usr/local/include/python2.7 -c samtools/bam_import.c.pysam.c -o build/temp.dragonfly-5.2-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 -I/construction/biology/py-pysam/pysam-0.14.1/htslib -I/construction/biology/py-pysam/pysam-0.14.1/samtools -I/construction/biology/py-pysam/pysam-0.14.1/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.14.1/bcftools -I/construction/biology/py-pysam/pysam-0.14.1/pysam -I/construction/biology/py-pysam/pysam-0.14.1 -I/usr/local/include/python2.7 -c samtools/padding.c.pysam.c -o build/temp.dragonfly-5.2-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 -I/construction/biology/py-pysam/pysam-0.14.1/htslib -I/construction/biology/py-pysam/pysam-0.14.1/samtools -I/construction/biology/py-pysam/pysam-0.14.1/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.14.1/bcftools -I/construction/biology/py-pysam/pysam-0.14.1/pysam -I/construction/biology/py-pysam/pysam-0.14.1 -I/usr/local/include/python2.7 -c samtools/sam.c.pysam.c -o build/temp.dragonfly-5.2-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 -I/construction/biology/py-pysam/pysam-0.14.1/htslib -I/construction/biology/py-pysam/pysam-0.14.1/samtools -I/construction/biology/py-pysam/pysam-0.14.1/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.14.1/bcftools -I/construction/biology/py-pysam/pysam-0.14.1/pysam -I/construction/biology/py-pysam/pysam-0.14.1 -I/usr/local/include/python2.7 -c samtools/stats.c.pysam.c -o build/temp.dragonfly-5.2-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 -I/construction/biology/py-pysam/pysam-0.14.1/htslib -I/construction/biology/py-pysam/pysam-0.14.1/samtools -I/construction/biology/py-pysam/pysam-0.14.1/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.14.1/bcftools -I/construction/biology/py-pysam/pysam-0.14.1/pysam -I/construction/biology/py-pysam/pysam-0.14.1 -I/usr/local/include/python2.7 -c samtools/dict.c.pysam.c -o build/temp.dragonfly-5.2-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 -I/construction/biology/py-pysam/pysam-0.14.1/htslib -I/construction/biology/py-pysam/pysam-0.14.1/samtools -I/construction/biology/py-pysam/pysam-0.14.1/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.14.1/bcftools -I/construction/biology/py-pysam/pysam-0.14.1/pysam -I/construction/biology/py-pysam/pysam-0.14.1 -I/usr/local/include/python2.7 -c samtools/bam2bcf_indel.c.pysam.c -o build/temp.dragonfly-5.2-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 -I/construction/biology/py-pysam/pysam-0.14.1/htslib -I/construction/biology/py-pysam/pysam-0.14.1/samtools -I/construction/biology/py-pysam/pysam-0.14.1/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.14.1/bcftools -I/construction/biology/py-pysam/pysam-0.14.1/pysam -I/construction/biology/py-pysam/pysam-0.14.1 -I/usr/local/include/python2.7 -c samtools/bam_color.c.pysam.c -o build/temp.dragonfly-5.2-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 -I/construction/biology/py-pysam/pysam-0.14.1/htslib -I/construction/biology/py-pysam/pysam-0.14.1/samtools -I/construction/biology/py-pysam/pysam-0.14.1/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.14.1/bcftools -I/construction/biology/py-pysam/pysam-0.14.1/pysam -I/construction/biology/py-pysam/pysam-0.14.1 -I/usr/local/include/python2.7 -c samtools/lz4/lz4.c -o build/temp.dragonfly-5.2-SYNTH-x86_64-2.7/samtools/lz4/lz4.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -shared -pipe -O2 -fno-strict-aliasing build/temp.dragonfly-5.2-SYNTH-x86_64-2.7/pysam/libcsamtools.o build/temp.dragonfly-5.2-SYNTH-x86_64-2.7/samtools/bam_sort.c.pysam.o build/temp.dragonfly-5.2-SYNTH-x86_64-2.7/samtools/bam_aux.c.pysam.o build/temp.dragonfly-5.2-SYNTH-x86_64-2.7/samtools/tmp_file.c.pysam.o build/temp.dragonfly-5.2-SYNTH-x86_64-2.7/samtools/bam_split.c.pysam.o build/temp.dragonfly-5.2-SYNTH-x86_64-2.7/samtools/sam_opts.c.pysam.o build/temp.dragonfly-5.2-SYNTH-x86_64-2.7/samtools/bam2bcf.c.pysam.o build/temp.dragonfly-5.2-SYNTH-x86_64-2.7/samtools/sam_view.c.pysam.o build/temp.dragonfly-5.2-SYNTH-x86_64-2.7/samtools/cut_target.c.pysam.o build/temp.dragonfly-5.2-SYNTH-x86_64-2.7/samtools/sam_header.c.pysam.o build/temp.dragonfly-5.2-SYNTH-x86_64-2.7/samtools/bam_markdup.c.pysam.o build/temp.dragonfly-5.2-SYNTH-x86_64-2.7/samtools/bam_index.c.pysam.o build/temp.dragonfly-5.2-SYNTH-x86_64-2.7/samtools/bam.c.pysam.o build/temp.dragonfly-5.2-SYNTH-x86_64-2.7/samtools/bam_mate.c.pysam.o build/temp.dragonfly-5.2-SYNTH-x86_64-2.7/samtools/bam_plbuf.c.pysam.o build/temp.dragonfly-5.2-SYNTH-x86_64-2.7/samtools/bedidx.c.pysam.o build/temp.dragonfly-5.2-SYNTH-x86_64-2.7/samtools/bam_reheader.c.pysam.o build/temp.dragonfly-5.2-SYNTH-x86_64-2.7/samtools/faidx.c.pysam.o build/temp.dragonfly-5.2-SYNTH-x86_64-2.7/samtools/bam_plcmd.c.pysam.o build/temp.dragonfly-5.2-SYNTH-x86_64-2.7/samtools/bam_addrprg.c.pysam.o build/temp.dragonfly-5.2-SYNTH-x86_64-2.7/samtools/bam_flags.c.pysam.o build/temp.dragonfly-5.2-SYNTH-x86_64-2.7/samtools/sam_utils.c.pysam.o build/temp.dragonfly-5.2-SYNTH-x86_64-2.7/samtools/samtools.pysam.o build/temp.dragonfly-5.2-SYNTH-x86_64-2.7/samtools/bam_stat.c.pysam.o build/temp.dragonfly-5.2-SYNTH-x86_64-2.7/samtools/bam_rmdup.c.pysam.o build/temp.dragonfly-5.2-SYNTH-x86_64-2.7/samtools/bamtk.c.pysam.o build/temp.dragonfly-5.2-SYNTH-x86_64-2.7/samtools/bam_quickcheck.c.pysam.o build/temp.dragonfly-5.2-SYNTH-x86_64-2.7/samtools/phase.c.pysam.o build/temp.dragonfly-5.2-SYNTH-x86_64-2.7/samtools/bam_cat.c.pysam.o build/temp.dragonfly-5.2-SYNTH-x86_64-2.7/samtools/bam2depth.c.pysam.o build/temp.dragonfly-5.2-SYNTH-x86_64-2.7/samtools/sample.c.pysam.o build/temp.dragonfly-5.2-SYNTH-x86_64-2.7/samtools/bam_md.c.pysam.o build/temp.dragonfly-5.2-SYNTH-x86_64-2.7/samtools/bedcov.c.pysam.o build/temp.dragonfly-5.2-SYNTH-x86_64-2.7/samtools/bam_rmdupse.c.pysam.o build/temp.dragonfly-5.2-SYNTH-x86_64-2.7/samtools/bam_lpileup.c.pysam.o build/temp.dragonfly-5.2-SYNTH-x86_64-2.7/samtools/stats_isize.c.pysam.o build/temp.dragonfly-5.2-SYNTH-x86_64-2.7/samtools/bamshuf.c.pysam.o build/temp.dragonfly-5.2-SYNTH-x86_64-2.7/samtools/bam_import.c.pysam.o build/temp.dragonfly-5.2-SYNTH-x86_64-2.7/samtools/padding.c.pysam.o build/temp.dragonfly-5.2-SYNTH-x86_64-2.7/samtools/sam.c.pysam.o build/temp.dragonfly-5.2-SYNTH-x86_64-2.7/samtools/stats.c.pysam.o build/temp.dragonfly-5.2-SYNTH-x86_64-2.7/samtools/dict.c.pysam.o build/temp.dragonfly-5.2-SYNTH-x86_64-2.7/samtools/bam2bcf_indel.c.pysam.o build/temp.dragonfly-5.2-SYNTH-x86_64-2.7/samtools/bam_color.c.pysam.o build/temp.dragonfly-5.2-SYNTH-x86_64-2.7/samtools/lz4/lz4.o -L/construction/biology/py-pysam/pysam-0.14.1/pysam -L/construction/biology/py-pysam/pysam-0.14.1/pysam -L/construction/biology/py-pysam/pysam-0.14.1 -L/construction/biology/py-pysam/pysam-0.14.1/build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/pysam -Lbuild/lib.dragonfly-5.2-SYNTH-x86_64-2.7/pysam -Lbuild/lib.dragonfly-5.2-SYNTH-x86_64-2.7/pysam -L/usr/local/lib -lz -llzma -lbz2 -lz -lm -lchtslib -lpython2.7 -o build/lib.dragonfly-5.2-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-5.2-SYNTH-x86_64-2.7/bcftools cc -DNDEBUG -pipe -O2 -fno-strict-aliasing -fPIC -I/construction/biology/py-pysam/pysam-0.14.1/htslib -I/construction/biology/py-pysam/pysam-0.14.1/samtools -I/construction/biology/py-pysam/pysam-0.14.1/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.14.1/bcftools -I/construction/biology/py-pysam/pysam-0.14.1/pysam -I/construction/biology/py-pysam/pysam-0.14.1 -I/usr/local/include/python2.7 -c pysam/libcbcftools.c -o build/temp.dragonfly-5.2-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 -I/construction/biology/py-pysam/pysam-0.14.1/htslib -I/construction/biology/py-pysam/pysam-0.14.1/samtools -I/construction/biology/py-pysam/pysam-0.14.1/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.14.1/bcftools -I/construction/biology/py-pysam/pysam-0.14.1/pysam -I/construction/biology/py-pysam/pysam-0.14.1 -I/usr/local/include/python2.7 -c bcftools/vcfisec.c.pysam.c -o build/temp.dragonfly-5.2-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 -I/construction/biology/py-pysam/pysam-0.14.1/htslib -I/construction/biology/py-pysam/pysam-0.14.1/samtools -I/construction/biology/py-pysam/pysam-0.14.1/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.14.1/bcftools -I/construction/biology/py-pysam/pysam-0.14.1/pysam -I/construction/biology/py-pysam/pysam-0.14.1 -I/usr/local/include/python2.7 -c bcftools/vcfplugin.c.pysam.c -o build/temp.dragonfly-5.2-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 -I/construction/biology/py-pysam/pysam-0.14.1/htslib -I/construction/biology/py-pysam/pysam-0.14.1/samtools -I/construction/biology/py-pysam/pysam-0.14.1/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.14.1/bcftools -I/construction/biology/py-pysam/pysam-0.14.1/pysam -I/construction/biology/py-pysam/pysam-0.14.1 -I/usr/local/include/python2.7 -c bcftools/vcfstats.c.pysam.c -o build/temp.dragonfly-5.2-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 -I/construction/biology/py-pysam/pysam-0.14.1/htslib -I/construction/biology/py-pysam/pysam-0.14.1/samtools -I/construction/biology/py-pysam/pysam-0.14.1/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.14.1/bcftools -I/construction/biology/py-pysam/pysam-0.14.1/pysam -I/construction/biology/py-pysam/pysam-0.14.1 -I/usr/local/include/python2.7 -c bcftools/HMM.c.pysam.c -o build/temp.dragonfly-5.2-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 -I/construction/biology/py-pysam/pysam-0.14.1/htslib -I/construction/biology/py-pysam/pysam-0.14.1/samtools -I/construction/biology/py-pysam/pysam-0.14.1/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.14.1/bcftools -I/construction/biology/py-pysam/pysam-0.14.1/pysam -I/construction/biology/py-pysam/pysam-0.14.1 -I/usr/local/include/python2.7 -c bcftools/vcfconvert.c.pysam.c -o build/temp.dragonfly-5.2-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 -I/construction/biology/py-pysam/pysam-0.14.1/htslib -I/construction/biology/py-pysam/pysam-0.14.1/samtools -I/construction/biology/py-pysam/pysam-0.14.1/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.14.1/bcftools -I/construction/biology/py-pysam/pysam-0.14.1/pysam -I/construction/biology/py-pysam/pysam-0.14.1 -I/usr/local/include/python2.7 -c bcftools/ploidy.c.pysam.c -o build/temp.dragonfly-5.2-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 -I/construction/biology/py-pysam/pysam-0.14.1/htslib -I/construction/biology/py-pysam/pysam-0.14.1/samtools -I/construction/biology/py-pysam/pysam-0.14.1/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.14.1/bcftools -I/construction/biology/py-pysam/pysam-0.14.1/pysam -I/construction/biology/py-pysam/pysam-0.14.1 -I/usr/local/include/python2.7 -c bcftools/vcfcnv.c.pysam.c -o build/temp.dragonfly-5.2-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 -I/construction/biology/py-pysam/pysam-0.14.1/htslib -I/construction/biology/py-pysam/pysam-0.14.1/samtools -I/construction/biology/py-pysam/pysam-0.14.1/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.14.1/bcftools -I/construction/biology/py-pysam/pysam-0.14.1/pysam -I/construction/biology/py-pysam/pysam-0.14.1 -I/usr/local/include/python2.7 -c bcftools/vcfbuf.c.pysam.c -o build/temp.dragonfly-5.2-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 -I/construction/biology/py-pysam/pysam-0.14.1/htslib -I/construction/biology/py-pysam/pysam-0.14.1/samtools -I/construction/biology/py-pysam/pysam-0.14.1/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.14.1/bcftools -I/construction/biology/py-pysam/pysam-0.14.1/pysam -I/construction/biology/py-pysam/pysam-0.14.1 -I/usr/local/include/python2.7 -c bcftools/gvcf.c.pysam.c -o build/temp.dragonfly-5.2-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 -I/construction/biology/py-pysam/pysam-0.14.1/htslib -I/construction/biology/py-pysam/pysam-0.14.1/samtools -I/construction/biology/py-pysam/pysam-0.14.1/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.14.1/bcftools -I/construction/biology/py-pysam/pysam-0.14.1/pysam -I/construction/biology/py-pysam/pysam-0.14.1 -I/usr/local/include/python2.7 -c bcftools/vcfannotate.c.pysam.c -o build/temp.dragonfly-5.2-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 -I/construction/biology/py-pysam/pysam-0.14.1/htslib -I/construction/biology/py-pysam/pysam-0.14.1/samtools -I/construction/biology/py-pysam/pysam-0.14.1/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.14.1/bcftools -I/construction/biology/py-pysam/pysam-0.14.1/pysam -I/construction/biology/py-pysam/pysam-0.14.1 -I/usr/local/include/python2.7 -c bcftools/bcftools.pysam.c -o build/temp.dragonfly-5.2-SYNTH-x86_64-2.7/bcftools/bcftools.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -DNDEBUG -pipe -O2 -fno-strict-aliasing -fPIC -I/construction/biology/py-pysam/pysam-0.14.1/htslib -I/construction/biology/py-pysam/pysam-0.14.1/samtools -I/construction/biology/py-pysam/pysam-0.14.1/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.14.1/bcftools -I/construction/biology/py-pysam/pysam-0.14.1/pysam -I/construction/biology/py-pysam/pysam-0.14.1 -I/usr/local/include/python2.7 -c bcftools/vcfview.c.pysam.c -o build/temp.dragonfly-5.2-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 -I/construction/biology/py-pysam/pysam-0.14.1/htslib -I/construction/biology/py-pysam/pysam-0.14.1/samtools -I/construction/biology/py-pysam/pysam-0.14.1/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.14.1/bcftools -I/construction/biology/py-pysam/pysam-0.14.1/pysam -I/construction/biology/py-pysam/pysam-0.14.1 -I/usr/local/include/python2.7 -c bcftools/vcfcall.c.pysam.c -o build/temp.dragonfly-5.2-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 -I/construction/biology/py-pysam/pysam-0.14.1/htslib -I/construction/biology/py-pysam/pysam-0.14.1/samtools -I/construction/biology/py-pysam/pysam-0.14.1/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.14.1/bcftools -I/construction/biology/py-pysam/pysam-0.14.1/pysam -I/construction/biology/py-pysam/pysam-0.14.1 -I/usr/local/include/python2.7 -c bcftools/smpl_ilist.c.pysam.c -o build/temp.dragonfly-5.2-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 -I/construction/biology/py-pysam/pysam-0.14.1/htslib -I/construction/biology/py-pysam/pysam-0.14.1/samtools -I/construction/biology/py-pysam/pysam-0.14.1/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.14.1/bcftools -I/construction/biology/py-pysam/pysam-0.14.1/pysam -I/construction/biology/py-pysam/pysam-0.14.1 -I/usr/local/include/python2.7 -c bcftools/main.c.pysam.c -o build/temp.dragonfly-5.2-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 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bcftools/tabix.c.pysam.c -o build/temp.dragonfly-5.2-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 -I/construction/biology/py-pysam/pysam-0.14.1/htslib -I/construction/biology/py-pysam/pysam-0.14.1/samtools -I/construction/biology/py-pysam/pysam-0.14.1/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.14.1/bcftools -I/construction/biology/py-pysam/pysam-0.14.1/pysam -I/construction/biology/py-pysam/pysam-0.14.1 -I/usr/local/include/python2.7 -c bcftools/convert.c.pysam.c -o build/temp.dragonfly-5.2-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 -I/construction/biology/py-pysam/pysam-0.14.1/htslib -I/construction/biology/py-pysam/pysam-0.14.1/samtools -I/construction/biology/py-pysam/pysam-0.14.1/samtools/lz4 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bcftools/bam2bcf_indel.c.pysam.c -o build/temp.dragonfly-5.2-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 -I/construction/biology/py-pysam/pysam-0.14.1/htslib -I/construction/biology/py-pysam/pysam-0.14.1/samtools -I/construction/biology/py-pysam/pysam-0.14.1/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.14.1/bcftools -I/construction/biology/py-pysam/pysam-0.14.1/pysam -I/construction/biology/py-pysam/pysam-0.14.1 -I/usr/local/include/python2.7 -c bcftools/bam_sample.c.pysam.c -o build/temp.dragonfly-5.2-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 -I/construction/biology/py-pysam/pysam-0.14.1/htslib -I/construction/biology/py-pysam/pysam-0.14.1/samtools 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-Wno-error=declaration-after-statement cc -DNDEBUG -pipe -O2 -fno-strict-aliasing -fPIC -I/construction/biology/py-pysam/pysam-0.14.1/htslib -I/construction/biology/py-pysam/pysam-0.14.1/samtools -I/construction/biology/py-pysam/pysam-0.14.1/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.14.1/bcftools -I/construction/biology/py-pysam/pysam-0.14.1/pysam -I/construction/biology/py-pysam/pysam-0.14.1 -I/usr/local/include/python2.7 -c bcftools/vcfroh.c.pysam.c -o build/temp.dragonfly-5.2-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 -I/construction/biology/py-pysam/pysam-0.14.1/htslib -I/construction/biology/py-pysam/pysam-0.14.1/samtools -I/construction/biology/py-pysam/pysam-0.14.1/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.14.1/bcftools -I/construction/biology/py-pysam/pysam-0.14.1/pysam -I/construction/biology/py-pysam/pysam-0.14.1 -I/usr/local/include/python2.7 -c bcftools/vcfmerge.c.pysam.c -o build/temp.dragonfly-5.2-SYNTH-x86_64-2.7/bcftools/vcfmerge.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -DNDEBUG -pipe -O2 -fno-strict-aliasing -fPIC -I/construction/biology/py-pysam/pysam-0.14.1/htslib -I/construction/biology/py-pysam/pysam-0.14.1/samtools -I/construction/biology/py-pysam/pysam-0.14.1/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.14.1/bcftools -I/construction/biology/py-pysam/pysam-0.14.1/pysam -I/construction/biology/py-pysam/pysam-0.14.1 -I/usr/local/include/python2.7 -c bcftools/vcfgtcheck.c.pysam.c -o build/temp.dragonfly-5.2-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 -I/construction/biology/py-pysam/pysam-0.14.1/htslib -I/construction/biology/py-pysam/pysam-0.14.1/samtools 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-Wno-error=declaration-after-statement cc -DNDEBUG -pipe -O2 -fno-strict-aliasing -fPIC -I/construction/biology/py-pysam/pysam-0.14.1/htslib -I/construction/biology/py-pysam/pysam-0.14.1/samtools -I/construction/biology/py-pysam/pysam-0.14.1/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.14.1/bcftools -I/construction/biology/py-pysam/pysam-0.14.1/pysam -I/construction/biology/py-pysam/pysam-0.14.1 -I/usr/local/include/python2.7 -c bcftools/filter.c.pysam.c -o build/temp.dragonfly-5.2-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 -I/construction/biology/py-pysam/pysam-0.14.1/htslib -I/construction/biology/py-pysam/pysam-0.14.1/samtools -I/construction/biology/py-pysam/pysam-0.14.1/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.14.1/bcftools -I/construction/biology/py-pysam/pysam-0.14.1/pysam -I/construction/biology/py-pysam/pysam-0.14.1 -I/usr/local/include/python2.7 -c bcftools/vcfconcat.c.pysam.c -o build/temp.dragonfly-5.2-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 -I/construction/biology/py-pysam/pysam-0.14.1/htslib -I/construction/biology/py-pysam/pysam-0.14.1/samtools -I/construction/biology/py-pysam/pysam-0.14.1/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.14.1/bcftools -I/construction/biology/py-pysam/pysam-0.14.1/pysam -I/construction/biology/py-pysam/pysam-0.14.1 -I/usr/local/include/python2.7 -c bcftools/bam2bcf.c.pysam.c -o build/temp.dragonfly-5.2-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 -I/construction/biology/py-pysam/pysam-0.14.1/htslib -I/construction/biology/py-pysam/pysam-0.14.1/samtools -I/construction/biology/py-pysam/pysam-0.14.1/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.14.1/bcftools -I/construction/biology/py-pysam/pysam-0.14.1/pysam -I/construction/biology/py-pysam/pysam-0.14.1 -I/usr/local/include/python2.7 -c bcftools/em.c.pysam.c -o build/temp.dragonfly-5.2-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 -I/construction/biology/py-pysam/pysam-0.14.1/htslib -I/construction/biology/py-pysam/pysam-0.14.1/samtools -I/construction/biology/py-pysam/pysam-0.14.1/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.14.1/bcftools -I/construction/biology/py-pysam/pysam-0.14.1/pysam -I/construction/biology/py-pysam/pysam-0.14.1 -I/usr/local/include/python2.7 -c bcftools/hclust.c.pysam.c -o build/temp.dragonfly-5.2-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 -I/construction/biology/py-pysam/pysam-0.14.1/htslib -I/construction/biology/py-pysam/pysam-0.14.1/samtools -I/construction/biology/py-pysam/pysam-0.14.1/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.14.1/bcftools -I/construction/biology/py-pysam/pysam-0.14.1/pysam -I/construction/biology/py-pysam/pysam-0.14.1 -I/usr/local/include/python2.7 -c bcftools/consensus.c.pysam.c -o build/temp.dragonfly-5.2-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 -I/construction/biology/py-pysam/pysam-0.14.1/htslib -I/construction/biology/py-pysam/pysam-0.14.1/samtools -I/construction/biology/py-pysam/pysam-0.14.1/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.14.1/bcftools -I/construction/biology/py-pysam/pysam-0.14.1/pysam -I/construction/biology/py-pysam/pysam-0.14.1 -I/usr/local/include/python2.7 -c bcftools/ccall.c.pysam.c -o build/temp.dragonfly-5.2-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 -I/construction/biology/py-pysam/pysam-0.14.1/htslib -I/construction/biology/py-pysam/pysam-0.14.1/samtools -I/construction/biology/py-pysam/pysam-0.14.1/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.14.1/bcftools -I/construction/biology/py-pysam/pysam-0.14.1/pysam -I/construction/biology/py-pysam/pysam-0.14.1 -I/usr/local/include/python2.7 -c bcftools/regidx.c.pysam.c -o build/temp.dragonfly-5.2-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 -I/construction/biology/py-pysam/pysam-0.14.1/htslib -I/construction/biology/py-pysam/pysam-0.14.1/samtools -I/construction/biology/py-pysam/pysam-0.14.1/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.14.1/bcftools -I/construction/biology/py-pysam/pysam-0.14.1/pysam -I/construction/biology/py-pysam/pysam-0.14.1 -I/usr/local/include/python2.7 -c bcftools/bin.c.pysam.c -o build/temp.dragonfly-5.2-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 -I/construction/biology/py-pysam/pysam-0.14.1/htslib -I/construction/biology/py-pysam/pysam-0.14.1/samtools -I/construction/biology/py-pysam/pysam-0.14.1/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.14.1/bcftools -I/construction/biology/py-pysam/pysam-0.14.1/pysam -I/construction/biology/py-pysam/pysam-0.14.1 -I/usr/local/include/python2.7 -c bcftools/vcfsort.c.pysam.c -o build/temp.dragonfly-5.2-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 -I/construction/biology/py-pysam/pysam-0.14.1/htslib -I/construction/biology/py-pysam/pysam-0.14.1/samtools -I/construction/biology/py-pysam/pysam-0.14.1/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.14.1/bcftools -I/construction/biology/py-pysam/pysam-0.14.1/pysam -I/construction/biology/py-pysam/pysam-0.14.1 -I/usr/local/include/python2.7 -c bcftools/csq.c.pysam.c -o build/temp.dragonfly-5.2-SYNTH-x86_64-2.7/bcftools/csq.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-5.2-SYNTH-x86_64-2.7/pysam/libcbcftools.o build/temp.dragonfly-5.2-SYNTH-x86_64-2.7/bcftools/vcfisec.c.pysam.o build/temp.dragonfly-5.2-SYNTH-x86_64-2.7/bcftools/vcfplugin.c.pysam.o build/temp.dragonfly-5.2-SYNTH-x86_64-2.7/bcftools/vcfstats.c.pysam.o build/temp.dragonfly-5.2-SYNTH-x86_64-2.7/bcftools/HMM.c.pysam.o build/temp.dragonfly-5.2-SYNTH-x86_64-2.7/bcftools/vcfconvert.c.pysam.o build/temp.dragonfly-5.2-SYNTH-x86_64-2.7/bcftools/ploidy.c.pysam.o build/temp.dragonfly-5.2-SYNTH-x86_64-2.7/bcftools/vcfcnv.c.pysam.o build/temp.dragonfly-5.2-SYNTH-x86_64-2.7/bcftools/vcfbuf.c.pysam.o build/temp.dragonfly-5.2-SYNTH-x86_64-2.7/bcftools/gvcf.c.pysam.o build/temp.dragonfly-5.2-SYNTH-x86_64-2.7/bcftools/vcfannotate.c.pysam.o build/temp.dragonfly-5.2-SYNTH-x86_64-2.7/bcftools/bcftools.pysam.o build/temp.dragonfly-5.2-SYNTH-x86_64-2.7/bcftools/vcfview.c.pysam.o build/temp.dragonfly-5.2-SYNTH-x86_64-2.7/bcftools/vcfcall.c.pysam.o build/temp.dragonfly-5.2-SYNTH-x86_64-2.7/bcftools/smpl_ilist.c.pysam.o build/temp.dragonfly-5.2-SYNTH-x86_64-2.7/bcftools/main.c.pysam.o build/temp.dragonfly-5.2-SYNTH-x86_64-2.7/bcftools/tsv2vcf.c.pysam.o build/temp.dragonfly-5.2-SYNTH-x86_64-2.7/bcftools/mpileup.c.pysam.o build/temp.dragonfly-5.2-SYNTH-x86_64-2.7/bcftools/mcall.c.pysam.o build/temp.dragonfly-5.2-SYNTH-x86_64-2.7/bcftools/vcfsom.c.pysam.o build/temp.dragonfly-5.2-SYNTH-x86_64-2.7/bcftools/prob1.c.pysam.o build/temp.dragonfly-5.2-SYNTH-x86_64-2.7/bcftools/vcfindex.c.pysam.o build/temp.dragonfly-5.2-SYNTH-x86_64-2.7/bcftools/tabix.c.pysam.o build/temp.dragonfly-5.2-SYNTH-x86_64-2.7/bcftools/convert.c.pysam.o build/temp.dragonfly-5.2-SYNTH-x86_64-2.7/bcftools/kmin.c.pysam.o build/temp.dragonfly-5.2-SYNTH-x86_64-2.7/bcftools/version.c.pysam.o build/temp.dragonfly-5.2-SYNTH-x86_64-2.7/bcftools/vcffilter.c.pysam.o build/temp.dragonfly-5.2-SYNTH-x86_64-2.7/bcftools/bam2bcf_indel.c.pysam.o build/temp.dragonfly-5.2-SYNTH-x86_64-2.7/bcftools/bam_sample.c.pysam.o build/temp.dragonfly-5.2-SYNTH-x86_64-2.7/bcftools/reheader.c.pysam.o build/temp.dragonfly-5.2-SYNTH-x86_64-2.7/bcftools/vcmp.c.pysam.o build/temp.dragonfly-5.2-SYNTH-x86_64-2.7/bcftools/vcfroh.c.pysam.o build/temp.dragonfly-5.2-SYNTH-x86_64-2.7/bcftools/vcfmerge.c.pysam.o build/temp.dragonfly-5.2-SYNTH-x86_64-2.7/bcftools/vcfgtcheck.c.pysam.o build/temp.dragonfly-5.2-SYNTH-x86_64-2.7/bcftools/vcfquery.c.pysam.o build/temp.dragonfly-5.2-SYNTH-x86_64-2.7/bcftools/vcfnorm.c.pysam.o build/temp.dragonfly-5.2-SYNTH-x86_64-2.7/bcftools/filter.c.pysam.o build/temp.dragonfly-5.2-SYNTH-x86_64-2.7/bcftools/vcfconcat.c.pysam.o build/temp.dragonfly-5.2-SYNTH-x86_64-2.7/bcftools/bam2bcf.c.pysam.o build/temp.dragonfly-5.2-SYNTH-x86_64-2.7/bcftools/em.c.pysam.o build/temp.dragonfly-5.2-SYNTH-x86_64-2.7/bcftools/hclust.c.pysam.o build/temp.dragonfly-5.2-SYNTH-x86_64-2.7/bcftools/consensus.c.pysam.o build/temp.dragonfly-5.2-SYNTH-x86_64-2.7/bcftools/ccall.c.pysam.o build/temp.dragonfly-5.2-SYNTH-x86_64-2.7/bcftools/regidx.c.pysam.o build/temp.dragonfly-5.2-SYNTH-x86_64-2.7/bcftools/bin.c.pysam.o build/temp.dragonfly-5.2-SYNTH-x86_64-2.7/bcftools/vcfsort.c.pysam.o build/temp.dragonfly-5.2-SYNTH-x86_64-2.7/bcftools/csq.c.pysam.o -L/construction/biology/py-pysam/pysam-0.14.1/pysam -L/construction/biology/py-pysam/pysam-0.14.1/pysam -L/construction/biology/py-pysam/pysam-0.14.1 -L/construction/biology/py-pysam/pysam-0.14.1/build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/pysam -Lbuild/lib.dragonfly-5.2-SYNTH-x86_64-2.7/pysam -Lbuild/lib.dragonfly-5.2-SYNTH-x86_64-2.7/pysam -Lbuild/lib.dragonfly-5.2-SYNTH-x86_64-2.7/pysam -L/usr/local/lib -lz -llzma -lbz2 -lz -lm -lchtslib -lpython2.7 -o build/lib.dragonfly-5.2-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 -I/construction/biology/py-pysam/pysam-0.14.1/htslib -I/construction/biology/py-pysam/pysam-0.14.1/samtools -I/construction/biology/py-pysam/pysam-0.14.1/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.14.1/bcftools -I/construction/biology/py-pysam/pysam-0.14.1/pysam -I/construction/biology/py-pysam/pysam-0.14.1 -I/usr/local/include/python2.7 -c pysam/libcutils.c -o build/temp.dragonfly-5.2-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 -I/construction/biology/py-pysam/pysam-0.14.1/htslib -I/construction/biology/py-pysam/pysam-0.14.1/samtools -I/construction/biology/py-pysam/pysam-0.14.1/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.14.1/bcftools -I/construction/biology/py-pysam/pysam-0.14.1/pysam -I/construction/biology/py-pysam/pysam-0.14.1 -I/usr/local/include/python2.7 -c pysam/pysam_util.c -o build/temp.dragonfly-5.2-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-5.2-SYNTH-x86_64-2.7/pysam/libcutils.o build/temp.dragonfly-5.2-SYNTH-x86_64-2.7/pysam/pysam_util.o -L/construction/biology/py-pysam/pysam-0.14.1/pysam -L/construction/biology/py-pysam/pysam-0.14.1/pysam -L/construction/biology/py-pysam/pysam-0.14.1 -L/construction/biology/py-pysam/pysam-0.14.1/build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/pysam -Lbuild/lib.dragonfly-5.2-SYNTH-x86_64-2.7/pysam -Lbuild/lib.dragonfly-5.2-SYNTH-x86_64-2.7/pysam -Lbuild/lib.dragonfly-5.2-SYNTH-x86_64-2.7/pysam -Lbuild/lib.dragonfly-5.2-SYNTH-x86_64-2.7/pysam -L/usr/local/lib -lz -llzma -lbz2 -lz -lm -lchtslib -lcsamtools -lcbcftools -lpython2.7 -o build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/pysam/libcutils.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 -I/construction/biology/py-pysam/pysam-0.14.1/htslib -I/construction/biology/py-pysam/pysam-0.14.1/samtools -I/construction/biology/py-pysam/pysam-0.14.1/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.14.1/bcftools -I/construction/biology/py-pysam/pysam-0.14.1/pysam -I/construction/biology/py-pysam/pysam-0.14.1 -I/usr/local/include/python2.7 -c pysam/libcalignmentfile.c -o build/temp.dragonfly-5.2-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:28523:126: warning: passing argument 5 of 'bam_mplp_auto' from incompatible pointer type [-Wincompatible-pointer-types] __pyx_v_ret = bam_mplp_auto(__pyx_v_self->pileup_iter, (&__pyx_v_self->tid), (&__pyx_v_self->pos), (&__pyx_v_self->n_plp), (&__pyx_v_self->plp)); ^ In file included from pysam/htslib_util.h:4:0, from pysam/libcalignmentfile.c:440: /construction/biology/py-pysam/pysam-0.14.1/htslib/htslib/sam.h:594:9: note: expected 'const bam_pileup1_t ** {aka const struct **}' but argument is of type 'bam_pileup1_t ** {aka struct **}' int bam_mplp_auto(bam_mplp_t iter, int *_tid, int *_pos, int *n_plp, const bam_pileup1_t **plp); ^ pysam/libcalignmentfile.c: In function '__pyx_f_5pysam_17libcalignmentfile_20IteratorRowSelection_cnext': pysam/libcalignmentfile.c:26898:9: 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:13411:13: 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_hdr); ^ cc -shared -pipe -O2 -fno-strict-aliasing build/temp.dragonfly-5.2-SYNTH-x86_64-2.7/pysam/libcalignmentfile.o -L/construction/biology/py-pysam/pysam-0.14.1/pysam -L/construction/biology/py-pysam/pysam-0.14.1/pysam -L/construction/biology/py-pysam/pysam-0.14.1 -L/construction/biology/py-pysam/pysam-0.14.1/build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/pysam -Lbuild/lib.dragonfly-5.2-SYNTH-x86_64-2.7/pysam -Lbuild/lib.dragonfly-5.2-SYNTH-x86_64-2.7/pysam -Lbuild/lib.dragonfly-5.2-SYNTH-x86_64-2.7/pysam -Lbuild/lib.dragonfly-5.2-SYNTH-x86_64-2.7/pysam -Lbuild/lib.dragonfly-5.2-SYNTH-x86_64-2.7/pysam -L/usr/local/lib -lz -llzma -lbz2 -lz -lm -lchtslib -lcutils -lpython2.7 -o build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/pysam/libcalignmentfile.so -Wl,-rpath,$ORIGIN skipping 'pysam/libcsamfile.c' Cython extension (up-to-date) building 'pysam.libcsamfile' extension cc -DNDEBUG -pipe -O2 -fno-strict-aliasing -fPIC -I/construction/biology/py-pysam/pysam-0.14.1/htslib -I/construction/biology/py-pysam/pysam-0.14.1/samtools -I/construction/biology/py-pysam/pysam-0.14.1/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.14.1/bcftools -I/construction/biology/py-pysam/pysam-0.14.1/pysam -I/construction/biology/py-pysam/pysam-0.14.1 -I/usr/local/include/python2.7 -c pysam/libcsamfile.c -o build/temp.dragonfly-5.2-SYNTH-x86_64-2.7/pysam/libcsamfile.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -shared -pipe -O2 -fno-strict-aliasing build/temp.dragonfly-5.2-SYNTH-x86_64-2.7/pysam/libcsamfile.o -L/construction/biology/py-pysam/pysam-0.14.1/pysam -L/construction/biology/py-pysam/pysam-0.14.1/pysam -L/construction/biology/py-pysam/pysam-0.14.1 -L/construction/biology/py-pysam/pysam-0.14.1/build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/pysam -Lbuild/lib.dragonfly-5.2-SYNTH-x86_64-2.7/pysam -Lbuild/lib.dragonfly-5.2-SYNTH-x86_64-2.7/pysam -Lbuild/lib.dragonfly-5.2-SYNTH-x86_64-2.7/pysam -Lbuild/lib.dragonfly-5.2-SYNTH-x86_64-2.7/pysam -Lbuild/lib.dragonfly-5.2-SYNTH-x86_64-2.7/pysam -Lbuild/lib.dragonfly-5.2-SYNTH-x86_64-2.7/pysam -L/usr/local/lib -lz -llzma -lbz2 -lz -lm -lchtslib -lcutils -lpython2.7 -o build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/pysam/libcsamfile.so -Wl,-rpath,$ORIGIN skipping 'pysam/libcalignedsegment.c' Cython extension (up-to-date) building 'pysam.libcalignedsegment' extension cc -DNDEBUG -pipe -O2 -fno-strict-aliasing -fPIC -I/construction/biology/py-pysam/pysam-0.14.1/htslib -I/construction/biology/py-pysam/pysam-0.14.1/samtools -I/construction/biology/py-pysam/pysam-0.14.1/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.14.1/bcftools -I/construction/biology/py-pysam/pysam-0.14.1/pysam -I/construction/biology/py-pysam/pysam-0.14.1 -I/usr/local/include/python2.7 -c pysam/libcalignedsegment.c -o build/temp.dragonfly-5.2-SYNTH-x86_64-2.7/pysam/libcalignedsegment.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement pysam/libcalignedsegment.c: In function '__pyx_pf_5pysam_18libcalignedsegment_14AlignedSegment_18fromstring': pysam/libcalignedsegment.c:13925:3: warning: ignoring return value of 'sam_parse1', declared with attribute warn_unused_result [-Wunused-result] sam_parse1((&__pyx_v_line), __pyx_v_dest->header->ptr, __pyx_v_dest->_delegate); ^ cc -shared -pipe -O2 -fno-strict-aliasing build/temp.dragonfly-5.2-SYNTH-x86_64-2.7/pysam/libcalignedsegment.o -L/construction/biology/py-pysam/pysam-0.14.1/pysam -L/construction/biology/py-pysam/pysam-0.14.1/pysam -L/construction/biology/py-pysam/pysam-0.14.1 -L/construction/biology/py-pysam/pysam-0.14.1/build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/pysam -Lbuild/lib.dragonfly-5.2-SYNTH-x86_64-2.7/pysam -Lbuild/lib.dragonfly-5.2-SYNTH-x86_64-2.7/pysam -Lbuild/lib.dragonfly-5.2-SYNTH-x86_64-2.7/pysam -Lbuild/lib.dragonfly-5.2-SYNTH-x86_64-2.7/pysam -Lbuild/lib.dragonfly-5.2-SYNTH-x86_64-2.7/pysam -Lbuild/lib.dragonfly-5.2-SYNTH-x86_64-2.7/pysam -Lbuild/lib.dragonfly-5.2-SYNTH-x86_64-2.7/pysam -L/usr/local/lib -lz -llzma -lbz2 -lz -lm -lchtslib -lcutils -lpython2.7 -o build/lib.dragonfly-5.2-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 -I/construction/biology/py-pysam/pysam-0.14.1/htslib -I/construction/biology/py-pysam/pysam-0.14.1/samtools -I/construction/biology/py-pysam/pysam-0.14.1/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.14.1/bcftools -I/construction/biology/py-pysam/pysam-0.14.1/pysam -I/construction/biology/py-pysam/pysam-0.14.1 -I/usr/local/include/python2.7 -c pysam/libctabix.c -o build/temp.dragonfly-5.2-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:6569:27: 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': /construction/biology/py-pysam/pysam-0.14.1/htslib/htslib/tbx.h:41:21: warning: overflow in implicit constant conversion [-Woverflow] #define TBX_UCSC 0x10000 ^ pysam/libctabix.c:11108:39: note: in expansion of macro 'TBX_UCSC' __pyx_t_1 = __Pyx_PyInt_From_int8_t(TBX_UCSC); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 965, __pyx_L1_error) ^ /construction/biology/py-pysam/pysam-0.14.1/htslib/htslib/tbx.h:41:21: warning: overflow in implicit constant conversion [-Woverflow] #define TBX_UCSC 0x10000 ^ pysam/libctabix.c:11140:39: 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, 966, __pyx_L1_error) ^ /construction/biology/py-pysam/pysam-0.14.1/htslib/htslib/tbx.h:41:21: warning: overflow in implicit constant conversion [-Woverflow] #define TBX_UCSC 0x10000 ^ pysam/libctabix.c:11517:43: 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, 995, __pyx_L1_error) ^ cc -shared -pipe -O2 -fno-strict-aliasing build/temp.dragonfly-5.2-SYNTH-x86_64-2.7/pysam/libctabix.o -L/construction/biology/py-pysam/pysam-0.14.1/pysam -L/construction/biology/py-pysam/pysam-0.14.1/pysam -L/construction/biology/py-pysam/pysam-0.14.1 -L/construction/biology/py-pysam/pysam-0.14.1/build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/pysam -Lbuild/lib.dragonfly-5.2-SYNTH-x86_64-2.7/pysam -Lbuild/lib.dragonfly-5.2-SYNTH-x86_64-2.7/pysam -Lbuild/lib.dragonfly-5.2-SYNTH-x86_64-2.7/pysam -Lbuild/lib.dragonfly-5.2-SYNTH-x86_64-2.7/pysam -Lbuild/lib.dragonfly-5.2-SYNTH-x86_64-2.7/pysam -Lbuild/lib.dragonfly-5.2-SYNTH-x86_64-2.7/pysam -Lbuild/lib.dragonfly-5.2-SYNTH-x86_64-2.7/pysam -Lbuild/lib.dragonfly-5.2-SYNTH-x86_64-2.7/pysam -L/usr/local/lib -lz -llzma -lbz2 -lz -lm -lchtslib -lcutils -lpython2.7 -o build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/pysam/libctabix.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 -I/construction/biology/py-pysam/pysam-0.14.1/htslib -I/construction/biology/py-pysam/pysam-0.14.1/samtools -I/construction/biology/py-pysam/pysam-0.14.1/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.14.1/bcftools -I/construction/biology/py-pysam/pysam-0.14.1/pysam -I/construction/biology/py-pysam/pysam-0.14.1 -I/usr/local/include/python2.7 -c pysam/libcfaidx.c -o build/temp.dragonfly-5.2-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-5.2-SYNTH-x86_64-2.7/pysam/libcfaidx.o -L/construction/biology/py-pysam/pysam-0.14.1/pysam -L/construction/biology/py-pysam/pysam-0.14.1/pysam -L/construction/biology/py-pysam/pysam-0.14.1 -L/construction/biology/py-pysam/pysam-0.14.1/build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/pysam -Lbuild/lib.dragonfly-5.2-SYNTH-x86_64-2.7/pysam -Lbuild/lib.dragonfly-5.2-SYNTH-x86_64-2.7/pysam -Lbuild/lib.dragonfly-5.2-SYNTH-x86_64-2.7/pysam -Lbuild/lib.dragonfly-5.2-SYNTH-x86_64-2.7/pysam -Lbuild/lib.dragonfly-5.2-SYNTH-x86_64-2.7/pysam -Lbuild/lib.dragonfly-5.2-SYNTH-x86_64-2.7/pysam -Lbuild/lib.dragonfly-5.2-SYNTH-x86_64-2.7/pysam -Lbuild/lib.dragonfly-5.2-SYNTH-x86_64-2.7/pysam -Lbuild/lib.dragonfly-5.2-SYNTH-x86_64-2.7/pysam -L/usr/local/lib -lz -llzma -lbz2 -lz -lm -lchtslib -lcutils -lpython2.7 -o build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/pysam/libcfaidx.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 -I/construction/biology/py-pysam/pysam-0.14.1/htslib -I/construction/biology/py-pysam/pysam-0.14.1/samtools -I/construction/biology/py-pysam/pysam-0.14.1/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.14.1/bcftools -I/construction/biology/py-pysam/pysam-0.14.1/pysam -I/construction/biology/py-pysam/pysam-0.14.1 -I/usr/local/include/python2.7 -c pysam/libcbcf.c -o build/temp.dragonfly-5.2-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:30662:3: 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: /construction/biology/py-pysam/pysam-0.14.1/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-5.2-SYNTH-x86_64-2.7/pysam/libcbcf.o -L/construction/biology/py-pysam/pysam-0.14.1/pysam -L/construction/biology/py-pysam/pysam-0.14.1/pysam -L/construction/biology/py-pysam/pysam-0.14.1 -L/construction/biology/py-pysam/pysam-0.14.1/build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/pysam -Lbuild/lib.dragonfly-5.2-SYNTH-x86_64-2.7/pysam -Lbuild/lib.dragonfly-5.2-SYNTH-x86_64-2.7/pysam -Lbuild/lib.dragonfly-5.2-SYNTH-x86_64-2.7/pysam -Lbuild/lib.dragonfly-5.2-SYNTH-x86_64-2.7/pysam -Lbuild/lib.dragonfly-5.2-SYNTH-x86_64-2.7/pysam -Lbuild/lib.dragonfly-5.2-SYNTH-x86_64-2.7/pysam -Lbuild/lib.dragonfly-5.2-SYNTH-x86_64-2.7/pysam -Lbuild/lib.dragonfly-5.2-SYNTH-x86_64-2.7/pysam -Lbuild/lib.dragonfly-5.2-SYNTH-x86_64-2.7/pysam -Lbuild/lib.dragonfly-5.2-SYNTH-x86_64-2.7/pysam -L/usr/local/lib -lz -llzma -lbz2 -lz -lm -lchtslib -lcutils -lpython2.7 -o build/lib.dragonfly-5.2-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 -I/construction/biology/py-pysam/pysam-0.14.1/htslib -I/construction/biology/py-pysam/pysam-0.14.1/samtools -I/construction/biology/py-pysam/pysam-0.14.1/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.14.1/bcftools -I/construction/biology/py-pysam/pysam-0.14.1/pysam -I/construction/biology/py-pysam/pysam-0.14.1 -I/usr/local/include/python2.7 -c pysam/libcbgzf.c -o build/temp.dragonfly-5.2-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-5.2-SYNTH-x86_64-2.7/pysam/libcbgzf.o -L/construction/biology/py-pysam/pysam-0.14.1/pysam -L/construction/biology/py-pysam/pysam-0.14.1/pysam -L/construction/biology/py-pysam/pysam-0.14.1 -L/construction/biology/py-pysam/pysam-0.14.1/build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/pysam -Lbuild/lib.dragonfly-5.2-SYNTH-x86_64-2.7/pysam -Lbuild/lib.dragonfly-5.2-SYNTH-x86_64-2.7/pysam -Lbuild/lib.dragonfly-5.2-SYNTH-x86_64-2.7/pysam -Lbuild/lib.dragonfly-5.2-SYNTH-x86_64-2.7/pysam -Lbuild/lib.dragonfly-5.2-SYNTH-x86_64-2.7/pysam -Lbuild/lib.dragonfly-5.2-SYNTH-x86_64-2.7/pysam -Lbuild/lib.dragonfly-5.2-SYNTH-x86_64-2.7/pysam -Lbuild/lib.dragonfly-5.2-SYNTH-x86_64-2.7/pysam -Lbuild/lib.dragonfly-5.2-SYNTH-x86_64-2.7/pysam -Lbuild/lib.dragonfly-5.2-SYNTH-x86_64-2.7/pysam -Lbuild/lib.dragonfly-5.2-SYNTH-x86_64-2.7/pysam -L/usr/local/lib -lz -llzma -lbz2 -lz -lm -lchtslib -lcutils -lpython2.7 -o build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/pysam/libcbgzf.so -Wl,-rpath,$ORIGIN skipping 'pysam/libctabixproxies.c' Cython extension (up-to-date) building 'pysam.libctabixproxies' extension cc -DNDEBUG -pipe -O2 -fno-strict-aliasing -fPIC -I/construction/biology/py-pysam/pysam-0.14.1/htslib -I/construction/biology/py-pysam/pysam-0.14.1/samtools -I/construction/biology/py-pysam/pysam-0.14.1/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.14.1/bcftools -I/construction/biology/py-pysam/pysam-0.14.1/pysam -I/construction/biology/py-pysam/pysam-0.14.1 -I/usr/local/include/python2.7 -c pysam/libctabixproxies.c -o build/temp.dragonfly-5.2-SYNTH-x86_64-2.7/pysam/libctabixproxies.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -shared -pipe -O2 -fno-strict-aliasing build/temp.dragonfly-5.2-SYNTH-x86_64-2.7/pysam/libctabixproxies.o -L/construction/biology/py-pysam/pysam-0.14.1/pysam -L/construction/biology/py-pysam/pysam-0.14.1/pysam -L/construction/biology/py-pysam/pysam-0.14.1 -L/construction/biology/py-pysam/pysam-0.14.1/build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/pysam -Lbuild/lib.dragonfly-5.2-SYNTH-x86_64-2.7/pysam -Lbuild/lib.dragonfly-5.2-SYNTH-x86_64-2.7/pysam -Lbuild/lib.dragonfly-5.2-SYNTH-x86_64-2.7/pysam -Lbuild/lib.dragonfly-5.2-SYNTH-x86_64-2.7/pysam -Lbuild/lib.dragonfly-5.2-SYNTH-x86_64-2.7/pysam -Lbuild/lib.dragonfly-5.2-SYNTH-x86_64-2.7/pysam -Lbuild/lib.dragonfly-5.2-SYNTH-x86_64-2.7/pysam -Lbuild/lib.dragonfly-5.2-SYNTH-x86_64-2.7/pysam -Lbuild/lib.dragonfly-5.2-SYNTH-x86_64-2.7/pysam -Lbuild/lib.dragonfly-5.2-SYNTH-x86_64-2.7/pysam -Lbuild/lib.dragonfly-5.2-SYNTH-x86_64-2.7/pysam -Lbuild/lib.dragonfly-5.2-SYNTH-x86_64-2.7/pysam -L/usr/local/lib -lz -llzma -lbz2 -lz -lm -lchtslib -lcutils -lpython2.7 -o build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/pysam/libctabixproxies.so -Wl,-rpath,$ORIGIN skipping 'pysam/libcvcf.c' Cython extension (up-to-date) building 'pysam.libcvcf' extension cc -DNDEBUG -pipe -O2 -fno-strict-aliasing -fPIC -I/construction/biology/py-pysam/pysam-0.14.1/htslib -I/construction/biology/py-pysam/pysam-0.14.1/samtools -I/construction/biology/py-pysam/pysam-0.14.1/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.14.1/bcftools -I/construction/biology/py-pysam/pysam-0.14.1/pysam -I/construction/biology/py-pysam/pysam-0.14.1 -I/usr/local/include/python2.7 -c pysam/libcvcf.c -o build/temp.dragonfly-5.2-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-5.2-SYNTH-x86_64-2.7/pysam/libcvcf.o -L/construction/biology/py-pysam/pysam-0.14.1/pysam -L/construction/biology/py-pysam/pysam-0.14.1/pysam -L/construction/biology/py-pysam/pysam-0.14.1 -L/construction/biology/py-pysam/pysam-0.14.1/build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/pysam -Lbuild/lib.dragonfly-5.2-SYNTH-x86_64-2.7/pysam -Lbuild/lib.dragonfly-5.2-SYNTH-x86_64-2.7/pysam -Lbuild/lib.dragonfly-5.2-SYNTH-x86_64-2.7/pysam -Lbuild/lib.dragonfly-5.2-SYNTH-x86_64-2.7/pysam -Lbuild/lib.dragonfly-5.2-SYNTH-x86_64-2.7/pysam -Lbuild/lib.dragonfly-5.2-SYNTH-x86_64-2.7/pysam -Lbuild/lib.dragonfly-5.2-SYNTH-x86_64-2.7/pysam -Lbuild/lib.dragonfly-5.2-SYNTH-x86_64-2.7/pysam -Lbuild/lib.dragonfly-5.2-SYNTH-x86_64-2.7/pysam -Lbuild/lib.dragonfly-5.2-SYNTH-x86_64-2.7/pysam -Lbuild/lib.dragonfly-5.2-SYNTH-x86_64-2.7/pysam -Lbuild/lib.dragonfly-5.2-SYNTH-x86_64-2.7/pysam -Lbuild/lib.dragonfly-5.2-SYNTH-x86_64-2.7/pysam -L/usr/local/lib -lz -llzma -lbz2 -lz -lm -lchtslib -lcutils -lpython2.7 -o build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/pysam/libcvcf.so -Wl,-rpath,$ORIGIN -------------------------------------------------------------------------------- -- Phase: run-depends -------------------------------------------------------------------------------- ===> py27-pysam-0.14.1 depends on executable: cython-2.7 - found ===> py27-pysam-0.14.1 depends on package: py27-setuptools>0 - found ===> py27-pysam-0.14.1 depends on file: /usr/local/bin/python2.7 - found -------------------------------------------------------------------------------- -- Phase: stage -------------------------------------------------------------------------------- ===> Staging for py27-pysam-0.14.1 ===> 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 grep that handles long lines and -e... /usr/bin/grep checking for C compiler warning flags... -Wall 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 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 . 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 grep that handles long lines and -e... /usr/bin/grep checking for C compiler warning flags... -Wall 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 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-5.2-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/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) skipping 'pysam/libcalignmentfile.c' Cython extension (up-to-date) skipping 'pysam/libcsamfile.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/libcfaidx.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/libctabixproxies.c' Cython extension (up-to-date) skipping 'pysam/libcvcf.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-5.2-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-5.2-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-5.2-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-5.2-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-5.2-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-5.2-SYNTH-x86_64-2.7/pysam/libcbgzf.so -> /construction/biology/py-pysam/stage/usr/local/lib/python2.7/site-packages/pysam copying build/lib.dragonfly-5.2-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-5.2-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-5.2-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-5.2-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-5.2-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-5.2-SYNTH-x86_64-2.7/pysam/samtools.py -> /construction/biology/py-pysam/stage/usr/local/lib/python2.7/site-packages/pysam copying build/lib.dragonfly-5.2-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-5.2-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-5.2-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-5.2-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-5.2-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-5.2-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-5.2-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-5.2-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-5.2-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-5.2-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-5.2-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-5.2-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-5.2-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-5.2-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-5.2-SYNTH-x86_64-2.7/pysam/htslib_util.h -> /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/bcftools copying build/lib.dragonfly-5.2-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-5.2-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-5.2-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-5.2-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-5.2-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-5.2-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-5.2-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-5.2-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-5.2-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-5.2-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-5.2-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-5.2-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-5.2-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-5.2-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-5.2-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-5.2-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-5.2-SYNTH-x86_64-2.7/pysam/include/bcftools/bcftools.pysam.h -> /construction/biology/py-pysam/stage/usr/local/lib/python2.7/site-packages/pysam/include/bcftools copying build/lib.dragonfly-5.2-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-5.2-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-5.2-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-5.2-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-5.2-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-5.2-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-5.2-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-5.2-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-5.2-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/samtools copying build/lib.dragonfly-5.2-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-5.2-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-5.2-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-5.2-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-5.2-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-5.2-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-5.2-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-5.2-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-5.2-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-5.2-SYNTH-x86_64-2.7/pysam/include/samtools/bedidx.h -> /construction/biology/py-pysam/stage/usr/local/lib/python2.7/site-packages/pysam/include/samtools copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/pysam/include/samtools/samtools.pysam.h -> /construction/biology/py-pysam/stage/usr/local/lib/python2.7/site-packages/pysam/include/samtools copying build/lib.dragonfly-5.2-SYNTH-x86_64-2.7/pysam/include/samtools/tmp_file.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-5.2-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-5.2-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-5.2-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-5.2-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-5.2-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-5.2-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-5.2-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 creating /construction/biology/py-pysam/stage/usr/local/lib/python2.7/site-packages/pysam/include/htslib copying build/lib.dragonfly-5.2-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-5.2-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-5.2-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-5.2-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-5.2-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-5.2-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-5.2-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-5.2-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-5.2-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-5.2-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-5.2-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-5.2-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-5.2-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-5.2-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-5.2-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-5.2-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-5.2-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-5.2-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-5.2-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-5.2-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-5.2-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-5.2-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-5.2-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-5.2-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-5.2-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-5.2-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-5.2-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-5.2-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 copying build/lib.dragonfly-5.2-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-5.2-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-5.2-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-5.2-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-5.2-SYNTH-x86_64-2.7/pysam/include/htslib/textutils_internal.h -> /construction/biology/py-pysam/stage/usr/local/lib/python2.7/site-packages/pysam/include/htslib copying build/lib.dragonfly-5.2-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-5.2-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-5.2-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-5.2-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-5.2-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-5.2-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-5.2-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-5.2-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-5.2-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-5.2-SYNTH-x86_64-2.7/pysam/libcbcftools.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/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/__init__.py to __init__.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/bcftools.py to bcftools.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/Pileup.py to Pileup.pyc writing byte-compilation script '/tmp/tmpne9uwx.py' /usr/local/bin/python2.7 -O /tmp/tmpne9uwx.py removing /tmp/tmpne9uwx.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' no previously-included directories found matching 'tests/' 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 'htslib/win/*.c' warning: no files found matching 'htslib/win/*.h' 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-0.14.1-py2.7.egg-info running install_scripts writing list of installed files to '/construction/biology/py-pysam/.PLIST.pymodtmp' ====> Compressing man pages (compress-man) -------------------------------------------------------------------------------- -- Phase: package -------------------------------------------------------------------------------- ===> Building package for py27-pysam-0.14.1 file sizes/checksums [139]: .. done packing files [139]: .. done packing directories [0]: . done -------------------------------------------------- -- Termination -------------------------------------------------- Finished: Friday, 20 JUL 2018 at 23:34:38 UTC Duration: 00:05:13