jaqx008 / repository

Pysam-installation-error

$ pip install pysam Collecting pysam Using cached https://files.pythonhosted.org/packages/fc/9b/4bb8d016406dcff47e2866e14d3dcb10741ec3920649e8c521996830944f/pysam-0.14.1.tar.gz Building wheels for collected packages: pysam Running setup.py bdist_wheel for pysam ... error Complete output from command /anaconda3/bin/python -u -c "import setuptools, tokenize;__file__='/private/var/folders/tz/89qgqyd97wj1cdrpq_d62n100000gr/T/pip-install-u6tryjwo/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 /private/var/folders/tz/89qgqyd97wj1cdrpq_d62n100000gr/T/pip-wheel-44u7nejn --python-tag cp36: # 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.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 grep that handles long lines and -e... /usr/bin/grep checking for C compiler warning flags... -Wall checking for special C compiler options needed for large files... no checking for _FILE_OFFSET_BITS value needed for large files... no checking for _LARGEFILE_SOURCE value needed for large files... no checking shared library type for unknown-Darwin... Darwin dylib checking how to run the C preprocessor... gcc -E checking for egrep... /usr/bin/grep -E checking for ANSI C header files... no checking for sys/types.h... yes checking for sys/stat.h... yes checking for stdlib.h... no checking for string.h... yes checking for memory.h... yes checking for strings.h... yes checking for inttypes.h... no checking for stdint.h... yes checking for unistd.h... yes checking for stdlib.h... (cached) no 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 lzma.h... no checking for lzma_easy_buffer_encode in -llzma... 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: --enable-libcurl make: ./version.sh: Command not found make: ./version.sh: Command not found # pysam: htslib_config LDFLAGS= # 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 LIBS=-llzma -lbz2 -lz -lcurl # pysam: htslib_config PLATFORM=Darwin # 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 bdist_wheel running build running build_py creating build creating build/lib.macosx-10.7-x86_64-3.6 creating build/lib.macosx-10.7-x86_64-3.6/pysam copying pysam/__init__.py -> build/lib.macosx-10.7-x86_64-3.6/pysam copying pysam/bcftools.py -> build/lib.macosx-10.7-x86_64-3.6/pysam copying pysam/config.py -> build/lib.macosx-10.7-x86_64-3.6/pysam copying pysam/Pileup.py -> build/lib.macosx-10.7-x86_64-3.6/pysam copying pysam/samtools.py -> build/lib.macosx-10.7-x86_64-3.6/pysam copying pysam/utils.py -> build/lib.macosx-10.7-x86_64-3.6/pysam copying pysam/version.py -> build/lib.macosx-10.7-x86_64-3.6/pysam creating build/lib.macosx-10.7-x86_64-3.6/pysam/include copying pysam/include/__init__.py -> build/lib.macosx-10.7-x86_64-3.6/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/libcalignedsegment.pxd -> build/lib.macosx-10.7-x86_64-3.6/pysam copying pysam/libcalignmentfile.pxd -> build/lib.macosx-10.7-x86_64-3.6/pysam copying pysam/libcbcf.pxd -> build/lib.macosx-10.7-x86_64-3.6/pysam copying pysam/libcbcftools.pxd -> build/lib.macosx-10.7-x86_64-3.6/pysam copying pysam/libcfaidx.pxd -> build/lib.macosx-10.7-x86_64-3.6/pysam copying pysam/libchtslib.pxd -> build/lib.macosx-10.7-x86_64-3.6/pysam copying pysam/libcsamfile.pxd -> build/lib.macosx-10.7-x86_64-3.6/pysam copying pysam/libcsamtools.pxd -> build/lib.macosx-10.7-x86_64-3.6/pysam copying pysam/libctabix.pxd -> build/lib.macosx-10.7-x86_64-3.6/pysam copying pysam/libctabixproxies.pxd -> build/lib.macosx-10.7-x86_64-3.6/pysam copying pysam/libcutils.pxd -> build/lib.macosx-10.7-x86_64-3.6/pysam copying pysam/libcvcf.pxd -> build/lib.macosx-10.7-x86_64-3.6/pysam copying pysam/cbcftools_util.h -> build/lib.macosx-10.7-x86_64-3.6/pysam copying pysam/csamtools_util.h -> build/lib.macosx-10.7-x86_64-3.6/pysam copying pysam/htslib_util.h -> build/lib.macosx-10.7-x86_64-3.6/pysam copying pysam/pysam_stream.h -> build/lib.macosx-10.7-x86_64-3.6/pysam copying pysam/pysam_util.h -> build/lib.macosx-10.7-x86_64-3.6/pysam creating build/lib.macosx-10.7-x86_64-3.6/pysam/include/samtools copying samtools/bam.h -> build/lib.macosx-10.7-x86_64-3.6/pysam/include/samtools copying samtools/bam2bcf.h -> build/lib.macosx-10.7-x86_64-3.6/pysam/include/samtools copying samtools/bam_endian.h -> build/lib.macosx-10.7-x86_64-3.6/pysam/include/samtools copying samtools/bam_lpileup.h -> build/lib.macosx-10.7-x86_64-3.6/pysam/include/samtools copying samtools/bam_plbuf.h -> build/lib.macosx-10.7-x86_64-3.6/pysam/include/samtools copying samtools/bedidx.h -> build/lib.macosx-10.7-x86_64-3.6/pysam/include/samtools copying samtools/config.h -> build/lib.macosx-10.7-x86_64-3.6/pysam/include/samtools copying samtools/sam.h -> build/lib.macosx-10.7-x86_64-3.6/pysam/include/samtools copying samtools/sam_header.h -> build/lib.macosx-10.7-x86_64-3.6/pysam/include/samtools copying samtools/sam_opts.h -> build/lib.macosx-10.7-x86_64-3.6/pysam/include/samtools copying samtools/sample.h -> build/lib.macosx-10.7-x86_64-3.6/pysam/include/samtools copying samtools/samtools.h -> build/lib.macosx-10.7-x86_64-3.6/pysam/include/samtools copying samtools/samtools.pysam.h -> build/lib.macosx-10.7-x86_64-3.6/pysam/include/samtools copying samtools/stats_isize.h -> build/lib.macosx-10.7-x86_64-3.6/pysam/include/samtools copying samtools/tmp_file.h -> build/lib.macosx-10.7-x86_64-3.6/pysam/include/samtools copying samtools/version.h -> build/lib.macosx-10.7-x86_64-3.6/pysam/include/samtools creating build/lib.macosx-10.7-x86_64-3.6/pysam/include/bcftools copying bcftools/bam2bcf.h -> build/lib.macosx-10.7-x86_64-3.6/pysam/include/bcftools copying bcftools/bam_sample.h -> build/lib.macosx-10.7-x86_64-3.6/pysam/include/bcftools copying bcftools/bcftools.h -> build/lib.macosx-10.7-x86_64-3.6/pysam/include/bcftools copying bcftools/bcftools.pysam.h -> build/lib.macosx-10.7-x86_64-3.6/pysam/include/bcftools copying bcftools/bin.h -> build/lib.macosx-10.7-x86_64-3.6/pysam/include/bcftools copying bcftools/call.h -> build/lib.macosx-10.7-x86_64-3.6/pysam/include/bcftools copying bcftools/config.h -> build/lib.macosx-10.7-x86_64-3.6/pysam/include/bcftools copying bcftools/convert.h -> build/lib.macosx-10.7-x86_64-3.6/pysam/include/bcftools copying bcftools/filter.h -> build/lib.macosx-10.7-x86_64-3.6/pysam/include/bcftools copying bcftools/gvcf.h -> build/lib.macosx-10.7-x86_64-3.6/pysam/include/bcftools copying bcftools/hclust.h -> build/lib.macosx-10.7-x86_64-3.6/pysam/include/bcftools copying bcftools/HMM.h -> build/lib.macosx-10.7-x86_64-3.6/pysam/include/bcftools copying bcftools/khash_str2str.h -> build/lib.macosx-10.7-x86_64-3.6/pysam/include/bcftools copying bcftools/kheap.h -> build/lib.macosx-10.7-x86_64-3.6/pysam/include/bcftools copying bcftools/kmin.h -> build/lib.macosx-10.7-x86_64-3.6/pysam/include/bcftools copying bcftools/mw.h -> build/lib.macosx-10.7-x86_64-3.6/pysam/include/bcftools copying bcftools/ploidy.h -> build/lib.macosx-10.7-x86_64-3.6/pysam/include/bcftools copying bcftools/prob1.h -> build/lib.macosx-10.7-x86_64-3.6/pysam/include/bcftools copying bcftools/rbuf.h -> build/lib.macosx-10.7-x86_64-3.6/pysam/include/bcftools copying bcftools/regidx.h -> build/lib.macosx-10.7-x86_64-3.6/pysam/include/bcftools copying bcftools/smpl_ilist.h -> build/lib.macosx-10.7-x86_64-3.6/pysam/include/bcftools copying bcftools/tsv2vcf.h -> build/lib.macosx-10.7-x86_64-3.6/pysam/include/bcftools copying bcftools/vcfbuf.h -> build/lib.macosx-10.7-x86_64-3.6/pysam/include/bcftools copying bcftools/vcmp.h -> build/lib.macosx-10.7-x86_64-3.6/pysam/include/bcftools copying bcftools/version.h -> build/lib.macosx-10.7-x86_64-3.6/pysam/include/bcftools creating build/lib.macosx-10.7-x86_64-3.6/pysam/include/samtools/win32 copying samtools/win32/xcurses.h -> build/lib.macosx-10.7-x86_64-3.6/pysam/include/samtools/win32 copying samtools/win32/zconf.h -> build/lib.macosx-10.7-x86_64-3.6/pysam/include/samtools/win32 copying samtools/win32/zlib.h -> build/lib.macosx-10.7-x86_64-3.6/pysam/include/samtools/win32 creating build/lib.macosx-10.7-x86_64-3.6/pysam/include/htslib copying htslib/bcf_sr_sort.h -> build/lib.macosx-10.7-x86_64-3.6/pysam/include/htslib copying htslib/config.h -> build/lib.macosx-10.7-x86_64-3.6/pysam/include/htslib copying htslib/hfile_internal.h -> build/lib.macosx-10.7-x86_64-3.6/pysam/include/htslib copying htslib/hts_internal.h -> build/lib.macosx-10.7-x86_64-3.6/pysam/include/htslib copying htslib/textutils_internal.h -> build/lib.macosx-10.7-x86_64-3.6/pysam/include/htslib copying htslib/thread_pool_internal.h -> build/lib.macosx-10.7-x86_64-3.6/pysam/include/htslib copying htslib/version.h -> build/lib.macosx-10.7-x86_64-3.6/pysam/include/htslib creating build/lib.macosx-10.7-x86_64-3.6/pysam/include/htslib/htslib copying htslib/htslib/bgzf.h -> build/lib.macosx-10.7-x86_64-3.6/pysam/include/htslib/htslib copying htslib/htslib/cram.h -> build/lib.macosx-10.7-x86_64-3.6/pysam/include/htslib/htslib copying htslib/htslib/faidx.h -> build/lib.macosx-10.7-x86_64-3.6/pysam/include/htslib/htslib copying htslib/htslib/hfile.h -> build/lib.macosx-10.7-x86_64-3.6/pysam/include/htslib/htslib copying htslib/htslib/hts.h -> build/lib.macosx-10.7-x86_64-3.6/pysam/include/htslib/htslib copying htslib/htslib/hts_defs.h -> build/lib.macosx-10.7-x86_64-3.6/pysam/include/htslib/htslib copying htslib/htslib/hts_endian.h -> build/lib.macosx-10.7-x86_64-3.6/pysam/include/htslib/htslib copying htslib/htslib/hts_log.h -> build/lib.macosx-10.7-x86_64-3.6/pysam/include/htslib/htslib copying htslib/htslib/hts_os.h -> build/lib.macosx-10.7-x86_64-3.6/pysam/include/htslib/htslib copying htslib/htslib/kbitset.h -> build/lib.macosx-10.7-x86_64-3.6/pysam/include/htslib/htslib copying htslib/htslib/kfunc.h -> build/lib.macosx-10.7-x86_64-3.6/pysam/include/htslib/htslib copying htslib/htslib/khash.h -> build/lib.macosx-10.7-x86_64-3.6/pysam/include/htslib/htslib copying htslib/htslib/khash_str2int.h -> build/lib.macosx-10.7-x86_64-3.6/pysam/include/htslib/htslib copying htslib/htslib/klist.h -> build/lib.macosx-10.7-x86_64-3.6/pysam/include/htslib/htslib copying htslib/htslib/knetfile.h -> build/lib.macosx-10.7-x86_64-3.6/pysam/include/htslib/htslib copying htslib/htslib/kseq.h -> build/lib.macosx-10.7-x86_64-3.6/pysam/include/htslib/htslib copying htslib/htslib/ksort.h -> build/lib.macosx-10.7-x86_64-3.6/pysam/include/htslib/htslib copying htslib/htslib/kstring.h -> build/lib.macosx-10.7-x86_64-3.6/pysam/include/htslib/htslib copying htslib/htslib/regidx.h -> build/lib.macosx-10.7-x86_64-3.6/pysam/include/htslib/htslib copying htslib/htslib/sam.h -> build/lib.macosx-10.7-x86_64-3.6/pysam/include/htslib/htslib copying htslib/htslib/synced_bcf_reader.h -> build/lib.macosx-10.7-x86_64-3.6/pysam/include/htslib/htslib copying htslib/htslib/tbx.h -> build/lib.macosx-10.7-x86_64-3.6/pysam/include/htslib/htslib copying htslib/htslib/thread_pool.h -> build/lib.macosx-10.7-x86_64-3.6/pysam/include/htslib/htslib copying htslib/htslib/vcf.h -> build/lib.macosx-10.7-x86_64-3.6/pysam/include/htslib/htslib copying htslib/htslib/vcf_sweep.h -> build/lib.macosx-10.7-x86_64-3.6/pysam/include/htslib/htslib copying htslib/htslib/vcfutils.h -> build/lib.macosx-10.7-x86_64-3.6/pysam/include/htslib/htslib Fixing build/lib.macosx-10.7-x86_64-3.6/pysam/__init__.py build/lib.macosx-10.7-x86_64-3.6/pysam/bcftools.py build/lib.macosx-10.7-x86_64-3.6/pysam/config.py build/lib.macosx-10.7-x86_64-3.6/pysam/Pileup.py build/lib.macosx-10.7-x86_64-3.6/pysam/samtools.py build/lib.macosx-10.7-x86_64-3.6/pysam/utils.py build/lib.macosx-10.7-x86_64-3.6/pysam/version.py build/lib.macosx-10.7-x86_64-3.6/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.macosx-10.7-x86_64-3.6/pysam/__init__.py build/lib.macosx-10.7-x86_64-3.6/pysam/bcftools.py build/lib.macosx-10.7-x86_64-3.6/pysam/config.py build/lib.macosx-10.7-x86_64-3.6/pysam/Pileup.py build/lib.macosx-10.7-x86_64-3.6/pysam/samtools.py build/lib.macosx-10.7-x86_64-3.6/pysam/utils.py build/lib.macosx-10.7-x86_64-3.6/pysam/version.py build/lib.macosx-10.7-x86_64-3.6/pysam/include/__init__.py Skipping optional fixer: buffer Skipping optional fixer: idioms Skipping optional fixer: set_literal Skipping optional fixer: ws_comma running build_ext skipping 'pysam/libchtslib.c' Cython extension (up-to-date) building 'pysam.libchtslib' extension creating build/temp.macosx-10.7-x86_64-3.6 creating build/temp.macosx-10.7-x86_64-3.6/pysam creating build/temp.macosx-10.7-x86_64-3.6/htslib creating build/temp.macosx-10.7-x86_64-3.6/htslib/cram gcc -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/anaconda3/include -arch x86_64 -I/anaconda3/include -arch x86_64 -I/private/var/folders/tz/89qgqyd97wj1cdrpq_d62n100000gr/T/pip-install-u6tryjwo/pysam/htslib -I/private/var/folders/tz/89qgqyd97wj1cdrpq_d62n100000gr/T/pip-install-u6tryjwo/pysam/samtools -I/private/var/folders/tz/89qgqyd97wj1cdrpq_d62n100000gr/T/pip-install-u6tryjwo/pysam/samtools/lz4 -I/private/var/folders/tz/89qgqyd97wj1cdrpq_d62n100000gr/T/pip-install-u6tryjwo/pysam/bcftools -I/private/var/folders/tz/89qgqyd97wj1cdrpq_d62n100000gr/T/pip-install-u6tryjwo/pysam/pysam -I/private/var/folders/tz/89qgqyd97wj1cdrpq_d62n100000gr/T/pip-install-u6tryjwo/pysam -I/anaconda3/include/python3.6m -c pysam/libchtslib.c -o build/temp.macosx-10.7-x86_64-3.6/pysam/libchtslib.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement In file included from pysam/libchtslib.c:4: In file included from /anaconda3/include/python3.6m/Python.h:34: In file included from /usr/include/stdlib.h:65: In file included from /usr/include/sys/wait.h:110: /usr/include/sys/resource.h:196:2: error: unknown type name 'uint8_t' uint8_t ri_uuid[16]; ^ /usr/include/sys/resource.h:197:2: error: unknown type name 'uint64_t' uint64_t ri_user_time; ^ /usr/include/sys/resource.h:198:2: error: unknown type name 'uint64_t' uint64_t ri_system_time; ^ /usr/include/sys/resource.h:199:2: error: unknown type name 'uint64_t' uint64_t ri_pkg_idle_wkups; ^ /usr/include/sys/resource.h:200:2: error: unknown type name 'uint64_t' uint64_t ri_interrupt_wkups; ^ /usr/include/sys/resource.h:201:2: error: unknown type name 'uint64_t' uint64_t ri_pageins; ^ /usr/include/sys/resource.h:202:2: error: unknown type name 'uint64_t' uint64_t ri_wired_size; ^ /usr/include/sys/resource.h:203:2: error: unknown type name 'uint64_t' uint64_t ri_resident_size; ^ /usr/include/sys/resource.h:204:2: error: unknown type name 'uint64_t' uint64_t ri_phys_footprint; ^ /usr/include/sys/resource.h:205:2: error: unknown type name 'uint64_t' uint64_t ri_proc_start_abstime; ^ /usr/include/sys/resource.h:206:2: error: unknown type name 'uint64_t' uint64_t ri_proc_exit_abstime; ^ /usr/include/sys/resource.h:210:2: error: unknown type name 'uint8_t' uint8_t ri_uuid[16]; ^ /usr/include/sys/resource.h:211:2: error: unknown type name 'uint64_t' uint64_t ri_user_time; ^ /usr/include/sys/resource.h:212:2: error: unknown type name 'uint64_t' uint64_t ri_system_time; ^ /usr/include/sys/resource.h:213:2: error: unknown type name 'uint64_t' uint64_t ri_pkg_idle_wkups; ^ /usr/include/sys/resource.h:214:2: error: unknown type name 'uint64_t' uint64_t ri_interrupt_wkups; ^ /usr/include/sys/resource.h:215:2: error: unknown type name 'uint64_t' uint64_t ri_pageins; ^ /usr/include/sys/resource.h:216:2: error: unknown type name 'uint64_t' uint64_t ri_wired_size; ^ /usr/include/sys/resource.h:217:2: error: unknown type name 'uint64_t' uint64_t ri_resident_size; ^ fatal error: too many errors emitted, stopping now [-ferror-limit=] 20 errors generated. error: command 'gcc' failed with exit status 1 ---------------------------------------- Failed building wheel for pysam Running setup.py clean for pysam Failed to build pysam distributed 1.19.1 has requirement tornado>=4.5.1, but you'll have tornado 4.3 which is incompatible. Installing collected packages: pysam Running setup.py install for pysam ... error Complete output from command /anaconda3/bin/python -u -c "import setuptools, tokenize;__file__='/private/var/folders/tz/89qgqyd97wj1cdrpq_d62n100000gr/T/pip-install-u6tryjwo/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 /private/var/folders/tz/89qgqyd97wj1cdrpq_d62n100000gr/T/pip-record-jmme4k_o/install-record.txt --single-version-externally-managed --compile: # 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.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 grep that handles long lines and -e... /usr/bin/grep checking for C compiler warning flags... -Wall checking for special C compiler options needed for large files... no checking for _FILE_OFFSET_BITS value needed for large files... no checking for _LARGEFILE_SOURCE value needed for large files... no checking shared library type for unknown-Darwin... Darwin dylib checking how to run the C preprocessor... gcc -E checking for egrep... /usr/bin/grep -E checking for ANSI C header files... no checking for sys/types.h... yes checking for sys/stat.h... yes checking for stdlib.h... no checking for string.h... yes checking for memory.h... yes checking for strings.h... yes checking for inttypes.h... no checking for stdint.h... yes checking for unistd.h... yes checking for stdlib.h... (cached) no 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 lzma.h... no checking for lzma_easy_buffer_encode in -llzma... 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: --enable-libcurl make: ./version.sh: Command not found make: ./version.sh: Command not found # pysam: htslib_config LDFLAGS= # 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 LIBS=-llzma -lbz2 -lz -lcurl # pysam: htslib_config PLATFORM=Darwin # 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 install running build running build_py creating build creating build/lib.macosx-10.7-x86_64-3.6 creating build/lib.macosx-10.7-x86_64-3.6/pysam copying pysam/__init__.py -> build/lib.macosx-10.7-x86_64-3.6/pysam copying pysam/bcftools.py -> build/lib.macosx-10.7-x86_64-3.6/pysam copying pysam/config.py -> build/lib.macosx-10.7-x86_64-3.6/pysam copying pysam/Pileup.py -> build/lib.macosx-10.7-x86_64-3.6/pysam copying pysam/samtools.py -> build/lib.macosx-10.7-x86_64-3.6/pysam copying pysam/utils.py -> build/lib.macosx-10.7-x86_64-3.6/pysam copying pysam/version.py -> build/lib.macosx-10.7-x86_64-3.6/pysam creating build/lib.macosx-10.7-x86_64-3.6/pysam/include copying pysam/include/__init__.py -> build/lib.macosx-10.7-x86_64-3.6/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/libcalignedsegment.pxd -> build/lib.macosx-10.7-x86_64-3.6/pysam copying pysam/libcalignmentfile.pxd -> build/lib.macosx-10.7-x86_64-3.6/pysam copying pysam/libcbcf.pxd -> build/lib.macosx-10.7-x86_64-3.6/pysam copying pysam/libcbcftools.pxd -> build/lib.macosx-10.7-x86_64-3.6/pysam copying pysam/libcfaidx.pxd -> build/lib.macosx-10.7-x86_64-3.6/pysam copying pysam/libchtslib.pxd -> build/lib.macosx-10.7-x86_64-3.6/pysam copying pysam/libcsamfile.pxd -> build/lib.macosx-10.7-x86_64-3.6/pysam copying pysam/libcsamtools.pxd -> build/lib.macosx-10.7-x86_64-3.6/pysam copying pysam/libctabix.pxd -> build/lib.macosx-10.7-x86_64-3.6/pysam copying pysam/libctabixproxies.pxd -> build/lib.macosx-10.7-x86_64-3.6/pysam copying pysam/libcutils.pxd -> build/lib.macosx-10.7-x86_64-3.6/pysam copying pysam/libcvcf.pxd -> build/lib.macosx-10.7-x86_64-3.6/pysam copying pysam/cbcftools_util.h -> build/lib.macosx-10.7-x86_64-3.6/pysam copying pysam/csamtools_util.h -> build/lib.macosx-10.7-x86_64-3.6/pysam copying pysam/htslib_util.h -> build/lib.macosx-10.7-x86_64-3.6/pysam copying pysam/pysam_stream.h -> build/lib.macosx-10.7-x86_64-3.6/pysam copying pysam/pysam_util.h -> build/lib.macosx-10.7-x86_64-3.6/pysam creating build/lib.macosx-10.7-x86_64-3.6/pysam/include/samtools copying samtools/bam.h -> build/lib.macosx-10.7-x86_64-3.6/pysam/include/samtools copying samtools/bam2bcf.h -> build/lib.macosx-10.7-x86_64-3.6/pysam/include/samtools copying samtools/bam_endian.h -> build/lib.macosx-10.7-x86_64-3.6/pysam/include/samtools copying samtools/bam_lpileup.h -> build/lib.macosx-10.7-x86_64-3.6/pysam/include/samtools copying samtools/bam_plbuf.h -> build/lib.macosx-10.7-x86_64-3.6/pysam/include/samtools copying samtools/bedidx.h -> build/lib.macosx-10.7-x86_64-3.6/pysam/include/samtools copying samtools/config.h -> build/lib.macosx-10.7-x86_64-3.6/pysam/include/samtools copying samtools/sam.h -> build/lib.macosx-10.7-x86_64-3.6/pysam/include/samtools copying samtools/sam_header.h -> build/lib.macosx-10.7-x86_64-3.6/pysam/include/samtools copying samtools/sam_opts.h -> build/lib.macosx-10.7-x86_64-3.6/pysam/include/samtools copying samtools/sample.h -> build/lib.macosx-10.7-x86_64-3.6/pysam/include/samtools copying samtools/samtools.h -> build/lib.macosx-10.7-x86_64-3.6/pysam/include/samtools copying samtools/samtools.pysam.h -> build/lib.macosx-10.7-x86_64-3.6/pysam/include/samtools copying samtools/stats_isize.h -> build/lib.macosx-10.7-x86_64-3.6/pysam/include/samtools copying samtools/tmp_file.h -> build/lib.macosx-10.7-x86_64-3.6/pysam/include/samtools copying samtools/version.h -> build/lib.macosx-10.7-x86_64-3.6/pysam/include/samtools creating build/lib.macosx-10.7-x86_64-3.6/pysam/include/bcftools copying bcftools/bam2bcf.h -> build/lib.macosx-10.7-x86_64-3.6/pysam/include/bcftools copying bcftools/bam_sample.h -> build/lib.macosx-10.7-x86_64-3.6/pysam/include/bcftools copying bcftools/bcftools.h -> build/lib.macosx-10.7-x86_64-3.6/pysam/include/bcftools copying bcftools/bcftools.pysam.h -> build/lib.macosx-10.7-x86_64-3.6/pysam/include/bcftools copying bcftools/bin.h -> build/lib.macosx-10.7-x86_64-3.6/pysam/include/bcftools copying bcftools/call.h -> build/lib.macosx-10.7-x86_64-3.6/pysam/include/bcftools copying bcftools/config.h -> build/lib.macosx-10.7-x86_64-3.6/pysam/include/bcftools copying bcftools/convert.h -> build/lib.macosx-10.7-x86_64-3.6/pysam/include/bcftools copying bcftools/filter.h -> build/lib.macosx-10.7-x86_64-3.6/pysam/include/bcftools copying bcftools/gvcf.h -> build/lib.macosx-10.7-x86_64-3.6/pysam/include/bcftools copying bcftools/hclust.h -> build/lib.macosx-10.7-x86_64-3.6/pysam/include/bcftools copying bcftools/HMM.h -> build/lib.macosx-10.7-x86_64-3.6/pysam/include/bcftools copying bcftools/khash_str2str.h -> build/lib.macosx-10.7-x86_64-3.6/pysam/include/bcftools copying bcftools/kheap.h -> build/lib.macosx-10.7-x86_64-3.6/pysam/include/bcftools copying bcftools/kmin.h -> build/lib.macosx-10.7-x86_64-3.6/pysam/include/bcftools copying bcftools/mw.h -> build/lib.macosx-10.7-x86_64-3.6/pysam/include/bcftools copying bcftools/ploidy.h -> build/lib.macosx-10.7-x86_64-3.6/pysam/include/bcftools copying bcftools/prob1.h -> build/lib.macosx-10.7-x86_64-3.6/pysam/include/bcftools copying bcftools/rbuf.h -> build/lib.macosx-10.7-x86_64-3.6/pysam/include/bcftools copying bcftools/regidx.h -> build/lib.macosx-10.7-x86_64-3.6/pysam/include/bcftools copying bcftools/smpl_ilist.h -> build/lib.macosx-10.7-x86_64-3.6/pysam/include/bcftools copying bcftools/tsv2vcf.h -> build/lib.macosx-10.7-x86_64-3.6/pysam/include/bcftools copying bcftools/vcfbuf.h -> build/lib.macosx-10.7-x86_64-3.6/pysam/include/bcftools copying bcftools/vcmp.h -> build/lib.macosx-10.7-x86_64-3.6/pysam/include/bcftools copying bcftools/version.h -> build/lib.macosx-10.7-x86_64-3.6/pysam/include/bcftools creating build/lib.macosx-10.7-x86_64-3.6/pysam/include/samtools/win32 copying samtools/win32/xcurses.h -> build/lib.macosx-10.7-x86_64-3.6/pysam/include/samtools/win32 copying samtools/win32/zconf.h -> build/lib.macosx-10.7-x86_64-3.6/pysam/include/samtools/win32 copying samtools/win32/zlib.h -> build/lib.macosx-10.7-x86_64-3.6/pysam/include/samtools/win32 creating build/lib.macosx-10.7-x86_64-3.6/pysam/include/htslib copying htslib/bcf_sr_sort.h -> build/lib.macosx-10.7-x86_64-3.6/pysam/include/htslib copying htslib/config.h -> build/lib.macosx-10.7-x86_64-3.6/pysam/include/htslib copying htslib/hfile_internal.h -> build/lib.macosx-10.7-x86_64-3.6/pysam/include/htslib copying htslib/hts_internal.h -> build/lib.macosx-10.7-x86_64-3.6/pysam/include/htslib copying htslib/textutils_internal.h -> build/lib.macosx-10.7-x86_64-3.6/pysam/include/htslib copying htslib/thread_pool_internal.h -> build/lib.macosx-10.7-x86_64-3.6/pysam/include/htslib copying htslib/version.h -> build/lib.macosx-10.7-x86_64-3.6/pysam/include/htslib creating build/lib.macosx-10.7-x86_64-3.6/pysam/include/htslib/htslib copying htslib/htslib/bgzf.h -> build/lib.macosx-10.7-x86_64-3.6/pysam/include/htslib/htslib copying htslib/htslib/cram.h -> build/lib.macosx-10.7-x86_64-3.6/pysam/include/htslib/htslib copying htslib/htslib/faidx.h -> build/lib.macosx-10.7-x86_64-3.6/pysam/include/htslib/htslib copying htslib/htslib/hfile.h -> build/lib.macosx-10.7-x86_64-3.6/pysam/include/htslib/htslib copying htslib/htslib/hts.h -> build/lib.macosx-10.7-x86_64-3.6/pysam/include/htslib/htslib copying htslib/htslib/hts_defs.h -> build/lib.macosx-10.7-x86_64-3.6/pysam/include/htslib/htslib copying htslib/htslib/hts_endian.h -> build/lib.macosx-10.7-x86_64-3.6/pysam/include/htslib/htslib copying htslib/htslib/hts_log.h -> build/lib.macosx-10.7-x86_64-3.6/pysam/include/htslib/htslib copying htslib/htslib/hts_os.h -> build/lib.macosx-10.7-x86_64-3.6/pysam/include/htslib/htslib copying htslib/htslib/kbitset.h -> build/lib.macosx-10.7-x86_64-3.6/pysam/include/htslib/htslib copying htslib/htslib/kfunc.h -> build/lib.macosx-10.7-x86_64-3.6/pysam/include/htslib/htslib copying htslib/htslib/khash.h -> build/lib.macosx-10.7-x86_64-3.6/pysam/include/htslib/htslib copying htslib/htslib/khash_str2int.h -> build/lib.macosx-10.7-x86_64-3.6/pysam/include/htslib/htslib copying htslib/htslib/klist.h -> build/lib.macosx-10.7-x86_64-3.6/pysam/include/htslib/htslib copying htslib/htslib/knetfile.h -> build/lib.macosx-10.7-x86_64-3.6/pysam/include/htslib/htslib copying htslib/htslib/kseq.h -> build/lib.macosx-10.7-x86_64-3.6/pysam/include/htslib/htslib copying htslib/htslib/ksort.h -> build/lib.macosx-10.7-x86_64-3.6/pysam/include/htslib/htslib copying htslib/htslib/kstring.h -> build/lib.macosx-10.7-x86_64-3.6/pysam/include/htslib/htslib copying htslib/htslib/regidx.h -> build/lib.macosx-10.7-x86_64-3.6/pysam/include/htslib/htslib copying htslib/htslib/sam.h -> build/lib.macosx-10.7-x86_64-3.6/pysam/include/htslib/htslib copying htslib/htslib/synced_bcf_reader.h -> build/lib.macosx-10.7-x86_64-3.6/pysam/include/htslib/htslib copying htslib/htslib/tbx.h -> build/lib.macosx-10.7-x86_64-3.6/pysam/include/htslib/htslib copying htslib/htslib/thread_pool.h -> build/lib.macosx-10.7-x86_64-3.6/pysam/include/htslib/htslib copying htslib/htslib/vcf.h -> build/lib.macosx-10.7-x86_64-3.6/pysam/include/htslib/htslib copying htslib/htslib/vcf_sweep.h -> build/lib.macosx-10.7-x86_64-3.6/pysam/include/htslib/htslib copying htslib/htslib/vcfutils.h -> build/lib.macosx-10.7-x86_64-3.6/pysam/include/htslib/htslib Fixing build/lib.macosx-10.7-x86_64-3.6/pysam/__init__.py build/lib.macosx-10.7-x86_64-3.6/pysam/bcftools.py build/lib.macosx-10.7-x86_64-3.6/pysam/config.py build/lib.macosx-10.7-x86_64-3.6/pysam/Pileup.py build/lib.macosx-10.7-x86_64-3.6/pysam/samtools.py build/lib.macosx-10.7-x86_64-3.6/pysam/utils.py build/lib.macosx-10.7-x86_64-3.6/pysam/version.py build/lib.macosx-10.7-x86_64-3.6/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.macosx-10.7-x86_64-3.6/pysam/__init__.py build/lib.macosx-10.7-x86_64-3.6/pysam/bcftools.py build/lib.macosx-10.7-x86_64-3.6/pysam/config.py build/lib.macosx-10.7-x86_64-3.6/pysam/Pileup.py build/lib.macosx-10.7-x86_64-3.6/pysam/samtools.py build/lib.macosx-10.7-x86_64-3.6/pysam/utils.py build/lib.macosx-10.7-x86_64-3.6/pysam/version.py build/lib.macosx-10.7-x86_64-3.6/pysam/include/__init__.py Skipping optional fixer: buffer Skipping optional fixer: idioms Skipping optional fixer: set_literal Skipping optional fixer: ws_comma running build_ext skipping 'pysam/libchtslib.c' Cython extension (up-to-date) building 'pysam.libchtslib' extension creating build/temp.macosx-10.7-x86_64-3.6 creating build/temp.macosx-10.7-x86_64-3.6/pysam creating build/temp.macosx-10.7-x86_64-3.6/htslib creating build/temp.macosx-10.7-x86_64-3.6/htslib/cram gcc -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/anaconda3/include -arch x86_64 -I/anaconda3/include -arch x86_64 -I/private/var/folders/tz/89qgqyd97wj1cdrpq_d62n100000gr/T/pip-install-u6tryjwo/pysam/htslib -I/private/var/folders/tz/89qgqyd97wj1cdrpq_d62n100000gr/T/pip-install-u6tryjwo/pysam/samtools -I/private/var/folders/tz/89qgqyd97wj1cdrpq_d62n100000gr/T/pip-install-u6tryjwo/pysam/samtools/lz4 -I/private/var/folders/tz/89qgqyd97wj1cdrpq_d62n100000gr/T/pip-install-u6tryjwo/pysam/bcftools -I/private/var/folders/tz/89qgqyd97wj1cdrpq_d62n100000gr/T/pip-install-u6tryjwo/pysam/pysam -I/private/var/folders/tz/89qgqyd97wj1cdrpq_d62n100000gr/T/pip-install-u6tryjwo/pysam -I/anaconda3/include/python3.6m -c pysam/libchtslib.c -o build/temp.macosx-10.7-x86_64-3.6/pysam/libchtslib.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement In file included from pysam/libchtslib.c:4: In file included from /anaconda3/include/python3.6m/Python.h:34: In file included from /usr/include/stdlib.h:65: In file included from /usr/include/sys/wait.h:110: /usr/include/sys/resource.h:196:2: error: unknown type name 'uint8_t' uint8_t ri_uuid[16]; ^ /usr/include/sys/resource.h:197:2: error: unknown type name 'uint64_t' uint64_t ri_user_time; ^ /usr/include/sys/resource.h:198:2: error: unknown type name 'uint64_t' uint64_t ri_system_time; ^ /usr/include/sys/resource.h:199:2: error: unknown type name 'uint64_t' uint64_t ri_pkg_idle_wkups; ^ /usr/include/sys/resource.h:200:2: error: unknown type name 'uint64_t' uint64_t ri_interrupt_wkups; ^ /usr/include/sys/resource.h:201:2: error: unknown type name 'uint64_t' uint64_t ri_pageins; ^ /usr/include/sys/resource.h:202:2: error: unknown type name 'uint64_t' uint64_t ri_wired_size; ^ /usr/include/sys/resource.h:203:2: error: unknown type name 'uint64_t' uint64_t ri_resident_size; ^ /usr/include/sys/resource.h:204:2: error: unknown type name 'uint64_t' uint64_t ri_phys_footprint; ^ /usr/include/sys/resource.h:205:2: error: unknown type name 'uint64_t' uint64_t ri_proc_start_abstime; ^ /usr/include/sys/resource.h:206:2: error: unknown type name 'uint64_t' uint64_t ri_proc_exit_abstime; ^ /usr/include/sys/resource.h:210:2: error: unknown type name 'uint8_t' uint8_t ri_uuid[16]; ^ /usr/include/sys/resource.h:211:2: error: unknown type name 'uint64_t' uint64_t ri_user_time; ^ /usr/include/sys/resource.h:212:2: error: unknown type name 'uint64_t' uint64_t ri_system_time; ^ /usr/include/sys/resource.h:213:2: error: unknown type name 'uint64_t' uint64_t ri_pkg_idle_wkups; ^ /usr/include/sys/resource.h:214:2: error: unknown type name 'uint64_t' uint64_t ri_interrupt_wkups; ^ /usr/include/sys/resource.h:215:2: error: unknown type name 'uint64_t' uint64_t ri_pageins; ^ /usr/include/sys/resource.h:216:2: error: unknown type name 'uint64_t' uint64_t ri_wired_size; ^ /usr/include/sys/resource.h:217:2: error: unknown type name 'uint64_t' uint64_t ri_resident_size; ^ fatal error: too many errors emitted, stopping now [-ferror-limit=] 20 errors generated. error: command 'gcc' failed with exit status 1 ---------------------------------------- Command "/anaconda3/bin/python -u -c "import setuptools, tokenize;__file__='/private/var/folders/tz/89qgqyd97wj1cdrpq_d62n100000gr/T/pip-install-u6tryjwo/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 /private/var/folders/tz/89qgqyd97wj1cdrpq_d62n100000gr/T/pip-record-jmme4k_o/install-record.txt --single-version-externally-managed --compile" failed with error code 1 in /private/var/folders/tz/89qgqyd97wj1cdrpq_d62n100000gr/T/pip-install-u6tryjwo/pysam/