------------------------------------------------------------------------------- -- Phase: Environment ------------------------------------------------------------------------------- NO_DEPENDS=1 FLAVOR=py37 UNAME_r=6.1 UNAME_m=x86_64 UNAME_p=x86_64 UNAME_v=unknown UNAME_s=DragonFly PATH=/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin SSL_NO_VERIFY_PEER=1 LANG=C HOME=/root USER=root TERM=dumb SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: showconfig ------------------------------------------------------------------------------- SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: CONFIGURE_ENV ------------------------------------------------------------------------------- MAKE=gmake PYTHON="/usr/local/bin/python3.7" 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=gcc80 SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: CONFIGURE_ARGS ------------------------------------------------------------------------------- SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: 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=gcc80 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" SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: MAKE_ARGS ------------------------------------------------------------------------------- DESTDIR=/construction/biology/py-pysam/stage SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: PLIST_SUB ------------------------------------------------------------------------------- PYTHON_INCLUDEDIR=include/python3.7m PYTHON_LIBDIR=lib/python3.7 PYTHON_PLATFORM=dragonfly6 PYTHON_SITELIBDIR=lib/python3.7/site-packages PYTHON_SUFFIX=37 PYTHON_EXT_SUFFIX= PYTHON_VER=3.7 PYTHON_VERSION=python3.7 PYTHON2="@comment " PYTHON3="" OSREL=6.1 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" SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: 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 SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: /etc/make.conf ------------------------------------------------------------------------------- DPORTS_BUILDER=yes DISABLE_LICENSES=yes DEFAULT_VERSIONS=ssl=openssl FORCE_PACKAGE=yes DEVELOPER=yes USE_PACKAGE_DEPENDS_ONLY=yes PORTSDIR=/xports PORT_DBDIR=/options PKG_DBDIR=/var/db/pkg PKG_CACHEDIR=/var/cache/pkg PKG_SUFX=.txz DEVELOPER=1 UID=0 ARCH=x86_64 OPSYS=DragonFly DFLYVERSION=600100 OSVERSION=9999999 OSREL=6.1 _OSRELEASE=6.1-SYNTH DISTDIR=/distfiles WRKDIRPREFIX=/construction BATCH=yes PACKAGE_BUILDING=yes PKG_CREATE_VERBOSE=yes MAKE_JOBS_NUMBER=10 SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: setup ------------------------------------------------------------------------------- Installing /packages/All/indexinfo-0.3.1.txz Installing /packages/All/gettext-runtime-0.21.txz Installing /packages/All/gmake-4.3_2.txz Installing /packages/All/libffi-3.3_1.txz Installing /packages/All/expat-2.2.10.txz Installing /packages/All/ncurses-6.2.20210313_1.txz ===== Message from ncurses-6.2.20210313_1: -- { type: install message: < py37-pysam-0.16.0.1 depends on file: /usr/local/sbin/pkg - found SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: fetch-depends ------------------------------------------------------------------------------- SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: fetch ------------------------------------------------------------------------------- ===> py37-pysam-0.16.0.1 depends on file: /usr/local/sbin/pkg - found ===> Fetching all distfiles required by py37-pysam-0.16.0.1 for building SUCCEEDED 00:00:01 ------------------------------------------------------------------------------- -- Phase: checksum ------------------------------------------------------------------------------- ===> py37-pysam-0.16.0.1 depends on file: /usr/local/sbin/pkg - found ===> Fetching all distfiles required by py37-pysam-0.16.0.1 for building => SHA256 Checksum OK for pysam-0.16.0.1.tar.gz. SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: extract-depends ------------------------------------------------------------------------------- SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: extract ------------------------------------------------------------------------------- ===> py37-pysam-0.16.0.1 depends on file: /usr/local/sbin/pkg - found ===> Fetching all distfiles required by py37-pysam-0.16.0.1 for building ===> Extracting for py37-pysam-0.16.0.1 => SHA256 Checksum OK for pysam-0.16.0.1.tar.gz. Extracted Memory Use: 23.47M SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: patch-depends ------------------------------------------------------------------------------- SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: patch ------------------------------------------------------------------------------- ===> Patching for py37-pysam-0.16.0.1 ===> Applying ports patches for py37-pysam-0.16.0.1 from /xports/biology/py-pysam/files SUCCEEDED 00:00:01 ------------------------------------------------------------------------------- -- Phase: build-depends ------------------------------------------------------------------------------- ===> py37-pysam-0.16.0.1 depends on package: gmake>=4.3 - found ===> py37-pysam-0.16.0.1 depends on executable: cython-3.7 - found ===> py37-pysam-0.16.0.1 depends on package: py37-setuptools>0 - found ===> py37-pysam-0.16.0.1 depends on file: /usr/local/bin/python3.7 - found SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: lib-depends ------------------------------------------------------------------------------- SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: configure ------------------------------------------------------------------------------- ===> py37-pysam-0.16.0.1 depends on package: gmake>=4.3 - found ===> py37-pysam-0.16.0.1 depends on executable: cython-3.7 - found ===> py37-pysam-0.16.0.1 depends on package: py37-setuptools>0 - found ===> py37-pysam-0.16.0.1 depends on file: /usr/local/bin/python3.7 - found ===> Configuring for py37-pysam-0.16.0.1 # pysam: cython is available - using cythonize if necessary # pysam: htslib mode is shared # pysam: HTSLIB_CONFIGURE_OPTIONS=None # pysam: (env) CC=cc # pysam: (env) CFLAGS=-pipe -O2 -fno-strict-aliasing # pysam: (env) LDFLAGS= 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 pkg-config... no checking for special C compiler options needed for large files... no checking for _FILE_OFFSET_BITS value needed for large files... no checking shared library type for unknown-DragonFly... plain .so checking whether the compiler accepts -fvisibility=hidden... yes 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 libdeflate.h... no checking for libdeflate_deflate_compress in -ldeflate... no 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 pkg-config... no checking for special C compiler options needed for large files... no checking for _FILE_OFFSET_BITS value needed for large files... no checking shared library type for unknown-DragonFly... plain .so checking whether the compiler accepts -fvisibility=hidden... yes 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 libdeflate.h... no checking for libdeflate_deflate_compress in -ldeflate... no 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 # pysam: htslib configure options: --disable-libcurl gmake[1]: ./version.sh: No such file or directory gmake[1]: ./version.sh: No such file or directory # pysam: htslib_config LIBHTS_OBJS=kfunc.o knetfile.o kstring.o bcf_sr_sort.o bgzf.o errmod.o faidx.o header.o hfile.o hfile_net.o hts.o hts_os.o md5.o multipart.o probaln.o realn.o regidx.o region.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/mFILE.o cram/open_trace_file.o cram/pooled_alloc.o cram/rANS_static.o cram/string_alloc.o # pysam: htslib_config LIBS=-llzma -lbz2 -lz -lm # pysam: htslib_config PLATFORM=default # pysam: config_option: ENABLE_GCS=0 # pysam: config_option: ENABLE_PLUGINS=0 # pysam: config_option: ENABLE_S3=0 # pysam: config_option: HAVE_COMMONCRYPTO=0 # pysam: config_option: HAVE_HMAC=0 # pysam: config_option: HAVE_LIBBZ2=1 # pysam: config_option: HAVE_LIBCURL=0 # pysam: config_option: HAVE_LIBDEFLATE=0 # pysam: config_option: HAVE_LIBLZMA=1 # pysam: config_option: HAVE_MMAP=1 running config SUCCEEDED 00:00:10 ------------------------------------------------------------------------------- -- Phase: build ------------------------------------------------------------------------------- ===> Building for py37-pysam-0.16.0.1 # pysam: cython is available - using cythonize if necessary # pysam: htslib mode is shared # pysam: HTSLIB_CONFIGURE_OPTIONS=None # pysam: (env) CC=cc # pysam: (env) CFLAGS=-pipe -O2 -fno-strict-aliasing # pysam: (env) LDFLAGS= 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 pkg-config... no checking for special C compiler options needed for large files... no checking for _FILE_OFFSET_BITS value needed for large files... no checking shared library type for unknown-DragonFly... plain .so checking whether the compiler accepts -fvisibility=hidden... yes 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 libdeflate.h... no checking for libdeflate_deflate_compress in -ldeflate... no 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 pkg-config... no checking for special C compiler options needed for large files... no checking for _FILE_OFFSET_BITS value needed for large files... no checking shared library type for unknown-DragonFly... plain .so checking whether the compiler accepts -fvisibility=hidden... yes 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 libdeflate.h... no checking for libdeflate_deflate_compress in -ldeflate... no 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 # pysam: htslib configure options: --disable-libcurl gmake[1]: ./version.sh: No such file or directory gmake[1]: ./version.sh: No such file or directory # pysam: htslib_config LIBHTS_OBJS=kfunc.o knetfile.o kstring.o bcf_sr_sort.o bgzf.o errmod.o faidx.o header.o hfile.o hfile_net.o hts.o hts_os.o md5.o multipart.o probaln.o realn.o regidx.o region.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/mFILE.o cram/open_trace_file.o cram/pooled_alloc.o cram/rANS_static.o cram/string_alloc.o # pysam: htslib_config LIBS=-llzma -lbz2 -lz -lm # pysam: htslib_config PLATFORM=default # pysam: config_option: ENABLE_GCS=0 # pysam: config_option: ENABLE_PLUGINS=0 # pysam: config_option: ENABLE_S3=0 # pysam: config_option: HAVE_COMMONCRYPTO=0 # pysam: config_option: HAVE_HMAC=0 # pysam: config_option: HAVE_LIBBZ2=1 # pysam: config_option: HAVE_LIBCURL=0 # pysam: config_option: HAVE_LIBDEFLATE=0 # pysam: config_option: HAVE_LIBLZMA=1 # pysam: config_option: HAVE_MMAP=1 running build running build_py creating build creating build/lib.dragonfly-6.1-x86_64-3.7 creating build/lib.dragonfly-6.1-x86_64-3.7/pysam copying pysam/samtools.py -> build/lib.dragonfly-6.1-x86_64-3.7/pysam copying pysam/utils.py -> build/lib.dragonfly-6.1-x86_64-3.7/pysam copying pysam/config.py -> build/lib.dragonfly-6.1-x86_64-3.7/pysam copying pysam/version.py -> build/lib.dragonfly-6.1-x86_64-3.7/pysam copying pysam/__init__.py -> build/lib.dragonfly-6.1-x86_64-3.7/pysam copying pysam/Pileup.py -> build/lib.dragonfly-6.1-x86_64-3.7/pysam copying pysam/bcftools.py -> build/lib.dragonfly-6.1-x86_64-3.7/pysam creating build/lib.dragonfly-6.1-x86_64-3.7/pysam/include copying pysam/include/__init__.py -> build/lib.dragonfly-6.1-x86_64-3.7/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 '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/libctabixproxies.pxd -> build/lib.dragonfly-6.1-x86_64-3.7/pysam copying pysam/libchtslib.pxd -> build/lib.dragonfly-6.1-x86_64-3.7/pysam copying pysam/libcsamtools.pxd -> build/lib.dragonfly-6.1-x86_64-3.7/pysam copying pysam/libcutils.pxd -> build/lib.dragonfly-6.1-x86_64-3.7/pysam copying pysam/libcfaidx.pxd -> build/lib.dragonfly-6.1-x86_64-3.7/pysam copying pysam/libcbcf.pxd -> build/lib.dragonfly-6.1-x86_64-3.7/pysam copying pysam/libctabix.pxd -> build/lib.dragonfly-6.1-x86_64-3.7/pysam copying pysam/libcalignedsegment.pxd -> build/lib.dragonfly-6.1-x86_64-3.7/pysam copying pysam/libcsamfile.pxd -> build/lib.dragonfly-6.1-x86_64-3.7/pysam copying pysam/libcalignmentfile.pxd -> build/lib.dragonfly-6.1-x86_64-3.7/pysam copying pysam/libcvcf.pxd -> build/lib.dragonfly-6.1-x86_64-3.7/pysam copying pysam/libcbcftools.pxd -> build/lib.dragonfly-6.1-x86_64-3.7/pysam copying pysam/csamtools_util.h -> build/lib.dragonfly-6.1-x86_64-3.7/pysam copying pysam/pysam_stream.h -> build/lib.dragonfly-6.1-x86_64-3.7/pysam copying pysam/version.h -> build/lib.dragonfly-6.1-x86_64-3.7/pysam copying pysam/pysam_util.h -> build/lib.dragonfly-6.1-x86_64-3.7/pysam copying pysam/cbcftools_util.h -> build/lib.dragonfly-6.1-x86_64-3.7/pysam copying pysam/htslib_util.h -> build/lib.dragonfly-6.1-x86_64-3.7/pysam creating build/lib.dragonfly-6.1-x86_64-3.7/pysam/include/samtools copying samtools/config.h -> build/lib.dragonfly-6.1-x86_64-3.7/pysam/include/samtools copying samtools/bam.h -> build/lib.dragonfly-6.1-x86_64-3.7/pysam/include/samtools copying samtools/bedidx.h -> build/lib.dragonfly-6.1-x86_64-3.7/pysam/include/samtools copying samtools/sam.h -> build/lib.dragonfly-6.1-x86_64-3.7/pysam/include/samtools copying samtools/samtools.h -> build/lib.dragonfly-6.1-x86_64-3.7/pysam/include/samtools copying samtools/bam_endian.h -> build/lib.dragonfly-6.1-x86_64-3.7/pysam/include/samtools copying samtools/sample.h -> build/lib.dragonfly-6.1-x86_64-3.7/pysam/include/samtools copying samtools/samtools.pysam.h -> build/lib.dragonfly-6.1-x86_64-3.7/pysam/include/samtools copying samtools/stats_isize.h -> build/lib.dragonfly-6.1-x86_64-3.7/pysam/include/samtools copying samtools/sam_opts.h -> build/lib.dragonfly-6.1-x86_64-3.7/pysam/include/samtools copying samtools/tmp_file.h -> build/lib.dragonfly-6.1-x86_64-3.7/pysam/include/samtools copying samtools/bam_lpileup.h -> build/lib.dragonfly-6.1-x86_64-3.7/pysam/include/samtools copying samtools/bam2bcf.h -> build/lib.dragonfly-6.1-x86_64-3.7/pysam/include/samtools copying samtools/bam_plbuf.h -> build/lib.dragonfly-6.1-x86_64-3.7/pysam/include/samtools creating build/lib.dragonfly-6.1-x86_64-3.7/pysam/include/bcftools copying bcftools/config.h -> build/lib.dragonfly-6.1-x86_64-3.7/pysam/include/bcftools copying bcftools/bcftools.h -> build/lib.dragonfly-6.1-x86_64-3.7/pysam/include/bcftools copying bcftools/hclust.h -> build/lib.dragonfly-6.1-x86_64-3.7/pysam/include/bcftools copying bcftools/bcftools.pysam.h -> build/lib.dragonfly-6.1-x86_64-3.7/pysam/include/bcftools copying bcftools/convert.h -> build/lib.dragonfly-6.1-x86_64-3.7/pysam/include/bcftools copying bcftools/bam_sample.h -> build/lib.dragonfly-6.1-x86_64-3.7/pysam/include/bcftools copying bcftools/tsv2vcf.h -> build/lib.dragonfly-6.1-x86_64-3.7/pysam/include/bcftools copying bcftools/HMM.h -> build/lib.dragonfly-6.1-x86_64-3.7/pysam/include/bcftools copying bcftools/regidx.h -> build/lib.dragonfly-6.1-x86_64-3.7/pysam/include/bcftools copying bcftools/vcmp.h -> build/lib.dragonfly-6.1-x86_64-3.7/pysam/include/bcftools copying bcftools/call.h -> build/lib.dragonfly-6.1-x86_64-3.7/pysam/include/bcftools copying bcftools/mw.h -> build/lib.dragonfly-6.1-x86_64-3.7/pysam/include/bcftools copying bcftools/prob1.h -> build/lib.dragonfly-6.1-x86_64-3.7/pysam/include/bcftools copying bcftools/vcfbuf.h -> build/lib.dragonfly-6.1-x86_64-3.7/pysam/include/bcftools copying bcftools/filter.h -> build/lib.dragonfly-6.1-x86_64-3.7/pysam/include/bcftools copying bcftools/cols.h -> build/lib.dragonfly-6.1-x86_64-3.7/pysam/include/bcftools copying bcftools/smpl_ilist.h -> build/lib.dragonfly-6.1-x86_64-3.7/pysam/include/bcftools copying bcftools/hex.h -> build/lib.dragonfly-6.1-x86_64-3.7/pysam/include/bcftools copying bcftools/gvcf.h -> build/lib.dragonfly-6.1-x86_64-3.7/pysam/include/bcftools copying bcftools/kmin.h -> build/lib.dragonfly-6.1-x86_64-3.7/pysam/include/bcftools copying bcftools/kheap.h -> build/lib.dragonfly-6.1-x86_64-3.7/pysam/include/bcftools copying bcftools/bin.h -> build/lib.dragonfly-6.1-x86_64-3.7/pysam/include/bcftools copying bcftools/khash_str2str.h -> build/lib.dragonfly-6.1-x86_64-3.7/pysam/include/bcftools copying bcftools/rbuf.h -> build/lib.dragonfly-6.1-x86_64-3.7/pysam/include/bcftools copying bcftools/ploidy.h -> build/lib.dragonfly-6.1-x86_64-3.7/pysam/include/bcftools copying bcftools/bam2bcf.h -> build/lib.dragonfly-6.1-x86_64-3.7/pysam/include/bcftools copying bcftools/variantkey.h -> build/lib.dragonfly-6.1-x86_64-3.7/pysam/include/bcftools creating build/lib.dragonfly-6.1-x86_64-3.7/pysam/include/htslib copying htslib/hts_internal.h -> build/lib.dragonfly-6.1-x86_64-3.7/pysam/include/htslib copying htslib/thread_pool_internal.h -> build/lib.dragonfly-6.1-x86_64-3.7/pysam/include/htslib copying htslib/hfile_internal.h -> build/lib.dragonfly-6.1-x86_64-3.7/pysam/include/htslib copying htslib/header.h -> build/lib.dragonfly-6.1-x86_64-3.7/pysam/include/htslib copying htslib/sam_internal.h -> build/lib.dragonfly-6.1-x86_64-3.7/pysam/include/htslib copying htslib/bcf_sr_sort.h -> build/lib.dragonfly-6.1-x86_64-3.7/pysam/include/htslib copying htslib/textutils_internal.h -> build/lib.dragonfly-6.1-x86_64-3.7/pysam/include/htslib copying htslib/config.h -> build/lib.dragonfly-6.1-x86_64-3.7/pysam/include/htslib creating build/lib.dragonfly-6.1-x86_64-3.7/pysam/include/htslib/htslib copying htslib/htslib/hts.h -> build/lib.dragonfly-6.1-x86_64-3.7/pysam/include/htslib/htslib copying htslib/htslib/hfile.h -> build/lib.dragonfly-6.1-x86_64-3.7/pysam/include/htslib/htslib copying htslib/htslib/kfunc.h -> build/lib.dragonfly-6.1-x86_64-3.7/pysam/include/htslib/htslib copying htslib/htslib/synced_bcf_reader.h -> build/lib.dragonfly-6.1-x86_64-3.7/pysam/include/htslib/htslib copying htslib/htslib/faidx.h -> build/lib.dragonfly-6.1-x86_64-3.7/pysam/include/htslib/htslib copying htslib/htslib/vcf_sweep.h -> build/lib.dragonfly-6.1-x86_64-3.7/pysam/include/htslib/htslib copying htslib/htslib/ksort.h -> build/lib.dragonfly-6.1-x86_64-3.7/pysam/include/htslib/htslib copying htslib/htslib/thread_pool.h -> build/lib.dragonfly-6.1-x86_64-3.7/pysam/include/htslib/htslib copying htslib/htslib/sam.h -> build/lib.dragonfly-6.1-x86_64-3.7/pysam/include/htslib/htslib copying htslib/htslib/khash.h -> build/lib.dragonfly-6.1-x86_64-3.7/pysam/include/htslib/htslib copying htslib/htslib/klist.h -> build/lib.dragonfly-6.1-x86_64-3.7/pysam/include/htslib/htslib copying htslib/htslib/knetfile.h -> build/lib.dragonfly-6.1-x86_64-3.7/pysam/include/htslib/htslib copying htslib/htslib/kstring.h -> build/lib.dragonfly-6.1-x86_64-3.7/pysam/include/htslib/htslib copying htslib/htslib/kseq.h -> build/lib.dragonfly-6.1-x86_64-3.7/pysam/include/htslib/htslib copying htslib/htslib/hts_defs.h -> build/lib.dragonfly-6.1-x86_64-3.7/pysam/include/htslib/htslib copying htslib/htslib/regidx.h -> build/lib.dragonfly-6.1-x86_64-3.7/pysam/include/htslib/htslib copying htslib/htslib/hts_log.h -> build/lib.dragonfly-6.1-x86_64-3.7/pysam/include/htslib/htslib copying htslib/htslib/tbx.h -> build/lib.dragonfly-6.1-x86_64-3.7/pysam/include/htslib/htslib copying htslib/htslib/kbitset.h -> build/lib.dragonfly-6.1-x86_64-3.7/pysam/include/htslib/htslib copying htslib/htslib/khash_str2int.h -> build/lib.dragonfly-6.1-x86_64-3.7/pysam/include/htslib/htslib copying htslib/htslib/hts_os.h -> build/lib.dragonfly-6.1-x86_64-3.7/pysam/include/htslib/htslib copying htslib/htslib/vcfutils.h -> build/lib.dragonfly-6.1-x86_64-3.7/pysam/include/htslib/htslib copying htslib/htslib/hts_endian.h -> build/lib.dragonfly-6.1-x86_64-3.7/pysam/include/htslib/htslib copying htslib/htslib/bgzf.h -> build/lib.dragonfly-6.1-x86_64-3.7/pysam/include/htslib/htslib copying htslib/htslib/cram.h -> build/lib.dragonfly-6.1-x86_64-3.7/pysam/include/htslib/htslib copying htslib/htslib/vcf.h -> build/lib.dragonfly-6.1-x86_64-3.7/pysam/include/htslib/htslib Fixing build/lib.dragonfly-6.1-x86_64-3.7/pysam/samtools.py build/lib.dragonfly-6.1-x86_64-3.7/pysam/utils.py build/lib.dragonfly-6.1-x86_64-3.7/pysam/config.py build/lib.dragonfly-6.1-x86_64-3.7/pysam/version.py build/lib.dragonfly-6.1-x86_64-3.7/pysam/__init__.py build/lib.dragonfly-6.1-x86_64-3.7/pysam/Pileup.py build/lib.dragonfly-6.1-x86_64-3.7/pysam/bcftools.py build/lib.dragonfly-6.1-x86_64-3.7/pysam/include/__init__.py Skipping optional fixer: buffer Skipping optional fixer: idioms Skipping optional fixer: set_literal Skipping optional fixer: ws_comma Fixing build/lib.dragonfly-6.1-x86_64-3.7/pysam/samtools.py build/lib.dragonfly-6.1-x86_64-3.7/pysam/utils.py build/lib.dragonfly-6.1-x86_64-3.7/pysam/config.py build/lib.dragonfly-6.1-x86_64-3.7/pysam/version.py build/lib.dragonfly-6.1-x86_64-3.7/pysam/__init__.py build/lib.dragonfly-6.1-x86_64-3.7/pysam/Pileup.py build/lib.dragonfly-6.1-x86_64-3.7/pysam/bcftools.py build/lib.dragonfly-6.1-x86_64-3.7/pysam/include/__init__.py Skipping optional fixer: buffer Skipping optional fixer: idioms Skipping optional fixer: set_literal Skipping optional fixer: ws_comma 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) building 'pysam.libchtslib' extension creating build/temp.dragonfly-6.1-x86_64-3.7 creating build/temp.dragonfly-6.1-x86_64-3.7/pysam creating build/temp.dragonfly-6.1-x86_64-3.7/htslib creating build/temp.dragonfly-6.1-x86_64-3.7/htslib/cram cc -Wno-unused-result -Wsign-compare -DNDEBUG -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -fPIC -I/construction/biology/py-pysam/pysam-0.16.0.1/htslib -I/construction/biology/py-pysam/pysam-0.16.0.1/samtools -I/construction/biology/py-pysam/pysam-0.16.0.1/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.16.0.1/bcftools -I/construction/biology/py-pysam/pysam-0.16.0.1/pysam -I/construction/biology/py-pysam/pysam-0.16.0.1 -I/usr/local/include/python3.7m -c pysam/libchtslib.c -o build/temp.dragonfly-6.1-x86_64-3.7/pysam/libchtslib.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -Wno-unused-result -Wsign-compare -DNDEBUG -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -fPIC -I/construction/biology/py-pysam/pysam-0.16.0.1/htslib -I/construction/biology/py-pysam/pysam-0.16.0.1/samtools -I/construction/biology/py-pysam/pysam-0.16.0.1/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.16.0.1/bcftools -I/construction/biology/py-pysam/pysam-0.16.0.1/pysam -I/construction/biology/py-pysam/pysam-0.16.0.1 -I/usr/local/include/python3.7m -c pysam/htslib_util.c -o build/temp.dragonfly-6.1-x86_64-3.7/pysam/htslib_util.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -Wno-unused-result -Wsign-compare -DNDEBUG -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -fPIC -I/construction/biology/py-pysam/pysam-0.16.0.1/htslib -I/construction/biology/py-pysam/pysam-0.16.0.1/samtools -I/construction/biology/py-pysam/pysam-0.16.0.1/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.16.0.1/bcftools -I/construction/biology/py-pysam/pysam-0.16.0.1/pysam -I/construction/biology/py-pysam/pysam-0.16.0.1 -I/usr/local/include/python3.7m -c htslib/kfunc.c -o build/temp.dragonfly-6.1-x86_64-3.7/htslib/kfunc.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -Wno-unused-result -Wsign-compare -DNDEBUG -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -fPIC -I/construction/biology/py-pysam/pysam-0.16.0.1/htslib -I/construction/biology/py-pysam/pysam-0.16.0.1/samtools -I/construction/biology/py-pysam/pysam-0.16.0.1/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.16.0.1/bcftools -I/construction/biology/py-pysam/pysam-0.16.0.1/pysam -I/construction/biology/py-pysam/pysam-0.16.0.1 -I/usr/local/include/python3.7m -c htslib/knetfile.c -o build/temp.dragonfly-6.1-x86_64-3.7/htslib/knetfile.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -Wno-unused-result -Wsign-compare -DNDEBUG -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -fPIC -I/construction/biology/py-pysam/pysam-0.16.0.1/htslib -I/construction/biology/py-pysam/pysam-0.16.0.1/samtools -I/construction/biology/py-pysam/pysam-0.16.0.1/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.16.0.1/bcftools -I/construction/biology/py-pysam/pysam-0.16.0.1/pysam -I/construction/biology/py-pysam/pysam-0.16.0.1 -I/usr/local/include/python3.7m -c htslib/kstring.c -o build/temp.dragonfly-6.1-x86_64-3.7/htslib/kstring.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -Wno-unused-result -Wsign-compare -DNDEBUG -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -fPIC -I/construction/biology/py-pysam/pysam-0.16.0.1/htslib -I/construction/biology/py-pysam/pysam-0.16.0.1/samtools -I/construction/biology/py-pysam/pysam-0.16.0.1/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.16.0.1/bcftools -I/construction/biology/py-pysam/pysam-0.16.0.1/pysam -I/construction/biology/py-pysam/pysam-0.16.0.1 -I/usr/local/include/python3.7m -c htslib/bcf_sr_sort.c -o build/temp.dragonfly-6.1-x86_64-3.7/htslib/bcf_sr_sort.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -Wno-unused-result -Wsign-compare -DNDEBUG -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -fPIC -I/construction/biology/py-pysam/pysam-0.16.0.1/htslib -I/construction/biology/py-pysam/pysam-0.16.0.1/samtools -I/construction/biology/py-pysam/pysam-0.16.0.1/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.16.0.1/bcftools -I/construction/biology/py-pysam/pysam-0.16.0.1/pysam -I/construction/biology/py-pysam/pysam-0.16.0.1 -I/usr/local/include/python3.7m -c htslib/bgzf.c -o build/temp.dragonfly-6.1-x86_64-3.7/htslib/bgzf.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -Wno-unused-result -Wsign-compare -DNDEBUG -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -fPIC -I/construction/biology/py-pysam/pysam-0.16.0.1/htslib -I/construction/biology/py-pysam/pysam-0.16.0.1/samtools -I/construction/biology/py-pysam/pysam-0.16.0.1/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.16.0.1/bcftools -I/construction/biology/py-pysam/pysam-0.16.0.1/pysam -I/construction/biology/py-pysam/pysam-0.16.0.1 -I/usr/local/include/python3.7m -c htslib/errmod.c -o build/temp.dragonfly-6.1-x86_64-3.7/htslib/errmod.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -Wno-unused-result -Wsign-compare -DNDEBUG -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -fPIC -I/construction/biology/py-pysam/pysam-0.16.0.1/htslib -I/construction/biology/py-pysam/pysam-0.16.0.1/samtools -I/construction/biology/py-pysam/pysam-0.16.0.1/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.16.0.1/bcftools -I/construction/biology/py-pysam/pysam-0.16.0.1/pysam -I/construction/biology/py-pysam/pysam-0.16.0.1 -I/usr/local/include/python3.7m -c htslib/faidx.c -o build/temp.dragonfly-6.1-x86_64-3.7/htslib/faidx.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -Wno-unused-result -Wsign-compare -DNDEBUG -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -fPIC -I/construction/biology/py-pysam/pysam-0.16.0.1/htslib -I/construction/biology/py-pysam/pysam-0.16.0.1/samtools -I/construction/biology/py-pysam/pysam-0.16.0.1/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.16.0.1/bcftools -I/construction/biology/py-pysam/pysam-0.16.0.1/pysam -I/construction/biology/py-pysam/pysam-0.16.0.1 -I/usr/local/include/python3.7m -c htslib/header.c -o build/temp.dragonfly-6.1-x86_64-3.7/htslib/header.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -Wno-unused-result -Wsign-compare -DNDEBUG -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -fPIC -I/construction/biology/py-pysam/pysam-0.16.0.1/htslib -I/construction/biology/py-pysam/pysam-0.16.0.1/samtools -I/construction/biology/py-pysam/pysam-0.16.0.1/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.16.0.1/bcftools -I/construction/biology/py-pysam/pysam-0.16.0.1/pysam -I/construction/biology/py-pysam/pysam-0.16.0.1 -I/usr/local/include/python3.7m -c htslib/hfile.c -o build/temp.dragonfly-6.1-x86_64-3.7/htslib/hfile.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -Wno-unused-result -Wsign-compare -DNDEBUG -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -fPIC -I/construction/biology/py-pysam/pysam-0.16.0.1/htslib -I/construction/biology/py-pysam/pysam-0.16.0.1/samtools -I/construction/biology/py-pysam/pysam-0.16.0.1/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.16.0.1/bcftools -I/construction/biology/py-pysam/pysam-0.16.0.1/pysam -I/construction/biology/py-pysam/pysam-0.16.0.1 -I/usr/local/include/python3.7m -c htslib/hfile_net.c -o build/temp.dragonfly-6.1-x86_64-3.7/htslib/hfile_net.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -Wno-unused-result -Wsign-compare -DNDEBUG -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -fPIC -I/construction/biology/py-pysam/pysam-0.16.0.1/htslib -I/construction/biology/py-pysam/pysam-0.16.0.1/samtools -I/construction/biology/py-pysam/pysam-0.16.0.1/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.16.0.1/bcftools -I/construction/biology/py-pysam/pysam-0.16.0.1/pysam -I/construction/biology/py-pysam/pysam-0.16.0.1 -I/usr/local/include/python3.7m -c htslib/hts.c -o build/temp.dragonfly-6.1-x86_64-3.7/htslib/hts.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -Wno-unused-result -Wsign-compare -DNDEBUG -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -fPIC -I/construction/biology/py-pysam/pysam-0.16.0.1/htslib -I/construction/biology/py-pysam/pysam-0.16.0.1/samtools -I/construction/biology/py-pysam/pysam-0.16.0.1/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.16.0.1/bcftools -I/construction/biology/py-pysam/pysam-0.16.0.1/pysam -I/construction/biology/py-pysam/pysam-0.16.0.1 -I/usr/local/include/python3.7m -c htslib/hts_os.c -o build/temp.dragonfly-6.1-x86_64-3.7/htslib/hts_os.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -Wno-unused-result -Wsign-compare -DNDEBUG -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -fPIC -I/construction/biology/py-pysam/pysam-0.16.0.1/htslib -I/construction/biology/py-pysam/pysam-0.16.0.1/samtools -I/construction/biology/py-pysam/pysam-0.16.0.1/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.16.0.1/bcftools -I/construction/biology/py-pysam/pysam-0.16.0.1/pysam -I/construction/biology/py-pysam/pysam-0.16.0.1 -I/usr/local/include/python3.7m -c htslib/md5.c -o build/temp.dragonfly-6.1-x86_64-3.7/htslib/md5.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -Wno-unused-result -Wsign-compare -DNDEBUG -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -fPIC -I/construction/biology/py-pysam/pysam-0.16.0.1/htslib -I/construction/biology/py-pysam/pysam-0.16.0.1/samtools -I/construction/biology/py-pysam/pysam-0.16.0.1/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.16.0.1/bcftools -I/construction/biology/py-pysam/pysam-0.16.0.1/pysam -I/construction/biology/py-pysam/pysam-0.16.0.1 -I/usr/local/include/python3.7m -c htslib/multipart.c -o build/temp.dragonfly-6.1-x86_64-3.7/htslib/multipart.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -Wno-unused-result -Wsign-compare -DNDEBUG -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -fPIC -I/construction/biology/py-pysam/pysam-0.16.0.1/htslib -I/construction/biology/py-pysam/pysam-0.16.0.1/samtools -I/construction/biology/py-pysam/pysam-0.16.0.1/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.16.0.1/bcftools -I/construction/biology/py-pysam/pysam-0.16.0.1/pysam -I/construction/biology/py-pysam/pysam-0.16.0.1 -I/usr/local/include/python3.7m -c htslib/probaln.c -o build/temp.dragonfly-6.1-x86_64-3.7/htslib/probaln.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -Wno-unused-result -Wsign-compare -DNDEBUG -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -fPIC -I/construction/biology/py-pysam/pysam-0.16.0.1/htslib -I/construction/biology/py-pysam/pysam-0.16.0.1/samtools -I/construction/biology/py-pysam/pysam-0.16.0.1/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.16.0.1/bcftools -I/construction/biology/py-pysam/pysam-0.16.0.1/pysam -I/construction/biology/py-pysam/pysam-0.16.0.1 -I/usr/local/include/python3.7m -c htslib/realn.c -o build/temp.dragonfly-6.1-x86_64-3.7/htslib/realn.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -Wno-unused-result -Wsign-compare -DNDEBUG -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -fPIC -I/construction/biology/py-pysam/pysam-0.16.0.1/htslib -I/construction/biology/py-pysam/pysam-0.16.0.1/samtools -I/construction/biology/py-pysam/pysam-0.16.0.1/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.16.0.1/bcftools -I/construction/biology/py-pysam/pysam-0.16.0.1/pysam -I/construction/biology/py-pysam/pysam-0.16.0.1 -I/usr/local/include/python3.7m -c htslib/regidx.c -o build/temp.dragonfly-6.1-x86_64-3.7/htslib/regidx.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -Wno-unused-result -Wsign-compare -DNDEBUG -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -fPIC -I/construction/biology/py-pysam/pysam-0.16.0.1/htslib -I/construction/biology/py-pysam/pysam-0.16.0.1/samtools -I/construction/biology/py-pysam/pysam-0.16.0.1/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.16.0.1/bcftools -I/construction/biology/py-pysam/pysam-0.16.0.1/pysam -I/construction/biology/py-pysam/pysam-0.16.0.1 -I/usr/local/include/python3.7m -c htslib/region.c -o build/temp.dragonfly-6.1-x86_64-3.7/htslib/region.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -Wno-unused-result -Wsign-compare -DNDEBUG -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -fPIC -I/construction/biology/py-pysam/pysam-0.16.0.1/htslib -I/construction/biology/py-pysam/pysam-0.16.0.1/samtools -I/construction/biology/py-pysam/pysam-0.16.0.1/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.16.0.1/bcftools -I/construction/biology/py-pysam/pysam-0.16.0.1/pysam -I/construction/biology/py-pysam/pysam-0.16.0.1 -I/usr/local/include/python3.7m -c htslib/sam.c -o build/temp.dragonfly-6.1-x86_64-3.7/htslib/sam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -Wno-unused-result -Wsign-compare -DNDEBUG -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -fPIC -I/construction/biology/py-pysam/pysam-0.16.0.1/htslib -I/construction/biology/py-pysam/pysam-0.16.0.1/samtools -I/construction/biology/py-pysam/pysam-0.16.0.1/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.16.0.1/bcftools -I/construction/biology/py-pysam/pysam-0.16.0.1/pysam -I/construction/biology/py-pysam/pysam-0.16.0.1 -I/usr/local/include/python3.7m -c htslib/synced_bcf_reader.c -o build/temp.dragonfly-6.1-x86_64-3.7/htslib/synced_bcf_reader.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -Wno-unused-result -Wsign-compare -DNDEBUG -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -fPIC -I/construction/biology/py-pysam/pysam-0.16.0.1/htslib -I/construction/biology/py-pysam/pysam-0.16.0.1/samtools -I/construction/biology/py-pysam/pysam-0.16.0.1/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.16.0.1/bcftools -I/construction/biology/py-pysam/pysam-0.16.0.1/pysam -I/construction/biology/py-pysam/pysam-0.16.0.1 -I/usr/local/include/python3.7m -c htslib/vcf_sweep.c -o build/temp.dragonfly-6.1-x86_64-3.7/htslib/vcf_sweep.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -Wno-unused-result -Wsign-compare -DNDEBUG -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -fPIC -I/construction/biology/py-pysam/pysam-0.16.0.1/htslib -I/construction/biology/py-pysam/pysam-0.16.0.1/samtools -I/construction/biology/py-pysam/pysam-0.16.0.1/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.16.0.1/bcftools -I/construction/biology/py-pysam/pysam-0.16.0.1/pysam -I/construction/biology/py-pysam/pysam-0.16.0.1 -I/usr/local/include/python3.7m -c htslib/tbx.c -o build/temp.dragonfly-6.1-x86_64-3.7/htslib/tbx.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -Wno-unused-result -Wsign-compare -DNDEBUG -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -fPIC -I/construction/biology/py-pysam/pysam-0.16.0.1/htslib -I/construction/biology/py-pysam/pysam-0.16.0.1/samtools -I/construction/biology/py-pysam/pysam-0.16.0.1/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.16.0.1/bcftools -I/construction/biology/py-pysam/pysam-0.16.0.1/pysam -I/construction/biology/py-pysam/pysam-0.16.0.1 -I/usr/local/include/python3.7m -c htslib/textutils.c -o build/temp.dragonfly-6.1-x86_64-3.7/htslib/textutils.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -Wno-unused-result -Wsign-compare -DNDEBUG -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -fPIC -I/construction/biology/py-pysam/pysam-0.16.0.1/htslib -I/construction/biology/py-pysam/pysam-0.16.0.1/samtools -I/construction/biology/py-pysam/pysam-0.16.0.1/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.16.0.1/bcftools -I/construction/biology/py-pysam/pysam-0.16.0.1/pysam -I/construction/biology/py-pysam/pysam-0.16.0.1 -I/usr/local/include/python3.7m -c htslib/thread_pool.c -o build/temp.dragonfly-6.1-x86_64-3.7/htslib/thread_pool.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -Wno-unused-result -Wsign-compare -DNDEBUG -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -fPIC -I/construction/biology/py-pysam/pysam-0.16.0.1/htslib -I/construction/biology/py-pysam/pysam-0.16.0.1/samtools -I/construction/biology/py-pysam/pysam-0.16.0.1/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.16.0.1/bcftools -I/construction/biology/py-pysam/pysam-0.16.0.1/pysam -I/construction/biology/py-pysam/pysam-0.16.0.1 -I/usr/local/include/python3.7m -c htslib/vcf.c -o build/temp.dragonfly-6.1-x86_64-3.7/htslib/vcf.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -Wno-unused-result -Wsign-compare -DNDEBUG -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -fPIC -I/construction/biology/py-pysam/pysam-0.16.0.1/htslib -I/construction/biology/py-pysam/pysam-0.16.0.1/samtools -I/construction/biology/py-pysam/pysam-0.16.0.1/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.16.0.1/bcftools -I/construction/biology/py-pysam/pysam-0.16.0.1/pysam -I/construction/biology/py-pysam/pysam-0.16.0.1 -I/usr/local/include/python3.7m -c htslib/vcfutils.c -o build/temp.dragonfly-6.1-x86_64-3.7/htslib/vcfutils.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -Wno-unused-result -Wsign-compare -DNDEBUG -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -fPIC -I/construction/biology/py-pysam/pysam-0.16.0.1/htslib -I/construction/biology/py-pysam/pysam-0.16.0.1/samtools -I/construction/biology/py-pysam/pysam-0.16.0.1/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.16.0.1/bcftools -I/construction/biology/py-pysam/pysam-0.16.0.1/pysam -I/construction/biology/py-pysam/pysam-0.16.0.1 -I/usr/local/include/python3.7m -c htslib/cram/cram_codecs.c -o build/temp.dragonfly-6.1-x86_64-3.7/htslib/cram/cram_codecs.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -Wno-unused-result -Wsign-compare -DNDEBUG -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -fPIC -I/construction/biology/py-pysam/pysam-0.16.0.1/htslib -I/construction/biology/py-pysam/pysam-0.16.0.1/samtools -I/construction/biology/py-pysam/pysam-0.16.0.1/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.16.0.1/bcftools -I/construction/biology/py-pysam/pysam-0.16.0.1/pysam -I/construction/biology/py-pysam/pysam-0.16.0.1 -I/usr/local/include/python3.7m -c htslib/cram/cram_decode.c -o build/temp.dragonfly-6.1-x86_64-3.7/htslib/cram/cram_decode.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -Wno-unused-result -Wsign-compare -DNDEBUG -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -fPIC -I/construction/biology/py-pysam/pysam-0.16.0.1/htslib -I/construction/biology/py-pysam/pysam-0.16.0.1/samtools -I/construction/biology/py-pysam/pysam-0.16.0.1/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.16.0.1/bcftools -I/construction/biology/py-pysam/pysam-0.16.0.1/pysam -I/construction/biology/py-pysam/pysam-0.16.0.1 -I/usr/local/include/python3.7m -c htslib/cram/cram_encode.c -o build/temp.dragonfly-6.1-x86_64-3.7/htslib/cram/cram_encode.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -Wno-unused-result -Wsign-compare -DNDEBUG -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -fPIC -I/construction/biology/py-pysam/pysam-0.16.0.1/htslib -I/construction/biology/py-pysam/pysam-0.16.0.1/samtools -I/construction/biology/py-pysam/pysam-0.16.0.1/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.16.0.1/bcftools -I/construction/biology/py-pysam/pysam-0.16.0.1/pysam -I/construction/biology/py-pysam/pysam-0.16.0.1 -I/usr/local/include/python3.7m -c htslib/cram/cram_external.c -o build/temp.dragonfly-6.1-x86_64-3.7/htslib/cram/cram_external.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -Wno-unused-result -Wsign-compare -DNDEBUG -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -fPIC -I/construction/biology/py-pysam/pysam-0.16.0.1/htslib -I/construction/biology/py-pysam/pysam-0.16.0.1/samtools -I/construction/biology/py-pysam/pysam-0.16.0.1/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.16.0.1/bcftools -I/construction/biology/py-pysam/pysam-0.16.0.1/pysam -I/construction/biology/py-pysam/pysam-0.16.0.1 -I/usr/local/include/python3.7m -c htslib/cram/cram_index.c -o build/temp.dragonfly-6.1-x86_64-3.7/htslib/cram/cram_index.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -Wno-unused-result -Wsign-compare -DNDEBUG -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -fPIC -I/construction/biology/py-pysam/pysam-0.16.0.1/htslib -I/construction/biology/py-pysam/pysam-0.16.0.1/samtools -I/construction/biology/py-pysam/pysam-0.16.0.1/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.16.0.1/bcftools -I/construction/biology/py-pysam/pysam-0.16.0.1/pysam -I/construction/biology/py-pysam/pysam-0.16.0.1 -I/usr/local/include/python3.7m -c htslib/cram/cram_io.c -o build/temp.dragonfly-6.1-x86_64-3.7/htslib/cram/cram_io.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -Wno-unused-result -Wsign-compare -DNDEBUG -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -fPIC -I/construction/biology/py-pysam/pysam-0.16.0.1/htslib -I/construction/biology/py-pysam/pysam-0.16.0.1/samtools -I/construction/biology/py-pysam/pysam-0.16.0.1/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.16.0.1/bcftools -I/construction/biology/py-pysam/pysam-0.16.0.1/pysam -I/construction/biology/py-pysam/pysam-0.16.0.1 -I/usr/local/include/python3.7m -c htslib/cram/cram_samtools.c -o build/temp.dragonfly-6.1-x86_64-3.7/htslib/cram/cram_samtools.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -Wno-unused-result -Wsign-compare -DNDEBUG -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -fPIC -I/construction/biology/py-pysam/pysam-0.16.0.1/htslib -I/construction/biology/py-pysam/pysam-0.16.0.1/samtools -I/construction/biology/py-pysam/pysam-0.16.0.1/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.16.0.1/bcftools -I/construction/biology/py-pysam/pysam-0.16.0.1/pysam -I/construction/biology/py-pysam/pysam-0.16.0.1 -I/usr/local/include/python3.7m -c htslib/cram/cram_stats.c -o build/temp.dragonfly-6.1-x86_64-3.7/htslib/cram/cram_stats.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -Wno-unused-result -Wsign-compare -DNDEBUG -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -fPIC -I/construction/biology/py-pysam/pysam-0.16.0.1/htslib -I/construction/biology/py-pysam/pysam-0.16.0.1/samtools -I/construction/biology/py-pysam/pysam-0.16.0.1/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.16.0.1/bcftools -I/construction/biology/py-pysam/pysam-0.16.0.1/pysam -I/construction/biology/py-pysam/pysam-0.16.0.1 -I/usr/local/include/python3.7m -c htslib/cram/mFILE.c -o build/temp.dragonfly-6.1-x86_64-3.7/htslib/cram/mFILE.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -Wno-unused-result -Wsign-compare -DNDEBUG -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -fPIC -I/construction/biology/py-pysam/pysam-0.16.0.1/htslib -I/construction/biology/py-pysam/pysam-0.16.0.1/samtools -I/construction/biology/py-pysam/pysam-0.16.0.1/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.16.0.1/bcftools -I/construction/biology/py-pysam/pysam-0.16.0.1/pysam -I/construction/biology/py-pysam/pysam-0.16.0.1 -I/usr/local/include/python3.7m -c htslib/cram/open_trace_file.c -o build/temp.dragonfly-6.1-x86_64-3.7/htslib/cram/open_trace_file.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -Wno-unused-result -Wsign-compare -DNDEBUG -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -fPIC -I/construction/biology/py-pysam/pysam-0.16.0.1/htslib -I/construction/biology/py-pysam/pysam-0.16.0.1/samtools -I/construction/biology/py-pysam/pysam-0.16.0.1/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.16.0.1/bcftools -I/construction/biology/py-pysam/pysam-0.16.0.1/pysam -I/construction/biology/py-pysam/pysam-0.16.0.1 -I/usr/local/include/python3.7m -c htslib/cram/pooled_alloc.c -o build/temp.dragonfly-6.1-x86_64-3.7/htslib/cram/pooled_alloc.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -Wno-unused-result -Wsign-compare -DNDEBUG -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -fPIC -I/construction/biology/py-pysam/pysam-0.16.0.1/htslib -I/construction/biology/py-pysam/pysam-0.16.0.1/samtools -I/construction/biology/py-pysam/pysam-0.16.0.1/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.16.0.1/bcftools -I/construction/biology/py-pysam/pysam-0.16.0.1/pysam -I/construction/biology/py-pysam/pysam-0.16.0.1 -I/usr/local/include/python3.7m -c htslib/cram/rANS_static.c -o build/temp.dragonfly-6.1-x86_64-3.7/htslib/cram/rANS_static.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -Wno-unused-result -Wsign-compare -DNDEBUG -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -fPIC -I/construction/biology/py-pysam/pysam-0.16.0.1/htslib -I/construction/biology/py-pysam/pysam-0.16.0.1/samtools -I/construction/biology/py-pysam/pysam-0.16.0.1/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.16.0.1/bcftools -I/construction/biology/py-pysam/pysam-0.16.0.1/pysam -I/construction/biology/py-pysam/pysam-0.16.0.1 -I/usr/local/include/python3.7m -c htslib/cram/string_alloc.c -o build/temp.dragonfly-6.1-x86_64-3.7/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-6.1-x86_64-3.7/pysam/libchtslib.o build/temp.dragonfly-6.1-x86_64-3.7/pysam/htslib_util.o build/temp.dragonfly-6.1-x86_64-3.7/htslib/kfunc.o build/temp.dragonfly-6.1-x86_64-3.7/htslib/knetfile.o build/temp.dragonfly-6.1-x86_64-3.7/htslib/kstring.o build/temp.dragonfly-6.1-x86_64-3.7/htslib/bcf_sr_sort.o build/temp.dragonfly-6.1-x86_64-3.7/htslib/bgzf.o build/temp.dragonfly-6.1-x86_64-3.7/htslib/errmod.o build/temp.dragonfly-6.1-x86_64-3.7/htslib/faidx.o build/temp.dragonfly-6.1-x86_64-3.7/htslib/header.o build/temp.dragonfly-6.1-x86_64-3.7/htslib/hfile.o build/temp.dragonfly-6.1-x86_64-3.7/htslib/hfile_net.o build/temp.dragonfly-6.1-x86_64-3.7/htslib/hts.o build/temp.dragonfly-6.1-x86_64-3.7/htslib/hts_os.o build/temp.dragonfly-6.1-x86_64-3.7/htslib/md5.o build/temp.dragonfly-6.1-x86_64-3.7/htslib/multipart.o build/temp.dragonfly-6.1-x86_64-3.7/htslib/probaln.o build/temp.dragonfly-6.1-x86_64-3.7/htslib/realn.o build/temp.dragonfly-6.1-x86_64-3.7/htslib/regidx.o build/temp.dragonfly-6.1-x86_64-3.7/htslib/region.o build/temp.dragonfly-6.1-x86_64-3.7/htslib/sam.o build/temp.dragonfly-6.1-x86_64-3.7/htslib/synced_bcf_reader.o build/temp.dragonfly-6.1-x86_64-3.7/htslib/vcf_sweep.o build/temp.dragonfly-6.1-x86_64-3.7/htslib/tbx.o build/temp.dragonfly-6.1-x86_64-3.7/htslib/textutils.o build/temp.dragonfly-6.1-x86_64-3.7/htslib/thread_pool.o build/temp.dragonfly-6.1-x86_64-3.7/htslib/vcf.o build/temp.dragonfly-6.1-x86_64-3.7/htslib/vcfutils.o build/temp.dragonfly-6.1-x86_64-3.7/htslib/cram/cram_codecs.o build/temp.dragonfly-6.1-x86_64-3.7/htslib/cram/cram_decode.o build/temp.dragonfly-6.1-x86_64-3.7/htslib/cram/cram_encode.o build/temp.dragonfly-6.1-x86_64-3.7/htslib/cram/cram_external.o build/temp.dragonfly-6.1-x86_64-3.7/htslib/cram/cram_index.o build/temp.dragonfly-6.1-x86_64-3.7/htslib/cram/cram_io.o build/temp.dragonfly-6.1-x86_64-3.7/htslib/cram/cram_samtools.o build/temp.dragonfly-6.1-x86_64-3.7/htslib/cram/cram_stats.o build/temp.dragonfly-6.1-x86_64-3.7/htslib/cram/mFILE.o build/temp.dragonfly-6.1-x86_64-3.7/htslib/cram/open_trace_file.o build/temp.dragonfly-6.1-x86_64-3.7/htslib/cram/pooled_alloc.o build/temp.dragonfly-6.1-x86_64-3.7/htslib/cram/rANS_static.o build/temp.dragonfly-6.1-x86_64-3.7/htslib/cram/string_alloc.o -L/construction/biology/py-pysam/pysam-0.16.0.1/pysam -L/construction/biology/py-pysam/pysam-0.16.0.1/pysam -L/construction/biology/py-pysam/pysam-0.16.0.1 -L/construction/biology/py-pysam/pysam-0.16.0.1/build/lib.dragonfly-6.1-x86_64-3.7/pysam -Lbuild/lib.dragonfly-6.1-x86_64-3.7/pysam -L/usr/local/lib -lz -llzma -lbz2 -lz -lm -lpython3.7m -o build/lib.dragonfly-6.1-x86_64-3.7/pysam/libchtslib.so -Wl,-rpath,$ORIGIN building 'pysam.libcsamtools' extension creating build/temp.dragonfly-6.1-x86_64-3.7/samtools creating build/temp.dragonfly-6.1-x86_64-3.7/samtools/lz4 cc -Wno-unused-result -Wsign-compare -DNDEBUG -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -fPIC -I/construction/biology/py-pysam/pysam-0.16.0.1/htslib -I/construction/biology/py-pysam/pysam-0.16.0.1/samtools -I/construction/biology/py-pysam/pysam-0.16.0.1/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.16.0.1/bcftools -I/construction/biology/py-pysam/pysam-0.16.0.1/pysam -I/construction/biology/py-pysam/pysam-0.16.0.1 -I/usr/local/include/python3.7m -c pysam/libcsamtools.c -o build/temp.dragonfly-6.1-x86_64-3.7/pysam/libcsamtools.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -Wno-unused-result -Wsign-compare -DNDEBUG -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -fPIC -I/construction/biology/py-pysam/pysam-0.16.0.1/htslib -I/construction/biology/py-pysam/pysam-0.16.0.1/samtools -I/construction/biology/py-pysam/pysam-0.16.0.1/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.16.0.1/bcftools -I/construction/biology/py-pysam/pysam-0.16.0.1/pysam -I/construction/biology/py-pysam/pysam-0.16.0.1 -I/usr/local/include/python3.7m -c samtools/padding.c.pysam.c -o build/temp.dragonfly-6.1-x86_64-3.7/samtools/padding.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -Wno-unused-result -Wsign-compare -DNDEBUG -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -fPIC -I/construction/biology/py-pysam/pysam-0.16.0.1/htslib -I/construction/biology/py-pysam/pysam-0.16.0.1/samtools -I/construction/biology/py-pysam/pysam-0.16.0.1/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.16.0.1/bcftools -I/construction/biology/py-pysam/pysam-0.16.0.1/pysam -I/construction/biology/py-pysam/pysam-0.16.0.1 -I/usr/local/include/python3.7m -c samtools/bam_quickcheck.c.pysam.c -o build/temp.dragonfly-6.1-x86_64-3.7/samtools/bam_quickcheck.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -Wno-unused-result -Wsign-compare -DNDEBUG -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -fPIC -I/construction/biology/py-pysam/pysam-0.16.0.1/htslib -I/construction/biology/py-pysam/pysam-0.16.0.1/samtools -I/construction/biology/py-pysam/pysam-0.16.0.1/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.16.0.1/bcftools -I/construction/biology/py-pysam/pysam-0.16.0.1/pysam -I/construction/biology/py-pysam/pysam-0.16.0.1 -I/usr/local/include/python3.7m -c samtools/bam_fastq.c.pysam.c -o build/temp.dragonfly-6.1-x86_64-3.7/samtools/bam_fastq.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -Wno-unused-result -Wsign-compare -DNDEBUG -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -fPIC -I/construction/biology/py-pysam/pysam-0.16.0.1/htslib -I/construction/biology/py-pysam/pysam-0.16.0.1/samtools -I/construction/biology/py-pysam/pysam-0.16.0.1/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.16.0.1/bcftools -I/construction/biology/py-pysam/pysam-0.16.0.1/pysam -I/construction/biology/py-pysam/pysam-0.16.0.1 -I/usr/local/include/python3.7m -c samtools/sample.c.pysam.c -o build/temp.dragonfly-6.1-x86_64-3.7/samtools/sample.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -Wno-unused-result -Wsign-compare -DNDEBUG -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -fPIC -I/construction/biology/py-pysam/pysam-0.16.0.1/htslib -I/construction/biology/py-pysam/pysam-0.16.0.1/samtools -I/construction/biology/py-pysam/pysam-0.16.0.1/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.16.0.1/bcftools -I/construction/biology/py-pysam/pysam-0.16.0.1/pysam -I/construction/biology/py-pysam/pysam-0.16.0.1 -I/usr/local/include/python3.7m -c samtools/sam_view.c.pysam.c -o build/temp.dragonfly-6.1-x86_64-3.7/samtools/sam_view.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -Wno-unused-result -Wsign-compare -DNDEBUG -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -fPIC -I/construction/biology/py-pysam/pysam-0.16.0.1/htslib -I/construction/biology/py-pysam/pysam-0.16.0.1/samtools -I/construction/biology/py-pysam/pysam-0.16.0.1/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.16.0.1/bcftools -I/construction/biology/py-pysam/pysam-0.16.0.1/pysam -I/construction/biology/py-pysam/pysam-0.16.0.1 -I/usr/local/include/python3.7m -c samtools/bam_index.c.pysam.c -o build/temp.dragonfly-6.1-x86_64-3.7/samtools/bam_index.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -Wno-unused-result -Wsign-compare -DNDEBUG -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -fPIC -I/construction/biology/py-pysam/pysam-0.16.0.1/htslib -I/construction/biology/py-pysam/pysam-0.16.0.1/samtools -I/construction/biology/py-pysam/pysam-0.16.0.1/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.16.0.1/bcftools -I/construction/biology/py-pysam/pysam-0.16.0.1/pysam -I/construction/biology/py-pysam/pysam-0.16.0.1 -I/usr/local/include/python3.7m -c samtools/bam2bcf.c.pysam.c -o build/temp.dragonfly-6.1-x86_64-3.7/samtools/bam2bcf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -Wno-unused-result -Wsign-compare -DNDEBUG -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -fPIC -I/construction/biology/py-pysam/pysam-0.16.0.1/htslib -I/construction/biology/py-pysam/pysam-0.16.0.1/samtools -I/construction/biology/py-pysam/pysam-0.16.0.1/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.16.0.1/bcftools -I/construction/biology/py-pysam/pysam-0.16.0.1/pysam -I/construction/biology/py-pysam/pysam-0.16.0.1 -I/usr/local/include/python3.7m -c samtools/bedidx.c.pysam.c -o build/temp.dragonfly-6.1-x86_64-3.7/samtools/bedidx.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -Wno-unused-result -Wsign-compare -DNDEBUG -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -fPIC -I/construction/biology/py-pysam/pysam-0.16.0.1/htslib -I/construction/biology/py-pysam/pysam-0.16.0.1/samtools -I/construction/biology/py-pysam/pysam-0.16.0.1/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.16.0.1/bcftools -I/construction/biology/py-pysam/pysam-0.16.0.1/pysam -I/construction/biology/py-pysam/pysam-0.16.0.1 -I/usr/local/include/python3.7m -c samtools/sam_opts.c.pysam.c -o build/temp.dragonfly-6.1-x86_64-3.7/samtools/sam_opts.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -Wno-unused-result -Wsign-compare -DNDEBUG -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -fPIC -I/construction/biology/py-pysam/pysam-0.16.0.1/htslib -I/construction/biology/py-pysam/pysam-0.16.0.1/samtools -I/construction/biology/py-pysam/pysam-0.16.0.1/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.16.0.1/bcftools -I/construction/biology/py-pysam/pysam-0.16.0.1/pysam -I/construction/biology/py-pysam/pysam-0.16.0.1 -I/usr/local/include/python3.7m -c samtools/bamshuf.c.pysam.c -o build/temp.dragonfly-6.1-x86_64-3.7/samtools/bamshuf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -Wno-unused-result -Wsign-compare -DNDEBUG -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -fPIC -I/construction/biology/py-pysam/pysam-0.16.0.1/htslib -I/construction/biology/py-pysam/pysam-0.16.0.1/samtools -I/construction/biology/py-pysam/pysam-0.16.0.1/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.16.0.1/bcftools -I/construction/biology/py-pysam/pysam-0.16.0.1/pysam -I/construction/biology/py-pysam/pysam-0.16.0.1 -I/usr/local/include/python3.7m -c samtools/bam_mate.c.pysam.c -o build/temp.dragonfly-6.1-x86_64-3.7/samtools/bam_mate.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -Wno-unused-result -Wsign-compare -DNDEBUG -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -fPIC -I/construction/biology/py-pysam/pysam-0.16.0.1/htslib -I/construction/biology/py-pysam/pysam-0.16.0.1/samtools -I/construction/biology/py-pysam/pysam-0.16.0.1/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.16.0.1/bcftools -I/construction/biology/py-pysam/pysam-0.16.0.1/pysam -I/construction/biology/py-pysam/pysam-0.16.0.1 -I/usr/local/include/python3.7m -c samtools/bam_lpileup.c.pysam.c -o build/temp.dragonfly-6.1-x86_64-3.7/samtools/bam_lpileup.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -Wno-unused-result -Wsign-compare -DNDEBUG -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -fPIC -I/construction/biology/py-pysam/pysam-0.16.0.1/htslib -I/construction/biology/py-pysam/pysam-0.16.0.1/samtools -I/construction/biology/py-pysam/pysam-0.16.0.1/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.16.0.1/bcftools -I/construction/biology/py-pysam/pysam-0.16.0.1/pysam -I/construction/biology/py-pysam/pysam-0.16.0.1 -I/usr/local/include/python3.7m -c samtools/phase.c.pysam.c -o build/temp.dragonfly-6.1-x86_64-3.7/samtools/phase.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -Wno-unused-result -Wsign-compare -DNDEBUG -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -fPIC -I/construction/biology/py-pysam/pysam-0.16.0.1/htslib -I/construction/biology/py-pysam/pysam-0.16.0.1/samtools -I/construction/biology/py-pysam/pysam-0.16.0.1/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.16.0.1/bcftools -I/construction/biology/py-pysam/pysam-0.16.0.1/pysam -I/construction/biology/py-pysam/pysam-0.16.0.1 -I/usr/local/include/python3.7m -c samtools/bam2bcf_indel.c.pysam.c -o build/temp.dragonfly-6.1-x86_64-3.7/samtools/bam2bcf_indel.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -Wno-unused-result -Wsign-compare -DNDEBUG -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -fPIC -I/construction/biology/py-pysam/pysam-0.16.0.1/htslib -I/construction/biology/py-pysam/pysam-0.16.0.1/samtools -I/construction/biology/py-pysam/pysam-0.16.0.1/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.16.0.1/bcftools -I/construction/biology/py-pysam/pysam-0.16.0.1/pysam -I/construction/biology/py-pysam/pysam-0.16.0.1 -I/usr/local/include/python3.7m -c samtools/bam_aux.c.pysam.c -o build/temp.dragonfly-6.1-x86_64-3.7/samtools/bam_aux.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -Wno-unused-result -Wsign-compare -DNDEBUG -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -fPIC -I/construction/biology/py-pysam/pysam-0.16.0.1/htslib -I/construction/biology/py-pysam/pysam-0.16.0.1/samtools -I/construction/biology/py-pysam/pysam-0.16.0.1/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.16.0.1/bcftools -I/construction/biology/py-pysam/pysam-0.16.0.1/pysam -I/construction/biology/py-pysam/pysam-0.16.0.1 -I/usr/local/include/python3.7m -c samtools/bam_flags.c.pysam.c -o build/temp.dragonfly-6.1-x86_64-3.7/samtools/bam_flags.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -Wno-unused-result -Wsign-compare -DNDEBUG -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -fPIC -I/construction/biology/py-pysam/pysam-0.16.0.1/htslib -I/construction/biology/py-pysam/pysam-0.16.0.1/samtools -I/construction/biology/py-pysam/pysam-0.16.0.1/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.16.0.1/bcftools -I/construction/biology/py-pysam/pysam-0.16.0.1/pysam -I/construction/biology/py-pysam/pysam-0.16.0.1 -I/usr/local/include/python3.7m -c samtools/sam_utils.c.pysam.c -o build/temp.dragonfly-6.1-x86_64-3.7/samtools/sam_utils.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -Wno-unused-result -Wsign-compare -DNDEBUG -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -fPIC -I/construction/biology/py-pysam/pysam-0.16.0.1/htslib -I/construction/biology/py-pysam/pysam-0.16.0.1/samtools -I/construction/biology/py-pysam/pysam-0.16.0.1/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.16.0.1/bcftools -I/construction/biology/py-pysam/pysam-0.16.0.1/pysam -I/construction/biology/py-pysam/pysam-0.16.0.1 -I/usr/local/include/python3.7m -c samtools/bam_plcmd.c.pysam.c -o build/temp.dragonfly-6.1-x86_64-3.7/samtools/bam_plcmd.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -Wno-unused-result -Wsign-compare -DNDEBUG -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -fPIC -I/construction/biology/py-pysam/pysam-0.16.0.1/htslib -I/construction/biology/py-pysam/pysam-0.16.0.1/samtools -I/construction/biology/py-pysam/pysam-0.16.0.1/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.16.0.1/bcftools -I/construction/biology/py-pysam/pysam-0.16.0.1/pysam -I/construction/biology/py-pysam/pysam-0.16.0.1 -I/usr/local/include/python3.7m -c samtools/bam_rmdupse.c.pysam.c -o build/temp.dragonfly-6.1-x86_64-3.7/samtools/bam_rmdupse.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -Wno-unused-result -Wsign-compare -DNDEBUG -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -fPIC -I/construction/biology/py-pysam/pysam-0.16.0.1/htslib -I/construction/biology/py-pysam/pysam-0.16.0.1/samtools -I/construction/biology/py-pysam/pysam-0.16.0.1/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.16.0.1/bcftools -I/construction/biology/py-pysam/pysam-0.16.0.1/pysam -I/construction/biology/py-pysam/pysam-0.16.0.1 -I/usr/local/include/python3.7m -c samtools/bam_addrprg.c.pysam.c -o build/temp.dragonfly-6.1-x86_64-3.7/samtools/bam_addrprg.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -Wno-unused-result -Wsign-compare -DNDEBUG -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -fPIC -I/construction/biology/py-pysam/pysam-0.16.0.1/htslib -I/construction/biology/py-pysam/pysam-0.16.0.1/samtools -I/construction/biology/py-pysam/pysam-0.16.0.1/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.16.0.1/bcftools -I/construction/biology/py-pysam/pysam-0.16.0.1/pysam -I/construction/biology/py-pysam/pysam-0.16.0.1 -I/usr/local/include/python3.7m -c samtools/samtools.pysam.c -o build/temp.dragonfly-6.1-x86_64-3.7/samtools/samtools.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -Wno-unused-result -Wsign-compare -DNDEBUG -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -fPIC -I/construction/biology/py-pysam/pysam-0.16.0.1/htslib -I/construction/biology/py-pysam/pysam-0.16.0.1/samtools -I/construction/biology/py-pysam/pysam-0.16.0.1/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.16.0.1/bcftools -I/construction/biology/py-pysam/pysam-0.16.0.1/pysam -I/construction/biology/py-pysam/pysam-0.16.0.1 -I/usr/local/include/python3.7m -c samtools/cut_target.c.pysam.c -o build/temp.dragonfly-6.1-x86_64-3.7/samtools/cut_target.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -Wno-unused-result -Wsign-compare -DNDEBUG -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -fPIC -I/construction/biology/py-pysam/pysam-0.16.0.1/htslib -I/construction/biology/py-pysam/pysam-0.16.0.1/samtools -I/construction/biology/py-pysam/pysam-0.16.0.1/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.16.0.1/bcftools -I/construction/biology/py-pysam/pysam-0.16.0.1/pysam -I/construction/biology/py-pysam/pysam-0.16.0.1 -I/usr/local/include/python3.7m -c samtools/bam_stat.c.pysam.c -o build/temp.dragonfly-6.1-x86_64-3.7/samtools/bam_stat.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -Wno-unused-result -Wsign-compare -DNDEBUG -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -fPIC -I/construction/biology/py-pysam/pysam-0.16.0.1/htslib -I/construction/biology/py-pysam/pysam-0.16.0.1/samtools -I/construction/biology/py-pysam/pysam-0.16.0.1/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.16.0.1/bcftools -I/construction/biology/py-pysam/pysam-0.16.0.1/pysam -I/construction/biology/py-pysam/pysam-0.16.0.1 -I/usr/local/include/python3.7m -c samtools/bam_color.c.pysam.c -o build/temp.dragonfly-6.1-x86_64-3.7/samtools/bam_color.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -Wno-unused-result -Wsign-compare -DNDEBUG -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -fPIC -I/construction/biology/py-pysam/pysam-0.16.0.1/htslib -I/construction/biology/py-pysam/pysam-0.16.0.1/samtools -I/construction/biology/py-pysam/pysam-0.16.0.1/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.16.0.1/bcftools -I/construction/biology/py-pysam/pysam-0.16.0.1/pysam -I/construction/biology/py-pysam/pysam-0.16.0.1 -I/usr/local/include/python3.7m -c samtools/bam_sort.c.pysam.c -o build/temp.dragonfly-6.1-x86_64-3.7/samtools/bam_sort.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -Wno-unused-result -Wsign-compare -DNDEBUG -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -fPIC -I/construction/biology/py-pysam/pysam-0.16.0.1/htslib -I/construction/biology/py-pysam/pysam-0.16.0.1/samtools -I/construction/biology/py-pysam/pysam-0.16.0.1/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.16.0.1/bcftools -I/construction/biology/py-pysam/pysam-0.16.0.1/pysam -I/construction/biology/py-pysam/pysam-0.16.0.1 -I/usr/local/include/python3.7m -c samtools/tmp_file.c.pysam.c -o build/temp.dragonfly-6.1-x86_64-3.7/samtools/tmp_file.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -Wno-unused-result -Wsign-compare -DNDEBUG -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -fPIC -I/construction/biology/py-pysam/pysam-0.16.0.1/htslib -I/construction/biology/py-pysam/pysam-0.16.0.1/samtools -I/construction/biology/py-pysam/pysam-0.16.0.1/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.16.0.1/bcftools -I/construction/biology/py-pysam/pysam-0.16.0.1/pysam -I/construction/biology/py-pysam/pysam-0.16.0.1 -I/usr/local/include/python3.7m -c samtools/bam_rmdup.c.pysam.c -o build/temp.dragonfly-6.1-x86_64-3.7/samtools/bam_rmdup.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -Wno-unused-result -Wsign-compare -DNDEBUG -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -fPIC -I/construction/biology/py-pysam/pysam-0.16.0.1/htslib -I/construction/biology/py-pysam/pysam-0.16.0.1/samtools -I/construction/biology/py-pysam/pysam-0.16.0.1/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.16.0.1/bcftools -I/construction/biology/py-pysam/pysam-0.16.0.1/pysam -I/construction/biology/py-pysam/pysam-0.16.0.1 -I/usr/local/include/python3.7m -c samtools/bedcov.c.pysam.c -o build/temp.dragonfly-6.1-x86_64-3.7/samtools/bedcov.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -Wno-unused-result -Wsign-compare -DNDEBUG -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -fPIC -I/construction/biology/py-pysam/pysam-0.16.0.1/htslib -I/construction/biology/py-pysam/pysam-0.16.0.1/samtools -I/construction/biology/py-pysam/pysam-0.16.0.1/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.16.0.1/bcftools -I/construction/biology/py-pysam/pysam-0.16.0.1/pysam -I/construction/biology/py-pysam/pysam-0.16.0.1 -I/usr/local/include/python3.7m -c samtools/bam_split.c.pysam.c -o build/temp.dragonfly-6.1-x86_64-3.7/samtools/bam_split.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -Wno-unused-result -Wsign-compare -DNDEBUG -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -fPIC -I/construction/biology/py-pysam/pysam-0.16.0.1/htslib -I/construction/biology/py-pysam/pysam-0.16.0.1/samtools -I/construction/biology/py-pysam/pysam-0.16.0.1/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.16.0.1/bcftools -I/construction/biology/py-pysam/pysam-0.16.0.1/pysam -I/construction/biology/py-pysam/pysam-0.16.0.1 -I/usr/local/include/python3.7m -c samtools/bam_markdup.c.pysam.c -o build/temp.dragonfly-6.1-x86_64-3.7/samtools/bam_markdup.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -Wno-unused-result -Wsign-compare -DNDEBUG -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -fPIC -I/construction/biology/py-pysam/pysam-0.16.0.1/htslib -I/construction/biology/py-pysam/pysam-0.16.0.1/samtools -I/construction/biology/py-pysam/pysam-0.16.0.1/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.16.0.1/bcftools -I/construction/biology/py-pysam/pysam-0.16.0.1/pysam -I/construction/biology/py-pysam/pysam-0.16.0.1 -I/usr/local/include/python3.7m -c samtools/bam_reheader.c.pysam.c -o build/temp.dragonfly-6.1-x86_64-3.7/samtools/bam_reheader.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -Wno-unused-result -Wsign-compare -DNDEBUG -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -fPIC -I/construction/biology/py-pysam/pysam-0.16.0.1/htslib -I/construction/biology/py-pysam/pysam-0.16.0.1/samtools -I/construction/biology/py-pysam/pysam-0.16.0.1/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.16.0.1/bcftools -I/construction/biology/py-pysam/pysam-0.16.0.1/pysam -I/construction/biology/py-pysam/pysam-0.16.0.1 -I/usr/local/include/python3.7m -c samtools/dict.c.pysam.c -o build/temp.dragonfly-6.1-x86_64-3.7/samtools/dict.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -Wno-unused-result -Wsign-compare -DNDEBUG -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -fPIC -I/construction/biology/py-pysam/pysam-0.16.0.1/htslib -I/construction/biology/py-pysam/pysam-0.16.0.1/samtools -I/construction/biology/py-pysam/pysam-0.16.0.1/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.16.0.1/bcftools -I/construction/biology/py-pysam/pysam-0.16.0.1/pysam -I/construction/biology/py-pysam/pysam-0.16.0.1 -I/usr/local/include/python3.7m -c samtools/coverage.c.pysam.c -o build/temp.dragonfly-6.1-x86_64-3.7/samtools/coverage.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -Wno-unused-result -Wsign-compare -DNDEBUG -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -fPIC -I/construction/biology/py-pysam/pysam-0.16.0.1/htslib -I/construction/biology/py-pysam/pysam-0.16.0.1/samtools -I/construction/biology/py-pysam/pysam-0.16.0.1/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.16.0.1/bcftools -I/construction/biology/py-pysam/pysam-0.16.0.1/pysam -I/construction/biology/py-pysam/pysam-0.16.0.1 -I/usr/local/include/python3.7m -c samtools/bam_cat.c.pysam.c -o build/temp.dragonfly-6.1-x86_64-3.7/samtools/bam_cat.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -Wno-unused-result -Wsign-compare -DNDEBUG -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -fPIC -I/construction/biology/py-pysam/pysam-0.16.0.1/htslib -I/construction/biology/py-pysam/pysam-0.16.0.1/samtools -I/construction/biology/py-pysam/pysam-0.16.0.1/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.16.0.1/bcftools -I/construction/biology/py-pysam/pysam-0.16.0.1/pysam -I/construction/biology/py-pysam/pysam-0.16.0.1 -I/usr/local/include/python3.7m -c samtools/bam2depth.c.pysam.c -o build/temp.dragonfly-6.1-x86_64-3.7/samtools/bam2depth.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -Wno-unused-result -Wsign-compare -DNDEBUG -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -fPIC -I/construction/biology/py-pysam/pysam-0.16.0.1/htslib -I/construction/biology/py-pysam/pysam-0.16.0.1/samtools -I/construction/biology/py-pysam/pysam-0.16.0.1/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.16.0.1/bcftools -I/construction/biology/py-pysam/pysam-0.16.0.1/pysam -I/construction/biology/py-pysam/pysam-0.16.0.1 -I/usr/local/include/python3.7m -c samtools/bam_plbuf.c.pysam.c -o build/temp.dragonfly-6.1-x86_64-3.7/samtools/bam_plbuf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -Wno-unused-result -Wsign-compare -DNDEBUG -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -fPIC -I/construction/biology/py-pysam/pysam-0.16.0.1/htslib -I/construction/biology/py-pysam/pysam-0.16.0.1/samtools -I/construction/biology/py-pysam/pysam-0.16.0.1/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.16.0.1/bcftools -I/construction/biology/py-pysam/pysam-0.16.0.1/pysam -I/construction/biology/py-pysam/pysam-0.16.0.1 -I/usr/local/include/python3.7m -c samtools/stats_isize.c.pysam.c -o build/temp.dragonfly-6.1-x86_64-3.7/samtools/stats_isize.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -Wno-unused-result -Wsign-compare -DNDEBUG -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -fPIC -I/construction/biology/py-pysam/pysam-0.16.0.1/htslib -I/construction/biology/py-pysam/pysam-0.16.0.1/samtools -I/construction/biology/py-pysam/pysam-0.16.0.1/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.16.0.1/bcftools -I/construction/biology/py-pysam/pysam-0.16.0.1/pysam -I/construction/biology/py-pysam/pysam-0.16.0.1 -I/usr/local/include/python3.7m -c samtools/stats.c.pysam.c -o build/temp.dragonfly-6.1-x86_64-3.7/samtools/stats.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -Wno-unused-result -Wsign-compare -DNDEBUG -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -fPIC -I/construction/biology/py-pysam/pysam-0.16.0.1/htslib -I/construction/biology/py-pysam/pysam-0.16.0.1/samtools -I/construction/biology/py-pysam/pysam-0.16.0.1/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.16.0.1/bcftools -I/construction/biology/py-pysam/pysam-0.16.0.1/pysam -I/construction/biology/py-pysam/pysam-0.16.0.1 -I/usr/local/include/python3.7m -c samtools/bam_md.c.pysam.c -o build/temp.dragonfly-6.1-x86_64-3.7/samtools/bam_md.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -Wno-unused-result -Wsign-compare -DNDEBUG -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -fPIC -I/construction/biology/py-pysam/pysam-0.16.0.1/htslib -I/construction/biology/py-pysam/pysam-0.16.0.1/samtools -I/construction/biology/py-pysam/pysam-0.16.0.1/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.16.0.1/bcftools -I/construction/biology/py-pysam/pysam-0.16.0.1/pysam -I/construction/biology/py-pysam/pysam-0.16.0.1 -I/usr/local/include/python3.7m -c samtools/bamtk.c.pysam.c -o build/temp.dragonfly-6.1-x86_64-3.7/samtools/bamtk.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -Wno-unused-result -Wsign-compare -DNDEBUG -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -fPIC -I/construction/biology/py-pysam/pysam-0.16.0.1/htslib -I/construction/biology/py-pysam/pysam-0.16.0.1/samtools -I/construction/biology/py-pysam/pysam-0.16.0.1/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.16.0.1/bcftools -I/construction/biology/py-pysam/pysam-0.16.0.1/pysam -I/construction/biology/py-pysam/pysam-0.16.0.1 -I/usr/local/include/python3.7m -c samtools/bam.c.pysam.c -o build/temp.dragonfly-6.1-x86_64-3.7/samtools/bam.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -Wno-unused-result -Wsign-compare -DNDEBUG -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -fPIC -I/construction/biology/py-pysam/pysam-0.16.0.1/htslib -I/construction/biology/py-pysam/pysam-0.16.0.1/samtools -I/construction/biology/py-pysam/pysam-0.16.0.1/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.16.0.1/bcftools -I/construction/biology/py-pysam/pysam-0.16.0.1/pysam -I/construction/biology/py-pysam/pysam-0.16.0.1 -I/usr/local/include/python3.7m -c samtools/sam.c.pysam.c -o build/temp.dragonfly-6.1-x86_64-3.7/samtools/sam.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -Wno-unused-result -Wsign-compare -DNDEBUG -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -fPIC -I/construction/biology/py-pysam/pysam-0.16.0.1/htslib -I/construction/biology/py-pysam/pysam-0.16.0.1/samtools -I/construction/biology/py-pysam/pysam-0.16.0.1/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.16.0.1/bcftools -I/construction/biology/py-pysam/pysam-0.16.0.1/pysam -I/construction/biology/py-pysam/pysam-0.16.0.1 -I/usr/local/include/python3.7m -c samtools/faidx.c.pysam.c -o build/temp.dragonfly-6.1-x86_64-3.7/samtools/faidx.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -Wno-unused-result -Wsign-compare -DNDEBUG -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -fPIC -I/construction/biology/py-pysam/pysam-0.16.0.1/htslib -I/construction/biology/py-pysam/pysam-0.16.0.1/samtools -I/construction/biology/py-pysam/pysam-0.16.0.1/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.16.0.1/bcftools -I/construction/biology/py-pysam/pysam-0.16.0.1/pysam -I/construction/biology/py-pysam/pysam-0.16.0.1 -I/usr/local/include/python3.7m -c samtools/lz4/lz4.c -o build/temp.dragonfly-6.1-x86_64-3.7/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-6.1-x86_64-3.7/pysam/libcsamtools.o build/temp.dragonfly-6.1-x86_64-3.7/samtools/padding.c.pysam.o build/temp.dragonfly-6.1-x86_64-3.7/samtools/bam_quickcheck.c.pysam.o build/temp.dragonfly-6.1-x86_64-3.7/samtools/bam_fastq.c.pysam.o build/temp.dragonfly-6.1-x86_64-3.7/samtools/sample.c.pysam.o build/temp.dragonfly-6.1-x86_64-3.7/samtools/sam_view.c.pysam.o build/temp.dragonfly-6.1-x86_64-3.7/samtools/bam_index.c.pysam.o build/temp.dragonfly-6.1-x86_64-3.7/samtools/bam2bcf.c.pysam.o build/temp.dragonfly-6.1-x86_64-3.7/samtools/bedidx.c.pysam.o build/temp.dragonfly-6.1-x86_64-3.7/samtools/sam_opts.c.pysam.o build/temp.dragonfly-6.1-x86_64-3.7/samtools/bamshuf.c.pysam.o build/temp.dragonfly-6.1-x86_64-3.7/samtools/bam_mate.c.pysam.o build/temp.dragonfly-6.1-x86_64-3.7/samtools/bam_lpileup.c.pysam.o build/temp.dragonfly-6.1-x86_64-3.7/samtools/phase.c.pysam.o build/temp.dragonfly-6.1-x86_64-3.7/samtools/bam2bcf_indel.c.pysam.o build/temp.dragonfly-6.1-x86_64-3.7/samtools/bam_aux.c.pysam.o build/temp.dragonfly-6.1-x86_64-3.7/samtools/bam_flags.c.pysam.o build/temp.dragonfly-6.1-x86_64-3.7/samtools/sam_utils.c.pysam.o build/temp.dragonfly-6.1-x86_64-3.7/samtools/bam_plcmd.c.pysam.o build/temp.dragonfly-6.1-x86_64-3.7/samtools/bam_rmdupse.c.pysam.o build/temp.dragonfly-6.1-x86_64-3.7/samtools/bam_addrprg.c.pysam.o build/temp.dragonfly-6.1-x86_64-3.7/samtools/samtools.pysam.o build/temp.dragonfly-6.1-x86_64-3.7/samtools/cut_target.c.pysam.o build/temp.dragonfly-6.1-x86_64-3.7/samtools/bam_stat.c.pysam.o build/temp.dragonfly-6.1-x86_64-3.7/samtools/bam_color.c.pysam.o build/temp.dragonfly-6.1-x86_64-3.7/samtools/bam_sort.c.pysam.o build/temp.dragonfly-6.1-x86_64-3.7/samtools/tmp_file.c.pysam.o build/temp.dragonfly-6.1-x86_64-3.7/samtools/bam_rmdup.c.pysam.o build/temp.dragonfly-6.1-x86_64-3.7/samtools/bedcov.c.pysam.o build/temp.dragonfly-6.1-x86_64-3.7/samtools/bam_split.c.pysam.o build/temp.dragonfly-6.1-x86_64-3.7/samtools/bam_markdup.c.pysam.o build/temp.dragonfly-6.1-x86_64-3.7/samtools/bam_reheader.c.pysam.o build/temp.dragonfly-6.1-x86_64-3.7/samtools/dict.c.pysam.o build/temp.dragonfly-6.1-x86_64-3.7/samtools/coverage.c.pysam.o build/temp.dragonfly-6.1-x86_64-3.7/samtools/bam_cat.c.pysam.o build/temp.dragonfly-6.1-x86_64-3.7/samtools/bam2depth.c.pysam.o build/temp.dragonfly-6.1-x86_64-3.7/samtools/bam_plbuf.c.pysam.o build/temp.dragonfly-6.1-x86_64-3.7/samtools/stats_isize.c.pysam.o build/temp.dragonfly-6.1-x86_64-3.7/samtools/stats.c.pysam.o build/temp.dragonfly-6.1-x86_64-3.7/samtools/bam_md.c.pysam.o build/temp.dragonfly-6.1-x86_64-3.7/samtools/bamtk.c.pysam.o build/temp.dragonfly-6.1-x86_64-3.7/samtools/bam.c.pysam.o build/temp.dragonfly-6.1-x86_64-3.7/samtools/sam.c.pysam.o build/temp.dragonfly-6.1-x86_64-3.7/samtools/faidx.c.pysam.o build/temp.dragonfly-6.1-x86_64-3.7/samtools/lz4/lz4.o -L/construction/biology/py-pysam/pysam-0.16.0.1/pysam -L/construction/biology/py-pysam/pysam-0.16.0.1/pysam -L/construction/biology/py-pysam/pysam-0.16.0.1 -L/construction/biology/py-pysam/pysam-0.16.0.1/build/lib.dragonfly-6.1-x86_64-3.7/pysam -Lbuild/lib.dragonfly-6.1-x86_64-3.7/pysam -Lbuild/lib.dragonfly-6.1-x86_64-3.7/pysam -L/usr/local/lib -lz -llzma -lbz2 -lz -lm -lchtslib -lpython3.7m -o build/lib.dragonfly-6.1-x86_64-3.7/pysam/libcsamtools.so -Wl,-rpath,$ORIGIN building 'pysam.libcbcftools' extension creating build/temp.dragonfly-6.1-x86_64-3.7/bcftools cc -Wno-unused-result -Wsign-compare -DNDEBUG -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -fPIC -I/construction/biology/py-pysam/pysam-0.16.0.1/htslib -I/construction/biology/py-pysam/pysam-0.16.0.1/samtools -I/construction/biology/py-pysam/pysam-0.16.0.1/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.16.0.1/bcftools -I/construction/biology/py-pysam/pysam-0.16.0.1/pysam -I/construction/biology/py-pysam/pysam-0.16.0.1 -I/usr/local/include/python3.7m -c pysam/libcbcftools.c -o build/temp.dragonfly-6.1-x86_64-3.7/pysam/libcbcftools.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -Wno-unused-result -Wsign-compare -DNDEBUG -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -fPIC -I/construction/biology/py-pysam/pysam-0.16.0.1/htslib -I/construction/biology/py-pysam/pysam-0.16.0.1/samtools -I/construction/biology/py-pysam/pysam-0.16.0.1/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.16.0.1/bcftools -I/construction/biology/py-pysam/pysam-0.16.0.1/pysam -I/construction/biology/py-pysam/pysam-0.16.0.1 -I/usr/local/include/python3.7m -c bcftools/vcmp.c.pysam.c -o build/temp.dragonfly-6.1-x86_64-3.7/bcftools/vcmp.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -Wno-unused-result -Wsign-compare -DNDEBUG -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -fPIC -I/construction/biology/py-pysam/pysam-0.16.0.1/htslib -I/construction/biology/py-pysam/pysam-0.16.0.1/samtools -I/construction/biology/py-pysam/pysam-0.16.0.1/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.16.0.1/bcftools -I/construction/biology/py-pysam/pysam-0.16.0.1/pysam -I/construction/biology/py-pysam/pysam-0.16.0.1 -I/usr/local/include/python3.7m -c bcftools/hclust.c.pysam.c -o build/temp.dragonfly-6.1-x86_64-3.7/bcftools/hclust.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -Wno-unused-result -Wsign-compare -DNDEBUG -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -fPIC -I/construction/biology/py-pysam/pysam-0.16.0.1/htslib -I/construction/biology/py-pysam/pysam-0.16.0.1/samtools -I/construction/biology/py-pysam/pysam-0.16.0.1/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.16.0.1/bcftools -I/construction/biology/py-pysam/pysam-0.16.0.1/pysam -I/construction/biology/py-pysam/pysam-0.16.0.1 -I/usr/local/include/python3.7m -c bcftools/cols.c.pysam.c -o build/temp.dragonfly-6.1-x86_64-3.7/bcftools/cols.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -Wno-unused-result -Wsign-compare -DNDEBUG -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -fPIC -I/construction/biology/py-pysam/pysam-0.16.0.1/htslib -I/construction/biology/py-pysam/pysam-0.16.0.1/samtools -I/construction/biology/py-pysam/pysam-0.16.0.1/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.16.0.1/bcftools -I/construction/biology/py-pysam/pysam-0.16.0.1/pysam -I/construction/biology/py-pysam/pysam-0.16.0.1 -I/usr/local/include/python3.7m -c bcftools/bam2bcf.c.pysam.c -o build/temp.dragonfly-6.1-x86_64-3.7/bcftools/bam2bcf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -Wno-unused-result -Wsign-compare -DNDEBUG -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -fPIC -I/construction/biology/py-pysam/pysam-0.16.0.1/htslib -I/construction/biology/py-pysam/pysam-0.16.0.1/samtools -I/construction/biology/py-pysam/pysam-0.16.0.1/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.16.0.1/bcftools -I/construction/biology/py-pysam/pysam-0.16.0.1/pysam -I/construction/biology/py-pysam/pysam-0.16.0.1 -I/usr/local/include/python3.7m -c bcftools/vcfmerge.c.pysam.c -o build/temp.dragonfly-6.1-x86_64-3.7/bcftools/vcfmerge.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -Wno-unused-result -Wsign-compare -DNDEBUG -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -fPIC -I/construction/biology/py-pysam/pysam-0.16.0.1/htslib -I/construction/biology/py-pysam/pysam-0.16.0.1/samtools -I/construction/biology/py-pysam/pysam-0.16.0.1/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.16.0.1/bcftools -I/construction/biology/py-pysam/pysam-0.16.0.1/pysam -I/construction/biology/py-pysam/pysam-0.16.0.1 -I/usr/local/include/python3.7m -c bcftools/version.c.pysam.c -o build/temp.dragonfly-6.1-x86_64-3.7/bcftools/version.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -Wno-unused-result -Wsign-compare -DNDEBUG -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -fPIC -I/construction/biology/py-pysam/pysam-0.16.0.1/htslib -I/construction/biology/py-pysam/pysam-0.16.0.1/samtools -I/construction/biology/py-pysam/pysam-0.16.0.1/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.16.0.1/bcftools -I/construction/biology/py-pysam/pysam-0.16.0.1/pysam -I/construction/biology/py-pysam/pysam-0.16.0.1 -I/usr/local/include/python3.7m -c bcftools/vcfconvert.c.pysam.c -o build/temp.dragonfly-6.1-x86_64-3.7/bcftools/vcfconvert.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -Wno-unused-result -Wsign-compare -DNDEBUG -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -fPIC -I/construction/biology/py-pysam/pysam-0.16.0.1/htslib -I/construction/biology/py-pysam/pysam-0.16.0.1/samtools -I/construction/biology/py-pysam/pysam-0.16.0.1/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.16.0.1/bcftools -I/construction/biology/py-pysam/pysam-0.16.0.1/pysam -I/construction/biology/py-pysam/pysam-0.16.0.1 -I/usr/local/include/python3.7m -c bcftools/mcall.c.pysam.c -o build/temp.dragonfly-6.1-x86_64-3.7/bcftools/mcall.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -Wno-unused-result -Wsign-compare -DNDEBUG -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -fPIC -I/construction/biology/py-pysam/pysam-0.16.0.1/htslib -I/construction/biology/py-pysam/pysam-0.16.0.1/samtools -I/construction/biology/py-pysam/pysam-0.16.0.1/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.16.0.1/bcftools -I/construction/biology/py-pysam/pysam-0.16.0.1/pysam -I/construction/biology/py-pysam/pysam-0.16.0.1 -I/usr/local/include/python3.7m -c bcftools/consensus.c.pysam.c -o build/temp.dragonfly-6.1-x86_64-3.7/bcftools/consensus.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -Wno-unused-result -Wsign-compare -DNDEBUG -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -fPIC -I/construction/biology/py-pysam/pysam-0.16.0.1/htslib -I/construction/biology/py-pysam/pysam-0.16.0.1/samtools -I/construction/biology/py-pysam/pysam-0.16.0.1/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.16.0.1/bcftools -I/construction/biology/py-pysam/pysam-0.16.0.1/pysam -I/construction/biology/py-pysam/pysam-0.16.0.1 -I/usr/local/include/python3.7m -c bcftools/vcfcnv.c.pysam.c -o build/temp.dragonfly-6.1-x86_64-3.7/bcftools/vcfcnv.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -Wno-unused-result -Wsign-compare -DNDEBUG -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -fPIC -I/construction/biology/py-pysam/pysam-0.16.0.1/htslib -I/construction/biology/py-pysam/pysam-0.16.0.1/samtools -I/construction/biology/py-pysam/pysam-0.16.0.1/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.16.0.1/bcftools -I/construction/biology/py-pysam/pysam-0.16.0.1/pysam -I/construction/biology/py-pysam/pysam-0.16.0.1 -I/usr/local/include/python3.7m -c bcftools/tsv2vcf.c.pysam.c -o build/temp.dragonfly-6.1-x86_64-3.7/bcftools/tsv2vcf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -Wno-unused-result -Wsign-compare -DNDEBUG -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -fPIC -I/construction/biology/py-pysam/pysam-0.16.0.1/htslib -I/construction/biology/py-pysam/pysam-0.16.0.1/samtools -I/construction/biology/py-pysam/pysam-0.16.0.1/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.16.0.1/bcftools -I/construction/biology/py-pysam/pysam-0.16.0.1/pysam -I/construction/biology/py-pysam/pysam-0.16.0.1 -I/usr/local/include/python3.7m -c bcftools/convert.c.pysam.c -o build/temp.dragonfly-6.1-x86_64-3.7/bcftools/convert.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -Wno-unused-result -Wsign-compare -DNDEBUG -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -fPIC -I/construction/biology/py-pysam/pysam-0.16.0.1/htslib -I/construction/biology/py-pysam/pysam-0.16.0.1/samtools -I/construction/biology/py-pysam/pysam-0.16.0.1/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.16.0.1/bcftools -I/construction/biology/py-pysam/pysam-0.16.0.1/pysam -I/construction/biology/py-pysam/pysam-0.16.0.1 -I/usr/local/include/python3.7m -c bcftools/vcfnorm.c.pysam.c -o build/temp.dragonfly-6.1-x86_64-3.7/bcftools/vcfnorm.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -Wno-unused-result -Wsign-compare -DNDEBUG -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -fPIC -I/construction/biology/py-pysam/pysam-0.16.0.1/htslib -I/construction/biology/py-pysam/pysam-0.16.0.1/samtools -I/construction/biology/py-pysam/pysam-0.16.0.1/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.16.0.1/bcftools -I/construction/biology/py-pysam/pysam-0.16.0.1/pysam -I/construction/biology/py-pysam/pysam-0.16.0.1 -I/usr/local/include/python3.7m -c bcftools/gvcf.c.pysam.c -o build/temp.dragonfly-6.1-x86_64-3.7/bcftools/gvcf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -Wno-unused-result -Wsign-compare -DNDEBUG -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -fPIC -I/construction/biology/py-pysam/pysam-0.16.0.1/htslib -I/construction/biology/py-pysam/pysam-0.16.0.1/samtools -I/construction/biology/py-pysam/pysam-0.16.0.1/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.16.0.1/bcftools -I/construction/biology/py-pysam/pysam-0.16.0.1/pysam -I/construction/biology/py-pysam/pysam-0.16.0.1 -I/usr/local/include/python3.7m -c bcftools/smpl_ilist.c.pysam.c -o build/temp.dragonfly-6.1-x86_64-3.7/bcftools/smpl_ilist.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -Wno-unused-result -Wsign-compare -DNDEBUG -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -fPIC -I/construction/biology/py-pysam/pysam-0.16.0.1/htslib -I/construction/biology/py-pysam/pysam-0.16.0.1/samtools -I/construction/biology/py-pysam/pysam-0.16.0.1/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.16.0.1/bcftools -I/construction/biology/py-pysam/pysam-0.16.0.1/pysam -I/construction/biology/py-pysam/pysam-0.16.0.1 -I/usr/local/include/python3.7m -c bcftools/em.c.pysam.c -o build/temp.dragonfly-6.1-x86_64-3.7/bcftools/em.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -Wno-unused-result -Wsign-compare -DNDEBUG -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -fPIC -I/construction/biology/py-pysam/pysam-0.16.0.1/htslib -I/construction/biology/py-pysam/pysam-0.16.0.1/samtools -I/construction/biology/py-pysam/pysam-0.16.0.1/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.16.0.1/bcftools -I/construction/biology/py-pysam/pysam-0.16.0.1/pysam -I/construction/biology/py-pysam/pysam-0.16.0.1 -I/usr/local/include/python3.7m -c bcftools/ploidy.c.pysam.c -o build/temp.dragonfly-6.1-x86_64-3.7/bcftools/ploidy.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -Wno-unused-result -Wsign-compare -DNDEBUG -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -fPIC -I/construction/biology/py-pysam/pysam-0.16.0.1/htslib -I/construction/biology/py-pysam/pysam-0.16.0.1/samtools -I/construction/biology/py-pysam/pysam-0.16.0.1/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.16.0.1/bcftools -I/construction/biology/py-pysam/pysam-0.16.0.1/pysam -I/construction/biology/py-pysam/pysam-0.16.0.1 -I/usr/local/include/python3.7m -c bcftools/kmin.c.pysam.c -o build/temp.dragonfly-6.1-x86_64-3.7/bcftools/kmin.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -Wno-unused-result -Wsign-compare -DNDEBUG -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -fPIC -I/construction/biology/py-pysam/pysam-0.16.0.1/htslib -I/construction/biology/py-pysam/pysam-0.16.0.1/samtools -I/construction/biology/py-pysam/pysam-0.16.0.1/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.16.0.1/bcftools -I/construction/biology/py-pysam/pysam-0.16.0.1/pysam -I/construction/biology/py-pysam/pysam-0.16.0.1 -I/usr/local/include/python3.7m -c bcftools/HMM.c.pysam.c -o build/temp.dragonfly-6.1-x86_64-3.7/bcftools/HMM.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -Wno-unused-result -Wsign-compare -DNDEBUG -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -fPIC -I/construction/biology/py-pysam/pysam-0.16.0.1/htslib -I/construction/biology/py-pysam/pysam-0.16.0.1/samtools -I/construction/biology/py-pysam/pysam-0.16.0.1/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.16.0.1/bcftools -I/construction/biology/py-pysam/pysam-0.16.0.1/pysam -I/construction/biology/py-pysam/pysam-0.16.0.1 -I/usr/local/include/python3.7m -c bcftools/vcfcall.c.pysam.c -o build/temp.dragonfly-6.1-x86_64-3.7/bcftools/vcfcall.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement In function 'init_data', inlined from 'main_vcfcall' at bcftools/vcfcall.c.pysam.c:1062:5: bcftools/vcfcall.c.pysam.c:655:39: warning: argument 1 range [18446744071562067968, 18446744073709551615] exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] args->aux.ploidy = (uint8_t*) malloc(args->nsamples); ^~~~~~~~~~~~~~~~~~~~~~ In file included from /construction/biology/py-pysam/pysam-0.16.0.1/htslib/htslib/kstring.h:30, from /construction/biology/py-pysam/pysam-0.16.0.1/htslib/htslib/vcf.h:41, from bcftools/vcfcall.c.pysam.c:34: bcftools/vcfcall.c.pysam.c: In function 'main_vcfcall': /usr/include/stdlib.h:105:7: note: in a call to allocation function 'malloc' declared here void *malloc(size_t) __malloclike __heedresult __alloc_size(1); ^~~~~~ cc -Wno-unused-result -Wsign-compare -DNDEBUG -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -fPIC -I/construction/biology/py-pysam/pysam-0.16.0.1/htslib -I/construction/biology/py-pysam/pysam-0.16.0.1/samtools -I/construction/biology/py-pysam/pysam-0.16.0.1/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.16.0.1/bcftools -I/construction/biology/py-pysam/pysam-0.16.0.1/pysam -I/construction/biology/py-pysam/pysam-0.16.0.1 -I/usr/local/include/python3.7m -c bcftools/bam2bcf_indel.c.pysam.c -o build/temp.dragonfly-6.1-x86_64-3.7/bcftools/bam2bcf_indel.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -Wno-unused-result -Wsign-compare -DNDEBUG -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -fPIC -I/construction/biology/py-pysam/pysam-0.16.0.1/htslib -I/construction/biology/py-pysam/pysam-0.16.0.1/samtools -I/construction/biology/py-pysam/pysam-0.16.0.1/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.16.0.1/bcftools -I/construction/biology/py-pysam/pysam-0.16.0.1/pysam -I/construction/biology/py-pysam/pysam-0.16.0.1 -I/usr/local/include/python3.7m -c bcftools/reheader.c.pysam.c -o build/temp.dragonfly-6.1-x86_64-3.7/bcftools/reheader.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -Wno-unused-result -Wsign-compare -DNDEBUG -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -fPIC -I/construction/biology/py-pysam/pysam-0.16.0.1/htslib -I/construction/biology/py-pysam/pysam-0.16.0.1/samtools -I/construction/biology/py-pysam/pysam-0.16.0.1/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.16.0.1/bcftools -I/construction/biology/py-pysam/pysam-0.16.0.1/pysam -I/construction/biology/py-pysam/pysam-0.16.0.1 -I/usr/local/include/python3.7m -c bcftools/vcfindex.c.pysam.c -o build/temp.dragonfly-6.1-x86_64-3.7/bcftools/vcfindex.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -Wno-unused-result -Wsign-compare -DNDEBUG -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -fPIC -I/construction/biology/py-pysam/pysam-0.16.0.1/htslib -I/construction/biology/py-pysam/pysam-0.16.0.1/samtools -I/construction/biology/py-pysam/pysam-0.16.0.1/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.16.0.1/bcftools -I/construction/biology/py-pysam/pysam-0.16.0.1/pysam -I/construction/biology/py-pysam/pysam-0.16.0.1 -I/usr/local/include/python3.7m -c bcftools/regidx.c.pysam.c -o build/temp.dragonfly-6.1-x86_64-3.7/bcftools/regidx.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -Wno-unused-result -Wsign-compare -DNDEBUG -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -fPIC -I/construction/biology/py-pysam/pysam-0.16.0.1/htslib -I/construction/biology/py-pysam/pysam-0.16.0.1/samtools -I/construction/biology/py-pysam/pysam-0.16.0.1/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.16.0.1/bcftools -I/construction/biology/py-pysam/pysam-0.16.0.1/pysam -I/construction/biology/py-pysam/pysam-0.16.0.1 -I/usr/local/include/python3.7m -c bcftools/bam_sample.c.pysam.c -o build/temp.dragonfly-6.1-x86_64-3.7/bcftools/bam_sample.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -Wno-unused-result -Wsign-compare -DNDEBUG -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -fPIC -I/construction/biology/py-pysam/pysam-0.16.0.1/htslib -I/construction/biology/py-pysam/pysam-0.16.0.1/samtools -I/construction/biology/py-pysam/pysam-0.16.0.1/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.16.0.1/bcftools -I/construction/biology/py-pysam/pysam-0.16.0.1/pysam -I/construction/biology/py-pysam/pysam-0.16.0.1 -I/usr/local/include/python3.7m -c bcftools/filter.c.pysam.c -o build/temp.dragonfly-6.1-x86_64-3.7/bcftools/filter.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -Wno-unused-result -Wsign-compare -DNDEBUG -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -fPIC -I/construction/biology/py-pysam/pysam-0.16.0.1/htslib -I/construction/biology/py-pysam/pysam-0.16.0.1/samtools -I/construction/biology/py-pysam/pysam-0.16.0.1/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.16.0.1/bcftools -I/construction/biology/py-pysam/pysam-0.16.0.1/pysam -I/construction/biology/py-pysam/pysam-0.16.0.1 -I/usr/local/include/python3.7m -c bcftools/bin.c.pysam.c -o build/temp.dragonfly-6.1-x86_64-3.7/bcftools/bin.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -Wno-unused-result -Wsign-compare -DNDEBUG -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -fPIC -I/construction/biology/py-pysam/pysam-0.16.0.1/htslib -I/construction/biology/py-pysam/pysam-0.16.0.1/samtools -I/construction/biology/py-pysam/pysam-0.16.0.1/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.16.0.1/bcftools -I/construction/biology/py-pysam/pysam-0.16.0.1/pysam -I/construction/biology/py-pysam/pysam-0.16.0.1 -I/usr/local/include/python3.7m -c bcftools/bcftools.pysam.c -o build/temp.dragonfly-6.1-x86_64-3.7/bcftools/bcftools.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -Wno-unused-result -Wsign-compare -DNDEBUG -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -fPIC -I/construction/biology/py-pysam/pysam-0.16.0.1/htslib -I/construction/biology/py-pysam/pysam-0.16.0.1/samtools -I/construction/biology/py-pysam/pysam-0.16.0.1/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.16.0.1/bcftools -I/construction/biology/py-pysam/pysam-0.16.0.1/pysam -I/construction/biology/py-pysam/pysam-0.16.0.1 -I/usr/local/include/python3.7m -c bcftools/vcfconcat.c.pysam.c -o build/temp.dragonfly-6.1-x86_64-3.7/bcftools/vcfconcat.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -Wno-unused-result -Wsign-compare -DNDEBUG -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -fPIC -I/construction/biology/py-pysam/pysam-0.16.0.1/htslib -I/construction/biology/py-pysam/pysam-0.16.0.1/samtools -I/construction/biology/py-pysam/pysam-0.16.0.1/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.16.0.1/bcftools -I/construction/biology/py-pysam/pysam-0.16.0.1/pysam -I/construction/biology/py-pysam/pysam-0.16.0.1 -I/usr/local/include/python3.7m -c bcftools/vcfstats.c.pysam.c -o build/temp.dragonfly-6.1-x86_64-3.7/bcftools/vcfstats.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -Wno-unused-result -Wsign-compare -DNDEBUG -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -fPIC -I/construction/biology/py-pysam/pysam-0.16.0.1/htslib -I/construction/biology/py-pysam/pysam-0.16.0.1/samtools -I/construction/biology/py-pysam/pysam-0.16.0.1/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.16.0.1/bcftools -I/construction/biology/py-pysam/pysam-0.16.0.1/pysam -I/construction/biology/py-pysam/pysam-0.16.0.1 -I/usr/local/include/python3.7m -c bcftools/vcfquery.c.pysam.c -o build/temp.dragonfly-6.1-x86_64-3.7/bcftools/vcfquery.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -Wno-unused-result -Wsign-compare -DNDEBUG -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -fPIC -I/construction/biology/py-pysam/pysam-0.16.0.1/htslib -I/construction/biology/py-pysam/pysam-0.16.0.1/samtools -I/construction/biology/py-pysam/pysam-0.16.0.1/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.16.0.1/bcftools -I/construction/biology/py-pysam/pysam-0.16.0.1/pysam -I/construction/biology/py-pysam/pysam-0.16.0.1 -I/usr/local/include/python3.7m -c bcftools/vcfview.c.pysam.c -o build/temp.dragonfly-6.1-x86_64-3.7/bcftools/vcfview.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -Wno-unused-result -Wsign-compare -DNDEBUG -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -fPIC -I/construction/biology/py-pysam/pysam-0.16.0.1/htslib -I/construction/biology/py-pysam/pysam-0.16.0.1/samtools -I/construction/biology/py-pysam/pysam-0.16.0.1/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.16.0.1/bcftools -I/construction/biology/py-pysam/pysam-0.16.0.1/pysam -I/construction/biology/py-pysam/pysam-0.16.0.1 -I/usr/local/include/python3.7m -c bcftools/vcfroh.c.pysam.c -o build/temp.dragonfly-6.1-x86_64-3.7/bcftools/vcfroh.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -Wno-unused-result -Wsign-compare -DNDEBUG -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -fPIC -I/construction/biology/py-pysam/pysam-0.16.0.1/htslib -I/construction/biology/py-pysam/pysam-0.16.0.1/samtools -I/construction/biology/py-pysam/pysam-0.16.0.1/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.16.0.1/bcftools -I/construction/biology/py-pysam/pysam-0.16.0.1/pysam -I/construction/biology/py-pysam/pysam-0.16.0.1 -I/usr/local/include/python3.7m -c bcftools/vcffilter.c.pysam.c -o build/temp.dragonfly-6.1-x86_64-3.7/bcftools/vcffilter.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -Wno-unused-result -Wsign-compare -DNDEBUG -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -fPIC -I/construction/biology/py-pysam/pysam-0.16.0.1/htslib -I/construction/biology/py-pysam/pysam-0.16.0.1/samtools -I/construction/biology/py-pysam/pysam-0.16.0.1/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.16.0.1/bcftools -I/construction/biology/py-pysam/pysam-0.16.0.1/pysam -I/construction/biology/py-pysam/pysam-0.16.0.1 -I/usr/local/include/python3.7m -c bcftools/mpileup.c.pysam.c -o build/temp.dragonfly-6.1-x86_64-3.7/bcftools/mpileup.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -Wno-unused-result -Wsign-compare -DNDEBUG -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -fPIC -I/construction/biology/py-pysam/pysam-0.16.0.1/htslib -I/construction/biology/py-pysam/pysam-0.16.0.1/samtools -I/construction/biology/py-pysam/pysam-0.16.0.1/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.16.0.1/bcftools -I/construction/biology/py-pysam/pysam-0.16.0.1/pysam -I/construction/biology/py-pysam/pysam-0.16.0.1 -I/usr/local/include/python3.7m -c bcftools/vcfbuf.c.pysam.c -o build/temp.dragonfly-6.1-x86_64-3.7/bcftools/vcfbuf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -Wno-unused-result -Wsign-compare -DNDEBUG -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -fPIC -I/construction/biology/py-pysam/pysam-0.16.0.1/htslib -I/construction/biology/py-pysam/pysam-0.16.0.1/samtools -I/construction/biology/py-pysam/pysam-0.16.0.1/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.16.0.1/bcftools -I/construction/biology/py-pysam/pysam-0.16.0.1/pysam -I/construction/biology/py-pysam/pysam-0.16.0.1 -I/usr/local/include/python3.7m -c bcftools/vcfisec.c.pysam.c -o build/temp.dragonfly-6.1-x86_64-3.7/bcftools/vcfisec.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -Wno-unused-result -Wsign-compare -DNDEBUG -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -fPIC -I/construction/biology/py-pysam/pysam-0.16.0.1/htslib -I/construction/biology/py-pysam/pysam-0.16.0.1/samtools -I/construction/biology/py-pysam/pysam-0.16.0.1/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.16.0.1/bcftools -I/construction/biology/py-pysam/pysam-0.16.0.1/pysam -I/construction/biology/py-pysam/pysam-0.16.0.1 -I/usr/local/include/python3.7m -c bcftools/prob1.c.pysam.c -o build/temp.dragonfly-6.1-x86_64-3.7/bcftools/prob1.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -Wno-unused-result -Wsign-compare -DNDEBUG -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -fPIC -I/construction/biology/py-pysam/pysam-0.16.0.1/htslib -I/construction/biology/py-pysam/pysam-0.16.0.1/samtools -I/construction/biology/py-pysam/pysam-0.16.0.1/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.16.0.1/bcftools -I/construction/biology/py-pysam/pysam-0.16.0.1/pysam -I/construction/biology/py-pysam/pysam-0.16.0.1 -I/usr/local/include/python3.7m -c bcftools/tabix.c.pysam.c -o build/temp.dragonfly-6.1-x86_64-3.7/bcftools/tabix.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -Wno-unused-result -Wsign-compare -DNDEBUG -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -fPIC -I/construction/biology/py-pysam/pysam-0.16.0.1/htslib -I/construction/biology/py-pysam/pysam-0.16.0.1/samtools -I/construction/biology/py-pysam/pysam-0.16.0.1/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.16.0.1/bcftools -I/construction/biology/py-pysam/pysam-0.16.0.1/pysam -I/construction/biology/py-pysam/pysam-0.16.0.1 -I/usr/local/include/python3.7m -c bcftools/main.c.pysam.c -o build/temp.dragonfly-6.1-x86_64-3.7/bcftools/main.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -Wno-unused-result -Wsign-compare -DNDEBUG -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -fPIC -I/construction/biology/py-pysam/pysam-0.16.0.1/htslib -I/construction/biology/py-pysam/pysam-0.16.0.1/samtools -I/construction/biology/py-pysam/pysam-0.16.0.1/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.16.0.1/bcftools -I/construction/biology/py-pysam/pysam-0.16.0.1/pysam -I/construction/biology/py-pysam/pysam-0.16.0.1 -I/usr/local/include/python3.7m -c bcftools/ccall.c.pysam.c -o build/temp.dragonfly-6.1-x86_64-3.7/bcftools/ccall.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -Wno-unused-result -Wsign-compare -DNDEBUG -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -fPIC -I/construction/biology/py-pysam/pysam-0.16.0.1/htslib -I/construction/biology/py-pysam/pysam-0.16.0.1/samtools -I/construction/biology/py-pysam/pysam-0.16.0.1/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.16.0.1/bcftools -I/construction/biology/py-pysam/pysam-0.16.0.1/pysam -I/construction/biology/py-pysam/pysam-0.16.0.1 -I/usr/local/include/python3.7m -c bcftools/vcfsort.c.pysam.c -o build/temp.dragonfly-6.1-x86_64-3.7/bcftools/vcfsort.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -Wno-unused-result -Wsign-compare -DNDEBUG -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -fPIC -I/construction/biology/py-pysam/pysam-0.16.0.1/htslib -I/construction/biology/py-pysam/pysam-0.16.0.1/samtools -I/construction/biology/py-pysam/pysam-0.16.0.1/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.16.0.1/bcftools -I/construction/biology/py-pysam/pysam-0.16.0.1/pysam -I/construction/biology/py-pysam/pysam-0.16.0.1 -I/usr/local/include/python3.7m -c bcftools/csq.c.pysam.c -o build/temp.dragonfly-6.1-x86_64-3.7/bcftools/csq.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -Wno-unused-result -Wsign-compare -DNDEBUG -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -fPIC -I/construction/biology/py-pysam/pysam-0.16.0.1/htslib -I/construction/biology/py-pysam/pysam-0.16.0.1/samtools -I/construction/biology/py-pysam/pysam-0.16.0.1/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.16.0.1/bcftools -I/construction/biology/py-pysam/pysam-0.16.0.1/pysam -I/construction/biology/py-pysam/pysam-0.16.0.1 -I/usr/local/include/python3.7m -c bcftools/vcfplugin.c.pysam.c -o build/temp.dragonfly-6.1-x86_64-3.7/bcftools/vcfplugin.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -Wno-unused-result -Wsign-compare -DNDEBUG -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -fPIC -I/construction/biology/py-pysam/pysam-0.16.0.1/htslib -I/construction/biology/py-pysam/pysam-0.16.0.1/samtools -I/construction/biology/py-pysam/pysam-0.16.0.1/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.16.0.1/bcftools -I/construction/biology/py-pysam/pysam-0.16.0.1/pysam -I/construction/biology/py-pysam/pysam-0.16.0.1 -I/usr/local/include/python3.7m -c bcftools/vcfsom.c.pysam.c -o build/temp.dragonfly-6.1-x86_64-3.7/bcftools/vcfsom.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -Wno-unused-result -Wsign-compare -DNDEBUG -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -fPIC -I/construction/biology/py-pysam/pysam-0.16.0.1/htslib -I/construction/biology/py-pysam/pysam-0.16.0.1/samtools -I/construction/biology/py-pysam/pysam-0.16.0.1/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.16.0.1/bcftools -I/construction/biology/py-pysam/pysam-0.16.0.1/pysam -I/construction/biology/py-pysam/pysam-0.16.0.1 -I/usr/local/include/python3.7m -c bcftools/vcfannotate.c.pysam.c -o build/temp.dragonfly-6.1-x86_64-3.7/bcftools/vcfannotate.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -Wno-unused-result -Wsign-compare -DNDEBUG -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -fPIC -I/construction/biology/py-pysam/pysam-0.16.0.1/htslib -I/construction/biology/py-pysam/pysam-0.16.0.1/samtools -I/construction/biology/py-pysam/pysam-0.16.0.1/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.16.0.1/bcftools -I/construction/biology/py-pysam/pysam-0.16.0.1/pysam -I/construction/biology/py-pysam/pysam-0.16.0.1 -I/usr/local/include/python3.7m -c bcftools/vcfgtcheck.c.pysam.c -o build/temp.dragonfly-6.1-x86_64-3.7/bcftools/vcfgtcheck.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-6.1-x86_64-3.7/pysam/libcbcftools.o build/temp.dragonfly-6.1-x86_64-3.7/bcftools/vcmp.c.pysam.o build/temp.dragonfly-6.1-x86_64-3.7/bcftools/hclust.c.pysam.o build/temp.dragonfly-6.1-x86_64-3.7/bcftools/cols.c.pysam.o build/temp.dragonfly-6.1-x86_64-3.7/bcftools/bam2bcf.c.pysam.o build/temp.dragonfly-6.1-x86_64-3.7/bcftools/vcfmerge.c.pysam.o build/temp.dragonfly-6.1-x86_64-3.7/bcftools/version.c.pysam.o build/temp.dragonfly-6.1-x86_64-3.7/bcftools/vcfconvert.c.pysam.o build/temp.dragonfly-6.1-x86_64-3.7/bcftools/mcall.c.pysam.o build/temp.dragonfly-6.1-x86_64-3.7/bcftools/consensus.c.pysam.o build/temp.dragonfly-6.1-x86_64-3.7/bcftools/vcfcnv.c.pysam.o build/temp.dragonfly-6.1-x86_64-3.7/bcftools/tsv2vcf.c.pysam.o build/temp.dragonfly-6.1-x86_64-3.7/bcftools/convert.c.pysam.o build/temp.dragonfly-6.1-x86_64-3.7/bcftools/vcfnorm.c.pysam.o build/temp.dragonfly-6.1-x86_64-3.7/bcftools/gvcf.c.pysam.o build/temp.dragonfly-6.1-x86_64-3.7/bcftools/smpl_ilist.c.pysam.o build/temp.dragonfly-6.1-x86_64-3.7/bcftools/em.c.pysam.o build/temp.dragonfly-6.1-x86_64-3.7/bcftools/ploidy.c.pysam.o build/temp.dragonfly-6.1-x86_64-3.7/bcftools/kmin.c.pysam.o build/temp.dragonfly-6.1-x86_64-3.7/bcftools/HMM.c.pysam.o build/temp.dragonfly-6.1-x86_64-3.7/bcftools/vcfcall.c.pysam.o build/temp.dragonfly-6.1-x86_64-3.7/bcftools/bam2bcf_indel.c.pysam.o build/temp.dragonfly-6.1-x86_64-3.7/bcftools/reheader.c.pysam.o build/temp.dragonfly-6.1-x86_64-3.7/bcftools/vcfindex.c.pysam.o build/temp.dragonfly-6.1-x86_64-3.7/bcftools/regidx.c.pysam.o build/temp.dragonfly-6.1-x86_64-3.7/bcftools/bam_sample.c.pysam.o build/temp.dragonfly-6.1-x86_64-3.7/bcftools/filter.c.pysam.o build/temp.dragonfly-6.1-x86_64-3.7/bcftools/bin.c.pysam.o build/temp.dragonfly-6.1-x86_64-3.7/bcftools/bcftools.pysam.o build/temp.dragonfly-6.1-x86_64-3.7/bcftools/vcfconcat.c.pysam.o build/temp.dragonfly-6.1-x86_64-3.7/bcftools/vcfstats.c.pysam.o build/temp.dragonfly-6.1-x86_64-3.7/bcftools/vcfquery.c.pysam.o build/temp.dragonfly-6.1-x86_64-3.7/bcftools/vcfview.c.pysam.o build/temp.dragonfly-6.1-x86_64-3.7/bcftools/vcfroh.c.pysam.o build/temp.dragonfly-6.1-x86_64-3.7/bcftools/vcffilter.c.pysam.o build/temp.dragonfly-6.1-x86_64-3.7/bcftools/mpileup.c.pysam.o build/temp.dragonfly-6.1-x86_64-3.7/bcftools/vcfbuf.c.pysam.o build/temp.dragonfly-6.1-x86_64-3.7/bcftools/vcfisec.c.pysam.o build/temp.dragonfly-6.1-x86_64-3.7/bcftools/prob1.c.pysam.o build/temp.dragonfly-6.1-x86_64-3.7/bcftools/tabix.c.pysam.o build/temp.dragonfly-6.1-x86_64-3.7/bcftools/main.c.pysam.o build/temp.dragonfly-6.1-x86_64-3.7/bcftools/ccall.c.pysam.o build/temp.dragonfly-6.1-x86_64-3.7/bcftools/vcfsort.c.pysam.o build/temp.dragonfly-6.1-x86_64-3.7/bcftools/csq.c.pysam.o build/temp.dragonfly-6.1-x86_64-3.7/bcftools/vcfplugin.c.pysam.o build/temp.dragonfly-6.1-x86_64-3.7/bcftools/vcfsom.c.pysam.o build/temp.dragonfly-6.1-x86_64-3.7/bcftools/vcfannotate.c.pysam.o build/temp.dragonfly-6.1-x86_64-3.7/bcftools/vcfgtcheck.c.pysam.o -L/construction/biology/py-pysam/pysam-0.16.0.1/pysam -L/construction/biology/py-pysam/pysam-0.16.0.1/pysam -L/construction/biology/py-pysam/pysam-0.16.0.1 -L/construction/biology/py-pysam/pysam-0.16.0.1/build/lib.dragonfly-6.1-x86_64-3.7/pysam -Lbuild/lib.dragonfly-6.1-x86_64-3.7/pysam -Lbuild/lib.dragonfly-6.1-x86_64-3.7/pysam -Lbuild/lib.dragonfly-6.1-x86_64-3.7/pysam -L/usr/local/lib -lz -llzma -lbz2 -lz -lm -lchtslib -lpython3.7m -o build/lib.dragonfly-6.1-x86_64-3.7/pysam/libcbcftools.so -Wl,-rpath,$ORIGIN building 'pysam.libcutils' extension cc -Wno-unused-result -Wsign-compare -DNDEBUG -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -fPIC -I/construction/biology/py-pysam/pysam-0.16.0.1/htslib -I/construction/biology/py-pysam/pysam-0.16.0.1/samtools -I/construction/biology/py-pysam/pysam-0.16.0.1/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.16.0.1/bcftools -I/construction/biology/py-pysam/pysam-0.16.0.1/pysam -I/construction/biology/py-pysam/pysam-0.16.0.1 -I/usr/local/include/python3.7m -c pysam/libcutils.c -o build/temp.dragonfly-6.1-x86_64-3.7/pysam/libcutils.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -Wno-unused-result -Wsign-compare -DNDEBUG -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -fPIC -I/construction/biology/py-pysam/pysam-0.16.0.1/htslib -I/construction/biology/py-pysam/pysam-0.16.0.1/samtools -I/construction/biology/py-pysam/pysam-0.16.0.1/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.16.0.1/bcftools -I/construction/biology/py-pysam/pysam-0.16.0.1/pysam -I/construction/biology/py-pysam/pysam-0.16.0.1 -I/usr/local/include/python3.7m -c pysam/pysam_util.c -o build/temp.dragonfly-6.1-x86_64-3.7/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-6.1-x86_64-3.7/pysam/libcutils.o build/temp.dragonfly-6.1-x86_64-3.7/pysam/pysam_util.o -L/construction/biology/py-pysam/pysam-0.16.0.1/pysam -L/construction/biology/py-pysam/pysam-0.16.0.1/pysam -L/construction/biology/py-pysam/pysam-0.16.0.1 -L/construction/biology/py-pysam/pysam-0.16.0.1/build/lib.dragonfly-6.1-x86_64-3.7/pysam -Lbuild/lib.dragonfly-6.1-x86_64-3.7/pysam -Lbuild/lib.dragonfly-6.1-x86_64-3.7/pysam -Lbuild/lib.dragonfly-6.1-x86_64-3.7/pysam -Lbuild/lib.dragonfly-6.1-x86_64-3.7/pysam -L/usr/local/lib -lz -llzma -lbz2 -lz -lm -lchtslib -lcsamtools -lcbcftools -lpython3.7m -o build/lib.dragonfly-6.1-x86_64-3.7/pysam/libcutils.so -Wl,-rpath,$ORIGIN building 'pysam.libcalignmentfile' extension cc -Wno-unused-result -Wsign-compare -DNDEBUG -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -fPIC -I/construction/biology/py-pysam/pysam-0.16.0.1/htslib -I/construction/biology/py-pysam/pysam-0.16.0.1/samtools -I/construction/biology/py-pysam/pysam-0.16.0.1/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.16.0.1/bcftools -I/construction/biology/py-pysam/pysam-0.16.0.1/pysam -I/construction/biology/py-pysam/pysam-0.16.0.1 -I/usr/local/include/python3.7m -c pysam/libcalignmentfile.c -o build/temp.dragonfly-6.1-x86_64-3.7/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:30108:127: 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, from pysam/libcalignmentfile.c:612: /construction/biology/py-pysam/pysam-0.16.0.1/htslib/htslib/sam.h:1709:96: 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); ~~~~~~~~~~~~~~~~~~~~~~^~~ cc -shared -pipe -O2 -fno-strict-aliasing build/temp.dragonfly-6.1-x86_64-3.7/pysam/libcalignmentfile.o -L/construction/biology/py-pysam/pysam-0.16.0.1/pysam -L/construction/biology/py-pysam/pysam-0.16.0.1/pysam -L/construction/biology/py-pysam/pysam-0.16.0.1 -L/construction/biology/py-pysam/pysam-0.16.0.1/build/lib.dragonfly-6.1-x86_64-3.7/pysam -Lbuild/lib.dragonfly-6.1-x86_64-3.7/pysam -Lbuild/lib.dragonfly-6.1-x86_64-3.7/pysam -Lbuild/lib.dragonfly-6.1-x86_64-3.7/pysam -Lbuild/lib.dragonfly-6.1-x86_64-3.7/pysam -Lbuild/lib.dragonfly-6.1-x86_64-3.7/pysam -L/usr/local/lib -lz -llzma -lbz2 -lz -lm -lchtslib -lcutils -lpython3.7m -o build/lib.dragonfly-6.1-x86_64-3.7/pysam/libcalignmentfile.so -Wl,-rpath,$ORIGIN building 'pysam.libcsamfile' extension cc -Wno-unused-result -Wsign-compare -DNDEBUG -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -fPIC -I/construction/biology/py-pysam/pysam-0.16.0.1/htslib -I/construction/biology/py-pysam/pysam-0.16.0.1/samtools -I/construction/biology/py-pysam/pysam-0.16.0.1/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.16.0.1/bcftools -I/construction/biology/py-pysam/pysam-0.16.0.1/pysam -I/construction/biology/py-pysam/pysam-0.16.0.1 -I/usr/local/include/python3.7m -c pysam/libcsamfile.c -o build/temp.dragonfly-6.1-x86_64-3.7/pysam/libcsamfile.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -shared -pipe -O2 -fno-strict-aliasing build/temp.dragonfly-6.1-x86_64-3.7/pysam/libcsamfile.o -L/construction/biology/py-pysam/pysam-0.16.0.1/pysam -L/construction/biology/py-pysam/pysam-0.16.0.1/pysam -L/construction/biology/py-pysam/pysam-0.16.0.1 -L/construction/biology/py-pysam/pysam-0.16.0.1/build/lib.dragonfly-6.1-x86_64-3.7/pysam -Lbuild/lib.dragonfly-6.1-x86_64-3.7/pysam -Lbuild/lib.dragonfly-6.1-x86_64-3.7/pysam -Lbuild/lib.dragonfly-6.1-x86_64-3.7/pysam -Lbuild/lib.dragonfly-6.1-x86_64-3.7/pysam -Lbuild/lib.dragonfly-6.1-x86_64-3.7/pysam -Lbuild/lib.dragonfly-6.1-x86_64-3.7/pysam -L/usr/local/lib -lz -llzma -lbz2 -lz -lm -lchtslib -lcutils -lpython3.7m -o build/lib.dragonfly-6.1-x86_64-3.7/pysam/libcsamfile.so -Wl,-rpath,$ORIGIN building 'pysam.libcalignedsegment' extension cc -Wno-unused-result -Wsign-compare -DNDEBUG -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -fPIC -I/construction/biology/py-pysam/pysam-0.16.0.1/htslib -I/construction/biology/py-pysam/pysam-0.16.0.1/samtools -I/construction/biology/py-pysam/pysam-0.16.0.1/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.16.0.1/bcftools -I/construction/biology/py-pysam/pysam-0.16.0.1/pysam -I/construction/biology/py-pysam/pysam-0.16.0.1 -I/usr/local/include/python3.7m -c pysam/libcalignedsegment.c -o build/temp.dragonfly-6.1-x86_64-3.7/pysam/libcalignedsegment.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -shared -pipe -O2 -fno-strict-aliasing build/temp.dragonfly-6.1-x86_64-3.7/pysam/libcalignedsegment.o -L/construction/biology/py-pysam/pysam-0.16.0.1/pysam -L/construction/biology/py-pysam/pysam-0.16.0.1/pysam -L/construction/biology/py-pysam/pysam-0.16.0.1 -L/construction/biology/py-pysam/pysam-0.16.0.1/build/lib.dragonfly-6.1-x86_64-3.7/pysam -Lbuild/lib.dragonfly-6.1-x86_64-3.7/pysam -Lbuild/lib.dragonfly-6.1-x86_64-3.7/pysam -Lbuild/lib.dragonfly-6.1-x86_64-3.7/pysam -Lbuild/lib.dragonfly-6.1-x86_64-3.7/pysam -Lbuild/lib.dragonfly-6.1-x86_64-3.7/pysam -Lbuild/lib.dragonfly-6.1-x86_64-3.7/pysam -Lbuild/lib.dragonfly-6.1-x86_64-3.7/pysam -L/usr/local/lib -lz -llzma -lbz2 -lz -lm -lchtslib -lcutils -lpython3.7m -o build/lib.dragonfly-6.1-x86_64-3.7/pysam/libcalignedsegment.so -Wl,-rpath,$ORIGIN building 'pysam.libctabix' extension cc -Wno-unused-result -Wsign-compare -DNDEBUG -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -fPIC -I/construction/biology/py-pysam/pysam-0.16.0.1/htslib -I/construction/biology/py-pysam/pysam-0.16.0.1/samtools -I/construction/biology/py-pysam/pysam-0.16.0.1/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.16.0.1/bcftools -I/construction/biology/py-pysam/pysam-0.16.0.1/pysam -I/construction/biology/py-pysam/pysam-0.16.0.1 -I/usr/local/include/python3.7m -c pysam/libctabix.c -o build/temp.dragonfly-6.1-x86_64-3.7/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:8759:27: warning: assignment to 'char **' from incompatible pointer type 'const char **' [-Wincompatible-pointer-types] __pyx_v_sequences = tbx_seqnames(__pyx_v_self->index, (&__pyx_v_nsequences)); ^ In file included from pysam/libctabix.c:619: pysam/libctabix.c: In function '__pyx_pf_5pysam_9libctabix_4tabix_index': /construction/biology/py-pysam/pysam-0.16.0.1/htslib/htslib/tbx.h:41:21: warning: overflow in conversion from 'int' to 'int8_t' {aka 'signed char'} changes value from '65536' to '0' [-Woverflow] #define TBX_UCSC 0x10000 ^~~~~~~ pysam/libctabix.c:13954:39: 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, 975, __pyx_L1_error) ^~~~~~~~ /construction/biology/py-pysam/pysam-0.16.0.1/htslib/htslib/tbx.h:41:21: warning: overflow in conversion from 'int' to 'int8_t' {aka 'signed char'} changes value from '65536' to '0' [-Woverflow] #define TBX_UCSC 0x10000 ^~~~~~~ pysam/libctabix.c:13986:39: 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, 976, __pyx_L1_error) ^~~~~~~~ /construction/biology/py-pysam/pysam-0.16.0.1/htslib/htslib/tbx.h:41:21: warning: overflow in conversion from 'int' to 'int8_t' {aka 'signed char'} changes value from '65536' to '0' [-Woverflow] #define TBX_UCSC 0x10000 ^~~~~~~ pysam/libctabix.c:14356:43: 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, 1005, __pyx_L1_error) ^~~~~~~~ cc -shared -pipe -O2 -fno-strict-aliasing build/temp.dragonfly-6.1-x86_64-3.7/pysam/libctabix.o -L/construction/biology/py-pysam/pysam-0.16.0.1/pysam -L/construction/biology/py-pysam/pysam-0.16.0.1/pysam -L/construction/biology/py-pysam/pysam-0.16.0.1 -L/construction/biology/py-pysam/pysam-0.16.0.1/build/lib.dragonfly-6.1-x86_64-3.7/pysam -Lbuild/lib.dragonfly-6.1-x86_64-3.7/pysam -Lbuild/lib.dragonfly-6.1-x86_64-3.7/pysam -Lbuild/lib.dragonfly-6.1-x86_64-3.7/pysam -Lbuild/lib.dragonfly-6.1-x86_64-3.7/pysam -Lbuild/lib.dragonfly-6.1-x86_64-3.7/pysam -Lbuild/lib.dragonfly-6.1-x86_64-3.7/pysam -Lbuild/lib.dragonfly-6.1-x86_64-3.7/pysam -Lbuild/lib.dragonfly-6.1-x86_64-3.7/pysam -L/usr/local/lib -lz -llzma -lbz2 -lz -lm -lchtslib -lcutils -lpython3.7m -o build/lib.dragonfly-6.1-x86_64-3.7/pysam/libctabix.so -Wl,-rpath,$ORIGIN building 'pysam.libcfaidx' extension cc -Wno-unused-result -Wsign-compare -DNDEBUG -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -fPIC -I/construction/biology/py-pysam/pysam-0.16.0.1/htslib -I/construction/biology/py-pysam/pysam-0.16.0.1/samtools -I/construction/biology/py-pysam/pysam-0.16.0.1/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.16.0.1/bcftools -I/construction/biology/py-pysam/pysam-0.16.0.1/pysam -I/construction/biology/py-pysam/pysam-0.16.0.1 -I/usr/local/include/python3.7m -c pysam/libcfaidx.c -o build/temp.dragonfly-6.1-x86_64-3.7/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-6.1-x86_64-3.7/pysam/libcfaidx.o -L/construction/biology/py-pysam/pysam-0.16.0.1/pysam -L/construction/biology/py-pysam/pysam-0.16.0.1/pysam -L/construction/biology/py-pysam/pysam-0.16.0.1 -L/construction/biology/py-pysam/pysam-0.16.0.1/build/lib.dragonfly-6.1-x86_64-3.7/pysam -Lbuild/lib.dragonfly-6.1-x86_64-3.7/pysam -Lbuild/lib.dragonfly-6.1-x86_64-3.7/pysam -Lbuild/lib.dragonfly-6.1-x86_64-3.7/pysam -Lbuild/lib.dragonfly-6.1-x86_64-3.7/pysam -Lbuild/lib.dragonfly-6.1-x86_64-3.7/pysam -Lbuild/lib.dragonfly-6.1-x86_64-3.7/pysam -Lbuild/lib.dragonfly-6.1-x86_64-3.7/pysam -Lbuild/lib.dragonfly-6.1-x86_64-3.7/pysam -Lbuild/lib.dragonfly-6.1-x86_64-3.7/pysam -L/usr/local/lib -lz -llzma -lbz2 -lz -lm -lchtslib -lcutils -lpython3.7m -o build/lib.dragonfly-6.1-x86_64-3.7/pysam/libcfaidx.so -Wl,-rpath,$ORIGIN building 'pysam.libcbcf' extension cc -Wno-unused-result -Wsign-compare -DNDEBUG -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -fPIC -I/construction/biology/py-pysam/pysam-0.16.0.1/htslib -I/construction/biology/py-pysam/pysam-0.16.0.1/samtools -I/construction/biology/py-pysam/pysam-0.16.0.1/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.16.0.1/bcftools -I/construction/biology/py-pysam/pysam-0.16.0.1/pysam -I/construction/biology/py-pysam/pysam-0.16.0.1 -I/usr/local/include/python3.7m -c pysam/libcbcf.c -o build/temp.dragonfly-6.1-x86_64-3.7/pysam/libcbcf.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -shared -pipe -O2 -fno-strict-aliasing build/temp.dragonfly-6.1-x86_64-3.7/pysam/libcbcf.o -L/construction/biology/py-pysam/pysam-0.16.0.1/pysam -L/construction/biology/py-pysam/pysam-0.16.0.1/pysam -L/construction/biology/py-pysam/pysam-0.16.0.1 -L/construction/biology/py-pysam/pysam-0.16.0.1/build/lib.dragonfly-6.1-x86_64-3.7/pysam -Lbuild/lib.dragonfly-6.1-x86_64-3.7/pysam -Lbuild/lib.dragonfly-6.1-x86_64-3.7/pysam -Lbuild/lib.dragonfly-6.1-x86_64-3.7/pysam -Lbuild/lib.dragonfly-6.1-x86_64-3.7/pysam -Lbuild/lib.dragonfly-6.1-x86_64-3.7/pysam -Lbuild/lib.dragonfly-6.1-x86_64-3.7/pysam -Lbuild/lib.dragonfly-6.1-x86_64-3.7/pysam -Lbuild/lib.dragonfly-6.1-x86_64-3.7/pysam -Lbuild/lib.dragonfly-6.1-x86_64-3.7/pysam -Lbuild/lib.dragonfly-6.1-x86_64-3.7/pysam -L/usr/local/lib -lz -llzma -lbz2 -lz -lm -lchtslib -lcutils -lpython3.7m -o build/lib.dragonfly-6.1-x86_64-3.7/pysam/libcbcf.so -Wl,-rpath,$ORIGIN building 'pysam.libcbgzf' extension cc -Wno-unused-result -Wsign-compare -DNDEBUG -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -fPIC -I/construction/biology/py-pysam/pysam-0.16.0.1/htslib -I/construction/biology/py-pysam/pysam-0.16.0.1/samtools -I/construction/biology/py-pysam/pysam-0.16.0.1/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.16.0.1/bcftools -I/construction/biology/py-pysam/pysam-0.16.0.1/pysam -I/construction/biology/py-pysam/pysam-0.16.0.1 -I/usr/local/include/python3.7m -c pysam/libcbgzf.c -o build/temp.dragonfly-6.1-x86_64-3.7/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-6.1-x86_64-3.7/pysam/libcbgzf.o -L/construction/biology/py-pysam/pysam-0.16.0.1/pysam -L/construction/biology/py-pysam/pysam-0.16.0.1/pysam -L/construction/biology/py-pysam/pysam-0.16.0.1 -L/construction/biology/py-pysam/pysam-0.16.0.1/build/lib.dragonfly-6.1-x86_64-3.7/pysam -Lbuild/lib.dragonfly-6.1-x86_64-3.7/pysam -Lbuild/lib.dragonfly-6.1-x86_64-3.7/pysam -Lbuild/lib.dragonfly-6.1-x86_64-3.7/pysam -Lbuild/lib.dragonfly-6.1-x86_64-3.7/pysam -Lbuild/lib.dragonfly-6.1-x86_64-3.7/pysam -Lbuild/lib.dragonfly-6.1-x86_64-3.7/pysam -Lbuild/lib.dragonfly-6.1-x86_64-3.7/pysam -Lbuild/lib.dragonfly-6.1-x86_64-3.7/pysam -Lbuild/lib.dragonfly-6.1-x86_64-3.7/pysam -Lbuild/lib.dragonfly-6.1-x86_64-3.7/pysam -Lbuild/lib.dragonfly-6.1-x86_64-3.7/pysam -L/usr/local/lib -lz -llzma -lbz2 -lz -lm -lchtslib -lcutils -lpython3.7m -o build/lib.dragonfly-6.1-x86_64-3.7/pysam/libcbgzf.so -Wl,-rpath,$ORIGIN building 'pysam.libctabixproxies' extension cc -Wno-unused-result -Wsign-compare -DNDEBUG -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -fPIC -I/construction/biology/py-pysam/pysam-0.16.0.1/htslib -I/construction/biology/py-pysam/pysam-0.16.0.1/samtools -I/construction/biology/py-pysam/pysam-0.16.0.1/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.16.0.1/bcftools -I/construction/biology/py-pysam/pysam-0.16.0.1/pysam -I/construction/biology/py-pysam/pysam-0.16.0.1 -I/usr/local/include/python3.7m -c pysam/libctabixproxies.c -o build/temp.dragonfly-6.1-x86_64-3.7/pysam/libctabixproxies.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -shared -pipe -O2 -fno-strict-aliasing build/temp.dragonfly-6.1-x86_64-3.7/pysam/libctabixproxies.o -L/construction/biology/py-pysam/pysam-0.16.0.1/pysam -L/construction/biology/py-pysam/pysam-0.16.0.1/pysam -L/construction/biology/py-pysam/pysam-0.16.0.1 -L/construction/biology/py-pysam/pysam-0.16.0.1/build/lib.dragonfly-6.1-x86_64-3.7/pysam -Lbuild/lib.dragonfly-6.1-x86_64-3.7/pysam -Lbuild/lib.dragonfly-6.1-x86_64-3.7/pysam -Lbuild/lib.dragonfly-6.1-x86_64-3.7/pysam -Lbuild/lib.dragonfly-6.1-x86_64-3.7/pysam -Lbuild/lib.dragonfly-6.1-x86_64-3.7/pysam -Lbuild/lib.dragonfly-6.1-x86_64-3.7/pysam -Lbuild/lib.dragonfly-6.1-x86_64-3.7/pysam -Lbuild/lib.dragonfly-6.1-x86_64-3.7/pysam -Lbuild/lib.dragonfly-6.1-x86_64-3.7/pysam -Lbuild/lib.dragonfly-6.1-x86_64-3.7/pysam -Lbuild/lib.dragonfly-6.1-x86_64-3.7/pysam -Lbuild/lib.dragonfly-6.1-x86_64-3.7/pysam -L/usr/local/lib -lz -llzma -lbz2 -lz -lm -lchtslib -lcutils -lpython3.7m -o build/lib.dragonfly-6.1-x86_64-3.7/pysam/libctabixproxies.so -Wl,-rpath,$ORIGIN building 'pysam.libcvcf' extension cc -Wno-unused-result -Wsign-compare -DNDEBUG -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -fPIC -I/construction/biology/py-pysam/pysam-0.16.0.1/htslib -I/construction/biology/py-pysam/pysam-0.16.0.1/samtools -I/construction/biology/py-pysam/pysam-0.16.0.1/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.16.0.1/bcftools -I/construction/biology/py-pysam/pysam-0.16.0.1/pysam -I/construction/biology/py-pysam/pysam-0.16.0.1 -I/usr/local/include/python3.7m -c pysam/libcvcf.c -o build/temp.dragonfly-6.1-x86_64-3.7/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-6.1-x86_64-3.7/pysam/libcvcf.o -L/construction/biology/py-pysam/pysam-0.16.0.1/pysam -L/construction/biology/py-pysam/pysam-0.16.0.1/pysam -L/construction/biology/py-pysam/pysam-0.16.0.1 -L/construction/biology/py-pysam/pysam-0.16.0.1/build/lib.dragonfly-6.1-x86_64-3.7/pysam -Lbuild/lib.dragonfly-6.1-x86_64-3.7/pysam -Lbuild/lib.dragonfly-6.1-x86_64-3.7/pysam -Lbuild/lib.dragonfly-6.1-x86_64-3.7/pysam -Lbuild/lib.dragonfly-6.1-x86_64-3.7/pysam -Lbuild/lib.dragonfly-6.1-x86_64-3.7/pysam -Lbuild/lib.dragonfly-6.1-x86_64-3.7/pysam -Lbuild/lib.dragonfly-6.1-x86_64-3.7/pysam -Lbuild/lib.dragonfly-6.1-x86_64-3.7/pysam -Lbuild/lib.dragonfly-6.1-x86_64-3.7/pysam -Lbuild/lib.dragonfly-6.1-x86_64-3.7/pysam -Lbuild/lib.dragonfly-6.1-x86_64-3.7/pysam -Lbuild/lib.dragonfly-6.1-x86_64-3.7/pysam -Lbuild/lib.dragonfly-6.1-x86_64-3.7/pysam -L/usr/local/lib -lz -llzma -lbz2 -lz -lm -lchtslib -lcutils -lpython3.7m -o build/lib.dragonfly-6.1-x86_64-3.7/pysam/libcvcf.so -Wl,-rpath,$ORIGIN SUCCEEDED 00:05:43 ------------------------------------------------------------------------------- -- Phase: run-depends ------------------------------------------------------------------------------- ===> py37-pysam-0.16.0.1 depends on executable: cython-3.7 - found ===> py37-pysam-0.16.0.1 depends on package: py37-setuptools>0 - found ===> py37-pysam-0.16.0.1 depends on file: /usr/local/bin/python3.7 - found SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: stage ------------------------------------------------------------------------------- ===> Staging for py37-pysam-0.16.0.1 ===> py37-pysam-0.16.0.1 depends on executable: cython-3.7 - found ===> py37-pysam-0.16.0.1 depends on package: py37-setuptools>0 - found ===> py37-pysam-0.16.0.1 depends on file: /usr/local/bin/python3.7 - found ===> Generating temporary packing list # pysam: cython is available - using cythonize if necessary # pysam: htslib mode is shared # pysam: HTSLIB_CONFIGURE_OPTIONS=None # pysam: (env) CC=cc # pysam: (env) CFLAGS=-pipe -O2 -fno-strict-aliasing # pysam: (env) LDFLAGS= 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 pkg-config... no checking for special C compiler options needed for large files... no checking for _FILE_OFFSET_BITS value needed for large files... no checking shared library type for unknown-DragonFly... plain .so checking whether the compiler accepts -fvisibility=hidden... yes 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 libdeflate.h... no checking for libdeflate_deflate_compress in -ldeflate... no 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 pkg-config... no checking for special C compiler options needed for large files... no checking for _FILE_OFFSET_BITS value needed for large files... no checking shared library type for unknown-DragonFly... plain .so checking whether the compiler accepts -fvisibility=hidden... yes 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 libdeflate.h... no checking for libdeflate_deflate_compress in -ldeflate... no 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 # pysam: htslib configure options: --disable-libcurl gmake[1]: ./version.sh: No such file or directory gmake[1]: ./version.sh: No such file or directory # pysam: htslib_config LIBHTS_OBJS=kfunc.o knetfile.o kstring.o bcf_sr_sort.o bgzf.o errmod.o faidx.o header.o hfile.o hfile_net.o hts.o hts_os.o md5.o multipart.o probaln.o realn.o regidx.o region.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/mFILE.o cram/open_trace_file.o cram/pooled_alloc.o cram/rANS_static.o cram/string_alloc.o # pysam: htslib_config LIBS=-llzma -lbz2 -lz -lm # pysam: htslib_config PLATFORM=default # pysam: config_option: ENABLE_GCS=0 # pysam: config_option: ENABLE_PLUGINS=0 # pysam: config_option: ENABLE_S3=0 # pysam: config_option: HAVE_COMMONCRYPTO=0 # pysam: config_option: HAVE_HMAC=0 # pysam: config_option: HAVE_LIBBZ2=1 # pysam: config_option: HAVE_LIBCURL=0 # pysam: config_option: HAVE_LIBDEFLATE=0 # pysam: config_option: HAVE_LIBLZMA=1 # pysam: config_option: HAVE_MMAP=1 running install running build running build_py copying pysam/config.py -> build/lib.dragonfly-6.1-x86_64-3.7/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 'htslib/__init__.py' not found (or not a regular file) package init file 'htslib/htslib/__init__.py' not found (or not a regular file) Fixing build/lib.dragonfly-6.1-x86_64-3.7/pysam/config.py Skipping optional fixer: buffer Skipping optional fixer: idioms Skipping optional fixer: set_literal Skipping optional fixer: ws_comma Fixing build/lib.dragonfly-6.1-x86_64-3.7/pysam/config.py Skipping optional fixer: buffer Skipping optional fixer: idioms Skipping optional fixer: set_literal Skipping optional fixer: ws_comma 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/python3.7 creating /construction/biology/py-pysam/stage/usr/local/lib/python3.7/site-packages creating /construction/biology/py-pysam/stage/usr/local/lib/python3.7/site-packages/pysam copying build/lib.dragonfly-6.1-x86_64-3.7/pysam/config.py -> /construction/biology/py-pysam/stage/usr/local/lib/python3.7/site-packages/pysam copying build/lib.dragonfly-6.1-x86_64-3.7/pysam/samtools.py -> /construction/biology/py-pysam/stage/usr/local/lib/python3.7/site-packages/pysam copying build/lib.dragonfly-6.1-x86_64-3.7/pysam/utils.py -> /construction/biology/py-pysam/stage/usr/local/lib/python3.7/site-packages/pysam copying build/lib.dragonfly-6.1-x86_64-3.7/pysam/version.py -> /construction/biology/py-pysam/stage/usr/local/lib/python3.7/site-packages/pysam copying build/lib.dragonfly-6.1-x86_64-3.7/pysam/__init__.py -> /construction/biology/py-pysam/stage/usr/local/lib/python3.7/site-packages/pysam copying build/lib.dragonfly-6.1-x86_64-3.7/pysam/Pileup.py -> /construction/biology/py-pysam/stage/usr/local/lib/python3.7/site-packages/pysam copying build/lib.dragonfly-6.1-x86_64-3.7/pysam/bcftools.py -> /construction/biology/py-pysam/stage/usr/local/lib/python3.7/site-packages/pysam creating /construction/biology/py-pysam/stage/usr/local/lib/python3.7/site-packages/pysam/include copying build/lib.dragonfly-6.1-x86_64-3.7/pysam/include/__init__.py -> /construction/biology/py-pysam/stage/usr/local/lib/python3.7/site-packages/pysam/include creating /construction/biology/py-pysam/stage/usr/local/lib/python3.7/site-packages/pysam/include/samtools copying build/lib.dragonfly-6.1-x86_64-3.7/pysam/include/samtools/config.h -> /construction/biology/py-pysam/stage/usr/local/lib/python3.7/site-packages/pysam/include/samtools copying build/lib.dragonfly-6.1-x86_64-3.7/pysam/include/samtools/bam.h -> /construction/biology/py-pysam/stage/usr/local/lib/python3.7/site-packages/pysam/include/samtools copying build/lib.dragonfly-6.1-x86_64-3.7/pysam/include/samtools/bedidx.h -> /construction/biology/py-pysam/stage/usr/local/lib/python3.7/site-packages/pysam/include/samtools copying build/lib.dragonfly-6.1-x86_64-3.7/pysam/include/samtools/sam.h -> /construction/biology/py-pysam/stage/usr/local/lib/python3.7/site-packages/pysam/include/samtools copying build/lib.dragonfly-6.1-x86_64-3.7/pysam/include/samtools/samtools.h -> /construction/biology/py-pysam/stage/usr/local/lib/python3.7/site-packages/pysam/include/samtools copying build/lib.dragonfly-6.1-x86_64-3.7/pysam/include/samtools/bam_endian.h -> /construction/biology/py-pysam/stage/usr/local/lib/python3.7/site-packages/pysam/include/samtools copying build/lib.dragonfly-6.1-x86_64-3.7/pysam/include/samtools/sample.h -> /construction/biology/py-pysam/stage/usr/local/lib/python3.7/site-packages/pysam/include/samtools copying build/lib.dragonfly-6.1-x86_64-3.7/pysam/include/samtools/samtools.pysam.h -> /construction/biology/py-pysam/stage/usr/local/lib/python3.7/site-packages/pysam/include/samtools copying build/lib.dragonfly-6.1-x86_64-3.7/pysam/include/samtools/stats_isize.h -> /construction/biology/py-pysam/stage/usr/local/lib/python3.7/site-packages/pysam/include/samtools copying build/lib.dragonfly-6.1-x86_64-3.7/pysam/include/samtools/sam_opts.h -> /construction/biology/py-pysam/stage/usr/local/lib/python3.7/site-packages/pysam/include/samtools copying build/lib.dragonfly-6.1-x86_64-3.7/pysam/include/samtools/tmp_file.h -> /construction/biology/py-pysam/stage/usr/local/lib/python3.7/site-packages/pysam/include/samtools copying build/lib.dragonfly-6.1-x86_64-3.7/pysam/include/samtools/bam_lpileup.h -> /construction/biology/py-pysam/stage/usr/local/lib/python3.7/site-packages/pysam/include/samtools copying build/lib.dragonfly-6.1-x86_64-3.7/pysam/include/samtools/bam2bcf.h -> /construction/biology/py-pysam/stage/usr/local/lib/python3.7/site-packages/pysam/include/samtools copying build/lib.dragonfly-6.1-x86_64-3.7/pysam/include/samtools/bam_plbuf.h -> /construction/biology/py-pysam/stage/usr/local/lib/python3.7/site-packages/pysam/include/samtools creating /construction/biology/py-pysam/stage/usr/local/lib/python3.7/site-packages/pysam/include/bcftools copying build/lib.dragonfly-6.1-x86_64-3.7/pysam/include/bcftools/config.h -> /construction/biology/py-pysam/stage/usr/local/lib/python3.7/site-packages/pysam/include/bcftools copying build/lib.dragonfly-6.1-x86_64-3.7/pysam/include/bcftools/bcftools.h -> /construction/biology/py-pysam/stage/usr/local/lib/python3.7/site-packages/pysam/include/bcftools copying build/lib.dragonfly-6.1-x86_64-3.7/pysam/include/bcftools/hclust.h -> /construction/biology/py-pysam/stage/usr/local/lib/python3.7/site-packages/pysam/include/bcftools copying build/lib.dragonfly-6.1-x86_64-3.7/pysam/include/bcftools/bcftools.pysam.h -> /construction/biology/py-pysam/stage/usr/local/lib/python3.7/site-packages/pysam/include/bcftools copying build/lib.dragonfly-6.1-x86_64-3.7/pysam/include/bcftools/convert.h -> /construction/biology/py-pysam/stage/usr/local/lib/python3.7/site-packages/pysam/include/bcftools copying build/lib.dragonfly-6.1-x86_64-3.7/pysam/include/bcftools/bam_sample.h -> /construction/biology/py-pysam/stage/usr/local/lib/python3.7/site-packages/pysam/include/bcftools copying build/lib.dragonfly-6.1-x86_64-3.7/pysam/include/bcftools/tsv2vcf.h -> /construction/biology/py-pysam/stage/usr/local/lib/python3.7/site-packages/pysam/include/bcftools copying build/lib.dragonfly-6.1-x86_64-3.7/pysam/include/bcftools/HMM.h -> /construction/biology/py-pysam/stage/usr/local/lib/python3.7/site-packages/pysam/include/bcftools copying build/lib.dragonfly-6.1-x86_64-3.7/pysam/include/bcftools/regidx.h -> /construction/biology/py-pysam/stage/usr/local/lib/python3.7/site-packages/pysam/include/bcftools copying build/lib.dragonfly-6.1-x86_64-3.7/pysam/include/bcftools/vcmp.h -> /construction/biology/py-pysam/stage/usr/local/lib/python3.7/site-packages/pysam/include/bcftools copying build/lib.dragonfly-6.1-x86_64-3.7/pysam/include/bcftools/call.h -> /construction/biology/py-pysam/stage/usr/local/lib/python3.7/site-packages/pysam/include/bcftools copying build/lib.dragonfly-6.1-x86_64-3.7/pysam/include/bcftools/mw.h -> /construction/biology/py-pysam/stage/usr/local/lib/python3.7/site-packages/pysam/include/bcftools copying build/lib.dragonfly-6.1-x86_64-3.7/pysam/include/bcftools/prob1.h -> /construction/biology/py-pysam/stage/usr/local/lib/python3.7/site-packages/pysam/include/bcftools copying build/lib.dragonfly-6.1-x86_64-3.7/pysam/include/bcftools/vcfbuf.h -> /construction/biology/py-pysam/stage/usr/local/lib/python3.7/site-packages/pysam/include/bcftools copying build/lib.dragonfly-6.1-x86_64-3.7/pysam/include/bcftools/filter.h -> /construction/biology/py-pysam/stage/usr/local/lib/python3.7/site-packages/pysam/include/bcftools copying build/lib.dragonfly-6.1-x86_64-3.7/pysam/include/bcftools/cols.h -> /construction/biology/py-pysam/stage/usr/local/lib/python3.7/site-packages/pysam/include/bcftools copying build/lib.dragonfly-6.1-x86_64-3.7/pysam/include/bcftools/smpl_ilist.h -> /construction/biology/py-pysam/stage/usr/local/lib/python3.7/site-packages/pysam/include/bcftools copying build/lib.dragonfly-6.1-x86_64-3.7/pysam/include/bcftools/hex.h -> /construction/biology/py-pysam/stage/usr/local/lib/python3.7/site-packages/pysam/include/bcftools copying build/lib.dragonfly-6.1-x86_64-3.7/pysam/include/bcftools/gvcf.h -> /construction/biology/py-pysam/stage/usr/local/lib/python3.7/site-packages/pysam/include/bcftools copying build/lib.dragonfly-6.1-x86_64-3.7/pysam/include/bcftools/kmin.h -> /construction/biology/py-pysam/stage/usr/local/lib/python3.7/site-packages/pysam/include/bcftools copying build/lib.dragonfly-6.1-x86_64-3.7/pysam/include/bcftools/kheap.h -> /construction/biology/py-pysam/stage/usr/local/lib/python3.7/site-packages/pysam/include/bcftools copying build/lib.dragonfly-6.1-x86_64-3.7/pysam/include/bcftools/bin.h -> /construction/biology/py-pysam/stage/usr/local/lib/python3.7/site-packages/pysam/include/bcftools copying build/lib.dragonfly-6.1-x86_64-3.7/pysam/include/bcftools/khash_str2str.h -> /construction/biology/py-pysam/stage/usr/local/lib/python3.7/site-packages/pysam/include/bcftools copying build/lib.dragonfly-6.1-x86_64-3.7/pysam/include/bcftools/rbuf.h -> /construction/biology/py-pysam/stage/usr/local/lib/python3.7/site-packages/pysam/include/bcftools copying build/lib.dragonfly-6.1-x86_64-3.7/pysam/include/bcftools/ploidy.h -> /construction/biology/py-pysam/stage/usr/local/lib/python3.7/site-packages/pysam/include/bcftools copying build/lib.dragonfly-6.1-x86_64-3.7/pysam/include/bcftools/bam2bcf.h -> /construction/biology/py-pysam/stage/usr/local/lib/python3.7/site-packages/pysam/include/bcftools copying build/lib.dragonfly-6.1-x86_64-3.7/pysam/include/bcftools/variantkey.h -> /construction/biology/py-pysam/stage/usr/local/lib/python3.7/site-packages/pysam/include/bcftools creating /construction/biology/py-pysam/stage/usr/local/lib/python3.7/site-packages/pysam/include/htslib copying build/lib.dragonfly-6.1-x86_64-3.7/pysam/include/htslib/hts_internal.h -> /construction/biology/py-pysam/stage/usr/local/lib/python3.7/site-packages/pysam/include/htslib copying build/lib.dragonfly-6.1-x86_64-3.7/pysam/include/htslib/thread_pool_internal.h -> /construction/biology/py-pysam/stage/usr/local/lib/python3.7/site-packages/pysam/include/htslib copying build/lib.dragonfly-6.1-x86_64-3.7/pysam/include/htslib/hfile_internal.h -> /construction/biology/py-pysam/stage/usr/local/lib/python3.7/site-packages/pysam/include/htslib copying build/lib.dragonfly-6.1-x86_64-3.7/pysam/include/htslib/header.h -> /construction/biology/py-pysam/stage/usr/local/lib/python3.7/site-packages/pysam/include/htslib copying build/lib.dragonfly-6.1-x86_64-3.7/pysam/include/htslib/sam_internal.h -> /construction/biology/py-pysam/stage/usr/local/lib/python3.7/site-packages/pysam/include/htslib copying build/lib.dragonfly-6.1-x86_64-3.7/pysam/include/htslib/bcf_sr_sort.h -> /construction/biology/py-pysam/stage/usr/local/lib/python3.7/site-packages/pysam/include/htslib copying build/lib.dragonfly-6.1-x86_64-3.7/pysam/include/htslib/textutils_internal.h -> /construction/biology/py-pysam/stage/usr/local/lib/python3.7/site-packages/pysam/include/htslib copying build/lib.dragonfly-6.1-x86_64-3.7/pysam/include/htslib/config.h -> /construction/biology/py-pysam/stage/usr/local/lib/python3.7/site-packages/pysam/include/htslib creating /construction/biology/py-pysam/stage/usr/local/lib/python3.7/site-packages/pysam/include/htslib/htslib copying build/lib.dragonfly-6.1-x86_64-3.7/pysam/include/htslib/htslib/hts.h -> /construction/biology/py-pysam/stage/usr/local/lib/python3.7/site-packages/pysam/include/htslib/htslib copying build/lib.dragonfly-6.1-x86_64-3.7/pysam/include/htslib/htslib/hfile.h -> /construction/biology/py-pysam/stage/usr/local/lib/python3.7/site-packages/pysam/include/htslib/htslib copying build/lib.dragonfly-6.1-x86_64-3.7/pysam/include/htslib/htslib/kfunc.h -> /construction/biology/py-pysam/stage/usr/local/lib/python3.7/site-packages/pysam/include/htslib/htslib copying build/lib.dragonfly-6.1-x86_64-3.7/pysam/include/htslib/htslib/synced_bcf_reader.h -> /construction/biology/py-pysam/stage/usr/local/lib/python3.7/site-packages/pysam/include/htslib/htslib copying build/lib.dragonfly-6.1-x86_64-3.7/pysam/include/htslib/htslib/faidx.h -> /construction/biology/py-pysam/stage/usr/local/lib/python3.7/site-packages/pysam/include/htslib/htslib copying build/lib.dragonfly-6.1-x86_64-3.7/pysam/include/htslib/htslib/vcf_sweep.h -> /construction/biology/py-pysam/stage/usr/local/lib/python3.7/site-packages/pysam/include/htslib/htslib copying build/lib.dragonfly-6.1-x86_64-3.7/pysam/include/htslib/htslib/ksort.h -> /construction/biology/py-pysam/stage/usr/local/lib/python3.7/site-packages/pysam/include/htslib/htslib copying build/lib.dragonfly-6.1-x86_64-3.7/pysam/include/htslib/htslib/thread_pool.h -> /construction/biology/py-pysam/stage/usr/local/lib/python3.7/site-packages/pysam/include/htslib/htslib copying build/lib.dragonfly-6.1-x86_64-3.7/pysam/include/htslib/htslib/sam.h -> /construction/biology/py-pysam/stage/usr/local/lib/python3.7/site-packages/pysam/include/htslib/htslib copying build/lib.dragonfly-6.1-x86_64-3.7/pysam/include/htslib/htslib/khash.h -> /construction/biology/py-pysam/stage/usr/local/lib/python3.7/site-packages/pysam/include/htslib/htslib copying build/lib.dragonfly-6.1-x86_64-3.7/pysam/include/htslib/htslib/klist.h -> /construction/biology/py-pysam/stage/usr/local/lib/python3.7/site-packages/pysam/include/htslib/htslib copying build/lib.dragonfly-6.1-x86_64-3.7/pysam/include/htslib/htslib/knetfile.h -> /construction/biology/py-pysam/stage/usr/local/lib/python3.7/site-packages/pysam/include/htslib/htslib copying build/lib.dragonfly-6.1-x86_64-3.7/pysam/include/htslib/htslib/kstring.h -> /construction/biology/py-pysam/stage/usr/local/lib/python3.7/site-packages/pysam/include/htslib/htslib copying build/lib.dragonfly-6.1-x86_64-3.7/pysam/include/htslib/htslib/kseq.h -> /construction/biology/py-pysam/stage/usr/local/lib/python3.7/site-packages/pysam/include/htslib/htslib copying build/lib.dragonfly-6.1-x86_64-3.7/pysam/include/htslib/htslib/hts_defs.h -> /construction/biology/py-pysam/stage/usr/local/lib/python3.7/site-packages/pysam/include/htslib/htslib copying build/lib.dragonfly-6.1-x86_64-3.7/pysam/include/htslib/htslib/regidx.h -> /construction/biology/py-pysam/stage/usr/local/lib/python3.7/site-packages/pysam/include/htslib/htslib copying build/lib.dragonfly-6.1-x86_64-3.7/pysam/include/htslib/htslib/hts_log.h -> /construction/biology/py-pysam/stage/usr/local/lib/python3.7/site-packages/pysam/include/htslib/htslib copying build/lib.dragonfly-6.1-x86_64-3.7/pysam/include/htslib/htslib/tbx.h -> /construction/biology/py-pysam/stage/usr/local/lib/python3.7/site-packages/pysam/include/htslib/htslib copying build/lib.dragonfly-6.1-x86_64-3.7/pysam/include/htslib/htslib/kbitset.h -> /construction/biology/py-pysam/stage/usr/local/lib/python3.7/site-packages/pysam/include/htslib/htslib copying build/lib.dragonfly-6.1-x86_64-3.7/pysam/include/htslib/htslib/khash_str2int.h -> /construction/biology/py-pysam/stage/usr/local/lib/python3.7/site-packages/pysam/include/htslib/htslib copying build/lib.dragonfly-6.1-x86_64-3.7/pysam/include/htslib/htslib/hts_os.h -> /construction/biology/py-pysam/stage/usr/local/lib/python3.7/site-packages/pysam/include/htslib/htslib copying build/lib.dragonfly-6.1-x86_64-3.7/pysam/include/htslib/htslib/vcfutils.h -> /construction/biology/py-pysam/stage/usr/local/lib/python3.7/site-packages/pysam/include/htslib/htslib copying build/lib.dragonfly-6.1-x86_64-3.7/pysam/include/htslib/htslib/hts_endian.h -> /construction/biology/py-pysam/stage/usr/local/lib/python3.7/site-packages/pysam/include/htslib/htslib copying build/lib.dragonfly-6.1-x86_64-3.7/pysam/include/htslib/htslib/bgzf.h -> /construction/biology/py-pysam/stage/usr/local/lib/python3.7/site-packages/pysam/include/htslib/htslib copying build/lib.dragonfly-6.1-x86_64-3.7/pysam/include/htslib/htslib/cram.h -> /construction/biology/py-pysam/stage/usr/local/lib/python3.7/site-packages/pysam/include/htslib/htslib copying build/lib.dragonfly-6.1-x86_64-3.7/pysam/include/htslib/htslib/vcf.h -> /construction/biology/py-pysam/stage/usr/local/lib/python3.7/site-packages/pysam/include/htslib/htslib copying build/lib.dragonfly-6.1-x86_64-3.7/pysam/libctabixproxies.pxd -> /construction/biology/py-pysam/stage/usr/local/lib/python3.7/site-packages/pysam copying build/lib.dragonfly-6.1-x86_64-3.7/pysam/libchtslib.pxd -> /construction/biology/py-pysam/stage/usr/local/lib/python3.7/site-packages/pysam copying build/lib.dragonfly-6.1-x86_64-3.7/pysam/libcsamtools.pxd -> /construction/biology/py-pysam/stage/usr/local/lib/python3.7/site-packages/pysam copying build/lib.dragonfly-6.1-x86_64-3.7/pysam/libcutils.pxd -> /construction/biology/py-pysam/stage/usr/local/lib/python3.7/site-packages/pysam copying build/lib.dragonfly-6.1-x86_64-3.7/pysam/libcfaidx.pxd -> /construction/biology/py-pysam/stage/usr/local/lib/python3.7/site-packages/pysam copying build/lib.dragonfly-6.1-x86_64-3.7/pysam/libcbcf.pxd -> /construction/biology/py-pysam/stage/usr/local/lib/python3.7/site-packages/pysam copying build/lib.dragonfly-6.1-x86_64-3.7/pysam/libctabix.pxd -> /construction/biology/py-pysam/stage/usr/local/lib/python3.7/site-packages/pysam copying build/lib.dragonfly-6.1-x86_64-3.7/pysam/libcalignedsegment.pxd -> /construction/biology/py-pysam/stage/usr/local/lib/python3.7/site-packages/pysam copying build/lib.dragonfly-6.1-x86_64-3.7/pysam/libcsamfile.pxd -> /construction/biology/py-pysam/stage/usr/local/lib/python3.7/site-packages/pysam copying build/lib.dragonfly-6.1-x86_64-3.7/pysam/libcalignmentfile.pxd -> /construction/biology/py-pysam/stage/usr/local/lib/python3.7/site-packages/pysam copying build/lib.dragonfly-6.1-x86_64-3.7/pysam/libcvcf.pxd -> /construction/biology/py-pysam/stage/usr/local/lib/python3.7/site-packages/pysam copying build/lib.dragonfly-6.1-x86_64-3.7/pysam/libcbcftools.pxd -> /construction/biology/py-pysam/stage/usr/local/lib/python3.7/site-packages/pysam copying build/lib.dragonfly-6.1-x86_64-3.7/pysam/csamtools_util.h -> /construction/biology/py-pysam/stage/usr/local/lib/python3.7/site-packages/pysam copying build/lib.dragonfly-6.1-x86_64-3.7/pysam/pysam_stream.h -> /construction/biology/py-pysam/stage/usr/local/lib/python3.7/site-packages/pysam copying build/lib.dragonfly-6.1-x86_64-3.7/pysam/version.h -> /construction/biology/py-pysam/stage/usr/local/lib/python3.7/site-packages/pysam copying build/lib.dragonfly-6.1-x86_64-3.7/pysam/pysam_util.h -> /construction/biology/py-pysam/stage/usr/local/lib/python3.7/site-packages/pysam copying build/lib.dragonfly-6.1-x86_64-3.7/pysam/cbcftools_util.h -> /construction/biology/py-pysam/stage/usr/local/lib/python3.7/site-packages/pysam copying build/lib.dragonfly-6.1-x86_64-3.7/pysam/htslib_util.h -> /construction/biology/py-pysam/stage/usr/local/lib/python3.7/site-packages/pysam copying build/lib.dragonfly-6.1-x86_64-3.7/pysam/libcsamtools.so -> /construction/biology/py-pysam/stage/usr/local/lib/python3.7/site-packages/pysam copying build/lib.dragonfly-6.1-x86_64-3.7/pysam/libcbcftools.so -> /construction/biology/py-pysam/stage/usr/local/lib/python3.7/site-packages/pysam copying build/lib.dragonfly-6.1-x86_64-3.7/pysam/libcbgzf.so -> /construction/biology/py-pysam/stage/usr/local/lib/python3.7/site-packages/pysam copying build/lib.dragonfly-6.1-x86_64-3.7/pysam/libcutils.so -> /construction/biology/py-pysam/stage/usr/local/lib/python3.7/site-packages/pysam copying build/lib.dragonfly-6.1-x86_64-3.7/pysam/libcalignmentfile.so -> /construction/biology/py-pysam/stage/usr/local/lib/python3.7/site-packages/pysam copying build/lib.dragonfly-6.1-x86_64-3.7/pysam/libcsamfile.so -> /construction/biology/py-pysam/stage/usr/local/lib/python3.7/site-packages/pysam copying build/lib.dragonfly-6.1-x86_64-3.7/pysam/libctabix.so -> /construction/biology/py-pysam/stage/usr/local/lib/python3.7/site-packages/pysam copying build/lib.dragonfly-6.1-x86_64-3.7/pysam/libcbcf.so -> /construction/biology/py-pysam/stage/usr/local/lib/python3.7/site-packages/pysam copying build/lib.dragonfly-6.1-x86_64-3.7/pysam/libctabixproxies.so -> /construction/biology/py-pysam/stage/usr/local/lib/python3.7/site-packages/pysam copying build/lib.dragonfly-6.1-x86_64-3.7/pysam/libcalignedsegment.so -> /construction/biology/py-pysam/stage/usr/local/lib/python3.7/site-packages/pysam copying build/lib.dragonfly-6.1-x86_64-3.7/pysam/libcfaidx.so -> /construction/biology/py-pysam/stage/usr/local/lib/python3.7/site-packages/pysam copying build/lib.dragonfly-6.1-x86_64-3.7/pysam/libcvcf.so -> /construction/biology/py-pysam/stage/usr/local/lib/python3.7/site-packages/pysam copying build/lib.dragonfly-6.1-x86_64-3.7/pysam/libchtslib.so -> /construction/biology/py-pysam/stage/usr/local/lib/python3.7/site-packages/pysam byte-compiling /construction/biology/py-pysam/stage/usr/local/lib/python3.7/site-packages/pysam/config.py to config.cpython-37.pyc byte-compiling /construction/biology/py-pysam/stage/usr/local/lib/python3.7/site-packages/pysam/samtools.py to samtools.cpython-37.pyc byte-compiling /construction/biology/py-pysam/stage/usr/local/lib/python3.7/site-packages/pysam/utils.py to utils.cpython-37.pyc byte-compiling /construction/biology/py-pysam/stage/usr/local/lib/python3.7/site-packages/pysam/version.py to version.cpython-37.pyc byte-compiling /construction/biology/py-pysam/stage/usr/local/lib/python3.7/site-packages/pysam/__init__.py to __init__.cpython-37.pyc byte-compiling /construction/biology/py-pysam/stage/usr/local/lib/python3.7/site-packages/pysam/Pileup.py to Pileup.cpython-37.pyc byte-compiling /construction/biology/py-pysam/stage/usr/local/lib/python3.7/site-packages/pysam/bcftools.py to bcftools.cpython-37.pyc byte-compiling /construction/biology/py-pysam/stage/usr/local/lib/python3.7/site-packages/pysam/include/__init__.py to __init__.cpython-37.pyc writing byte-compilation script '/tmp/tmp4n797b1g.py' /usr/local/bin/python3.7 /tmp/tmp4n797b1g.py removing /tmp/tmp4n797b1g.py running install_egg_info running egg_info writing pysam.egg-info/PKG-INFO writing dependency_links to pysam.egg-info/dependency_links.txt writing top-level names to pysam.egg-info/top_level.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/INSTALL' warning: no files found matching 'htslib/NEWS' writing manifest file 'pysam.egg-info/SOURCES.txt' Copying pysam.egg-info to /construction/biology/py-pysam/stage/usr/local/lib/python3.7/site-packages/pysam-0.16.0.1-py3.7.egg-info running install_scripts writing list of installed files to '/construction/biology/py-pysam/.PLIST.pymodtmp' ====> Compressing man pages (compress-man) ====> Running Q/A tests (stage-qa) Warning: 'lib/python3.7/site-packages/pysam/libcutils.so' is not stripped consider trying INSTALL_TARGET=install-strip or using ${STRIP_CMD} Warning: 'lib/python3.7/site-packages/pysam/libcalignmentfile.so' is not stripped consider trying INSTALL_TARGET=install-strip or using ${STRIP_CMD} Warning: 'lib/python3.7/site-packages/pysam/libcsamfile.so' is not stripped consider trying INSTALL_TARGET=install-strip or using ${STRIP_CMD} Warning: 'lib/python3.7/site-packages/pysam/libctabix.so' is not stripped consider trying INSTALL_TARGET=install-strip or using ${STRIP_CMD} Warning: 'lib/python3.7/site-packages/pysam/libcbcf.so' is not stripped consider trying INSTALL_TARGET=install-strip or using ${STRIP_CMD} Warning: 'lib/python3.7/site-packages/pysam/libctabixproxies.so' is not stripped consider trying INSTALL_TARGET=install-strip or using ${STRIP_CMD} Warning: 'lib/python3.7/site-packages/pysam/libcalignedsegment.so' is not stripped consider trying INSTALL_TARGET=install-strip or using ${STRIP_CMD} Warning: 'lib/python3.7/site-packages/pysam/libcfaidx.so' is not stripped consider trying INSTALL_TARGET=install-strip or using ${STRIP_CMD} Warning: 'lib/python3.7/site-packages/pysam/libcvcf.so' is not stripped consider trying INSTALL_TARGET=install-strip or using ${STRIP_CMD} Warning: 'lib/python3.7/site-packages/pysam/libchtslib.so' is not stripped consider trying INSTALL_TARGET=install-strip or using ${STRIP_CMD} Warning: 'lib/python3.7/site-packages/pysam/libcsamtools.so' is not stripped consider trying INSTALL_TARGET=install-strip or using ${STRIP_CMD} Warning: 'lib/python3.7/site-packages/pysam/libcbcftools.so' is not stripped consider trying INSTALL_TARGET=install-strip or using ${STRIP_CMD} Warning: 'lib/python3.7/site-packages/pysam/libcbgzf.so' is not stripped consider trying INSTALL_TARGET=install-strip or using ${STRIP_CMD} Error: /usr/local/lib/python3.7/site-packages/pysam/libcalignedsegment.so is linked to /usr/local/lib/libintl.so.8 from devel/gettext-runtime but it is not declared as a dependency Warning: you need USES+=gettext-runtime Warning: You have disabled the licenses framework with DISABLE_LICENSES, unable to run checks SUCCEEDED 00:00:12 ------------------------------------------------------------------------------- -- Phase: check-plist ------------------------------------------------------------------------------- ====> Checking for pkg-plist issues (check-plist) ===> Parsing plist ===> Checking for items in STAGEDIR missing from pkg-plist ===> Checking for items in pkg-plist which are not in STAGEDIR ===> No pkg-plist issues found (check-plist) SUCCEEDED 00:00:01 ------------------------------------------------------------------------------- -- Phase: package ------------------------------------------------------------------------------- ===> Building package for py37-pysam-0.16.0.1 file sizes/checksums [135]: 0% file sizes/checksums [135]: 74% file sizes/checksums [135]: 100% packing files [135]: 0% packing files [135]: 74% packing files [135]: 100% packing directories [0]: 0% packing directories [0]: 100% SUCCEEDED 00:00:06 TOTAL TIME 00:06:22