Created
November 14, 2016 18:59
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svviz install error
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| $ pip install --user -I -U svviz | |
| Collecting svviz | |
| Collecting flask (from svviz) | |
| Using cached Flask-0.11.1-py2.py3-none-any.whl | |
| Collecting numpy (from svviz) | |
| Collecting pyfaidx (from svviz) | |
| Collecting requests (from svviz) | |
| Using cached requests-2.11.1-py2.py3-none-any.whl | |
| Collecting pysam>=0.7.8 (from svviz) | |
| Using cached pysam-0.9.1.4.tar.gz | |
| Collecting Werkzeug>=0.7 (from flask->svviz) | |
| Using cached Werkzeug-0.11.11-py2.py3-none-any.whl | |
| Collecting click>=2.0 (from flask->svviz) | |
| Collecting itsdangerous>=0.21 (from flask->svviz) | |
| Collecting Jinja2>=2.4 (from flask->svviz) | |
| Using cached Jinja2-2.8-py2.py3-none-any.whl | |
| Collecting six (from pyfaidx->svviz) | |
| Using cached six-1.10.0-py2.py3-none-any.whl | |
| Collecting setuptools>=0.7 (from pyfaidx->svviz) | |
| Using cached setuptools-28.8.0-py2.py3-none-any.whl | |
| Collecting MarkupSafe (from Jinja2>=2.4->flask->svviz) | |
| Building wheels for collected packages: pysam | |
| Running setup.py bdist_wheel for pysam ... error | |
| Complete output from command /bin/python3 -u -c "import setuptools, tokenize;__file__='/tmp/pip-build-ouyje9w1/pysam/setup.py';f=getattr(tokenize, 'open', open)(__file__);code=f.read().replace('\r\n', '\n');f.close();exec(compile(code, __file__, 'exec'))" bdist_wheel -d /tmp/tmpx_93hp50pip-wheel- --python-tag cp34: | |
| # pysam: cython is available - using cythonize if necessary | |
| # pysam: htslib mode is shared | |
| # pysam: HTSLIB_CONFIGURE_OPTIONS=None | |
| checking for gcc... gcc | |
| checking whether the C compiler works... yes | |
| checking for C compiler default output file name... a.exe | |
| checking for suffix of executables... .exe | |
| 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 how to run the C preprocessor... gcc -E | |
| checking for grep that handles long lines and -e... /bin/grep | |
| checking for egrep... /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 zlib.h... yes | |
| checking for inflate in -lz... yes | |
| checking for curl_easy_pause in -lcurl... no | |
| checking for curl_easy_init in -lcurl... no | |
| configure: error: libcurl library not found | |
| Support for HTTPS and other SSL-based URLs requires routines from the libcurl | |
| library <http://curl.haxx.se/libcurl/>. Building HTSlib with libcurl enabled | |
| requires libcurl development files to be installed on the build machine; you | |
| may need to ensure a package such as libcurl4-{gnutls,nss,openssl}-dev (on | |
| Debian or Ubuntu Linux) or libcurl-devel (on RPM-based Linux distributions) | |
| is installed. | |
| Either configure with --disable-libcurl or resolve this error to build HTSlib. | |
| checking for gcc... gcc | |
| checking whether the C compiler works... yes | |
| checking for C compiler default output file name... a.exe | |
| checking for suffix of executables... .exe | |
| 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 how to run the C preprocessor... gcc -E | |
| checking for grep that handles long lines and -e... /bin/grep | |
| checking for egrep... /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 zlib.h... yes | |
| checking for inflate in -lz... yes | |
| configure: creating ./config.status | |
| config.status: creating config.mk | |
| config.status: creating config.h | |
| config.status: config.h is unchanged | |
| # pysam: htslib configure options: --disable-libcurl | |
| # pysam: htslib_config PLATFORM=CYGWIN_NT-6.1 | |
| # pysam: htslib_config LDFLAGS= | |
| # pysam: htslib_config LIBHTS_OBJS=kfunc.o knetfile.o kstring.o bgzf.o faidx.o hfile.o hfile_net.o hts.o md5.o regidx.o sam.o synced_bcf_reader.o vcf_sweep.o tbx.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 cram/thread_pool.o cram/vlen.o cram/zfio.o | |
| # pysam: htslib_config LIBS= | |
| # pysam: config_option: ENABLE_PLUGINS=0 | |
| # pysam: config_option: HAVE_COMMONCRYPTO=0 | |
| # pysam: config_option: HAVE_GMTIME_R=1 | |
| # pysam: config_option: HAVE_HMAC=0 | |
| # pysam: config_option: HAVE_IRODS=0 | |
| # pysam: config_option: HAVE_LIBCURL=0 | |
| # pysam: config_option: HAVE_MMAP=1 | |
| running bdist_wheel | |
| running build | |
| running build_py | |
| creating build | |
| creating build/lib.cygwin-2.6.0-x86_64-3.4 | |
| creating build/lib.cygwin-2.6.0-x86_64-3.4/pysam | |
| copying pysam/bcftools.py -> build/lib.cygwin-2.6.0-x86_64-3.4/pysam | |
| copying pysam/config.py -> build/lib.cygwin-2.6.0-x86_64-3.4/pysam | |
| copying pysam/namedtuple.py -> build/lib.cygwin-2.6.0-x86_64-3.4/pysam | |
| copying pysam/Pileup.py -> build/lib.cygwin-2.6.0-x86_64-3.4/pysam | |
| copying pysam/samtools.py -> build/lib.cygwin-2.6.0-x86_64-3.4/pysam | |
| copying pysam/utils.py -> build/lib.cygwin-2.6.0-x86_64-3.4/pysam | |
| copying pysam/version.py -> build/lib.cygwin-2.6.0-x86_64-3.4/pysam | |
| copying pysam/__init__.py -> build/lib.cygwin-2.6.0-x86_64-3.4/pysam | |
| creating build/lib.cygwin-2.6.0-x86_64-3.4/pysam/include | |
| copying pysam/include/__init__.py -> build/lib.cygwin-2.6.0-x86_64-3.4/pysam/include | |
| package init file 'samtools/__init__.py' not found (or not a regular file) | |
| package init file 'bcftools/__init__.py' not found (or not a regular file) | |
| package init file 'samtools/win32/__init__.py' not found (or not a regular file) | |
| package init file 'htslib/__init__.py' not found (or not a regular file) | |
| package init file 'htslib/htslib/__init__.py' not found (or not a regular file) | |
| copying pysam/calignedsegment.pxd -> build/lib.cygwin-2.6.0-x86_64-3.4/pysam | |
| copying pysam/calignmentfile.pxd -> build/lib.cygwin-2.6.0-x86_64-3.4/pysam | |
| copying pysam/cbcf.pxd -> build/lib.cygwin-2.6.0-x86_64-3.4/pysam | |
| copying pysam/cfaidx.pxd -> build/lib.cygwin-2.6.0-x86_64-3.4/pysam | |
| copying pysam/chtslib.pxd -> build/lib.cygwin-2.6.0-x86_64-3.4/pysam | |
| copying pysam/csamfile.pxd -> build/lib.cygwin-2.6.0-x86_64-3.4/pysam | |
| copying pysam/ctabix.pxd -> build/lib.cygwin-2.6.0-x86_64-3.4/pysam | |
| copying pysam/ctabixproxies.pxd -> build/lib.cygwin-2.6.0-x86_64-3.4/pysam | |
| copying pysam/cutils.pxd -> build/lib.cygwin-2.6.0-x86_64-3.4/pysam | |
| copying pysam/cvcf.pxd -> build/lib.cygwin-2.6.0-x86_64-3.4/pysam | |
| copying pysam/htslib_util.h -> build/lib.cygwin-2.6.0-x86_64-3.4/pysam | |
| copying pysam/pysam_stream.h -> build/lib.cygwin-2.6.0-x86_64-3.4/pysam | |
| copying pysam/pysam_util.h -> build/lib.cygwin-2.6.0-x86_64-3.4/pysam | |
| copying pysam/samfile_util.h -> build/lib.cygwin-2.6.0-x86_64-3.4/pysam | |
| copying pysam/tabix_util.h -> build/lib.cygwin-2.6.0-x86_64-3.4/pysam | |
| creating build/lib.cygwin-2.6.0-x86_64-3.4/pysam/include/samtools | |
| copying samtools/bam.h -> build/lib.cygwin-2.6.0-x86_64-3.4/pysam/include/samtools | |
| copying samtools/bam2bcf.h -> build/lib.cygwin-2.6.0-x86_64-3.4/pysam/include/samtools | |
| copying samtools/bam_endian.h -> build/lib.cygwin-2.6.0-x86_64-3.4/pysam/include/samtools | |
| copying samtools/bam_lpileup.h -> build/lib.cygwin-2.6.0-x86_64-3.4/pysam/include/samtools | |
| copying samtools/bam_plbuf.h -> build/lib.cygwin-2.6.0-x86_64-3.4/pysam/include/samtools | |
| copying samtools/bam_tview.h -> build/lib.cygwin-2.6.0-x86_64-3.4/pysam/include/samtools | |
| copying samtools/config.h -> build/lib.cygwin-2.6.0-x86_64-3.4/pysam/include/samtools | |
| copying samtools/errmod.h -> build/lib.cygwin-2.6.0-x86_64-3.4/pysam/include/samtools | |
| copying samtools/kprobaln.h -> build/lib.cygwin-2.6.0-x86_64-3.4/pysam/include/samtools | |
| copying samtools/pysam.h -> build/lib.cygwin-2.6.0-x86_64-3.4/pysam/include/samtools | |
| copying samtools/sam.h -> build/lib.cygwin-2.6.0-x86_64-3.4/pysam/include/samtools | |
| copying samtools/sample.h -> build/lib.cygwin-2.6.0-x86_64-3.4/pysam/include/samtools | |
| copying samtools/samtools.h -> build/lib.cygwin-2.6.0-x86_64-3.4/pysam/include/samtools | |
| copying samtools/sam_header.h -> build/lib.cygwin-2.6.0-x86_64-3.4/pysam/include/samtools | |
| copying samtools/sam_opts.h -> build/lib.cygwin-2.6.0-x86_64-3.4/pysam/include/samtools | |
| copying samtools/stats_isize.h -> build/lib.cygwin-2.6.0-x86_64-3.4/pysam/include/samtools | |
| copying samtools/version.h -> build/lib.cygwin-2.6.0-x86_64-3.4/pysam/include/samtools | |
| creating build/lib.cygwin-2.6.0-x86_64-3.4/pysam/include/bcftools | |
| copying bcftools/bcftools.h -> build/lib.cygwin-2.6.0-x86_64-3.4/pysam/include/bcftools | |
| copying bcftools/call.h -> build/lib.cygwin-2.6.0-x86_64-3.4/pysam/include/bcftools | |
| copying bcftools/convert.h -> build/lib.cygwin-2.6.0-x86_64-3.4/pysam/include/bcftools | |
| copying bcftools/filter.h -> build/lib.cygwin-2.6.0-x86_64-3.4/pysam/include/bcftools | |
| copying bcftools/gvcf.h -> build/lib.cygwin-2.6.0-x86_64-3.4/pysam/include/bcftools | |
| copying bcftools/HMM.h -> build/lib.cygwin-2.6.0-x86_64-3.4/pysam/include/bcftools | |
| copying bcftools/khash_str2str.h -> build/lib.cygwin-2.6.0-x86_64-3.4/pysam/include/bcftools | |
| copying bcftools/kmin.h -> build/lib.cygwin-2.6.0-x86_64-3.4/pysam/include/bcftools | |
| copying bcftools/ploidy.h -> build/lib.cygwin-2.6.0-x86_64-3.4/pysam/include/bcftools | |
| copying bcftools/prob1.h -> build/lib.cygwin-2.6.0-x86_64-3.4/pysam/include/bcftools | |
| copying bcftools/pysam.h -> build/lib.cygwin-2.6.0-x86_64-3.4/pysam/include/bcftools | |
| copying bcftools/rbuf.h -> build/lib.cygwin-2.6.0-x86_64-3.4/pysam/include/bcftools | |
| copying bcftools/tsv2vcf.h -> build/lib.cygwin-2.6.0-x86_64-3.4/pysam/include/bcftools | |
| copying bcftools/vcmp.h -> build/lib.cygwin-2.6.0-x86_64-3.4/pysam/include/bcftools | |
| copying bcftools/version.h -> build/lib.cygwin-2.6.0-x86_64-3.4/pysam/include/bcftools | |
| creating build/lib.cygwin-2.6.0-x86_64-3.4/pysam/include/samtools/win32 | |
| copying samtools/win32/xcurses.h -> build/lib.cygwin-2.6.0-x86_64-3.4/pysam/include/samtools/win32 | |
| copying samtools/win32/zconf.h -> build/lib.cygwin-2.6.0-x86_64-3.4/pysam/include/samtools/win32 | |
| copying samtools/win32/zlib.h -> build/lib.cygwin-2.6.0-x86_64-3.4/pysam/include/samtools/win32 | |
| creating build/lib.cygwin-2.6.0-x86_64-3.4/pysam/include/htslib | |
| copying htslib/config.h -> build/lib.cygwin-2.6.0-x86_64-3.4/pysam/include/htslib | |
| copying htslib/hfile_internal.h -> build/lib.cygwin-2.6.0-x86_64-3.4/pysam/include/htslib | |
| copying htslib/hts_internal.h -> build/lib.cygwin-2.6.0-x86_64-3.4/pysam/include/htslib | |
| copying htslib/pysam.h -> build/lib.cygwin-2.6.0-x86_64-3.4/pysam/include/htslib | |
| copying htslib/version.h -> build/lib.cygwin-2.6.0-x86_64-3.4/pysam/include/htslib | |
| creating build/lib.cygwin-2.6.0-x86_64-3.4/pysam/include/htslib/htslib | |
| copying htslib/htslib/bgzf.h -> build/lib.cygwin-2.6.0-x86_64-3.4/pysam/include/htslib/htslib | |
| copying htslib/htslib/cram.h -> build/lib.cygwin-2.6.0-x86_64-3.4/pysam/include/htslib/htslib | |
| copying htslib/htslib/faidx.h -> build/lib.cygwin-2.6.0-x86_64-3.4/pysam/include/htslib/htslib | |
| copying htslib/htslib/hfile.h -> build/lib.cygwin-2.6.0-x86_64-3.4/pysam/include/htslib/htslib | |
| copying htslib/htslib/hts.h -> build/lib.cygwin-2.6.0-x86_64-3.4/pysam/include/htslib/htslib | |
| copying htslib/htslib/hts_defs.h -> build/lib.cygwin-2.6.0-x86_64-3.4/pysam/include/htslib/htslib | |
| copying htslib/htslib/kbitset.h -> build/lib.cygwin-2.6.0-x86_64-3.4/pysam/include/htslib/htslib | |
| copying htslib/htslib/kfunc.h -> build/lib.cygwin-2.6.0-x86_64-3.4/pysam/include/htslib/htslib | |
| copying htslib/htslib/khash.h -> build/lib.cygwin-2.6.0-x86_64-3.4/pysam/include/htslib/htslib | |
| copying htslib/htslib/khash_str2int.h -> build/lib.cygwin-2.6.0-x86_64-3.4/pysam/include/htslib/htslib | |
| copying htslib/htslib/klist.h -> build/lib.cygwin-2.6.0-x86_64-3.4/pysam/include/htslib/htslib | |
| copying htslib/htslib/knetfile.h -> build/lib.cygwin-2.6.0-x86_64-3.4/pysam/include/htslib/htslib | |
| copying htslib/htslib/kseq.h -> build/lib.cygwin-2.6.0-x86_64-3.4/pysam/include/htslib/htslib | |
| copying htslib/htslib/ksort.h -> build/lib.cygwin-2.6.0-x86_64-3.4/pysam/include/htslib/htslib | |
| copying htslib/htslib/kstring.h -> build/lib.cygwin-2.6.0-x86_64-3.4/pysam/include/htslib/htslib | |
| copying htslib/htslib/regidx.h -> build/lib.cygwin-2.6.0-x86_64-3.4/pysam/include/htslib/htslib | |
| copying htslib/htslib/sam.h -> build/lib.cygwin-2.6.0-x86_64-3.4/pysam/include/htslib/htslib | |
| copying htslib/htslib/synced_bcf_reader.h -> build/lib.cygwin-2.6.0-x86_64-3.4/pysam/include/htslib/htslib | |
| copying htslib/htslib/tbx.h -> build/lib.cygwin-2.6.0-x86_64-3.4/pysam/include/htslib/htslib | |
| copying htslib/htslib/vcf.h -> build/lib.cygwin-2.6.0-x86_64-3.4/pysam/include/htslib/htslib | |
| copying htslib/htslib/vcfutils.h -> build/lib.cygwin-2.6.0-x86_64-3.4/pysam/include/htslib/htslib | |
| copying htslib/htslib/vcf_sweep.h -> build/lib.cygwin-2.6.0-x86_64-3.4/pysam/include/htslib/htslib | |
| Fixing build/lib.cygwin-2.6.0-x86_64-3.4/pysam/bcftools.py build/lib.cygwin-2.6.0-x86_64-3.4/pysam/config.py build/lib.cygwin-2.6.0-x86_64-3.4/pysam/namedtuple.py build/lib.cygwin-2.6.0-x86_64-3.4/pysam/Pileup.py build/lib.cygwin-2.6.0-x86_64-3.4/pysam/samtools.py build/lib.cygwin-2.6.0-x86_64-3.4/pysam/utils.py build/lib.cygwin-2.6.0-x86_64-3.4/pysam/version.py build/lib.cygwin-2.6.0-x86_64-3.4/pysam/__init__.py build/lib.cygwin-2.6.0-x86_64-3.4/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.cygwin-2.6.0-x86_64-3.4/pysam/bcftools.py build/lib.cygwin-2.6.0-x86_64-3.4/pysam/config.py build/lib.cygwin-2.6.0-x86_64-3.4/pysam/namedtuple.py build/lib.cygwin-2.6.0-x86_64-3.4/pysam/Pileup.py build/lib.cygwin-2.6.0-x86_64-3.4/pysam/samtools.py build/lib.cygwin-2.6.0-x86_64-3.4/pysam/utils.py build/lib.cygwin-2.6.0-x86_64-3.4/pysam/version.py build/lib.cygwin-2.6.0-x86_64-3.4/pysam/__init__.py build/lib.cygwin-2.6.0-x86_64-3.4/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/chtslib.c' Cython extension (up-to-date) | |
| building 'pysam.libchtslib' extension | |
| creating build/temp.cygwin-2.6.0-x86_64-3.4 | |
| creating build/temp.cygwin-2.6.0-x86_64-3.4/pysam | |
| creating build/temp.cygwin-2.6.0-x86_64-3.4/htslib | |
| creating build/temp.cygwin-2.6.0-x86_64-3.4/htslib/cram | |
| gcc -Wno-unused-result -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -ggdb -O2 -pipe -Wimplicit-function-declaration -fdebug-prefix-map=/usr/src/ports/python3/python3-3.4.5-1.x86_64/build=/usr/src/debug/python3-3.4.5-1 -fdebug-prefix-map=/usr/src/ports/python3/python3-3.4.5-1.x86_64/src/Python-3.4.5=/usr/src/debug/python3-3.4.5-1 -Ipysam -I. -Ihtslib -I/usr/include/python3.4m -c pysam/chtslib.c -o build/temp.cygwin-2.6.0-x86_64-3.4/pysam/chtslib.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement | |
| gcc -Wno-unused-result -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -ggdb -O2 -pipe -Wimplicit-function-declaration -fdebug-prefix-map=/usr/src/ports/python3/python3-3.4.5-1.x86_64/build=/usr/src/debug/python3-3.4.5-1 -fdebug-prefix-map=/usr/src/ports/python3/python3-3.4.5-1.x86_64/src/Python-3.4.5=/usr/src/debug/python3-3.4.5-1 -Ipysam -I. -Ihtslib -I/usr/include/python3.4m -c pysam/htslib_util.c -o build/temp.cygwin-2.6.0-x86_64-3.4/pysam/htslib_util.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement | |
| gcc -Wno-unused-result -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -ggdb -O2 -pipe -Wimplicit-function-declaration -fdebug-prefix-map=/usr/src/ports/python3/python3-3.4.5-1.x86_64/build=/usr/src/debug/python3-3.4.5-1 -fdebug-prefix-map=/usr/src/ports/python3/python3-3.4.5-1.x86_64/src/Python-3.4.5=/usr/src/debug/python3-3.4.5-1 -Ipysam -I. -Ihtslib -I/usr/include/python3.4m -c htslib/kfunc.c -o build/temp.cygwin-2.6.0-x86_64-3.4/htslib/kfunc.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement | |
| gcc -Wno-unused-result -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -ggdb -O2 -pipe -Wimplicit-function-declaration -fdebug-prefix-map=/usr/src/ports/python3/python3-3.4.5-1.x86_64/build=/usr/src/debug/python3-3.4.5-1 -fdebug-prefix-map=/usr/src/ports/python3/python3-3.4.5-1.x86_64/src/Python-3.4.5=/usr/src/debug/python3-3.4.5-1 -Ipysam -I. -Ihtslib -I/usr/include/python3.4m -c htslib/knetfile.c -o build/temp.cygwin-2.6.0-x86_64-3.4/htslib/knetfile.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement | |
| gcc -Wno-unused-result -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -ggdb -O2 -pipe -Wimplicit-function-declaration -fdebug-prefix-map=/usr/src/ports/python3/python3-3.4.5-1.x86_64/build=/usr/src/debug/python3-3.4.5-1 -fdebug-prefix-map=/usr/src/ports/python3/python3-3.4.5-1.x86_64/src/Python-3.4.5=/usr/src/debug/python3-3.4.5-1 -Ipysam -I. -Ihtslib -I/usr/include/python3.4m -c htslib/kstring.c -o build/temp.cygwin-2.6.0-x86_64-3.4/htslib/kstring.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement | |
| gcc -Wno-unused-result -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -ggdb -O2 -pipe -Wimplicit-function-declaration -fdebug-prefix-map=/usr/src/ports/python3/python3-3.4.5-1.x86_64/build=/usr/src/debug/python3-3.4.5-1 -fdebug-prefix-map=/usr/src/ports/python3/python3-3.4.5-1.x86_64/src/Python-3.4.5=/usr/src/debug/python3-3.4.5-1 -Ipysam -I. -Ihtslib -I/usr/include/python3.4m -c htslib/bgzf.c -o build/temp.cygwin-2.6.0-x86_64-3.4/htslib/bgzf.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement | |
| gcc -Wno-unused-result -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -ggdb -O2 -pipe -Wimplicit-function-declaration -fdebug-prefix-map=/usr/src/ports/python3/python3-3.4.5-1.x86_64/build=/usr/src/debug/python3-3.4.5-1 -fdebug-prefix-map=/usr/src/ports/python3/python3-3.4.5-1.x86_64/src/Python-3.4.5=/usr/src/debug/python3-3.4.5-1 -Ipysam -I. -Ihtslib -I/usr/include/python3.4m -c htslib/faidx.c -o build/temp.cygwin-2.6.0-x86_64-3.4/htslib/faidx.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement | |
| gcc -Wno-unused-result -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -ggdb -O2 -pipe -Wimplicit-function-declaration -fdebug-prefix-map=/usr/src/ports/python3/python3-3.4.5-1.x86_64/build=/usr/src/debug/python3-3.4.5-1 -fdebug-prefix-map=/usr/src/ports/python3/python3-3.4.5-1.x86_64/src/Python-3.4.5=/usr/src/debug/python3-3.4.5-1 -Ipysam -I. -Ihtslib -I/usr/include/python3.4m -c htslib/hfile.c -o build/temp.cygwin-2.6.0-x86_64-3.4/htslib/hfile.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement | |
| gcc -Wno-unused-result -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -ggdb -O2 -pipe -Wimplicit-function-declaration -fdebug-prefix-map=/usr/src/ports/python3/python3-3.4.5-1.x86_64/build=/usr/src/debug/python3-3.4.5-1 -fdebug-prefix-map=/usr/src/ports/python3/python3-3.4.5-1.x86_64/src/Python-3.4.5=/usr/src/debug/python3-3.4.5-1 -Ipysam -I. -Ihtslib -I/usr/include/python3.4m -c htslib/hfile_net.c -o build/temp.cygwin-2.6.0-x86_64-3.4/htslib/hfile_net.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement | |
| gcc -Wno-unused-result -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -ggdb -O2 -pipe -Wimplicit-function-declaration -fdebug-prefix-map=/usr/src/ports/python3/python3-3.4.5-1.x86_64/build=/usr/src/debug/python3-3.4.5-1 -fdebug-prefix-map=/usr/src/ports/python3/python3-3.4.5-1.x86_64/src/Python-3.4.5=/usr/src/debug/python3-3.4.5-1 -Ipysam -I. -Ihtslib -I/usr/include/python3.4m -c htslib/hts.c -o build/temp.cygwin-2.6.0-x86_64-3.4/htslib/hts.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement | |
| gcc -Wno-unused-result -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -ggdb -O2 -pipe -Wimplicit-function-declaration -fdebug-prefix-map=/usr/src/ports/python3/python3-3.4.5-1.x86_64/build=/usr/src/debug/python3-3.4.5-1 -fdebug-prefix-map=/usr/src/ports/python3/python3-3.4.5-1.x86_64/src/Python-3.4.5=/usr/src/debug/python3-3.4.5-1 -Ipysam -I. -Ihtslib -I/usr/include/python3.4m -c htslib/md5.c -o build/temp.cygwin-2.6.0-x86_64-3.4/htslib/md5.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement | |
| gcc -Wno-unused-result -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -ggdb -O2 -pipe -Wimplicit-function-declaration -fdebug-prefix-map=/usr/src/ports/python3/python3-3.4.5-1.x86_64/build=/usr/src/debug/python3-3.4.5-1 -fdebug-prefix-map=/usr/src/ports/python3/python3-3.4.5-1.x86_64/src/Python-3.4.5=/usr/src/debug/python3-3.4.5-1 -Ipysam -I. -Ihtslib -I/usr/include/python3.4m -c htslib/regidx.c -o build/temp.cygwin-2.6.0-x86_64-3.4/htslib/regidx.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement | |
| gcc -Wno-unused-result -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -ggdb -O2 -pipe -Wimplicit-function-declaration -fdebug-prefix-map=/usr/src/ports/python3/python3-3.4.5-1.x86_64/build=/usr/src/debug/python3-3.4.5-1 -fdebug-prefix-map=/usr/src/ports/python3/python3-3.4.5-1.x86_64/src/Python-3.4.5=/usr/src/debug/python3-3.4.5-1 -Ipysam -I. -Ihtslib -I/usr/include/python3.4m -c htslib/sam.c -o build/temp.cygwin-2.6.0-x86_64-3.4/htslib/sam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement | |
| gcc -Wno-unused-result -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -ggdb -O2 -pipe -Wimplicit-function-declaration -fdebug-prefix-map=/usr/src/ports/python3/python3-3.4.5-1.x86_64/build=/usr/src/debug/python3-3.4.5-1 -fdebug-prefix-map=/usr/src/ports/python3/python3-3.4.5-1.x86_64/src/Python-3.4.5=/usr/src/debug/python3-3.4.5-1 -Ipysam -I. -Ihtslib -I/usr/include/python3.4m -c htslib/synced_bcf_reader.c -o build/temp.cygwin-2.6.0-x86_64-3.4/htslib/synced_bcf_reader.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement | |
| gcc -Wno-unused-result -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -ggdb -O2 -pipe -Wimplicit-function-declaration -fdebug-prefix-map=/usr/src/ports/python3/python3-3.4.5-1.x86_64/build=/usr/src/debug/python3-3.4.5-1 -fdebug-prefix-map=/usr/src/ports/python3/python3-3.4.5-1.x86_64/src/Python-3.4.5=/usr/src/debug/python3-3.4.5-1 -Ipysam -I. -Ihtslib -I/usr/include/python3.4m -c htslib/vcf_sweep.c -o build/temp.cygwin-2.6.0-x86_64-3.4/htslib/vcf_sweep.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement | |
| gcc -Wno-unused-result -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -ggdb -O2 -pipe -Wimplicit-function-declaration -fdebug-prefix-map=/usr/src/ports/python3/python3-3.4.5-1.x86_64/build=/usr/src/debug/python3-3.4.5-1 -fdebug-prefix-map=/usr/src/ports/python3/python3-3.4.5-1.x86_64/src/Python-3.4.5=/usr/src/debug/python3-3.4.5-1 -Ipysam -I. -Ihtslib -I/usr/include/python3.4m -c htslib/tbx.c -o build/temp.cygwin-2.6.0-x86_64-3.4/htslib/tbx.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement | |
| gcc -Wno-unused-result -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -ggdb -O2 -pipe -Wimplicit-function-declaration -fdebug-prefix-map=/usr/src/ports/python3/python3-3.4.5-1.x86_64/build=/usr/src/debug/python3-3.4.5-1 -fdebug-prefix-map=/usr/src/ports/python3/python3-3.4.5-1.x86_64/src/Python-3.4.5=/usr/src/debug/python3-3.4.5-1 -Ipysam -I. -Ihtslib -I/usr/include/python3.4m -c htslib/vcf.c -o build/temp.cygwin-2.6.0-x86_64-3.4/htslib/vcf.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement | |
| gcc -Wno-unused-result -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -ggdb -O2 -pipe -Wimplicit-function-declaration -fdebug-prefix-map=/usr/src/ports/python3/python3-3.4.5-1.x86_64/build=/usr/src/debug/python3-3.4.5-1 -fdebug-prefix-map=/usr/src/ports/python3/python3-3.4.5-1.x86_64/src/Python-3.4.5=/usr/src/debug/python3-3.4.5-1 -Ipysam -I. -Ihtslib -I/usr/include/python3.4m -c htslib/vcfutils.c -o build/temp.cygwin-2.6.0-x86_64-3.4/htslib/vcfutils.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement | |
| gcc -Wno-unused-result -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -ggdb -O2 -pipe -Wimplicit-function-declaration -fdebug-prefix-map=/usr/src/ports/python3/python3-3.4.5-1.x86_64/build=/usr/src/debug/python3-3.4.5-1 -fdebug-prefix-map=/usr/src/ports/python3/python3-3.4.5-1.x86_64/src/Python-3.4.5=/usr/src/debug/python3-3.4.5-1 -Ipysam -I. -Ihtslib -I/usr/include/python3.4m -c htslib/cram/cram_codecs.c -o build/temp.cygwin-2.6.0-x86_64-3.4/htslib/cram/cram_codecs.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement | |
| gcc -Wno-unused-result -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -ggdb -O2 -pipe -Wimplicit-function-declaration -fdebug-prefix-map=/usr/src/ports/python3/python3-3.4.5-1.x86_64/build=/usr/src/debug/python3-3.4.5-1 -fdebug-prefix-map=/usr/src/ports/python3/python3-3.4.5-1.x86_64/src/Python-3.4.5=/usr/src/debug/python3-3.4.5-1 -Ipysam -I. -Ihtslib -I/usr/include/python3.4m -c htslib/cram/cram_decode.c -o build/temp.cygwin-2.6.0-x86_64-3.4/htslib/cram/cram_decode.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement | |
| gcc -Wno-unused-result -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -ggdb -O2 -pipe -Wimplicit-function-declaration -fdebug-prefix-map=/usr/src/ports/python3/python3-3.4.5-1.x86_64/build=/usr/src/debug/python3-3.4.5-1 -fdebug-prefix-map=/usr/src/ports/python3/python3-3.4.5-1.x86_64/src/Python-3.4.5=/usr/src/debug/python3-3.4.5-1 -Ipysam -I. -Ihtslib -I/usr/include/python3.4m -c htslib/cram/cram_encode.c -o build/temp.cygwin-2.6.0-x86_64-3.4/htslib/cram/cram_encode.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement | |
| gcc -Wno-unused-result -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -ggdb -O2 -pipe -Wimplicit-function-declaration -fdebug-prefix-map=/usr/src/ports/python3/python3-3.4.5-1.x86_64/build=/usr/src/debug/python3-3.4.5-1 -fdebug-prefix-map=/usr/src/ports/python3/python3-3.4.5-1.x86_64/src/Python-3.4.5=/usr/src/debug/python3-3.4.5-1 -Ipysam -I. -Ihtslib -I/usr/include/python3.4m -c htslib/cram/cram_external.c -o build/temp.cygwin-2.6.0-x86_64-3.4/htslib/cram/cram_external.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement | |
| gcc -Wno-unused-result -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -ggdb -O2 -pipe -Wimplicit-function-declaration -fdebug-prefix-map=/usr/src/ports/python3/python3-3.4.5-1.x86_64/build=/usr/src/debug/python3-3.4.5-1 -fdebug-prefix-map=/usr/src/ports/python3/python3-3.4.5-1.x86_64/src/Python-3.4.5=/usr/src/debug/python3-3.4.5-1 -Ipysam -I. -Ihtslib -I/usr/include/python3.4m -c htslib/cram/cram_index.c -o build/temp.cygwin-2.6.0-x86_64-3.4/htslib/cram/cram_index.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement | |
| gcc -Wno-unused-result -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -ggdb -O2 -pipe -Wimplicit-function-declaration -fdebug-prefix-map=/usr/src/ports/python3/python3-3.4.5-1.x86_64/build=/usr/src/debug/python3-3.4.5-1 -fdebug-prefix-map=/usr/src/ports/python3/python3-3.4.5-1.x86_64/src/Python-3.4.5=/usr/src/debug/python3-3.4.5-1 -Ipysam -I. -Ihtslib -I/usr/include/python3.4m -c htslib/cram/cram_io.c -o build/temp.cygwin-2.6.0-x86_64-3.4/htslib/cram/cram_io.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement | |
| gcc -Wno-unused-result -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -ggdb -O2 -pipe -Wimplicit-function-declaration -fdebug-prefix-map=/usr/src/ports/python3/python3-3.4.5-1.x86_64/build=/usr/src/debug/python3-3.4.5-1 -fdebug-prefix-map=/usr/src/ports/python3/python3-3.4.5-1.x86_64/src/Python-3.4.5=/usr/src/debug/python3-3.4.5-1 -Ipysam -I. -Ihtslib -I/usr/include/python3.4m -c htslib/cram/cram_samtools.c -o build/temp.cygwin-2.6.0-x86_64-3.4/htslib/cram/cram_samtools.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement | |
| gcc -Wno-unused-result -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -ggdb -O2 -pipe -Wimplicit-function-declaration -fdebug-prefix-map=/usr/src/ports/python3/python3-3.4.5-1.x86_64/build=/usr/src/debug/python3-3.4.5-1 -fdebug-prefix-map=/usr/src/ports/python3/python3-3.4.5-1.x86_64/src/Python-3.4.5=/usr/src/debug/python3-3.4.5-1 -Ipysam -I. -Ihtslib -I/usr/include/python3.4m -c htslib/cram/cram_stats.c -o build/temp.cygwin-2.6.0-x86_64-3.4/htslib/cram/cram_stats.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement | |
| gcc -Wno-unused-result -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -ggdb -O2 -pipe -Wimplicit-function-declaration -fdebug-prefix-map=/usr/src/ports/python3/python3-3.4.5-1.x86_64/build=/usr/src/debug/python3-3.4.5-1 -fdebug-prefix-map=/usr/src/ports/python3/python3-3.4.5-1.x86_64/src/Python-3.4.5=/usr/src/debug/python3-3.4.5-1 -Ipysam -I. -Ihtslib -I/usr/include/python3.4m -c htslib/cram/files.c -o build/temp.cygwin-2.6.0-x86_64-3.4/htslib/cram/files.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement | |
| gcc -Wno-unused-result -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -ggdb -O2 -pipe -Wimplicit-function-declaration -fdebug-prefix-map=/usr/src/ports/python3/python3-3.4.5-1.x86_64/build=/usr/src/debug/python3-3.4.5-1 -fdebug-prefix-map=/usr/src/ports/python3/python3-3.4.5-1.x86_64/src/Python-3.4.5=/usr/src/debug/python3-3.4.5-1 -Ipysam -I. -Ihtslib -I/usr/include/python3.4m -c htslib/cram/mFILE.c -o build/temp.cygwin-2.6.0-x86_64-3.4/htslib/cram/mFILE.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement | |
| gcc -Wno-unused-result -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -ggdb -O2 -pipe -Wimplicit-function-declaration -fdebug-prefix-map=/usr/src/ports/python3/python3-3.4.5-1.x86_64/build=/usr/src/debug/python3-3.4.5-1 -fdebug-prefix-map=/usr/src/ports/python3/python3-3.4.5-1.x86_64/src/Python-3.4.5=/usr/src/debug/python3-3.4.5-1 -Ipysam -I. -Ihtslib -I/usr/include/python3.4m -c htslib/cram/open_trace_file.c -o build/temp.cygwin-2.6.0-x86_64-3.4/htslib/cram/open_trace_file.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement | |
| gcc -Wno-unused-result -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -ggdb -O2 -pipe -Wimplicit-function-declaration -fdebug-prefix-map=/usr/src/ports/python3/python3-3.4.5-1.x86_64/build=/usr/src/debug/python3-3.4.5-1 -fdebug-prefix-map=/usr/src/ports/python3/python3-3.4.5-1.x86_64/src/Python-3.4.5=/usr/src/debug/python3-3.4.5-1 -Ipysam -I. -Ihtslib -I/usr/include/python3.4m -c htslib/cram/pooled_alloc.c -o build/temp.cygwin-2.6.0-x86_64-3.4/htslib/cram/pooled_alloc.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement | |
| gcc -Wno-unused-result -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -ggdb -O2 -pipe -Wimplicit-function-declaration -fdebug-prefix-map=/usr/src/ports/python3/python3-3.4.5-1.x86_64/build=/usr/src/debug/python3-3.4.5-1 -fdebug-prefix-map=/usr/src/ports/python3/python3-3.4.5-1.x86_64/src/Python-3.4.5=/usr/src/debug/python3-3.4.5-1 -Ipysam -I. -Ihtslib -I/usr/include/python3.4m -c htslib/cram/rANS_static.c -o build/temp.cygwin-2.6.0-x86_64-3.4/htslib/cram/rANS_static.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement | |
| gcc -Wno-unused-result -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -ggdb -O2 -pipe -Wimplicit-function-declaration -fdebug-prefix-map=/usr/src/ports/python3/python3-3.4.5-1.x86_64/build=/usr/src/debug/python3-3.4.5-1 -fdebug-prefix-map=/usr/src/ports/python3/python3-3.4.5-1.x86_64/src/Python-3.4.5=/usr/src/debug/python3-3.4.5-1 -Ipysam -I. -Ihtslib -I/usr/include/python3.4m -c htslib/cram/sam_header.c -o build/temp.cygwin-2.6.0-x86_64-3.4/htslib/cram/sam_header.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement | |
| gcc -Wno-unused-result -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -ggdb -O2 -pipe -Wimplicit-function-declaration -fdebug-prefix-map=/usr/src/ports/python3/python3-3.4.5-1.x86_64/build=/usr/src/debug/python3-3.4.5-1 -fdebug-prefix-map=/usr/src/ports/python3/python3-3.4.5-1.x86_64/src/Python-3.4.5=/usr/src/debug/python3-3.4.5-1 -Ipysam -I. -Ihtslib -I/usr/include/python3.4m -c htslib/cram/string_alloc.c -o build/temp.cygwin-2.6.0-x86_64-3.4/htslib/cram/string_alloc.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement | |
| gcc -Wno-unused-result -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -ggdb -O2 -pipe -Wimplicit-function-declaration -fdebug-prefix-map=/usr/src/ports/python3/python3-3.4.5-1.x86_64/build=/usr/src/debug/python3-3.4.5-1 -fdebug-prefix-map=/usr/src/ports/python3/python3-3.4.5-1.x86_64/src/Python-3.4.5=/usr/src/debug/python3-3.4.5-1 -Ipysam -I. -Ihtslib -I/usr/include/python3.4m -c htslib/cram/thread_pool.c -o build/temp.cygwin-2.6.0-x86_64-3.4/htslib/cram/thread_pool.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement | |
| gcc -Wno-unused-result -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -ggdb -O2 -pipe -Wimplicit-function-declaration -fdebug-prefix-map=/usr/src/ports/python3/python3-3.4.5-1.x86_64/build=/usr/src/debug/python3-3.4.5-1 -fdebug-prefix-map=/usr/src/ports/python3/python3-3.4.5-1.x86_64/src/Python-3.4.5=/usr/src/debug/python3-3.4.5-1 -Ipysam -I. -Ihtslib -I/usr/include/python3.4m -c htslib/cram/vlen.c -o build/temp.cygwin-2.6.0-x86_64-3.4/htslib/cram/vlen.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement | |
| gcc -Wno-unused-result -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -ggdb -O2 -pipe -Wimplicit-function-declaration -fdebug-prefix-map=/usr/src/ports/python3/python3-3.4.5-1.x86_64/build=/usr/src/debug/python3-3.4.5-1 -fdebug-prefix-map=/usr/src/ports/python3/python3-3.4.5-1.x86_64/src/Python-3.4.5=/usr/src/debug/python3-3.4.5-1 -Ipysam -I. -Ihtslib -I/usr/include/python3.4m -c htslib/cram/zfio.c -o build/temp.cygwin-2.6.0-x86_64-3.4/htslib/cram/zfio.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement | |
| gcc -shared -Wl,--enable-auto-image-base build/temp.cygwin-2.6.0-x86_64-3.4/pysam/chtslib.o build/temp.cygwin-2.6.0-x86_64-3.4/pysam/htslib_util.o build/temp.cygwin-2.6.0-x86_64-3.4/htslib/kfunc.o build/temp.cygwin-2.6.0-x86_64-3.4/htslib/knetfile.o build/temp.cygwin-2.6.0-x86_64-3.4/htslib/kstring.o build/temp.cygwin-2.6.0-x86_64-3.4/htslib/bgzf.o build/temp.cygwin-2.6.0-x86_64-3.4/htslib/faidx.o build/temp.cygwin-2.6.0-x86_64-3.4/htslib/hfile.o build/temp.cygwin-2.6.0-x86_64-3.4/htslib/hfile_net.o build/temp.cygwin-2.6.0-x86_64-3.4/htslib/hts.o build/temp.cygwin-2.6.0-x86_64-3.4/htslib/md5.o build/temp.cygwin-2.6.0-x86_64-3.4/htslib/regidx.o build/temp.cygwin-2.6.0-x86_64-3.4/htslib/sam.o build/temp.cygwin-2.6.0-x86_64-3.4/htslib/synced_bcf_reader.o build/temp.cygwin-2.6.0-x86_64-3.4/htslib/vcf_sweep.o build/temp.cygwin-2.6.0-x86_64-3.4/htslib/tbx.o build/temp.cygwin-2.6.0-x86_64-3.4/htslib/vcf.o build/temp.cygwin-2.6.0-x86_64-3.4/htslib/vcfutils.o build/temp.cygwin-2.6.0-x86_64-3.4/htslib/cram/cram_codecs.o build/temp.cygwin-2.6.0-x86_64-3.4/htslib/cram/cram_decode.o build/temp.cygwin-2.6.0-x86_64-3.4/htslib/cram/cram_encode.o build/temp.cygwin-2.6.0-x86_64-3.4/htslib/cram/cram_external.o build/temp.cygwin-2.6.0-x86_64-3.4/htslib/cram/cram_index.o build/temp.cygwin-2.6.0-x86_64-3.4/htslib/cram/cram_io.o build/temp.cygwin-2.6.0-x86_64-3.4/htslib/cram/cram_samtools.o build/temp.cygwin-2.6.0-x86_64-3.4/htslib/cram/cram_stats.o build/temp.cygwin-2.6.0-x86_64-3.4/htslib/cram/files.o build/temp.cygwin-2.6.0-x86_64-3.4/htslib/cram/mFILE.o build/temp.cygwin-2.6.0-x86_64-3.4/htslib/cram/open_trace_file.o build/temp.cygwin-2.6.0-x86_64-3.4/htslib/cram/pooled_alloc.o build/temp.cygwin-2.6.0-x86_64-3.4/htslib/cram/rANS_static.o build/temp.cygwin-2.6.0-x86_64-3.4/htslib/cram/sam_header.o build/temp.cygwin-2.6.0-x86_64-3.4/htslib/cram/string_alloc.o build/temp.cygwin-2.6.0-x86_64-3.4/htslib/cram/thread_pool.o build/temp.cygwin-2.6.0-x86_64-3.4/htslib/cram/vlen.o build/temp.cygwin-2.6.0-x86_64-3.4/htslib/cram/zfio.o -Lpysam -L. -Lbuild/lib.cygwin-2.6.0-x86_64-3.4/pysam -Lbuild/lib.cygwin-2.6.0-x86_64-3.4/pysam -L. -L/usr/lib -Lpysam -L. -Lbuild/lib.cygwin-2.6.0-x86_64-3.4/pysam -Lbuild/lib.cygwin-2.6.0-x86_64-3.4/pysam -lz -lpython3.4m -o build/lib.cygwin-2.6.0-x86_64-3.4/pysam/libchtslib.cpython-34m.dll -Wl,-rpath,$ORIGIN | |
| skipping 'pysam/csamfile.c' Cython extension (up-to-date) | |
| building 'pysam.csamfile' extension | |
| creating build/temp.cygwin-2.6.0-x86_64-3.4/samtools | |
| gcc -Wno-unused-result -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -ggdb -O2 -pipe -Wimplicit-function-declaration -fdebug-prefix-map=/usr/src/ports/python3/python3-3.4.5-1.x86_64/build=/usr/src/debug/python3-3.4.5-1 -fdebug-prefix-map=/usr/src/ports/python3/python3-3.4.5-1.x86_64/src/Python-3.4.5=/usr/src/debug/python3-3.4.5-1 -Ipysam -Isamtools -I. -Ihtslib -I/usr/include/python3.4m -c pysam/csamfile.c -o build/temp.cygwin-2.6.0-x86_64-3.4/pysam/csamfile.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement | |
| gcc -Wno-unused-result -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -ggdb -O2 -pipe -Wimplicit-function-declaration -fdebug-prefix-map=/usr/src/ports/python3/python3-3.4.5-1.x86_64/build=/usr/src/debug/python3-3.4.5-1 -fdebug-prefix-map=/usr/src/ports/python3/python3-3.4.5-1.x86_64/src/Python-3.4.5=/usr/src/debug/python3-3.4.5-1 -Ipysam -Isamtools -I. -Ihtslib -I/usr/include/python3.4m -c pysam/htslib_util.c -o build/temp.cygwin-2.6.0-x86_64-3.4/pysam/htslib_util.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement | |
| gcc -Wno-unused-result -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -ggdb -O2 -pipe -Wimplicit-function-declaration -fdebug-prefix-map=/usr/src/ports/python3/python3-3.4.5-1.x86_64/build=/usr/src/debug/python3-3.4.5-1 -fdebug-prefix-map=/usr/src/ports/python3/python3-3.4.5-1.x86_64/src/Python-3.4.5=/usr/src/debug/python3-3.4.5-1 -Ipysam -Isamtools -I. -Ihtslib -I/usr/include/python3.4m -c pysam/samfile_util.c -o build/temp.cygwin-2.6.0-x86_64-3.4/pysam/samfile_util.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement | |
| gcc -Wno-unused-result -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -ggdb -O2 -pipe -Wimplicit-function-declaration -fdebug-prefix-map=/usr/src/ports/python3/python3-3.4.5-1.x86_64/build=/usr/src/debug/python3-3.4.5-1 -fdebug-prefix-map=/usr/src/ports/python3/python3-3.4.5-1.x86_64/src/Python-3.4.5=/usr/src/debug/python3-3.4.5-1 -Ipysam -Isamtools -I. -Ihtslib -I/usr/include/python3.4m -c samtools/kprobaln.c -o build/temp.cygwin-2.6.0-x86_64-3.4/samtools/kprobaln.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement | |
| gcc -shared -Wl,--enable-auto-image-base build/temp.cygwin-2.6.0-x86_64-3.4/pysam/csamfile.o build/temp.cygwin-2.6.0-x86_64-3.4/pysam/htslib_util.o build/temp.cygwin-2.6.0-x86_64-3.4/pysam/samfile_util.o build/temp.cygwin-2.6.0-x86_64-3.4/samtools/kprobaln.o -Lpysam -L. -Lbuild/lib.cygwin-2.6.0-x86_64-3.4/pysam -Lbuild/lib.cygwin-2.6.0-x86_64-3.4/pysam -Lbuild/lib.cygwin-2.6.0-x86_64-3.4/pysam -L. -L/usr/lib -lz -lchtslib.cpython-34m -lpython3.4m -o build/lib.cygwin-2.6.0-x86_64-3.4/pysam/csamfile.cpython-34m.dll -Wl,-rpath,$ORIGIN | |
| build/temp.cygwin-2.6.0-x86_64-3.4/pysam/htslib_util.o:htslib_util.c:(.rdata$.refptr.seq_nt16_table[.refptr.seq_nt16_table]+0x0): undefined reference to `seq_nt16_table' | |
| build/temp.cygwin-2.6.0-x86_64-3.4/pysam/htslib_util.o:htslib_util.c:(.rdata$.refptr.hts_verbose[.refptr.hts_verbose]+0x0): undefined reference to `hts_verbose' | |
| build/temp.cygwin-2.6.0-x86_64-3.4/pysam/samfile_util.o: In function `bam_prob_realn_core': | |
| /tmp/pip-build-ouyje9w1/pysam/pysam/samfile_util.c:78: undefined reference to `bam_aux_get' | |
| /tmp/pip-build-ouyje9w1/pysam/pysam/samfile_util.c:78:(.text+0x427): relocation truncated to fit: R_X86_64_PC32 against undefined symbol `bam_aux_get' | |
| /tmp/pip-build-ouyje9w1/pysam/pysam/samfile_util.c:79: undefined reference to `bam_aux_get' | |
| /tmp/pip-build-ouyje9w1/pysam/pysam/samfile_util.c:79:(.text+0x446): relocation truncated to fit: R_X86_64_PC32 against undefined symbol `bam_aux_get' | |
| /tmp/pip-build-ouyje9w1/pysam/pysam/samfile_util.c:86: undefined reference to `bam_aux_del' | |
| /tmp/pip-build-ouyje9w1/pysam/pysam/samfile_util.c:86:(.text+0x49d): relocation truncated to fit: R_X86_64_PC32 against undefined symbol `bam_aux_del' | |
| /tmp/pip-build-ouyje9w1/pysam/pysam/samfile_util.c:82: undefined reference to `bam_aux_del' | |
| /tmp/pip-build-ouyje9w1/pysam/pysam/samfile_util.c:82:(.text+0x53b): relocation truncated to fit: R_X86_64_PC32 against undefined symbol `bam_aux_del' | |
| /tmp/pip-build-ouyje9w1/pysam/pysam/samfile_util.c:176: undefined reference to `bam_aux_append' | |
| /tmp/pip-build-ouyje9w1/pysam/pysam/samfile_util.c:176:(.text+0x969): relocation truncated to fit: R_X86_64_PC32 against undefined symbol `bam_aux_append' | |
| /tmp/pip-build-ouyje9w1/pysam/pysam/samfile_util.c:79: undefined reference to `bam_aux_get' | |
| /tmp/pip-build-ouyje9w1/pysam/pysam/samfile_util.c:79:(.text+0x9ad): relocation truncated to fit: R_X86_64_PC32 against undefined symbol `bam_aux_get' | |
| /tmp/pip-build-ouyje9w1/pysam/pysam/samfile_util.c:177: undefined reference to `bam_aux_append' | |
| /tmp/pip-build-ouyje9w1/pysam/pysam/samfile_util.c:177:(.text+0xb4c): relocation truncated to fit: R_X86_64_PC32 against undefined symbol `bam_aux_append' | |
| collect2: error: ld returned 1 exit status | |
| error: command 'gcc' failed with exit status 1 | |
| ---------------------------------------- | |
| Failed building wheel for pysam | |
| Running setup.py clean for pysam | |
| Failed to build pysam | |
| Installing collected packages: Werkzeug, click, itsdangerous, MarkupSafe, Jinja2, flask, numpy, six, setuptools, pyfaidx, requests, pysam, svviz | |
| Running setup.py install for pysam ... error | |
| Complete output from command /bin/python3 -u -c "import setuptools, tokenize;__file__='/tmp/pip-build-ouyje9w1/pysam/setup.py';f=getattr(tokenize, 'open', open)(__file__);code=f.read().replace('\r\n', '\n');f.close();exec(compile(code, __file__, 'exec'))" install --record /tmp/pip-lxwufq2p-record/install-record.txt --single-version-externally-managed --compile --user --prefix=: | |
| # pysam: cython is available - using cythonize if necessary | |
| # pysam: htslib mode is shared | |
| # pysam: HTSLIB_CONFIGURE_OPTIONS=None | |
| checking for gcc... gcc | |
| checking whether the C compiler works... yes | |
| checking for C compiler default output file name... a.exe | |
| checking for suffix of executables... .exe | |
| 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 how to run the C preprocessor... gcc -E | |
| checking for grep that handles long lines and -e... /bin/grep | |
| checking for egrep... /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 zlib.h... yes | |
| checking for inflate in -lz... yes | |
| checking for curl_easy_pause in -lcurl... no | |
| checking for curl_easy_init in -lcurl... no | |
| configure: error: libcurl library not found | |
| Support for HTTPS and other SSL-based URLs requires routines from the libcurl | |
| library <http://curl.haxx.se/libcurl/>. Building HTSlib with libcurl enabled | |
| requires libcurl development files to be installed on the build machine; you | |
| may need to ensure a package such as libcurl4-{gnutls,nss,openssl}-dev (on | |
| Debian or Ubuntu Linux) or libcurl-devel (on RPM-based Linux distributions) | |
| is installed. | |
| Either configure with --disable-libcurl or resolve this error to build HTSlib. | |
| checking for gcc... gcc | |
| checking whether the C compiler works... yes | |
| checking for C compiler default output file name... a.exe | |
| checking for suffix of executables... .exe | |
| 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 how to run the C preprocessor... gcc -E | |
| checking for grep that handles long lines and -e... /bin/grep | |
| checking for egrep... /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 zlib.h... yes | |
| checking for inflate in -lz... yes | |
| configure: creating ./config.status | |
| config.status: creating config.mk | |
| config.status: creating config.h | |
| config.status: config.h is unchanged | |
| # pysam: htslib configure options: --disable-libcurl | |
| # pysam: htslib_config LIBS= | |
| # pysam: htslib_config PLATFORM=CYGWIN_NT-6.1 | |
| # pysam: htslib_config LDFLAGS= | |
| # pysam: htslib_config LIBHTS_OBJS=kfunc.o knetfile.o kstring.o bgzf.o faidx.o hfile.o hfile_net.o hts.o md5.o regidx.o sam.o synced_bcf_reader.o vcf_sweep.o tbx.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 cram/thread_pool.o cram/vlen.o cram/zfio.o | |
| # pysam: config_option: ENABLE_PLUGINS=0 | |
| # pysam: config_option: HAVE_COMMONCRYPTO=0 | |
| # pysam: config_option: HAVE_GMTIME_R=1 | |
| # pysam: config_option: HAVE_HMAC=0 | |
| # pysam: config_option: HAVE_IRODS=0 | |
| # pysam: config_option: HAVE_LIBCURL=0 | |
| # pysam: config_option: HAVE_MMAP=1 | |
| running install | |
| running build | |
| running build_py | |
| creating build | |
| creating build/lib.cygwin-2.6.0-x86_64-3.4 | |
| creating build/lib.cygwin-2.6.0-x86_64-3.4/pysam | |
| copying pysam/bcftools.py -> build/lib.cygwin-2.6.0-x86_64-3.4/pysam | |
| copying pysam/config.py -> build/lib.cygwin-2.6.0-x86_64-3.4/pysam | |
| copying pysam/namedtuple.py -> build/lib.cygwin-2.6.0-x86_64-3.4/pysam | |
| copying pysam/Pileup.py -> build/lib.cygwin-2.6.0-x86_64-3.4/pysam | |
| copying pysam/samtools.py -> build/lib.cygwin-2.6.0-x86_64-3.4/pysam | |
| copying pysam/utils.py -> build/lib.cygwin-2.6.0-x86_64-3.4/pysam | |
| copying pysam/version.py -> build/lib.cygwin-2.6.0-x86_64-3.4/pysam | |
| copying pysam/__init__.py -> build/lib.cygwin-2.6.0-x86_64-3.4/pysam | |
| creating build/lib.cygwin-2.6.0-x86_64-3.4/pysam/include | |
| copying pysam/include/__init__.py -> build/lib.cygwin-2.6.0-x86_64-3.4/pysam/include | |
| package init file 'samtools/__init__.py' not found (or not a regular file) | |
| package init file 'bcftools/__init__.py' not found (or not a regular file) | |
| package init file 'samtools/win32/__init__.py' not found (or not a regular file) | |
| package init file 'htslib/__init__.py' not found (or not a regular file) | |
| package init file 'htslib/htslib/__init__.py' not found (or not a regular file) | |
| copying pysam/calignedsegment.pxd -> build/lib.cygwin-2.6.0-x86_64-3.4/pysam | |
| copying pysam/calignmentfile.pxd -> build/lib.cygwin-2.6.0-x86_64-3.4/pysam | |
| copying pysam/cbcf.pxd -> build/lib.cygwin-2.6.0-x86_64-3.4/pysam | |
| copying pysam/cfaidx.pxd -> build/lib.cygwin-2.6.0-x86_64-3.4/pysam | |
| copying pysam/chtslib.pxd -> build/lib.cygwin-2.6.0-x86_64-3.4/pysam | |
| copying pysam/csamfile.pxd -> build/lib.cygwin-2.6.0-x86_64-3.4/pysam | |
| copying pysam/ctabix.pxd -> build/lib.cygwin-2.6.0-x86_64-3.4/pysam | |
| copying pysam/ctabixproxies.pxd -> build/lib.cygwin-2.6.0-x86_64-3.4/pysam | |
| copying pysam/cutils.pxd -> build/lib.cygwin-2.6.0-x86_64-3.4/pysam | |
| copying pysam/cvcf.pxd -> build/lib.cygwin-2.6.0-x86_64-3.4/pysam | |
| copying pysam/htslib_util.h -> build/lib.cygwin-2.6.0-x86_64-3.4/pysam | |
| copying pysam/pysam_stream.h -> build/lib.cygwin-2.6.0-x86_64-3.4/pysam | |
| copying pysam/pysam_util.h -> build/lib.cygwin-2.6.0-x86_64-3.4/pysam | |
| copying pysam/samfile_util.h -> build/lib.cygwin-2.6.0-x86_64-3.4/pysam | |
| copying pysam/tabix_util.h -> build/lib.cygwin-2.6.0-x86_64-3.4/pysam | |
| creating build/lib.cygwin-2.6.0-x86_64-3.4/pysam/include/samtools | |
| copying samtools/bam.h -> build/lib.cygwin-2.6.0-x86_64-3.4/pysam/include/samtools | |
| copying samtools/bam2bcf.h -> build/lib.cygwin-2.6.0-x86_64-3.4/pysam/include/samtools | |
| copying samtools/bam_endian.h -> build/lib.cygwin-2.6.0-x86_64-3.4/pysam/include/samtools | |
| copying samtools/bam_lpileup.h -> build/lib.cygwin-2.6.0-x86_64-3.4/pysam/include/samtools | |
| copying samtools/bam_plbuf.h -> build/lib.cygwin-2.6.0-x86_64-3.4/pysam/include/samtools | |
| copying samtools/bam_tview.h -> build/lib.cygwin-2.6.0-x86_64-3.4/pysam/include/samtools | |
| copying samtools/config.h -> build/lib.cygwin-2.6.0-x86_64-3.4/pysam/include/samtools | |
| copying samtools/errmod.h -> build/lib.cygwin-2.6.0-x86_64-3.4/pysam/include/samtools | |
| copying samtools/kprobaln.h -> build/lib.cygwin-2.6.0-x86_64-3.4/pysam/include/samtools | |
| copying samtools/pysam.h -> build/lib.cygwin-2.6.0-x86_64-3.4/pysam/include/samtools | |
| copying samtools/sam.h -> build/lib.cygwin-2.6.0-x86_64-3.4/pysam/include/samtools | |
| copying samtools/sample.h -> build/lib.cygwin-2.6.0-x86_64-3.4/pysam/include/samtools | |
| copying samtools/samtools.h -> build/lib.cygwin-2.6.0-x86_64-3.4/pysam/include/samtools | |
| copying samtools/sam_header.h -> build/lib.cygwin-2.6.0-x86_64-3.4/pysam/include/samtools | |
| copying samtools/sam_opts.h -> build/lib.cygwin-2.6.0-x86_64-3.4/pysam/include/samtools | |
| copying samtools/stats_isize.h -> build/lib.cygwin-2.6.0-x86_64-3.4/pysam/include/samtools | |
| copying samtools/version.h -> build/lib.cygwin-2.6.0-x86_64-3.4/pysam/include/samtools | |
| creating build/lib.cygwin-2.6.0-x86_64-3.4/pysam/include/bcftools | |
| copying bcftools/bcftools.h -> build/lib.cygwin-2.6.0-x86_64-3.4/pysam/include/bcftools | |
| copying bcftools/call.h -> build/lib.cygwin-2.6.0-x86_64-3.4/pysam/include/bcftools | |
| copying bcftools/convert.h -> build/lib.cygwin-2.6.0-x86_64-3.4/pysam/include/bcftools | |
| copying bcftools/filter.h -> build/lib.cygwin-2.6.0-x86_64-3.4/pysam/include/bcftools | |
| copying bcftools/gvcf.h -> build/lib.cygwin-2.6.0-x86_64-3.4/pysam/include/bcftools | |
| copying bcftools/HMM.h -> build/lib.cygwin-2.6.0-x86_64-3.4/pysam/include/bcftools | |
| copying bcftools/khash_str2str.h -> build/lib.cygwin-2.6.0-x86_64-3.4/pysam/include/bcftools | |
| copying bcftools/kmin.h -> build/lib.cygwin-2.6.0-x86_64-3.4/pysam/include/bcftools | |
| copying bcftools/ploidy.h -> build/lib.cygwin-2.6.0-x86_64-3.4/pysam/include/bcftools | |
| copying bcftools/prob1.h -> build/lib.cygwin-2.6.0-x86_64-3.4/pysam/include/bcftools | |
| copying bcftools/pysam.h -> build/lib.cygwin-2.6.0-x86_64-3.4/pysam/include/bcftools | |
| copying bcftools/rbuf.h -> build/lib.cygwin-2.6.0-x86_64-3.4/pysam/include/bcftools | |
| copying bcftools/tsv2vcf.h -> build/lib.cygwin-2.6.0-x86_64-3.4/pysam/include/bcftools | |
| copying bcftools/vcmp.h -> build/lib.cygwin-2.6.0-x86_64-3.4/pysam/include/bcftools | |
| copying bcftools/version.h -> build/lib.cygwin-2.6.0-x86_64-3.4/pysam/include/bcftools | |
| creating build/lib.cygwin-2.6.0-x86_64-3.4/pysam/include/samtools/win32 | |
| copying samtools/win32/xcurses.h -> build/lib.cygwin-2.6.0-x86_64-3.4/pysam/include/samtools/win32 | |
| copying samtools/win32/zconf.h -> build/lib.cygwin-2.6.0-x86_64-3.4/pysam/include/samtools/win32 | |
| copying samtools/win32/zlib.h -> build/lib.cygwin-2.6.0-x86_64-3.4/pysam/include/samtools/win32 | |
| creating build/lib.cygwin-2.6.0-x86_64-3.4/pysam/include/htslib | |
| copying htslib/config.h -> build/lib.cygwin-2.6.0-x86_64-3.4/pysam/include/htslib | |
| copying htslib/hfile_internal.h -> build/lib.cygwin-2.6.0-x86_64-3.4/pysam/include/htslib | |
| copying htslib/hts_internal.h -> build/lib.cygwin-2.6.0-x86_64-3.4/pysam/include/htslib | |
| copying htslib/pysam.h -> build/lib.cygwin-2.6.0-x86_64-3.4/pysam/include/htslib | |
| copying htslib/version.h -> build/lib.cygwin-2.6.0-x86_64-3.4/pysam/include/htslib | |
| creating build/lib.cygwin-2.6.0-x86_64-3.4/pysam/include/htslib/htslib | |
| copying htslib/htslib/bgzf.h -> build/lib.cygwin-2.6.0-x86_64-3.4/pysam/include/htslib/htslib | |
| copying htslib/htslib/cram.h -> build/lib.cygwin-2.6.0-x86_64-3.4/pysam/include/htslib/htslib | |
| copying htslib/htslib/faidx.h -> build/lib.cygwin-2.6.0-x86_64-3.4/pysam/include/htslib/htslib | |
| copying htslib/htslib/hfile.h -> build/lib.cygwin-2.6.0-x86_64-3.4/pysam/include/htslib/htslib | |
| copying htslib/htslib/hts.h -> build/lib.cygwin-2.6.0-x86_64-3.4/pysam/include/htslib/htslib | |
| copying htslib/htslib/hts_defs.h -> build/lib.cygwin-2.6.0-x86_64-3.4/pysam/include/htslib/htslib | |
| copying htslib/htslib/kbitset.h -> build/lib.cygwin-2.6.0-x86_64-3.4/pysam/include/htslib/htslib | |
| copying htslib/htslib/kfunc.h -> build/lib.cygwin-2.6.0-x86_64-3.4/pysam/include/htslib/htslib | |
| copying htslib/htslib/khash.h -> build/lib.cygwin-2.6.0-x86_64-3.4/pysam/include/htslib/htslib | |
| copying htslib/htslib/khash_str2int.h -> build/lib.cygwin-2.6.0-x86_64-3.4/pysam/include/htslib/htslib | |
| copying htslib/htslib/klist.h -> build/lib.cygwin-2.6.0-x86_64-3.4/pysam/include/htslib/htslib | |
| copying htslib/htslib/knetfile.h -> build/lib.cygwin-2.6.0-x86_64-3.4/pysam/include/htslib/htslib | |
| copying htslib/htslib/kseq.h -> build/lib.cygwin-2.6.0-x86_64-3.4/pysam/include/htslib/htslib | |
| copying htslib/htslib/ksort.h -> build/lib.cygwin-2.6.0-x86_64-3.4/pysam/include/htslib/htslib | |
| copying htslib/htslib/kstring.h -> build/lib.cygwin-2.6.0-x86_64-3.4/pysam/include/htslib/htslib | |
| copying htslib/htslib/regidx.h -> build/lib.cygwin-2.6.0-x86_64-3.4/pysam/include/htslib/htslib | |
| copying htslib/htslib/sam.h -> build/lib.cygwin-2.6.0-x86_64-3.4/pysam/include/htslib/htslib | |
| copying htslib/htslib/synced_bcf_reader.h -> build/lib.cygwin-2.6.0-x86_64-3.4/pysam/include/htslib/htslib | |
| copying htslib/htslib/tbx.h -> build/lib.cygwin-2.6.0-x86_64-3.4/pysam/include/htslib/htslib | |
| copying htslib/htslib/vcf.h -> build/lib.cygwin-2.6.0-x86_64-3.4/pysam/include/htslib/htslib | |
| copying htslib/htslib/vcfutils.h -> build/lib.cygwin-2.6.0-x86_64-3.4/pysam/include/htslib/htslib | |
| copying htslib/htslib/vcf_sweep.h -> build/lib.cygwin-2.6.0-x86_64-3.4/pysam/include/htslib/htslib | |
| Fixing build/lib.cygwin-2.6.0-x86_64-3.4/pysam/bcftools.py build/lib.cygwin-2.6.0-x86_64-3.4/pysam/config.py build/lib.cygwin-2.6.0-x86_64-3.4/pysam/namedtuple.py build/lib.cygwin-2.6.0-x86_64-3.4/pysam/Pileup.py build/lib.cygwin-2.6.0-x86_64-3.4/pysam/samtools.py build/lib.cygwin-2.6.0-x86_64-3.4/pysam/utils.py build/lib.cygwin-2.6.0-x86_64-3.4/pysam/version.py build/lib.cygwin-2.6.0-x86_64-3.4/pysam/__init__.py build/lib.cygwin-2.6.0-x86_64-3.4/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.cygwin-2.6.0-x86_64-3.4/pysam/bcftools.py build/lib.cygwin-2.6.0-x86_64-3.4/pysam/config.py build/lib.cygwin-2.6.0-x86_64-3.4/pysam/namedtuple.py build/lib.cygwin-2.6.0-x86_64-3.4/pysam/Pileup.py build/lib.cygwin-2.6.0-x86_64-3.4/pysam/samtools.py build/lib.cygwin-2.6.0-x86_64-3.4/pysam/utils.py build/lib.cygwin-2.6.0-x86_64-3.4/pysam/version.py build/lib.cygwin-2.6.0-x86_64-3.4/pysam/__init__.py build/lib.cygwin-2.6.0-x86_64-3.4/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/chtslib.c' Cython extension (up-to-date) | |
| building 'pysam.libchtslib' extension | |
| creating build/temp.cygwin-2.6.0-x86_64-3.4 | |
| creating build/temp.cygwin-2.6.0-x86_64-3.4/pysam | |
| creating build/temp.cygwin-2.6.0-x86_64-3.4/htslib | |
| creating build/temp.cygwin-2.6.0-x86_64-3.4/htslib/cram | |
| gcc -Wno-unused-result -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -ggdb -O2 -pipe -Wimplicit-function-declaration -fdebug-prefix-map=/usr/src/ports/python3/python3-3.4.5-1.x86_64/build=/usr/src/debug/python3-3.4.5-1 -fdebug-prefix-map=/usr/src/ports/python3/python3-3.4.5-1.x86_64/src/Python-3.4.5=/usr/src/debug/python3-3.4.5-1 -Ipysam -I. -Ihtslib -I/usr/include/python3.4m -c pysam/chtslib.c -o build/temp.cygwin-2.6.0-x86_64-3.4/pysam/chtslib.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement | |
| gcc -Wno-unused-result -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -ggdb -O2 -pipe -Wimplicit-function-declaration -fdebug-prefix-map=/usr/src/ports/python3/python3-3.4.5-1.x86_64/build=/usr/src/debug/python3-3.4.5-1 -fdebug-prefix-map=/usr/src/ports/python3/python3-3.4.5-1.x86_64/src/Python-3.4.5=/usr/src/debug/python3-3.4.5-1 -Ipysam -I. -Ihtslib -I/usr/include/python3.4m -c pysam/htslib_util.c -o build/temp.cygwin-2.6.0-x86_64-3.4/pysam/htslib_util.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement | |
| gcc -Wno-unused-result -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -ggdb -O2 -pipe -Wimplicit-function-declaration -fdebug-prefix-map=/usr/src/ports/python3/python3-3.4.5-1.x86_64/build=/usr/src/debug/python3-3.4.5-1 -fdebug-prefix-map=/usr/src/ports/python3/python3-3.4.5-1.x86_64/src/Python-3.4.5=/usr/src/debug/python3-3.4.5-1 -Ipysam -I. -Ihtslib -I/usr/include/python3.4m -c htslib/kfunc.c -o build/temp.cygwin-2.6.0-x86_64-3.4/htslib/kfunc.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement | |
| gcc -Wno-unused-result -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -ggdb -O2 -pipe -Wimplicit-function-declaration -fdebug-prefix-map=/usr/src/ports/python3/python3-3.4.5-1.x86_64/build=/usr/src/debug/python3-3.4.5-1 -fdebug-prefix-map=/usr/src/ports/python3/python3-3.4.5-1.x86_64/src/Python-3.4.5=/usr/src/debug/python3-3.4.5-1 -Ipysam -I. -Ihtslib -I/usr/include/python3.4m -c htslib/knetfile.c -o build/temp.cygwin-2.6.0-x86_64-3.4/htslib/knetfile.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement | |
| gcc -Wno-unused-result -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -ggdb -O2 -pipe -Wimplicit-function-declaration -fdebug-prefix-map=/usr/src/ports/python3/python3-3.4.5-1.x86_64/build=/usr/src/debug/python3-3.4.5-1 -fdebug-prefix-map=/usr/src/ports/python3/python3-3.4.5-1.x86_64/src/Python-3.4.5=/usr/src/debug/python3-3.4.5-1 -Ipysam -I. -Ihtslib -I/usr/include/python3.4m -c htslib/kstring.c -o build/temp.cygwin-2.6.0-x86_64-3.4/htslib/kstring.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement | |
| gcc -Wno-unused-result -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -ggdb -O2 -pipe -Wimplicit-function-declaration -fdebug-prefix-map=/usr/src/ports/python3/python3-3.4.5-1.x86_64/build=/usr/src/debug/python3-3.4.5-1 -fdebug-prefix-map=/usr/src/ports/python3/python3-3.4.5-1.x86_64/src/Python-3.4.5=/usr/src/debug/python3-3.4.5-1 -Ipysam -I. -Ihtslib -I/usr/include/python3.4m -c htslib/bgzf.c -o build/temp.cygwin-2.6.0-x86_64-3.4/htslib/bgzf.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement | |
| gcc -Wno-unused-result -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -ggdb -O2 -pipe -Wimplicit-function-declaration -fdebug-prefix-map=/usr/src/ports/python3/python3-3.4.5-1.x86_64/build=/usr/src/debug/python3-3.4.5-1 -fdebug-prefix-map=/usr/src/ports/python3/python3-3.4.5-1.x86_64/src/Python-3.4.5=/usr/src/debug/python3-3.4.5-1 -Ipysam -I. -Ihtslib -I/usr/include/python3.4m -c htslib/faidx.c -o build/temp.cygwin-2.6.0-x86_64-3.4/htslib/faidx.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement | |
| gcc -Wno-unused-result -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -ggdb -O2 -pipe -Wimplicit-function-declaration -fdebug-prefix-map=/usr/src/ports/python3/python3-3.4.5-1.x86_64/build=/usr/src/debug/python3-3.4.5-1 -fdebug-prefix-map=/usr/src/ports/python3/python3-3.4.5-1.x86_64/src/Python-3.4.5=/usr/src/debug/python3-3.4.5-1 -Ipysam -I. -Ihtslib -I/usr/include/python3.4m -c htslib/hfile.c -o build/temp.cygwin-2.6.0-x86_64-3.4/htslib/hfile.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement | |
| gcc -Wno-unused-result -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -ggdb -O2 -pipe -Wimplicit-function-declaration -fdebug-prefix-map=/usr/src/ports/python3/python3-3.4.5-1.x86_64/build=/usr/src/debug/python3-3.4.5-1 -fdebug-prefix-map=/usr/src/ports/python3/python3-3.4.5-1.x86_64/src/Python-3.4.5=/usr/src/debug/python3-3.4.5-1 -Ipysam -I. -Ihtslib -I/usr/include/python3.4m -c htslib/hfile_net.c -o build/temp.cygwin-2.6.0-x86_64-3.4/htslib/hfile_net.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement | |
| gcc -Wno-unused-result -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -ggdb -O2 -pipe -Wimplicit-function-declaration -fdebug-prefix-map=/usr/src/ports/python3/python3-3.4.5-1.x86_64/build=/usr/src/debug/python3-3.4.5-1 -fdebug-prefix-map=/usr/src/ports/python3/python3-3.4.5-1.x86_64/src/Python-3.4.5=/usr/src/debug/python3-3.4.5-1 -Ipysam -I. -Ihtslib -I/usr/include/python3.4m -c htslib/hts.c -o build/temp.cygwin-2.6.0-x86_64-3.4/htslib/hts.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement | |
| gcc -Wno-unused-result -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -ggdb -O2 -pipe -Wimplicit-function-declaration -fdebug-prefix-map=/usr/src/ports/python3/python3-3.4.5-1.x86_64/build=/usr/src/debug/python3-3.4.5-1 -fdebug-prefix-map=/usr/src/ports/python3/python3-3.4.5-1.x86_64/src/Python-3.4.5=/usr/src/debug/python3-3.4.5-1 -Ipysam -I. -Ihtslib -I/usr/include/python3.4m -c htslib/md5.c -o build/temp.cygwin-2.6.0-x86_64-3.4/htslib/md5.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement | |
| gcc -Wno-unused-result -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -ggdb -O2 -pipe -Wimplicit-function-declaration -fdebug-prefix-map=/usr/src/ports/python3/python3-3.4.5-1.x86_64/build=/usr/src/debug/python3-3.4.5-1 -fdebug-prefix-map=/usr/src/ports/python3/python3-3.4.5-1.x86_64/src/Python-3.4.5=/usr/src/debug/python3-3.4.5-1 -Ipysam -I. -Ihtslib -I/usr/include/python3.4m -c htslib/regidx.c -o build/temp.cygwin-2.6.0-x86_64-3.4/htslib/regidx.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement | |
| gcc -Wno-unused-result -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -ggdb -O2 -pipe -Wimplicit-function-declaration -fdebug-prefix-map=/usr/src/ports/python3/python3-3.4.5-1.x86_64/build=/usr/src/debug/python3-3.4.5-1 -fdebug-prefix-map=/usr/src/ports/python3/python3-3.4.5-1.x86_64/src/Python-3.4.5=/usr/src/debug/python3-3.4.5-1 -Ipysam -I. -Ihtslib -I/usr/include/python3.4m -c htslib/sam.c -o build/temp.cygwin-2.6.0-x86_64-3.4/htslib/sam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement | |
| gcc -Wno-unused-result -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -ggdb -O2 -pipe -Wimplicit-function-declaration -fdebug-prefix-map=/usr/src/ports/python3/python3-3.4.5-1.x86_64/build=/usr/src/debug/python3-3.4.5-1 -fdebug-prefix-map=/usr/src/ports/python3/python3-3.4.5-1.x86_64/src/Python-3.4.5=/usr/src/debug/python3-3.4.5-1 -Ipysam -I. -Ihtslib -I/usr/include/python3.4m -c htslib/synced_bcf_reader.c -o build/temp.cygwin-2.6.0-x86_64-3.4/htslib/synced_bcf_reader.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement | |
| gcc -Wno-unused-result -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -ggdb -O2 -pipe -Wimplicit-function-declaration -fdebug-prefix-map=/usr/src/ports/python3/python3-3.4.5-1.x86_64/build=/usr/src/debug/python3-3.4.5-1 -fdebug-prefix-map=/usr/src/ports/python3/python3-3.4.5-1.x86_64/src/Python-3.4.5=/usr/src/debug/python3-3.4.5-1 -Ipysam -I. -Ihtslib -I/usr/include/python3.4m -c htslib/vcf_sweep.c -o build/temp.cygwin-2.6.0-x86_64-3.4/htslib/vcf_sweep.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement | |
| gcc -Wno-unused-result -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -ggdb -O2 -pipe -Wimplicit-function-declaration -fdebug-prefix-map=/usr/src/ports/python3/python3-3.4.5-1.x86_64/build=/usr/src/debug/python3-3.4.5-1 -fdebug-prefix-map=/usr/src/ports/python3/python3-3.4.5-1.x86_64/src/Python-3.4.5=/usr/src/debug/python3-3.4.5-1 -Ipysam -I. -Ihtslib -I/usr/include/python3.4m -c htslib/tbx.c -o build/temp.cygwin-2.6.0-x86_64-3.4/htslib/tbx.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement | |
| gcc -Wno-unused-result -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -ggdb -O2 -pipe -Wimplicit-function-declaration -fdebug-prefix-map=/usr/src/ports/python3/python3-3.4.5-1.x86_64/build=/usr/src/debug/python3-3.4.5-1 -fdebug-prefix-map=/usr/src/ports/python3/python3-3.4.5-1.x86_64/src/Python-3.4.5=/usr/src/debug/python3-3.4.5-1 -Ipysam -I. -Ihtslib -I/usr/include/python3.4m -c htslib/vcf.c -o build/temp.cygwin-2.6.0-x86_64-3.4/htslib/vcf.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement | |
| gcc -Wno-unused-result -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -ggdb -O2 -pipe -Wimplicit-function-declaration -fdebug-prefix-map=/usr/src/ports/python3/python3-3.4.5-1.x86_64/build=/usr/src/debug/python3-3.4.5-1 -fdebug-prefix-map=/usr/src/ports/python3/python3-3.4.5-1.x86_64/src/Python-3.4.5=/usr/src/debug/python3-3.4.5-1 -Ipysam -I. -Ihtslib -I/usr/include/python3.4m -c htslib/vcfutils.c -o build/temp.cygwin-2.6.0-x86_64-3.4/htslib/vcfutils.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement | |
| gcc -Wno-unused-result -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -ggdb -O2 -pipe -Wimplicit-function-declaration -fdebug-prefix-map=/usr/src/ports/python3/python3-3.4.5-1.x86_64/build=/usr/src/debug/python3-3.4.5-1 -fdebug-prefix-map=/usr/src/ports/python3/python3-3.4.5-1.x86_64/src/Python-3.4.5=/usr/src/debug/python3-3.4.5-1 -Ipysam -I. -Ihtslib -I/usr/include/python3.4m -c htslib/cram/cram_codecs.c -o build/temp.cygwin-2.6.0-x86_64-3.4/htslib/cram/cram_codecs.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement | |
| gcc -Wno-unused-result -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -ggdb -O2 -pipe -Wimplicit-function-declaration -fdebug-prefix-map=/usr/src/ports/python3/python3-3.4.5-1.x86_64/build=/usr/src/debug/python3-3.4.5-1 -fdebug-prefix-map=/usr/src/ports/python3/python3-3.4.5-1.x86_64/src/Python-3.4.5=/usr/src/debug/python3-3.4.5-1 -Ipysam -I. -Ihtslib -I/usr/include/python3.4m -c htslib/cram/cram_decode.c -o build/temp.cygwin-2.6.0-x86_64-3.4/htslib/cram/cram_decode.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement | |
| gcc -Wno-unused-result -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -ggdb -O2 -pipe -Wimplicit-function-declaration -fdebug-prefix-map=/usr/src/ports/python3/python3-3.4.5-1.x86_64/build=/usr/src/debug/python3-3.4.5-1 -fdebug-prefix-map=/usr/src/ports/python3/python3-3.4.5-1.x86_64/src/Python-3.4.5=/usr/src/debug/python3-3.4.5-1 -Ipysam -I. -Ihtslib -I/usr/include/python3.4m -c htslib/cram/cram_encode.c -o build/temp.cygwin-2.6.0-x86_64-3.4/htslib/cram/cram_encode.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement | |
| gcc -Wno-unused-result -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -ggdb -O2 -pipe -Wimplicit-function-declaration -fdebug-prefix-map=/usr/src/ports/python3/python3-3.4.5-1.x86_64/build=/usr/src/debug/python3-3.4.5-1 -fdebug-prefix-map=/usr/src/ports/python3/python3-3.4.5-1.x86_64/src/Python-3.4.5=/usr/src/debug/python3-3.4.5-1 -Ipysam -I. -Ihtslib -I/usr/include/python3.4m -c htslib/cram/cram_external.c -o build/temp.cygwin-2.6.0-x86_64-3.4/htslib/cram/cram_external.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement | |
| gcc -Wno-unused-result -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -ggdb -O2 -pipe -Wimplicit-function-declaration -fdebug-prefix-map=/usr/src/ports/python3/python3-3.4.5-1.x86_64/build=/usr/src/debug/python3-3.4.5-1 -fdebug-prefix-map=/usr/src/ports/python3/python3-3.4.5-1.x86_64/src/Python-3.4.5=/usr/src/debug/python3-3.4.5-1 -Ipysam -I. -Ihtslib -I/usr/include/python3.4m -c htslib/cram/cram_index.c -o build/temp.cygwin-2.6.0-x86_64-3.4/htslib/cram/cram_index.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement | |
| gcc -Wno-unused-result -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -ggdb -O2 -pipe -Wimplicit-function-declaration -fdebug-prefix-map=/usr/src/ports/python3/python3-3.4.5-1.x86_64/build=/usr/src/debug/python3-3.4.5-1 -fdebug-prefix-map=/usr/src/ports/python3/python3-3.4.5-1.x86_64/src/Python-3.4.5=/usr/src/debug/python3-3.4.5-1 -Ipysam -I. -Ihtslib -I/usr/include/python3.4m -c htslib/cram/cram_io.c -o build/temp.cygwin-2.6.0-x86_64-3.4/htslib/cram/cram_io.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement | |
| gcc -Wno-unused-result -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -ggdb -O2 -pipe -Wimplicit-function-declaration -fdebug-prefix-map=/usr/src/ports/python3/python3-3.4.5-1.x86_64/build=/usr/src/debug/python3-3.4.5-1 -fdebug-prefix-map=/usr/src/ports/python3/python3-3.4.5-1.x86_64/src/Python-3.4.5=/usr/src/debug/python3-3.4.5-1 -Ipysam -I. -Ihtslib -I/usr/include/python3.4m -c htslib/cram/cram_samtools.c -o build/temp.cygwin-2.6.0-x86_64-3.4/htslib/cram/cram_samtools.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement | |
| gcc -Wno-unused-result -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -ggdb -O2 -pipe -Wimplicit-function-declaration -fdebug-prefix-map=/usr/src/ports/python3/python3-3.4.5-1.x86_64/build=/usr/src/debug/python3-3.4.5-1 -fdebug-prefix-map=/usr/src/ports/python3/python3-3.4.5-1.x86_64/src/Python-3.4.5=/usr/src/debug/python3-3.4.5-1 -Ipysam -I. -Ihtslib -I/usr/include/python3.4m -c htslib/cram/cram_stats.c -o build/temp.cygwin-2.6.0-x86_64-3.4/htslib/cram/cram_stats.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement | |
| gcc -Wno-unused-result -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -ggdb -O2 -pipe -Wimplicit-function-declaration -fdebug-prefix-map=/usr/src/ports/python3/python3-3.4.5-1.x86_64/build=/usr/src/debug/python3-3.4.5-1 -fdebug-prefix-map=/usr/src/ports/python3/python3-3.4.5-1.x86_64/src/Python-3.4.5=/usr/src/debug/python3-3.4.5-1 -Ipysam -I. -Ihtslib -I/usr/include/python3.4m -c htslib/cram/files.c -o build/temp.cygwin-2.6.0-x86_64-3.4/htslib/cram/files.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement | |
| gcc -Wno-unused-result -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -ggdb -O2 -pipe -Wimplicit-function-declaration -fdebug-prefix-map=/usr/src/ports/python3/python3-3.4.5-1.x86_64/build=/usr/src/debug/python3-3.4.5-1 -fdebug-prefix-map=/usr/src/ports/python3/python3-3.4.5-1.x86_64/src/Python-3.4.5=/usr/src/debug/python3-3.4.5-1 -Ipysam -I. -Ihtslib -I/usr/include/python3.4m -c htslib/cram/mFILE.c -o build/temp.cygwin-2.6.0-x86_64-3.4/htslib/cram/mFILE.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement | |
| gcc -Wno-unused-result -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -ggdb -O2 -pipe -Wimplicit-function-declaration -fdebug-prefix-map=/usr/src/ports/python3/python3-3.4.5-1.x86_64/build=/usr/src/debug/python3-3.4.5-1 -fdebug-prefix-map=/usr/src/ports/python3/python3-3.4.5-1.x86_64/src/Python-3.4.5=/usr/src/debug/python3-3.4.5-1 -Ipysam -I. -Ihtslib -I/usr/include/python3.4m -c htslib/cram/open_trace_file.c -o build/temp.cygwin-2.6.0-x86_64-3.4/htslib/cram/open_trace_file.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement | |
| gcc -Wno-unused-result -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -ggdb -O2 -pipe -Wimplicit-function-declaration -fdebug-prefix-map=/usr/src/ports/python3/python3-3.4.5-1.x86_64/build=/usr/src/debug/python3-3.4.5-1 -fdebug-prefix-map=/usr/src/ports/python3/python3-3.4.5-1.x86_64/src/Python-3.4.5=/usr/src/debug/python3-3.4.5-1 -Ipysam -I. -Ihtslib -I/usr/include/python3.4m -c htslib/cram/pooled_alloc.c -o build/temp.cygwin-2.6.0-x86_64-3.4/htslib/cram/pooled_alloc.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement | |
| gcc -Wno-unused-result -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -ggdb -O2 -pipe -Wimplicit-function-declaration -fdebug-prefix-map=/usr/src/ports/python3/python3-3.4.5-1.x86_64/build=/usr/src/debug/python3-3.4.5-1 -fdebug-prefix-map=/usr/src/ports/python3/python3-3.4.5-1.x86_64/src/Python-3.4.5=/usr/src/debug/python3-3.4.5-1 -Ipysam -I. -Ihtslib -I/usr/include/python3.4m -c htslib/cram/rANS_static.c -o build/temp.cygwin-2.6.0-x86_64-3.4/htslib/cram/rANS_static.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement | |
| gcc -Wno-unused-result -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -ggdb -O2 -pipe -Wimplicit-function-declaration -fdebug-prefix-map=/usr/src/ports/python3/python3-3.4.5-1.x86_64/build=/usr/src/debug/python3-3.4.5-1 -fdebug-prefix-map=/usr/src/ports/python3/python3-3.4.5-1.x86_64/src/Python-3.4.5=/usr/src/debug/python3-3.4.5-1 -Ipysam -I. -Ihtslib -I/usr/include/python3.4m -c htslib/cram/sam_header.c -o build/temp.cygwin-2.6.0-x86_64-3.4/htslib/cram/sam_header.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement | |
| gcc -Wno-unused-result -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -ggdb -O2 -pipe -Wimplicit-function-declaration -fdebug-prefix-map=/usr/src/ports/python3/python3-3.4.5-1.x86_64/build=/usr/src/debug/python3-3.4.5-1 -fdebug-prefix-map=/usr/src/ports/python3/python3-3.4.5-1.x86_64/src/Python-3.4.5=/usr/src/debug/python3-3.4.5-1 -Ipysam -I. -Ihtslib -I/usr/include/python3.4m -c htslib/cram/string_alloc.c -o build/temp.cygwin-2.6.0-x86_64-3.4/htslib/cram/string_alloc.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement | |
| gcc -Wno-unused-result -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -ggdb -O2 -pipe -Wimplicit-function-declaration -fdebug-prefix-map=/usr/src/ports/python3/python3-3.4.5-1.x86_64/build=/usr/src/debug/python3-3.4.5-1 -fdebug-prefix-map=/usr/src/ports/python3/python3-3.4.5-1.x86_64/src/Python-3.4.5=/usr/src/debug/python3-3.4.5-1 -Ipysam -I. -Ihtslib -I/usr/include/python3.4m -c htslib/cram/thread_pool.c -o build/temp.cygwin-2.6.0-x86_64-3.4/htslib/cram/thread_pool.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement | |
| gcc -Wno-unused-result -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -ggdb -O2 -pipe -Wimplicit-function-declaration -fdebug-prefix-map=/usr/src/ports/python3/python3-3.4.5-1.x86_64/build=/usr/src/debug/python3-3.4.5-1 -fdebug-prefix-map=/usr/src/ports/python3/python3-3.4.5-1.x86_64/src/Python-3.4.5=/usr/src/debug/python3-3.4.5-1 -Ipysam -I. -Ihtslib -I/usr/include/python3.4m -c htslib/cram/vlen.c -o build/temp.cygwin-2.6.0-x86_64-3.4/htslib/cram/vlen.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement | |
| gcc -Wno-unused-result -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -ggdb -O2 -pipe -Wimplicit-function-declaration -fdebug-prefix-map=/usr/src/ports/python3/python3-3.4.5-1.x86_64/build=/usr/src/debug/python3-3.4.5-1 -fdebug-prefix-map=/usr/src/ports/python3/python3-3.4.5-1.x86_64/src/Python-3.4.5=/usr/src/debug/python3-3.4.5-1 -Ipysam -I. -Ihtslib -I/usr/include/python3.4m -c htslib/cram/zfio.c -o build/temp.cygwin-2.6.0-x86_64-3.4/htslib/cram/zfio.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement | |
| gcc -shared -Wl,--enable-auto-image-base build/temp.cygwin-2.6.0-x86_64-3.4/pysam/chtslib.o build/temp.cygwin-2.6.0-x86_64-3.4/pysam/htslib_util.o build/temp.cygwin-2.6.0-x86_64-3.4/htslib/kfunc.o build/temp.cygwin-2.6.0-x86_64-3.4/htslib/knetfile.o build/temp.cygwin-2.6.0-x86_64-3.4/htslib/kstring.o build/temp.cygwin-2.6.0-x86_64-3.4/htslib/bgzf.o build/temp.cygwin-2.6.0-x86_64-3.4/htslib/faidx.o build/temp.cygwin-2.6.0-x86_64-3.4/htslib/hfile.o build/temp.cygwin-2.6.0-x86_64-3.4/htslib/hfile_net.o build/temp.cygwin-2.6.0-x86_64-3.4/htslib/hts.o build/temp.cygwin-2.6.0-x86_64-3.4/htslib/md5.o build/temp.cygwin-2.6.0-x86_64-3.4/htslib/regidx.o build/temp.cygwin-2.6.0-x86_64-3.4/htslib/sam.o build/temp.cygwin-2.6.0-x86_64-3.4/htslib/synced_bcf_reader.o build/temp.cygwin-2.6.0-x86_64-3.4/htslib/vcf_sweep.o build/temp.cygwin-2.6.0-x86_64-3.4/htslib/tbx.o build/temp.cygwin-2.6.0-x86_64-3.4/htslib/vcf.o build/temp.cygwin-2.6.0-x86_64-3.4/htslib/vcfutils.o build/temp.cygwin-2.6.0-x86_64-3.4/htslib/cram/cram_codecs.o build/temp.cygwin-2.6.0-x86_64-3.4/htslib/cram/cram_decode.o build/temp.cygwin-2.6.0-x86_64-3.4/htslib/cram/cram_encode.o build/temp.cygwin-2.6.0-x86_64-3.4/htslib/cram/cram_external.o build/temp.cygwin-2.6.0-x86_64-3.4/htslib/cram/cram_index.o build/temp.cygwin-2.6.0-x86_64-3.4/htslib/cram/cram_io.o build/temp.cygwin-2.6.0-x86_64-3.4/htslib/cram/cram_samtools.o build/temp.cygwin-2.6.0-x86_64-3.4/htslib/cram/cram_stats.o build/temp.cygwin-2.6.0-x86_64-3.4/htslib/cram/files.o build/temp.cygwin-2.6.0-x86_64-3.4/htslib/cram/mFILE.o build/temp.cygwin-2.6.0-x86_64-3.4/htslib/cram/open_trace_file.o build/temp.cygwin-2.6.0-x86_64-3.4/htslib/cram/pooled_alloc.o build/temp.cygwin-2.6.0-x86_64-3.4/htslib/cram/rANS_static.o build/temp.cygwin-2.6.0-x86_64-3.4/htslib/cram/sam_header.o build/temp.cygwin-2.6.0-x86_64-3.4/htslib/cram/string_alloc.o build/temp.cygwin-2.6.0-x86_64-3.4/htslib/cram/thread_pool.o build/temp.cygwin-2.6.0-x86_64-3.4/htslib/cram/vlen.o build/temp.cygwin-2.6.0-x86_64-3.4/htslib/cram/zfio.o -Lpysam -L. -Lbuild/lib.cygwin-2.6.0-x86_64-3.4/pysam -Lbuild/lib.cygwin-2.6.0-x86_64-3.4/pysam -L. -L/usr/lib -Lpysam -L. -Lbuild/lib.cygwin-2.6.0-x86_64-3.4/pysam -Lbuild/lib.cygwin-2.6.0-x86_64-3.4/pysam -lz -lpython3.4m -o build/lib.cygwin-2.6.0-x86_64-3.4/pysam/libchtslib.cpython-34m.dll -Wl,-rpath,$ORIGIN | |
| skipping 'pysam/csamfile.c' Cython extension (up-to-date) | |
| building 'pysam.csamfile' extension | |
| creating build/temp.cygwin-2.6.0-x86_64-3.4/samtools | |
| gcc -Wno-unused-result -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -ggdb -O2 -pipe -Wimplicit-function-declaration -fdebug-prefix-map=/usr/src/ports/python3/python3-3.4.5-1.x86_64/build=/usr/src/debug/python3-3.4.5-1 -fdebug-prefix-map=/usr/src/ports/python3/python3-3.4.5-1.x86_64/src/Python-3.4.5=/usr/src/debug/python3-3.4.5-1 -Ipysam -Isamtools -I. -Ihtslib -I/usr/include/python3.4m -c pysam/csamfile.c -o build/temp.cygwin-2.6.0-x86_64-3.4/pysam/csamfile.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement | |
| gcc -Wno-unused-result -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -ggdb -O2 -pipe -Wimplicit-function-declaration -fdebug-prefix-map=/usr/src/ports/python3/python3-3.4.5-1.x86_64/build=/usr/src/debug/python3-3.4.5-1 -fdebug-prefix-map=/usr/src/ports/python3/python3-3.4.5-1.x86_64/src/Python-3.4.5=/usr/src/debug/python3-3.4.5-1 -Ipysam -Isamtools -I. -Ihtslib -I/usr/include/python3.4m -c pysam/htslib_util.c -o build/temp.cygwin-2.6.0-x86_64-3.4/pysam/htslib_util.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement | |
| gcc -Wno-unused-result -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -ggdb -O2 -pipe -Wimplicit-function-declaration -fdebug-prefix-map=/usr/src/ports/python3/python3-3.4.5-1.x86_64/build=/usr/src/debug/python3-3.4.5-1 -fdebug-prefix-map=/usr/src/ports/python3/python3-3.4.5-1.x86_64/src/Python-3.4.5=/usr/src/debug/python3-3.4.5-1 -Ipysam -Isamtools -I. -Ihtslib -I/usr/include/python3.4m -c pysam/samfile_util.c -o build/temp.cygwin-2.6.0-x86_64-3.4/pysam/samfile_util.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement | |
| gcc -Wno-unused-result -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -ggdb -O2 -pipe -Wimplicit-function-declaration -fdebug-prefix-map=/usr/src/ports/python3/python3-3.4.5-1.x86_64/build=/usr/src/debug/python3-3.4.5-1 -fdebug-prefix-map=/usr/src/ports/python3/python3-3.4.5-1.x86_64/src/Python-3.4.5=/usr/src/debug/python3-3.4.5-1 -Ipysam -Isamtools -I. -Ihtslib -I/usr/include/python3.4m -c samtools/kprobaln.c -o build/temp.cygwin-2.6.0-x86_64-3.4/samtools/kprobaln.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement | |
| gcc -shared -Wl,--enable-auto-image-base build/temp.cygwin-2.6.0-x86_64-3.4/pysam/csamfile.o build/temp.cygwin-2.6.0-x86_64-3.4/pysam/htslib_util.o build/temp.cygwin-2.6.0-x86_64-3.4/pysam/samfile_util.o build/temp.cygwin-2.6.0-x86_64-3.4/samtools/kprobaln.o -Lpysam -L. -Lbuild/lib.cygwin-2.6.0-x86_64-3.4/pysam -Lbuild/lib.cygwin-2.6.0-x86_64-3.4/pysam -Lbuild/lib.cygwin-2.6.0-x86_64-3.4/pysam -L. -L/usr/lib -lz -lchtslib.cpython-34m -lpython3.4m -o build/lib.cygwin-2.6.0-x86_64-3.4/pysam/csamfile.cpython-34m.dll -Wl,-rpath,$ORIGIN | |
| build/temp.cygwin-2.6.0-x86_64-3.4/pysam/htslib_util.o:htslib_util.c:(.rdata$.refptr.seq_nt16_table[.refptr.seq_nt16_table]+0x0): undefined reference to `seq_nt16_table' | |
| build/temp.cygwin-2.6.0-x86_64-3.4/pysam/htslib_util.o:htslib_util.c:(.rdata$.refptr.hts_verbose[.refptr.hts_verbose]+0x0): undefined reference to `hts_verbose' | |
| build/temp.cygwin-2.6.0-x86_64-3.4/pysam/samfile_util.o: In function `bam_prob_realn_core': | |
| /tmp/pip-build-ouyje9w1/pysam/pysam/samfile_util.c:78: undefined reference to `bam_aux_get' | |
| /tmp/pip-build-ouyje9w1/pysam/pysam/samfile_util.c:78:(.text+0x427): relocation truncated to fit: R_X86_64_PC32 against undefined symbol `bam_aux_get' | |
| /tmp/pip-build-ouyje9w1/pysam/pysam/samfile_util.c:79: undefined reference to `bam_aux_get' | |
| /tmp/pip-build-ouyje9w1/pysam/pysam/samfile_util.c:79:(.text+0x446): relocation truncated to fit: R_X86_64_PC32 against undefined symbol `bam_aux_get' | |
| /tmp/pip-build-ouyje9w1/pysam/pysam/samfile_util.c:86: undefined reference to `bam_aux_del' | |
| /tmp/pip-build-ouyje9w1/pysam/pysam/samfile_util.c:86:(.text+0x49d): relocation truncated to fit: R_X86_64_PC32 against undefined symbol `bam_aux_del' | |
| /tmp/pip-build-ouyje9w1/pysam/pysam/samfile_util.c:82: undefined reference to `bam_aux_del' | |
| /tmp/pip-build-ouyje9w1/pysam/pysam/samfile_util.c:82:(.text+0x53b): relocation truncated to fit: R_X86_64_PC32 against undefined symbol `bam_aux_del' | |
| /tmp/pip-build-ouyje9w1/pysam/pysam/samfile_util.c:176: undefined reference to `bam_aux_append' | |
| /tmp/pip-build-ouyje9w1/pysam/pysam/samfile_util.c:176:(.text+0x969): relocation truncated to fit: R_X86_64_PC32 against undefined symbol `bam_aux_append' | |
| /tmp/pip-build-ouyje9w1/pysam/pysam/samfile_util.c:79: undefined reference to `bam_aux_get' | |
| /tmp/pip-build-ouyje9w1/pysam/pysam/samfile_util.c:79:(.text+0x9ad): relocation truncated to fit: R_X86_64_PC32 against undefined symbol `bam_aux_get' | |
| /tmp/pip-build-ouyje9w1/pysam/pysam/samfile_util.c:177: undefined reference to `bam_aux_append' | |
| /tmp/pip-build-ouyje9w1/pysam/pysam/samfile_util.c:177:(.text+0xb4c): relocation truncated to fit: R_X86_64_PC32 against undefined symbol `bam_aux_append' | |
| collect2: error: ld returned 1 exit status | |
| error: command 'gcc' failed with exit status 1 | |
| ---------------------------------------- | |
| Command "/bin/python3 -u -c "import setuptools, tokenize;__file__='/tmp/pip-build-ouyje9w1/pysam/setup.py';f=getattr(tokenize, 'open', open)(__file__);code=f.read().replace('\r\n', '\n');f.close();exec(compile(code, __file__, 'exec'))" install --record /tmp/pip-lxwufq2p-record/install-record.txt --single-version-externally-managed --compile --user --prefix=" failed with error code 1 in /tmp/pip-build-ouyje9w1/pysam/ |
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