pysam.log

☕ Aichan ☕ >> python setup.py develop
# pysam: cython is available - using cythonize if necessary
# pysam: htslib mode is shared
# pysam: HTSLIB_CONFIGURE_OPTIONS=--disable-lzma
checking for gcc... gcc
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 gcc accepts -g... yes
checking for gcc option to accept ISO C89... none needed
checking for ranlib... ranlib
checking for special C compiler options needed for large files... no
checking for _FILE_OFFSET_BITS value needed for large files... no
checking for _LARGEFILE_SOURCE value needed for large files... no
checking shared library type for unknown-Darwin... Darwin dylib
checking how to run the C preprocessor... gcc -E
checking for grep that handles long lines and -e... /usr/bin/grep
checking for egrep... /usr/bin/grep -E
checking for ANSI C header files... yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking for stdlib.h... (cached) yes
checking for unistd.h... (cached) yes
checking for sys/param.h... yes
checking for getpagesize... yes
checking for working mmap... yes
checking for gmtime_r... yes
checking for fsync... yes
checking for drand48... yes
checking whether fdatasync is declared... no
checking for library containing log... none required
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 curl_easy_pause in -lcurl... yes
checking for CCHmac... yes
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-lzma
make: ./version.sh: Command not found
make: ./version.sh: Command not found
# pysam: htslib_config LIBS=-lbz2 -lz -lcurl
# pysam: htslib_config PLATFORM=Darwin
# pysam: htslib_config LIBHTS_OBJS=kfunc.o knetfile.o kstring.o bcf_sr_sort.o bgzf.o errmod.o faidx.o hfile.o hfile_net.o hts.o hts_os.o md5.o multipart.o probaln.o realn.o regidx.o sam.o synced_bcf_reader.o vcf_sweep.o tbx.o textutils.o thread_pool.o vcf.o vcfutils.o cram/cram_codecs.o cram/cram_decode.o cram/cram_encode.o cram/cram_external.o cram/cram_index.o cram/cram_io.o cram/cram_samtools.o cram/cram_stats.o cram/files.o cram/mFILE.o cram/open_trace_file.o cram/pooled_alloc.o cram/rANS_static.o cram/sam_header.o cram/string_alloc.o hfile_libcurl.o hfile_gcs.o hfile_s3.o
# pysam: htslib_config LDFLAGS=
# pysam: config_option: ENABLE_PLUGINS=0
# pysam: config_option: HAVE_COMMONCRYPTO=1
# pysam: config_option: HAVE_GMTIME_R=1
# pysam: config_option: HAVE_HMAC=0
# pysam: config_option: HAVE_IRODS=0
# pysam: config_option: HAVE_LIBCURL=1
# pysam: config_option: HAVE_MMAP=1
running develop
running egg_info
writing pysam.egg-info/PKG-INFO
writing top-level names to pysam.egg-info/top_level.txt
writing dependency_links to pysam.egg-info/dependency_links.txt
writing pbr to pysam.egg-info/pbr.json
package init file 'samtools/__init__.py' not found (or not a regular file)
package init file 'bcftools/__init__.py' not found (or not a regular file)
package init file 'samtools/win32/__init__.py' not found (or not a regular file)
package init file 'htslib/__init__.py' not found (or not a regular file)
package init file 'htslib/htslib/__init__.py' not found (or not a regular file)
reading manifest file 'pysam.egg-info/SOURCES.txt'
reading manifest template 'MANIFEST.in'
warning: no files found matching 'KNOWN_BUGS'
warning: no files found matching 'THANKS'
warning: no files found matching 'samtools/configure'
warning: no files found matching 'samtools/config.mk.in'
warning: no files found matching 'samtools/config.h.in'
warning: no files found matching 'tests/pysam_data'
warning: no files found matching 'tests/tabix_data'
writing manifest file 'pysam.egg-info/SOURCES.txt'
running build_ext
skipping 'pysam/libchtslib.c' Cython extension (up-to-date)
building 'pysam.libchtslib' extension
creating build/temp.macosx-10.4-x86_64-2.7
creating build/temp.macosx-10.4-x86_64-2.7/pysam
creating build/temp.macosx-10.4-x86_64-2.7/htslib
creating build/temp.macosx-10.4-x86_64-2.7/htslib/cram
/usr/bin/gcc -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -Ipysam -I. -Ihtslib -I/Users/yukke/.pyenv/versions/2.7.5/include/python2.7 -c pysam/libchtslib.c -o build/temp.macosx-10.4-x86_64-2.7/pysam/libchtslib.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
/usr/bin/gcc -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -Ipysam -I. -Ihtslib -I/Users/yukke/.pyenv/versions/2.7.5/include/python2.7 -c pysam/htslib_util.c -o build/temp.macosx-10.4-x86_64-2.7/pysam/htslib_util.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
/usr/bin/gcc -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -Ipysam -I. -Ihtslib -I/Users/yukke/.pyenv/versions/2.7.5/include/python2.7 -c htslib/kfunc.c -o build/temp.macosx-10.4-x86_64-2.7/htslib/kfunc.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
/usr/bin/gcc -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -Ipysam -I. -Ihtslib -I/Users/yukke/.pyenv/versions/2.7.5/include/python2.7 -c htslib/knetfile.c -o build/temp.macosx-10.4-x86_64-2.7/htslib/knetfile.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
/usr/bin/gcc -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -Ipysam -I. -Ihtslib -I/Users/yukke/.pyenv/versions/2.7.5/include/python2.7 -c htslib/kstring.c -o build/temp.macosx-10.4-x86_64-2.7/htslib/kstring.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
/usr/bin/gcc -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -Ipysam -I. -Ihtslib -I/Users/yukke/.pyenv/versions/2.7.5/include/python2.7 -c htslib/bcf_sr_sort.c -o build/temp.macosx-10.4-x86_64-2.7/htslib/bcf_sr_sort.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
/usr/bin/gcc -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -Ipysam -I. -Ihtslib -I/Users/yukke/.pyenv/versions/2.7.5/include/python2.7 -c htslib/bgzf.c -o build/temp.macosx-10.4-x86_64-2.7/htslib/bgzf.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
/usr/bin/gcc -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -Ipysam -I. -Ihtslib -I/Users/yukke/.pyenv/versions/2.7.5/include/python2.7 -c htslib/errmod.c -o build/temp.macosx-10.4-x86_64-2.7/htslib/errmod.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
/usr/bin/gcc -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -Ipysam -I. -Ihtslib -I/Users/yukke/.pyenv/versions/2.7.5/include/python2.7 -c htslib/faidx.c -o build/temp.macosx-10.4-x86_64-2.7/htslib/faidx.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
/usr/bin/gcc -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -Ipysam -I. -Ihtslib -I/Users/yukke/.pyenv/versions/2.7.5/include/python2.7 -c htslib/hfile.c -o build/temp.macosx-10.4-x86_64-2.7/htslib/hfile.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
/usr/bin/gcc -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -Ipysam -I. -Ihtslib -I/Users/yukke/.pyenv/versions/2.7.5/include/python2.7 -c htslib/hfile_net.c -o build/temp.macosx-10.4-x86_64-2.7/htslib/hfile_net.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
/usr/bin/gcc -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -Ipysam -I. -Ihtslib -I/Users/yukke/.pyenv/versions/2.7.5/include/python2.7 -c htslib/hts.c -o build/temp.macosx-10.4-x86_64-2.7/htslib/hts.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
/usr/bin/gcc -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -Ipysam -I. -Ihtslib -I/Users/yukke/.pyenv/versions/2.7.5/include/python2.7 -c htslib/hts_os.c -o build/temp.macosx-10.4-x86_64-2.7/htslib/hts_os.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
/usr/bin/gcc -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -Ipysam -I. -Ihtslib -I/Users/yukke/.pyenv/versions/2.7.5/include/python2.7 -c htslib/md5.c -o build/temp.macosx-10.4-x86_64-2.7/htslib/md5.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
/usr/bin/gcc -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -Ipysam -I. -Ihtslib -I/Users/yukke/.pyenv/versions/2.7.5/include/python2.7 -c htslib/multipart.c -o build/temp.macosx-10.4-x86_64-2.7/htslib/multipart.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
/usr/bin/gcc -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -Ipysam -I. -Ihtslib -I/Users/yukke/.pyenv/versions/2.7.5/include/python2.7 -c htslib/probaln.c -o build/temp.macosx-10.4-x86_64-2.7/htslib/probaln.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
/usr/bin/gcc -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -Ipysam -I. -Ihtslib -I/Users/yukke/.pyenv/versions/2.7.5/include/python2.7 -c htslib/realn.c -o build/temp.macosx-10.4-x86_64-2.7/htslib/realn.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
/usr/bin/gcc -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -Ipysam -I. -Ihtslib -I/Users/yukke/.pyenv/versions/2.7.5/include/python2.7 -c htslib/regidx.c -o build/temp.macosx-10.4-x86_64-2.7/htslib/regidx.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
/usr/bin/gcc -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -Ipysam -I. -Ihtslib -I/Users/yukke/.pyenv/versions/2.7.5/include/python2.7 -c htslib/sam.c -o build/temp.macosx-10.4-x86_64-2.7/htslib/sam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
/usr/bin/gcc -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -Ipysam -I. -Ihtslib -I/Users/yukke/.pyenv/versions/2.7.5/include/python2.7 -c htslib/synced_bcf_reader.c -o build/temp.macosx-10.4-x86_64-2.7/htslib/synced_bcf_reader.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
/usr/bin/gcc -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -Ipysam -I. -Ihtslib -I/Users/yukke/.pyenv/versions/2.7.5/include/python2.7 -c htslib/vcf_sweep.c -o build/temp.macosx-10.4-x86_64-2.7/htslib/vcf_sweep.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
/usr/bin/gcc -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -Ipysam -I. -Ihtslib -I/Users/yukke/.pyenv/versions/2.7.5/include/python2.7 -c htslib/tbx.c -o build/temp.macosx-10.4-x86_64-2.7/htslib/tbx.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
/usr/bin/gcc -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -Ipysam -I. -Ihtslib -I/Users/yukke/.pyenv/versions/2.7.5/include/python2.7 -c htslib/textutils.c -o build/temp.macosx-10.4-x86_64-2.7/htslib/textutils.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
/usr/bin/gcc -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -Ipysam -I. -Ihtslib -I/Users/yukke/.pyenv/versions/2.7.5/include/python2.7 -c htslib/thread_pool.c -o build/temp.macosx-10.4-x86_64-2.7/htslib/thread_pool.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
/usr/bin/gcc -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -Ipysam -I. -Ihtslib -I/Users/yukke/.pyenv/versions/2.7.5/include/python2.7 -c htslib/vcf.c -o build/temp.macosx-10.4-x86_64-2.7/htslib/vcf.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
/usr/bin/gcc -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -Ipysam -I. -Ihtslib -I/Users/yukke/.pyenv/versions/2.7.5/include/python2.7 -c htslib/vcfutils.c -o build/temp.macosx-10.4-x86_64-2.7/htslib/vcfutils.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
/usr/bin/gcc -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -Ipysam -I. -Ihtslib -I/Users/yukke/.pyenv/versions/2.7.5/include/python2.7 -c htslib/cram/cram_codecs.c -o build/temp.macosx-10.4-x86_64-2.7/htslib/cram/cram_codecs.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
/usr/bin/gcc -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -Ipysam -I. -Ihtslib -I/Users/yukke/.pyenv/versions/2.7.5/include/python2.7 -c htslib/cram/cram_decode.c -o build/temp.macosx-10.4-x86_64-2.7/htslib/cram/cram_decode.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
/usr/bin/gcc -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -Ipysam -I. -Ihtslib -I/Users/yukke/.pyenv/versions/2.7.5/include/python2.7 -c htslib/cram/cram_encode.c -o build/temp.macosx-10.4-x86_64-2.7/htslib/cram/cram_encode.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
/usr/bin/gcc -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -Ipysam -I. -Ihtslib -I/Users/yukke/.pyenv/versions/2.7.5/include/python2.7 -c htslib/cram/cram_external.c -o build/temp.macosx-10.4-x86_64-2.7/htslib/cram/cram_external.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
/usr/bin/gcc -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -Ipysam -I. -Ihtslib -I/Users/yukke/.pyenv/versions/2.7.5/include/python2.7 -c htslib/cram/cram_index.c -o build/temp.macosx-10.4-x86_64-2.7/htslib/cram/cram_index.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
/usr/bin/gcc -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -Ipysam -I. -Ihtslib -I/Users/yukke/.pyenv/versions/2.7.5/include/python2.7 -c htslib/cram/cram_io.c -o build/temp.macosx-10.4-x86_64-2.7/htslib/cram/cram_io.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
/usr/bin/gcc -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -Ipysam -I. -Ihtslib -I/Users/yukke/.pyenv/versions/2.7.5/include/python2.7 -c htslib/cram/cram_samtools.c -o build/temp.macosx-10.4-x86_64-2.7/htslib/cram/cram_samtools.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
/usr/bin/gcc -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -Ipysam -I. -Ihtslib -I/Users/yukke/.pyenv/versions/2.7.5/include/python2.7 -c htslib/cram/cram_stats.c -o build/temp.macosx-10.4-x86_64-2.7/htslib/cram/cram_stats.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
/usr/bin/gcc -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -Ipysam -I. -Ihtslib -I/Users/yukke/.pyenv/versions/2.7.5/include/python2.7 -c htslib/cram/files.c -o build/temp.macosx-10.4-x86_64-2.7/htslib/cram/files.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
/usr/bin/gcc -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -Ipysam -I. -Ihtslib -I/Users/yukke/.pyenv/versions/2.7.5/include/python2.7 -c htslib/cram/mFILE.c -o build/temp.macosx-10.4-x86_64-2.7/htslib/cram/mFILE.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
/usr/bin/gcc -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -Ipysam -I. -Ihtslib -I/Users/yukke/.pyenv/versions/2.7.5/include/python2.7 -c htslib/cram/open_trace_file.c -o build/temp.macosx-10.4-x86_64-2.7/htslib/cram/open_trace_file.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
/usr/bin/gcc -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -Ipysam -I. -Ihtslib -I/Users/yukke/.pyenv/versions/2.7.5/include/python2.7 -c htslib/cram/pooled_alloc.c -o build/temp.macosx-10.4-x86_64-2.7/htslib/cram/pooled_alloc.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
/usr/bin/gcc -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -Ipysam -I. -Ihtslib -I/Users/yukke/.pyenv/versions/2.7.5/include/python2.7 -c htslib/cram/rANS_static.c -o build/temp.macosx-10.4-x86_64-2.7/htslib/cram/rANS_static.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
/usr/bin/gcc -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -Ipysam -I. -Ihtslib -I/Users/yukke/.pyenv/versions/2.7.5/include/python2.7 -c htslib/cram/sam_header.c -o build/temp.macosx-10.4-x86_64-2.7/htslib/cram/sam_header.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
/usr/bin/gcc -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -Ipysam -I. -Ihtslib -I/Users/yukke/.pyenv/versions/2.7.5/include/python2.7 -c htslib/cram/string_alloc.c -o build/temp.macosx-10.4-x86_64-2.7/htslib/cram/string_alloc.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
/usr/bin/gcc -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -Ipysam -I. -Ihtslib -I/Users/yukke/.pyenv/versions/2.7.5/include/python2.7 -c htslib/hfile_libcurl.c -o build/temp.macosx-10.4-x86_64-2.7/htslib/hfile_libcurl.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
/usr/bin/gcc -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -Ipysam -I. -Ihtslib -I/Users/yukke/.pyenv/versions/2.7.5/include/python2.7 -c htslib/hfile_gcs.c -o build/temp.macosx-10.4-x86_64-2.7/htslib/hfile_gcs.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
/usr/bin/gcc -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -Ipysam -I. -Ihtslib -I/Users/yukke/.pyenv/versions/2.7.5/include/python2.7 -c htslib/hfile_s3.c -o build/temp.macosx-10.4-x86_64-2.7/htslib/hfile_s3.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
/usr/bin/gcc -undefined dynamic_lookup -L/Users/yukke/.pyenv/versions/2.7.5/lib build/temp.macosx-10.4-x86_64-2.7/pysam/libchtslib.o build/temp.macosx-10.4-x86_64-2.7/pysam/htslib_util.o build/temp.macosx-10.4-x86_64-2.7/htslib/kfunc.o build/temp.macosx-10.4-x86_64-2.7/htslib/knetfile.o build/temp.macosx-10.4-x86_64-2.7/htslib/kstring.o build/temp.macosx-10.4-x86_64-2.7/htslib/bcf_sr_sort.o build/temp.macosx-10.4-x86_64-2.7/htslib/bgzf.o build/temp.macosx-10.4-x86_64-2.7/htslib/errmod.o build/temp.macosx-10.4-x86_64-2.7/htslib/faidx.o build/temp.macosx-10.4-x86_64-2.7/htslib/hfile.o build/temp.macosx-10.4-x86_64-2.7/htslib/hfile_net.o build/temp.macosx-10.4-x86_64-2.7/htslib/hts.o build/temp.macosx-10.4-x86_64-2.7/htslib/hts_os.o build/temp.macosx-10.4-x86_64-2.7/htslib/md5.o build/temp.macosx-10.4-x86_64-2.7/htslib/multipart.o build/temp.macosx-10.4-x86_64-2.7/htslib/probaln.o build/temp.macosx-10.4-x86_64-2.7/htslib/realn.o build/temp.macosx-10.4-x86_64-2.7/htslib/regidx.o build/temp.macosx-10.4-x86_64-2.7/htslib/sam.o build/temp.macosx-10.4-x86_64-2.7/htslib/synced_bcf_reader.o build/temp.macosx-10.4-x86_64-2.7/htslib/vcf_sweep.o build/temp.macosx-10.4-x86_64-2.7/htslib/tbx.o build/temp.macosx-10.4-x86_64-2.7/htslib/textutils.o build/temp.macosx-10.4-x86_64-2.7/htslib/thread_pool.o build/temp.macosx-10.4-x86_64-2.7/htslib/vcf.o build/temp.macosx-10.4-x86_64-2.7/htslib/vcfutils.o build/temp.macosx-10.4-x86_64-2.7/htslib/cram/cram_codecs.o build/temp.macosx-10.4-x86_64-2.7/htslib/cram/cram_decode.o build/temp.macosx-10.4-x86_64-2.7/htslib/cram/cram_encode.o build/temp.macosx-10.4-x86_64-2.7/htslib/cram/cram_external.o build/temp.macosx-10.4-x86_64-2.7/htslib/cram/cram_index.o build/temp.macosx-10.4-x86_64-2.7/htslib/cram/cram_io.o build/temp.macosx-10.4-x86_64-2.7/htslib/cram/cram_samtools.o build/temp.macosx-10.4-x86_64-2.7/htslib/cram/cram_stats.o build/temp.macosx-10.4-x86_64-2.7/htslib/cram/files.o build/temp.macosx-10.4-x86_64-2.7/htslib/cram/mFILE.o build/temp.macosx-10.4-x86_64-2.7/htslib/cram/open_trace_file.o build/temp.macosx-10.4-x86_64-2.7/htslib/cram/pooled_alloc.o build/temp.macosx-10.4-x86_64-2.7/htslib/cram/rANS_static.o build/temp.macosx-10.4-x86_64-2.7/htslib/cram/sam_header.o build/temp.macosx-10.4-x86_64-2.7/htslib/cram/string_alloc.o build/temp.macosx-10.4-x86_64-2.7/htslib/hfile_libcurl.o build/temp.macosx-10.4-x86_64-2.7/htslib/hfile_gcs.o build/temp.macosx-10.4-x86_64-2.7/htslib/hfile_s3.o -Lpysam -L. -Lbuild/lib.macosx-10.4-x86_64-2.7/pysam -lz -lbz2 -lz -lcurl -o /Users/yukke/dev/pysam/pysam/libchtslib.so -dynamiclib -rpath @loader_path -Wl,-headerpad_max_install_names -Wl,-install_name,@rpath/libchtslib.so -Wl,-x
ld: -rpath can only be used when targeting Mac OS X 10.5 or later
clang: error: linker command failed with exit code 1 (use -v to see invocation)
error: command '/usr/bin/gcc' failed with exit status 1