Error installing pysam 0.14.1 with pip on OS X / python 3.7 #697

dancooke · 2018-07-05T13:44:59Z

I'm getting the following error when trying to install pysam with pip:

$ pip3 install pysam
Collecting pysam
  Downloading https://files.pythonhosted.org/packages/fc/9b/4bb8d016406dcff47e2866e14d3dcb10741ec3920649e8c521996830944f/pysam-0.14.1.tar.gz (3.2MB)
    100% |████████████████████████████████| 3.2MB 10.4MB/s 
Installing collected packages: pysam
  Running setup.py install for pysam ... error
    Complete output from command /usr/local/opt/python/bin/python3.7 -u -c "import setuptools, tokenize;__file__='/private/var/folders/3s/tv3skdy90hd6thwmgfwtdmhm0000gn/T/pip-install-5l6qatku/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/3s/tv3skdy90hd6thwmgfwtdmhm0000gn/T/pip-record-y057lddy/install-record.txt --single-version-externally-managed --compile:
    # pysam: no cython available - using pre-compiled C
    # 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... yes
    checking for sys/types.h... yes
    checking for sys/stat.h... yes
    checking for stdlib.h... yes
    checking for string.h... yes
    checking for memory.h... yes
    checking for strings.h... yes
    checking for inttypes.h... yes
    checking for stdint.h... yes
    checking for unistd.h... yes
    checking for stdlib.h... (cached) yes
    checking for unistd.h... (cached) yes
    checking for sys/param.h... yes
    checking for getpagesize... yes
    checking for working mmap... yes
    checking for gmtime_r... yes
    checking for fsync... yes
    checking for drand48... yes
    checking whether fdatasync is declared... no
    checking for library containing log... none required
    checking for zlib.h... yes
    checking for inflate in -lz... yes
    checking for library containing recv... none required
    checking for bzlib.h... yes
    checking for BZ2_bzBuffToBuffCompress in -lbz2... yes
    checking for lzma.h... yes
    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-10.13-x86_64-3.7
    creating build/lib.macosx-10.13-x86_64-3.7/pysam
    copying pysam/bcftools.py -> build/lib.macosx-10.13-x86_64-3.7/pysam
    copying pysam/config.py -> build/lib.macosx-10.13-x86_64-3.7/pysam
    copying pysam/version.py -> build/lib.macosx-10.13-x86_64-3.7/pysam
    copying pysam/samtools.py -> build/lib.macosx-10.13-x86_64-3.7/pysam
    copying pysam/__init__.py -> build/lib.macosx-10.13-x86_64-3.7/pysam
    copying pysam/Pileup.py -> build/lib.macosx-10.13-x86_64-3.7/pysam
    copying pysam/utils.py -> build/lib.macosx-10.13-x86_64-3.7/pysam
    creating build/lib.macosx-10.13-x86_64-3.7/pysam/include
    copying pysam/include/__init__.py -> build/lib.macosx-10.13-x86_64-3.7/pysam/include
    package init file 'samtools/__init__.py' not found (or not a regular file)
    package init file 'bcftools/__init__.py' not found (or not a regular file)
    package init file '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/libcsamtools.pxd -> build/lib.macosx-10.13-x86_64-3.7/pysam
    copying pysam/libcalignedsegment.pxd -> build/lib.macosx-10.13-x86_64-3.7/pysam
    copying pysam/libcbcf.pxd -> build/lib.macosx-10.13-x86_64-3.7/pysam
    copying pysam/libctabixproxies.pxd -> build/lib.macosx-10.13-x86_64-3.7/pysam
    copying pysam/libcutils.pxd -> build/lib.macosx-10.13-x86_64-3.7/pysam
    copying pysam/libchtslib.pxd -> build/lib.macosx-10.13-x86_64-3.7/pysam
    copying pysam/libcalignmentfile.pxd -> build/lib.macosx-10.13-x86_64-3.7/pysam
    copying pysam/libcvcf.pxd -> build/lib.macosx-10.13-x86_64-3.7/pysam
    copying pysam/libctabix.pxd -> build/lib.macosx-10.13-x86_64-3.7/pysam
    copying pysam/libcsamfile.pxd -> build/lib.macosx-10.13-x86_64-3.7/pysam
    copying pysam/libcbcftools.pxd -> build/lib.macosx-10.13-x86_64-3.7/pysam
    copying pysam/libcfaidx.pxd -> build/lib.macosx-10.13-x86_64-3.7/pysam
    copying pysam/pysam_stream.h -> build/lib.macosx-10.13-x86_64-3.7/pysam
    copying pysam/htslib_util.h -> build/lib.macosx-10.13-x86_64-3.7/pysam
    copying pysam/pysam_util.h -> build/lib.macosx-10.13-x86_64-3.7/pysam
    copying pysam/csamtools_util.h -> build/lib.macosx-10.13-x86_64-3.7/pysam
    copying pysam/cbcftools_util.h -> build/lib.macosx-10.13-x86_64-3.7/pysam
    creating build/lib.macosx-10.13-x86_64-3.7/pysam/include/samtools
    copying samtools/sam.h -> build/lib.macosx-10.13-x86_64-3.7/pysam/include/samtools
    copying samtools/tmp_file.h -> build/lib.macosx-10.13-x86_64-3.7/pysam/include/samtools
    copying samtools/sam_opts.h -> build/lib.macosx-10.13-x86_64-3.7/pysam/include/samtools
    copying samtools/bedidx.h -> build/lib.macosx-10.13-x86_64-3.7/pysam/include/samtools
    copying samtools/version.h -> build/lib.macosx-10.13-x86_64-3.7/pysam/include/samtools
    copying samtools/bam.h -> build/lib.macosx-10.13-x86_64-3.7/pysam/include/samtools
    copying samtools/config.h -> build/lib.macosx-10.13-x86_64-3.7/pysam/include/samtools
    copying samtools/samtools.h -> build/lib.macosx-10.13-x86_64-3.7/pysam/include/samtools
    copying samtools/bam2bcf.h -> build/lib.macosx-10.13-x86_64-3.7/pysam/include/samtools
    copying samtools/bam_plbuf.h -> build/lib.macosx-10.13-x86_64-3.7/pysam/include/samtools
    copying samtools/sam_header.h -> build/lib.macosx-10.13-x86_64-3.7/pysam/include/samtools
    copying samtools/bam_endian.h -> build/lib.macosx-10.13-x86_64-3.7/pysam/include/samtools
    copying samtools/stats_isize.h -> build/lib.macosx-10.13-x86_64-3.7/pysam/include/samtools
    copying samtools/bam_lpileup.h -> build/lib.macosx-10.13-x86_64-3.7/pysam/include/samtools
    copying samtools/sample.h -> build/lib.macosx-10.13-x86_64-3.7/pysam/include/samtools
    copying samtools/samtools.pysam.h -> build/lib.macosx-10.13-x86_64-3.7/pysam/include/samtools
    creating build/lib.macosx-10.13-x86_64-3.7/pysam/include/bcftools
    copying bcftools/bam_sample.h -> build/lib.macosx-10.13-x86_64-3.7/pysam/include/bcftools
    copying bcftools/bcftools.h -> build/lib.macosx-10.13-x86_64-3.7/pysam/include/bcftools
    copying bcftools/version.h -> build/lib.macosx-10.13-x86_64-3.7/pysam/include/bcftools
    copying bcftools/smpl_ilist.h -> build/lib.macosx-10.13-x86_64-3.7/pysam/include/bcftools
    copying bcftools/vcfbuf.h -> build/lib.macosx-10.13-x86_64-3.7/pysam/include/bcftools
    copying bcftools/config.h -> build/lib.macosx-10.13-x86_64-3.7/pysam/include/bcftools
    copying bcftools/prob1.h -> build/lib.macosx-10.13-x86_64-3.7/pysam/include/bcftools
    copying bcftools/ploidy.h -> build/lib.macosx-10.13-x86_64-3.7/pysam/include/bcftools
    copying bcftools/vcmp.h -> build/lib.macosx-10.13-x86_64-3.7/pysam/include/bcftools
    copying bcftools/tsv2vcf.h -> build/lib.macosx-10.13-x86_64-3.7/pysam/include/bcftools
    copying bcftools/call.h -> build/lib.macosx-10.13-x86_64-3.7/pysam/include/bcftools
    copying bcftools/HMM.h -> build/lib.macosx-10.13-x86_64-3.7/pysam/include/bcftools
    copying bcftools/bam2bcf.h -> build/lib.macosx-10.13-x86_64-3.7/pysam/include/bcftools
    copying bcftools/gvcf.h -> build/lib.macosx-10.13-x86_64-3.7/pysam/include/bcftools
    copying bcftools/regidx.h -> build/lib.macosx-10.13-x86_64-3.7/pysam/include/bcftools
    copying bcftools/mw.h -> build/lib.macosx-10.13-x86_64-3.7/pysam/include/bcftools
    copying bcftools/khash_str2str.h -> build/lib.macosx-10.13-x86_64-3.7/pysam/include/bcftools
    copying bcftools/kmin.h -> build/lib.macosx-10.13-x86_64-3.7/pysam/include/bcftools
    copying bcftools/rbuf.h -> build/lib.macosx-10.13-x86_64-3.7/pysam/include/bcftools
    copying bcftools/hclust.h -> build/lib.macosx-10.13-x86_64-3.7/pysam/include/bcftools
    copying bcftools/kheap.h -> build/lib.macosx-10.13-x86_64-3.7/pysam/include/bcftools
    copying bcftools/convert.h -> build/lib.macosx-10.13-x86_64-3.7/pysam/include/bcftools
    copying bcftools/filter.h -> build/lib.macosx-10.13-x86_64-3.7/pysam/include/bcftools
    copying bcftools/bcftools.pysam.h -> build/lib.macosx-10.13-x86_64-3.7/pysam/include/bcftools
    copying bcftools/bin.h -> build/lib.macosx-10.13-x86_64-3.7/pysam/include/bcftools
    creating build/lib.macosx-10.13-x86_64-3.7/pysam/include/samtools/win32
    copying samtools/win32/zlib.h -> build/lib.macosx-10.13-x86_64-3.7/pysam/include/samtools/win32
    copying samtools/win32/xcurses.h -> build/lib.macosx-10.13-x86_64-3.7/pysam/include/samtools/win32
    copying samtools/win32/zconf.h -> build/lib.macosx-10.13-x86_64-3.7/pysam/include/samtools/win32
    creating build/lib.macosx-10.13-x86_64-3.7/pysam/include/htslib
    copying htslib/bcf_sr_sort.h -> build/lib.macosx-10.13-x86_64-3.7/pysam/include/htslib
    copying htslib/version.h -> build/lib.macosx-10.13-x86_64-3.7/pysam/include/htslib
    copying htslib/config.h -> build/lib.macosx-10.13-x86_64-3.7/pysam/include/htslib
    copying htslib/hfile_internal.h -> build/lib.macosx-10.13-x86_64-3.7/pysam/include/htslib
    copying htslib/hts_internal.h -> build/lib.macosx-10.13-x86_64-3.7/pysam/include/htslib
    copying htslib/textutils_internal.h -> build/lib.macosx-10.13-x86_64-3.7/pysam/include/htslib
    copying htslib/thread_pool_internal.h -> build/lib.macosx-10.13-x86_64-3.7/pysam/include/htslib
    creating build/lib.macosx-10.13-x86_64-3.7/pysam/include/htslib/htslib
    copying htslib/htslib/sam.h -> build/lib.macosx-10.13-x86_64-3.7/pysam/include/htslib/htslib
    copying htslib/htslib/synced_bcf_reader.h -> build/lib.macosx-10.13-x86_64-3.7/pysam/include/htslib/htslib
    copying htslib/htslib/vcf_sweep.h -> build/lib.macosx-10.13-x86_64-3.7/pysam/include/htslib/htslib
    copying htslib/htslib/vcf.h -> build/lib.macosx-10.13-x86_64-3.7/pysam/include/htslib/htslib
    copying htslib/htslib/khash_str2int.h -> build/lib.macosx-10.13-x86_64-3.7/pysam/include/htslib/htslib
    copying htslib/htslib/bgzf.h -> build/lib.macosx-10.13-x86_64-3.7/pysam/include/htslib/htslib
    copying htslib/htslib/cram.h -> build/lib.macosx-10.13-x86_64-3.7/pysam/include/htslib/htslib
    copying htslib/htslib/kstring.h -> build/lib.macosx-10.13-x86_64-3.7/pysam/include/htslib/htslib
    copying htslib/htslib/knetfile.h -> build/lib.macosx-10.13-x86_64-3.7/pysam/include/htslib/htslib
    copying htslib/htslib/hts_log.h -> build/lib.macosx-10.13-x86_64-3.7/pysam/include/htslib/htslib
    copying htslib/htslib/hfile.h -> build/lib.macosx-10.13-x86_64-3.7/pysam/include/htslib/htslib
    copying htslib/htslib/thread_pool.h -> build/lib.macosx-10.13-x86_64-3.7/pysam/include/htslib/htslib
    copying htslib/htslib/hts_defs.h -> build/lib.macosx-10.13-x86_64-3.7/pysam/include/htslib/htslib
    copying htslib/htslib/khash.h -> build/lib.macosx-10.13-x86_64-3.7/pysam/include/htslib/htslib
    copying htslib/htslib/regidx.h -> build/lib.macosx-10.13-x86_64-3.7/pysam/include/htslib/htslib
    copying htslib/htslib/faidx.h -> build/lib.macosx-10.13-x86_64-3.7/pysam/include/htslib/htslib
    copying htslib/htslib/vcfutils.h -> build/lib.macosx-10.13-x86_64-3.7/pysam/include/htslib/htslib
    copying htslib/htslib/kseq.h -> build/lib.macosx-10.13-x86_64-3.7/pysam/include/htslib/htslib
    copying htslib/htslib/kfunc.h -> build/lib.macosx-10.13-x86_64-3.7/pysam/include/htslib/htslib
    copying htslib/htslib/tbx.h -> build/lib.macosx-10.13-x86_64-3.7/pysam/include/htslib/htslib
    copying htslib/htslib/ksort.h -> build/lib.macosx-10.13-x86_64-3.7/pysam/include/htslib/htslib
    copying htslib/htslib/kbitset.h -> build/lib.macosx-10.13-x86_64-3.7/pysam/include/htslib/htslib
    copying htslib/htslib/hts_os.h -> build/lib.macosx-10.13-x86_64-3.7/pysam/include/htslib/htslib
    copying htslib/htslib/klist.h -> build/lib.macosx-10.13-x86_64-3.7/pysam/include/htslib/htslib
    copying htslib/htslib/hts.h -> build/lib.macosx-10.13-x86_64-3.7/pysam/include/htslib/htslib
    copying htslib/htslib/hts_endian.h -> build/lib.macosx-10.13-x86_64-3.7/pysam/include/htslib/htslib
    Fixing build/lib.macosx-10.13-x86_64-3.7/pysam/bcftools.py build/lib.macosx-10.13-x86_64-3.7/pysam/config.py build/lib.macosx-10.13-x86_64-3.7/pysam/version.py build/lib.macosx-10.13-x86_64-3.7/pysam/samtools.py build/lib.macosx-10.13-x86_64-3.7/pysam/__init__.py build/lib.macosx-10.13-x86_64-3.7/pysam/Pileup.py build/lib.macosx-10.13-x86_64-3.7/pysam/utils.py build/lib.macosx-10.13-x86_64-3.7/pysam/include/__init__.py
    Skipping optional fixer: buffer
    Skipping optional fixer: idioms
    Skipping optional fixer: set_literal
    Skipping optional fixer: ws_comma
    Fixing build/lib.macosx-10.13-x86_64-3.7/pysam/bcftools.py build/lib.macosx-10.13-x86_64-3.7/pysam/config.py build/lib.macosx-10.13-x86_64-3.7/pysam/version.py build/lib.macosx-10.13-x86_64-3.7/pysam/samtools.py build/lib.macosx-10.13-x86_64-3.7/pysam/__init__.py build/lib.macosx-10.13-x86_64-3.7/pysam/Pileup.py build/lib.macosx-10.13-x86_64-3.7/pysam/utils.py build/lib.macosx-10.13-x86_64-3.7/pysam/include/__init__.py
    Skipping optional fixer: buffer
    Skipping optional fixer: idioms
    Skipping optional fixer: set_literal
    Skipping optional fixer: ws_comma
    running build_ext
    building 'pysam.libchtslib' extension
    creating build/temp.macosx-10.13-x86_64-3.7
    creating build/temp.macosx-10.13-x86_64-3.7/pysam
    creating build/temp.macosx-10.13-x86_64-3.7/htslib
    creating build/temp.macosx-10.13-x86_64-3.7/htslib/cram
    clang -Wno-unused-result -Wsign-compare -Wunreachable-code -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -I/private/var/folders/3s/tv3skdy90hd6thwmgfwtdmhm0000gn/T/pip-install-5l6qatku/pysam/htslib -I/private/var/folders/3s/tv3skdy90hd6thwmgfwtdmhm0000gn/T/pip-install-5l6qatku/pysam/samtools -I/private/var/folders/3s/tv3skdy90hd6thwmgfwtdmhm0000gn/T/pip-install-5l6qatku/pysam/samtools/lz4 -I/private/var/folders/3s/tv3skdy90hd6thwmgfwtdmhm0000gn/T/pip-install-5l6qatku/pysam/bcftools -I/private/var/folders/3s/tv3skdy90hd6thwmgfwtdmhm0000gn/T/pip-install-5l6qatku/pysam/pysam -I/private/var/folders/3s/tv3skdy90hd6thwmgfwtdmhm0000gn/T/pip-install-5l6qatku/pysam -I/usr/local/include -I/usr/local/opt/openssl/include -I/usr/local/opt/sqlite/include -I/usr/local/Cellar/python/3.7.0/Frameworks/Python.framework/Versions/3.7/include/python3.7m -c pysam/libchtslib.c -o build/temp.macosx-10.13-x86_64-3.7/pysam/libchtslib.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
    pysam/libchtslib.c:15077:65: error: too many arguments to function call, expected 3, have 4
        return (*((__Pyx_PyCFunctionFast)meth)) (self, args, nargs, NULL);
               ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~                     ^~~~
    /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/lib/clang/9.1.0/include/stddef.h:105:16: note: expanded from macro 'NULL'
    #  define NULL ((void*)0)
                   ^~~~~~~~~~
    pysam/libchtslib.c:15665:24: error: no member named 'exc_type' in 'struct _ts'
        tmp_type = tstate->exc_type;
                   ~~~~~~  ^
    pysam/libchtslib.c:15666:25: error: no member named 'exc_value' in 'struct _ts'; did you mean 'curexc_value'?
        tmp_value = tstate->exc_value;
                            ^~~~~~~~~
                            curexc_value
    /usr/local/Cellar/python/3.7.0/Frameworks/Python.framework/Versions/3.7/include/python3.7m/pystate.h:237:15: note: 'curexc_value' declared here
        PyObject *curexc_value;
                  ^
    pysam/libchtslib.c:15667:22: error: no member named 'exc_traceback' in 'struct _ts'; did you mean 'curexc_traceback'?
        tmp_tb = tstate->exc_traceback;
                         ^~~~~~~~~~~~~
                         curexc_traceback
    /usr/local/Cellar/python/3.7.0/Frameworks/Python.framework/Versions/3.7/include/python3.7m/pystate.h:238:15: note: 'curexc_traceback' declared here
        PyObject *curexc_traceback;
                  ^
    pysam/libchtslib.c:15668:13: error: no member named 'exc_type' in 'struct _ts'
        tstate->exc_type = local_type;
        ~~~~~~  ^
    pysam/libchtslib.c:15669:13: error: no member named 'exc_value' in 'struct _ts'; did you mean 'curexc_value'?
        tstate->exc_value = local_value;
                ^~~~~~~~~
                curexc_value
    /usr/local/Cellar/python/3.7.0/Frameworks/Python.framework/Versions/3.7/include/python3.7m/pystate.h:237:15: note: 'curexc_value' declared here
        PyObject *curexc_value;
                  ^
    pysam/libchtslib.c:15670:13: error: no member named 'exc_traceback' in 'struct _ts'; did you mean 'curexc_traceback'?
        tstate->exc_traceback = local_tb;
                ^~~~~~~~~~~~~
                curexc_traceback
    /usr/local/Cellar/python/3.7.0/Frameworks/Python.framework/Versions/3.7/include/python3.7m/pystate.h:238:15: note: 'curexc_traceback' declared here
        PyObject *curexc_traceback;
                  ^
    pysam/libchtslib.c:15692:24: error: no member named 'exc_type' in 'struct _ts'
        tmp_type = tstate->exc_type;
                   ~~~~~~  ^
    pysam/libchtslib.c:15693:25: error: no member named 'exc_value' in 'struct _ts'; did you mean 'curexc_value'?
        tmp_value = tstate->exc_value;
                            ^~~~~~~~~
                            curexc_value
    /usr/local/Cellar/python/3.7.0/Frameworks/Python.framework/Versions/3.7/include/python3.7m/pystate.h:237:15: note: 'curexc_value' declared here
        PyObject *curexc_value;
                  ^
    pysam/libchtslib.c:15694:22: error: no member named 'exc_traceback' in 'struct _ts'; did you mean 'curexc_traceback'?
        tmp_tb = tstate->exc_traceback;
                         ^~~~~~~~~~~~~
                         curexc_traceback
    /usr/local/Cellar/python/3.7.0/Frameworks/Python.framework/Versions/3.7/include/python3.7m/pystate.h:238:15: note: 'curexc_traceback' declared here
        PyObject *curexc_traceback;
                  ^
    pysam/libchtslib.c:15695:13: error: no member named 'exc_type' in 'struct _ts'
        tstate->exc_type = *type;
        ~~~~~~  ^
    pysam/libchtslib.c:15696:13: error: no member named 'exc_value' in 'struct _ts'; did you mean 'curexc_value'?
        tstate->exc_value = *value;
                ^~~~~~~~~
                curexc_value
    /usr/local/Cellar/python/3.7.0/Frameworks/Python.framework/Versions/3.7/include/python3.7m/pystate.h:237:15: note: 'curexc_value' declared here
        PyObject *curexc_value;
                  ^
    pysam/libchtslib.c:15697:13: error: no member named 'exc_traceback' in 'struct _ts'; did you mean 'curexc_traceback'?
        tstate->exc_traceback = *tb;
                ^~~~~~~~~~~~~
                curexc_traceback
    /usr/local/Cellar/python/3.7.0/Frameworks/Python.framework/Versions/3.7/include/python3.7m/pystate.h:238:15: note: 'curexc_traceback' declared here
        PyObject *curexc_traceback;
                  ^
    pysam/libchtslib.c:15716:21: error: no member named 'exc_type' in 'struct _ts'
        *type = tstate->exc_type;
                ~~~~~~  ^
    pysam/libchtslib.c:15717:22: error: no member named 'exc_value' in 'struct _ts'; did you mean 'curexc_value'?
        *value = tstate->exc_value;
                         ^~~~~~~~~
                         curexc_value
    /usr/local/Cellar/python/3.7.0/Frameworks/Python.framework/Versions/3.7/include/python3.7m/pystate.h:237:15: note: 'curexc_value' declared here
        PyObject *curexc_value;
                  ^
    pysam/libchtslib.c:15718:19: error: no member named 'exc_traceback' in 'struct _ts'; did you mean 'curexc_traceback'?
        *tb = tstate->exc_traceback;
                      ^~~~~~~~~~~~~
                      curexc_traceback
    /usr/local/Cellar/python/3.7.0/Frameworks/Python.framework/Versions/3.7/include/python3.7m/pystate.h:238:15: note: 'curexc_traceback' declared here
        PyObject *curexc_traceback;
                  ^
    pysam/libchtslib.c:15725:24: error: no member named 'exc_type' in 'struct _ts'
        tmp_type = tstate->exc_type;
                   ~~~~~~  ^
    pysam/libchtslib.c:15726:25: error: no member named 'exc_value' in 'struct _ts'; did you mean 'curexc_value'?
        tmp_value = tstate->exc_value;
                            ^~~~~~~~~
                            curexc_value
    /usr/local/Cellar/python/3.7.0/Frameworks/Python.framework/Versions/3.7/include/python3.7m/pystate.h:237:15: note: 'curexc_value' declared here
        PyObject *curexc_value;
                  ^
    pysam/libchtslib.c:15727:22: error: no member named 'exc_traceback' in 'struct _ts'; did you mean 'curexc_traceback'?
        tmp_tb = tstate->exc_traceback;
                         ^~~~~~~~~~~~~
                         curexc_traceback
    /usr/local/Cellar/python/3.7.0/Frameworks/Python.framework/Versions/3.7/include/python3.7m/pystate.h:238:15: note: 'curexc_traceback' declared here
        PyObject *curexc_traceback;
                  ^
    fatal error: too many errors emitted, stopping now [-ferror-limit=]
    20 errors generated.
    error: command 'clang' failed with exit status 1
    
    ----------------------------------------
Command "/usr/local/opt/python/bin/python3.7 -u -c "import setuptools, tokenize;__file__='/private/var/folders/3s/tv3skdy90hd6thwmgfwtdmhm0000gn/T/pip-install-5l6qatku/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/3s/tv3skdy90hd6thwmgfwtdmhm0000gn/T/pip-record-y057lddy/install-record.txt --single-version-externally-managed --compile" failed with error code 1 in /private/var/folders/3s/tv3skdy90hd6thwmgfwtdmhm0000gn/T/pip-install-5l6qatku/pysam/

System information:

MacOS High Sierra 10.13.5
Python 3.7.0 [Clang 9.1.0 (clang-902.0.39.2)]
pip 10.0.1
Apple LLVM version 9.1.0 (clang-902.0.39.2)

dancooke · 2018-07-05T14:13:01Z

I managed to successfully build the master branch:

$ pip install https://github.com/pysam-developers/pysam/archive/master.zip
Collecting https://github.com/pysam-developers/pysam/archive/master.zip
  Downloading https://github.com/pysam-developers/pysam/archive/master.zip
     \ 3.7MB 45.8MB/s
Building wheels for collected packages: pysam
  Running setup.py bdist_wheel for pysam ... done
  Stored in directory: /private/var/folders/3s/tv3skdy90hd6thwmgfwtdmhm0000gn/T/pip-ephem-wheel-cache-6fwehcmx/wheels/21/c6/43/3514cc51e28a807a49e50b4b57e4fac75ccc3305a9930be76a
Successfully built pysam
Installing collected packages: pysam
Successfully installed pysam-0.14.1

Time for a new release?

jmarshall · 2018-07-05T14:43:01Z

Complete output from command /usr/local/opt/python/bin/python3.7 -u -c […]
# pysam: no cython available - using pre-compiled C

Presumably this is what happens when you try to build C previously generated with a 3.6-aimed Cython against a new-fangled Python 3.7 released last week.

dancooke · 2018-07-05T14:44:31Z

@jmarshall I did actually update the Cython after posting this issue but got the same error.

AndreasHeger · 2018-07-26T20:24:43Z

Thanks, will need to test with python 3.7.

andersgs · 2018-07-30T22:47:19Z

I have had a similar issue with the latest version (0.15), python 3.7, and linux (REHL 7). Running pip 18.0, and cython 0.28.4.

Installing directly from the master branch works.

Downloading the tar, and building locally (python setup.py build and python setup.py install) finishes nicely, but then I can't load pysam. Claims it can't find pysam.libchtslib, although I do find it in the installed location (which is in the path).

Thank you.

HadrienG · 2018-08-01T19:32:14Z

Hi,

I encounter the same issue on ubuntu 14.04 (Travis image):

gcc 4.8.4
python 3.7.0a4+
pip 9.0.1
pysam 0.14.1

Traceback:

Building wheels for collected packages: pysam
  Running setup.py bdist_wheel for pysam: started
  Running setup.py bdist_wheel for pysam: finished with status 'error'
  Complete output from command /home/travis/virtualenv/python3.7-dev/bin/python -u -c "import setuptools, tokenize;__file__='/tmp/pip-build-_24amo_b/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/tmplgwp4s7dpip-wheel- --python-tag cp37:
  # 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... /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-Linux... plain .so
  checking how to run the C preprocessor... gcc -E
  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 fsync... yes
  checking for drand48... yes
  checking whether fdatasync is declared... yes
  checking for fdatasync... yes
  checking for library containing log... -lm
  checking for zlib.h... yes
  checking for inflate in -lz... yes
  checking for library containing recv... none required
  checking for bzlib.h... yes
  checking for BZ2_bzBuffToBuffCompress in -lbz2... yes
  checking for lzma.h... yes
  checking for lzma_easy_buffer_encode in -llzma... yes
  checking for curl_easy_pause in -lcurl... yes
  checking for CCHmac... no
  checking for library containing HMAC... -lcrypto
  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 -lm -lcurl -lcrypto
  # pysam: htslib_config PLATFORM=default
  # pysam: config_option: ENABLE_PLUGINS=0
  # pysam: config_option: HAVE_COMMONCRYPTO=0
  # pysam: config_option: HAVE_GMTIME_R=1
  # pysam: config_option: HAVE_HMAC=1
  # 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.linux-x86_64-3.7
  creating build/lib.linux-x86_64-3.7/pysam
  copying pysam/Pileup.py -> build/lib.linux-x86_64-3.7/pysam
  copying pysam/samtools.py -> build/lib.linux-x86_64-3.7/pysam
  copying pysam/config.py -> build/lib.linux-x86_64-3.7/pysam
  copying pysam/utils.py -> build/lib.linux-x86_64-3.7/pysam
  copying pysam/version.py -> build/lib.linux-x86_64-3.7/pysam
  copying pysam/__init__.py -> build/lib.linux-x86_64-3.7/pysam
  copying pysam/bcftools.py -> build/lib.linux-x86_64-3.7/pysam
  creating build/lib.linux-x86_64-3.7/pysam/include
  copying pysam/include/__init__.py -> build/lib.linux-x86_64-3.7/pysam/include
  package init file 'samtools/__init__.py' not found (or not a regular file)
  package init file 'bcftools/__init__.py' not found (or not a regular file)
  package init file '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/libchtslib.pxd -> build/lib.linux-x86_64-3.7/pysam
  copying pysam/libcalignmentfile.pxd -> build/lib.linux-x86_64-3.7/pysam
  copying pysam/libcbcftools.pxd -> build/lib.linux-x86_64-3.7/pysam
  copying pysam/libcbcf.pxd -> build/lib.linux-x86_64-3.7/pysam
  copying pysam/libcutils.pxd -> build/lib.linux-x86_64-3.7/pysam
  copying pysam/libctabixproxies.pxd -> build/lib.linux-x86_64-3.7/pysam
  copying pysam/libcfaidx.pxd -> build/lib.linux-x86_64-3.7/pysam
  copying pysam/libcsamfile.pxd -> build/lib.linux-x86_64-3.7/pysam
  copying pysam/libcalignedsegment.pxd -> build/lib.linux-x86_64-3.7/pysam
  copying pysam/libctabix.pxd -> build/lib.linux-x86_64-3.7/pysam
  copying pysam/libcvcf.pxd -> build/lib.linux-x86_64-3.7/pysam
  copying pysam/libcsamtools.pxd -> build/lib.linux-x86_64-3.7/pysam
  copying pysam/htslib_util.h -> build/lib.linux-x86_64-3.7/pysam
  copying pysam/csamtools_util.h -> build/lib.linux-x86_64-3.7/pysam
  copying pysam/cbcftools_util.h -> build/lib.linux-x86_64-3.7/pysam
  copying pysam/pysam_util.h -> build/lib.linux-x86_64-3.7/pysam
  copying pysam/pysam_stream.h -> build/lib.linux-x86_64-3.7/pysam
  creating build/lib.linux-x86_64-3.7/pysam/include/samtools
  copying samtools/samtools.h -> build/lib.linux-x86_64-3.7/pysam/include/samtools
  copying samtools/bam2bcf.h -> build/lib.linux-x86_64-3.7/pysam/include/samtools
  copying samtools/sam_opts.h -> build/lib.linux-x86_64-3.7/pysam/include/samtools
  copying samtools/sample.h -> build/lib.linux-x86_64-3.7/pysam/include/samtools
  copying samtools/stats_isize.h -> build/lib.linux-x86_64-3.7/pysam/include/samtools
  copying samtools/bam.h -> build/lib.linux-x86_64-3.7/pysam/include/samtools
  copying samtools/samtools.pysam.h -> build/lib.linux-x86_64-3.7/pysam/include/samtools
  copying samtools/bam_plbuf.h -> build/lib.linux-x86_64-3.7/pysam/include/samtools
  copying samtools/tmp_file.h -> build/lib.linux-x86_64-3.7/pysam/include/samtools
  copying samtools/bam_endian.h -> build/lib.linux-x86_64-3.7/pysam/include/samtools
  copying samtools/bedidx.h -> build/lib.linux-x86_64-3.7/pysam/include/samtools
  copying samtools/version.h -> build/lib.linux-x86_64-3.7/pysam/include/samtools
  copying samtools/sam.h -> build/lib.linux-x86_64-3.7/pysam/include/samtools
  copying samtools/bam_lpileup.h -> build/lib.linux-x86_64-3.7/pysam/include/samtools
  copying samtools/sam_header.h -> build/lib.linux-x86_64-3.7/pysam/include/samtools
  copying samtools/config.h -> build/lib.linux-x86_64-3.7/pysam/include/samtools
  creating build/lib.linux-x86_64-3.7/pysam/include/bcftools
  copying bcftools/smpl_ilist.h -> build/lib.linux-x86_64-3.7/pysam/include/bcftools
  copying bcftools/mw.h -> build/lib.linux-x86_64-3.7/pysam/include/bcftools
  copying bcftools/vcfbuf.h -> build/lib.linux-x86_64-3.7/pysam/include/bcftools
  copying bcftools/gvcf.h -> build/lib.linux-x86_64-3.7/pysam/include/bcftools
  copying bcftools/bam2bcf.h -> build/lib.linux-x86_64-3.7/pysam/include/bcftools
  copying bcftools/kmin.h -> build/lib.linux-x86_64-3.7/pysam/include/bcftools
  copying bcftools/khash_str2str.h -> build/lib.linux-x86_64-3.7/pysam/include/bcftools
  copying bcftools/prob1.h -> build/lib.linux-x86_64-3.7/pysam/include/bcftools
  copying bcftools/bin.h -> build/lib.linux-x86_64-3.7/pysam/include/bcftools
  copying bcftools/bam_sample.h -> build/lib.linux-x86_64-3.7/pysam/include/bcftools
  copying bcftools/bcftools.pysam.h -> build/lib.linux-x86_64-3.7/pysam/include/bcftools
  copying bcftools/ploidy.h -> build/lib.linux-x86_64-3.7/pysam/include/bcftools
  copying bcftools/regidx.h -> build/lib.linux-x86_64-3.7/pysam/include/bcftools
  copying bcftools/kheap.h -> build/lib.linux-x86_64-3.7/pysam/include/bcftools
  copying bcftools/filter.h -> build/lib.linux-x86_64-3.7/pysam/include/bcftools
  copying bcftools/call.h -> build/lib.linux-x86_64-3.7/pysam/include/bcftools
  copying bcftools/tsv2vcf.h -> build/lib.linux-x86_64-3.7/pysam/include/bcftools
  copying bcftools/bcftools.h -> build/lib.linux-x86_64-3.7/pysam/include/bcftools
  copying bcftools/hclust.h -> build/lib.linux-x86_64-3.7/pysam/include/bcftools
  copying bcftools/vcmp.h -> build/lib.linux-x86_64-3.7/pysam/include/bcftools
  copying bcftools/rbuf.h -> build/lib.linux-x86_64-3.7/pysam/include/bcftools
  copying bcftools/convert.h -> build/lib.linux-x86_64-3.7/pysam/include/bcftools
  copying bcftools/version.h -> build/lib.linux-x86_64-3.7/pysam/include/bcftools
  copying bcftools/HMM.h -> build/lib.linux-x86_64-3.7/pysam/include/bcftools
  copying bcftools/config.h -> build/lib.linux-x86_64-3.7/pysam/include/bcftools
  creating build/lib.linux-x86_64-3.7/pysam/include/samtools/win32
  copying samtools/win32/zlib.h -> build/lib.linux-x86_64-3.7/pysam/include/samtools/win32
  copying samtools/win32/xcurses.h -> build/lib.linux-x86_64-3.7/pysam/include/samtools/win32
  copying samtools/win32/zconf.h -> build/lib.linux-x86_64-3.7/pysam/include/samtools/win32
  creating build/lib.linux-x86_64-3.7/pysam/include/htslib
  copying htslib/bcf_sr_sort.h -> build/lib.linux-x86_64-3.7/pysam/include/htslib
  copying htslib/textutils_internal.h -> build/lib.linux-x86_64-3.7/pysam/include/htslib
  copying htslib/thread_pool_internal.h -> build/lib.linux-x86_64-3.7/pysam/include/htslib
  copying htslib/hts_internal.h -> build/lib.linux-x86_64-3.7/pysam/include/htslib
  copying htslib/hfile_internal.h -> build/lib.linux-x86_64-3.7/pysam/include/htslib
  copying htslib/version.h -> build/lib.linux-x86_64-3.7/pysam/include/htslib
  copying htslib/config.h -> build/lib.linux-x86_64-3.7/pysam/include/htslib
  creating build/lib.linux-x86_64-3.7/pysam/include/htslib/htslib
  copying htslib/htslib/khash_str2int.h -> build/lib.linux-x86_64-3.7/pysam/include/htslib/htslib
  copying htslib/htslib/kfunc.h -> build/lib.linux-x86_64-3.7/pysam/include/htslib/htslib
  copying htslib/htslib/faidx.h -> build/lib.linux-x86_64-3.7/pysam/include/htslib/htslib
  copying htslib/htslib/khash.h -> build/lib.linux-x86_64-3.7/pysam/include/htslib/htslib
  copying htslib/htslib/ksort.h -> build/lib.linux-x86_64-3.7/pysam/include/htslib/htslib
  copying htslib/htslib/tbx.h -> build/lib.linux-x86_64-3.7/pysam/include/htslib/htslib
  copying htslib/htslib/vcf.h -> build/lib.linux-x86_64-3.7/pysam/include/htslib/htslib
  copying htslib/htslib/hts_endian.h -> build/lib.linux-x86_64-3.7/pysam/include/htslib/htslib
  copying htslib/htslib/regidx.h -> build/lib.linux-x86_64-3.7/pysam/include/htslib/htslib
  copying htslib/htslib/hts.h -> build/lib.linux-x86_64-3.7/pysam/include/htslib/htslib
  copying htslib/htslib/hfile.h -> build/lib.linux-x86_64-3.7/pysam/include/htslib/htslib
  copying htslib/htslib/vcfutils.h -> build/lib.linux-x86_64-3.7/pysam/include/htslib/htslib
  copying htslib/htslib/synced_bcf_reader.h -> build/lib.linux-x86_64-3.7/pysam/include/htslib/htslib
  copying htslib/htslib/hts_defs.h -> build/lib.linux-x86_64-3.7/pysam/include/htslib/htslib
  copying htslib/htslib/kstring.h -> build/lib.linux-x86_64-3.7/pysam/include/htslib/htslib
  copying htslib/htslib/kseq.h -> build/lib.linux-x86_64-3.7/pysam/include/htslib/htslib
  copying htslib/htslib/kbitset.h -> build/lib.linux-x86_64-3.7/pysam/include/htslib/htslib
  copying htslib/htslib/hts_log.h -> build/lib.linux-x86_64-3.7/pysam/include/htslib/htslib
  copying htslib/htslib/vcf_sweep.h -> build/lib.linux-x86_64-3.7/pysam/include/htslib/htslib
  copying htslib/htslib/knetfile.h -> build/lib.linux-x86_64-3.7/pysam/include/htslib/htslib
  copying htslib/htslib/hts_os.h -> build/lib.linux-x86_64-3.7/pysam/include/htslib/htslib
  copying htslib/htslib/sam.h -> build/lib.linux-x86_64-3.7/pysam/include/htslib/htslib
  copying htslib/htslib/klist.h -> build/lib.linux-x86_64-3.7/pysam/include/htslib/htslib
  copying htslib/htslib/thread_pool.h -> build/lib.linux-x86_64-3.7/pysam/include/htslib/htslib
  copying htslib/htslib/cram.h -> build/lib.linux-x86_64-3.7/pysam/include/htslib/htslib
  copying htslib/htslib/bgzf.h -> build/lib.linux-x86_64-3.7/pysam/include/htslib/htslib
  Fixing build/lib.linux-x86_64-3.7/pysam/Pileup.py build/lib.linux-x86_64-3.7/pysam/samtools.py build/lib.linux-x86_64-3.7/pysam/config.py build/lib.linux-x86_64-3.7/pysam/utils.py build/lib.linux-x86_64-3.7/pysam/version.py build/lib.linux-x86_64-3.7/pysam/__init__.py build/lib.linux-x86_64-3.7/pysam/bcftools.py build/lib.linux-x86_64-3.7/pysam/include/__init__.py
  Skipping optional fixer: buffer
  Skipping optional fixer: idioms
  Skipping optional fixer: set_literal
  Skipping optional fixer: ws_comma
  Fixing build/lib.linux-x86_64-3.7/pysam/Pileup.py build/lib.linux-x86_64-3.7/pysam/samtools.py build/lib.linux-x86_64-3.7/pysam/config.py build/lib.linux-x86_64-3.7/pysam/utils.py build/lib.linux-x86_64-3.7/pysam/version.py build/lib.linux-x86_64-3.7/pysam/__init__.py build/lib.linux-x86_64-3.7/pysam/bcftools.py build/lib.linux-x86_64-3.7/pysam/include/__init__.py
  Skipping optional fixer: buffer
  Skipping optional fixer: idioms
  Skipping optional fixer: set_literal
  Skipping optional fixer: ws_comma
  warning: build_py: byte-compiling is disabled, skipping.
  
  running build_ext
  skipping 'pysam/libchtslib.c' Cython extension (up-to-date)
  building 'pysam.libchtslib' extension
  creating build/temp.linux-x86_64-3.7
  creating build/temp.linux-x86_64-3.7/pysam
  creating build/temp.linux-x86_64-3.7/htslib
  creating build/temp.linux-x86_64-3.7/htslib/cram
  gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -g -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -fPIC -I/tmp/pip-build-_24amo_b/pysam/htslib -I/tmp/pip-build-_24amo_b/pysam/samtools -I/tmp/pip-build-_24amo_b/pysam/samtools/lz4 -I/tmp/pip-build-_24amo_b/pysam/bcftools -I/tmp/pip-build-_24amo_b/pysam/pysam -I/tmp/pip-build-_24amo_b/pysam -I/opt/python/3.7-dev/include/python3.7m -c pysam/libchtslib.c -o build/temp.linux-x86_64-3.7/pysam/libchtslib.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
  pysam/libchtslib.c: In function ‘__Pyx_PyCFunction_FastCall’:
  pysam/libchtslib.c:15077:5: error: too many arguments to function ‘(struct PyObject * (*)(struct PyObject *, struct PyObject * const*, Py_ssize_t))meth’
       return (*((__Pyx_PyCFunctionFast)meth)) (self, args, nargs, NULL);
       ^
  pysam/libchtslib.c: In function ‘__Pyx__GetException’:
  pysam/libchtslib.c:15665:22: error: ‘PyThreadState’ has no member named ‘exc_type’
       tmp_type = tstate->exc_type;
                        ^
  pysam/libchtslib.c:15666:23: error: ‘PyThreadState’ has no member named ‘exc_value’
       tmp_value = tstate->exc_value;
                         ^
  pysam/libchtslib.c:15667:20: error: ‘PyThreadState’ has no member named ‘exc_traceback’
       tmp_tb = tstate->exc_traceback;
                      ^
  pysam/libchtslib.c:15668:11: error: ‘PyThreadState’ has no member named ‘exc_type’
       tstate->exc_type = local_type;
             ^
  pysam/libchtslib.c:15669:11: error: ‘PyThreadState’ has no member named ‘exc_value’
       tstate->exc_value = local_value;
             ^
  pysam/libchtslib.c:15670:11: error: ‘PyThreadState’ has no member named ‘exc_traceback’
       tstate->exc_traceback = local_tb;
             ^
  pysam/libchtslib.c: In function ‘__Pyx__ExceptionSwap’:
  pysam/libchtslib.c:15692:22: error: ‘PyThreadState’ has no member named ‘exc_type’
       tmp_type = tstate->exc_type;
                        ^
  pysam/libchtslib.c:15693:23: error: ‘PyThreadState’ has no member named ‘exc_value’
       tmp_value = tstate->exc_value;
                         ^
  pysam/libchtslib.c:15694:20: error: ‘PyThreadState’ has no member named ‘exc_traceback’
       tmp_tb = tstate->exc_traceback;
                      ^
  pysam/libchtslib.c:15695:11: error: ‘PyThreadState’ has no member named ‘exc_type’
       tstate->exc_type = *type;
             ^
  pysam/libchtslib.c:15696:11: error: ‘PyThreadState’ has no member named ‘exc_value’
       tstate->exc_value = *value;
             ^
  pysam/libchtslib.c:15697:11: error: ‘PyThreadState’ has no member named ‘exc_traceback’
       tstate->exc_traceback = *tb;
             ^
  pysam/libchtslib.c: In function ‘__Pyx__ExceptionSave’:
  pysam/libchtslib.c:15716:19: error: ‘PyThreadState’ has no member named ���exc_type’
       *type = tstate->exc_type;
                     ^
  pysam/libchtslib.c:15717:20: error: ‘PyThreadState’ has no member named ‘exc_value’
       *value = tstate->exc_value;
                      ^
  pysam/libchtslib.c:15718:17: error: ‘PyThreadState’ has no member named ‘exc_traceback’
       *tb = tstate->exc_traceback;
                   ^
  pysam/libchtslib.c: In function ‘__Pyx__ExceptionReset’:
  pysam/libchtslib.c:15725:22: error: ‘PyThreadState’ has no member named ‘exc_type’
       tmp_type = tstate->exc_type;
                        ^
  pysam/libchtslib.c:15726:23: error: ‘PyThreadState’ has no member named ‘exc_value’
       tmp_value = tstate->exc_value;
                         ^
  pysam/libchtslib.c:15727:20: error: ‘PyThreadState’ has no member named ‘exc_traceback’
       tmp_tb = tstate->exc_traceback;
                      ^
  pysam/libchtslib.c:15728:11: error: ‘PyThreadState’ has no member named ‘exc_type’
       tstate->exc_type = type;
             ^
  pysam/libchtslib.c:15729:11: error: ‘PyThreadState’ has no member named ‘exc_value’
       tstate->exc_value = value;
             ^
  pysam/libchtslib.c:15730:11: error: ‘PyThreadState’ has no member named ‘exc_traceback’
       tstate->exc_traceback = tb;
             ^
  error: command 'gcc' failed with exit status 1
  
  ----------------------------------------
  Running setup.py clean for pysam
Failed to build pysam
Installing collected packages: pysam
  Running setup.py install for pysam: started
    Running setup.py install for pysam: finished with status 'error'
    Complete output from command /home/travis/virtualenv/python3.7-dev/bin/python -u -c "import setuptools, tokenize;__file__='/tmp/pip-build-_24amo_b/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-whmfjk8e-record/install-record.txt --single-version-externally-managed --compile --install-headers /home/travis/virtualenv/python3.7-dev/include/site/python3.7/pysam:
    # 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... /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-Linux... plain .so
    checking how to run the C preprocessor... gcc -E
    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 fsync... yes
    checking for drand48... yes
    checking whether fdatasync is declared... yes
    checking for fdatasync... yes
    checking for library containing log... -lm
    checking for zlib.h... yes
    checking for inflate in -lz... yes
    checking for library containing recv... none required
    checking for bzlib.h... yes
    checking for BZ2_bzBuffToBuffCompress in -lbz2... yes
    checking for lzma.h... yes
    checking for lzma_easy_buffer_encode in -llzma... yes
    checking for curl_easy_pause in -lcurl... yes
    checking for CCHmac... no
    checking for library containing HMAC... -lcrypto
    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 -lm -lcurl -lcrypto
    # pysam: htslib_config PLATFORM=default
    # pysam: config_option: ENABLE_PLUGINS=0
    # pysam: config_option: HAVE_COMMONCRYPTO=0
    # pysam: config_option: HAVE_GMTIME_R=1
    # pysam: config_option: HAVE_HMAC=1
    # 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.linux-x86_64-3.7
    creating build/lib.linux-x86_64-3.7/pysam
    copying pysam/Pileup.py -> build/lib.linux-x86_64-3.7/pysam
    copying pysam/samtools.py -> build/lib.linux-x86_64-3.7/pysam
    copying pysam/config.py -> build/lib.linux-x86_64-3.7/pysam
    copying pysam/utils.py -> build/lib.linux-x86_64-3.7/pysam
    copying pysam/version.py -> build/lib.linux-x86_64-3.7/pysam
    copying pysam/__init__.py -> build/lib.linux-x86_64-3.7/pysam
    copying pysam/bcftools.py -> build/lib.linux-x86_64-3.7/pysam
    creating build/lib.linux-x86_64-3.7/pysam/include
    copying pysam/include/__init__.py -> build/lib.linux-x86_64-3.7/pysam/include
    package init file 'samtools/__init__.py' not found (or not a regular file)
    package init file 'bcftools/__init__.py' not found (or not a regular file)
    package init file '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/libchtslib.pxd -> build/lib.linux-x86_64-3.7/pysam
    copying pysam/libcalignmentfile.pxd -> build/lib.linux-x86_64-3.7/pysam
    copying pysam/libcbcftools.pxd -> build/lib.linux-x86_64-3.7/pysam
    copying pysam/libcbcf.pxd -> build/lib.linux-x86_64-3.7/pysam
    copying pysam/libcutils.pxd -> build/lib.linux-x86_64-3.7/pysam
    copying pysam/libctabixproxies.pxd -> build/lib.linux-x86_64-3.7/pysam
    copying pysam/libcfaidx.pxd -> build/lib.linux-x86_64-3.7/pysam
    copying pysam/libcsamfile.pxd -> build/lib.linux-x86_64-3.7/pysam
    copying pysam/libcalignedsegment.pxd -> build/lib.linux-x86_64-3.7/pysam
    copying pysam/libctabix.pxd -> build/lib.linux-x86_64-3.7/pysam
    copying pysam/libcvcf.pxd -> build/lib.linux-x86_64-3.7/pysam
    copying pysam/libcsamtools.pxd -> build/lib.linux-x86_64-3.7/pysam
    copying pysam/htslib_util.h -> build/lib.linux-x86_64-3.7/pysam
    copying pysam/csamtools_util.h -> build/lib.linux-x86_64-3.7/pysam
    copying pysam/cbcftools_util.h -> build/lib.linux-x86_64-3.7/pysam
    copying pysam/pysam_util.h -> build/lib.linux-x86_64-3.7/pysam
    copying pysam/pysam_stream.h -> build/lib.linux-x86_64-3.7/pysam
    creating build/lib.linux-x86_64-3.7/pysam/include/samtools
    copying samtools/samtools.h -> build/lib.linux-x86_64-3.7/pysam/include/samtools
    copying samtools/bam2bcf.h -> build/lib.linux-x86_64-3.7/pysam/include/samtools
    copying samtools/sam_opts.h -> build/lib.linux-x86_64-3.7/pysam/include/samtools
    copying samtools/sample.h -> build/lib.linux-x86_64-3.7/pysam/include/samtools
    copying samtools/stats_isize.h -> build/lib.linux-x86_64-3.7/pysam/include/samtools
    copying samtools/bam.h -> build/lib.linux-x86_64-3.7/pysam/include/samtools
    copying samtools/samtools.pysam.h -> build/lib.linux-x86_64-3.7/pysam/include/samtools
    copying samtools/bam_plbuf.h -> build/lib.linux-x86_64-3.7/pysam/include/samtools
    copying samtools/tmp_file.h -> build/lib.linux-x86_64-3.7/pysam/include/samtools
    copying samtools/bam_endian.h -> build/lib.linux-x86_64-3.7/pysam/include/samtools
    copying samtools/bedidx.h -> build/lib.linux-x86_64-3.7/pysam/include/samtools
    copying samtools/version.h -> build/lib.linux-x86_64-3.7/pysam/include/samtools
    copying samtools/sam.h -> build/lib.linux-x86_64-3.7/pysam/include/samtools
    copying samtools/bam_lpileup.h -> build/lib.linux-x86_64-3.7/pysam/include/samtools
    copying samtools/sam_header.h -> build/lib.linux-x86_64-3.7/pysam/include/samtools
    copying samtools/config.h -> build/lib.linux-x86_64-3.7/pysam/include/samtools
    creating build/lib.linux-x86_64-3.7/pysam/include/bcftools
    copying bcftools/smpl_ilist.h -> build/lib.linux-x86_64-3.7/pysam/include/bcftools
    copying bcftools/mw.h -> build/lib.linux-x86_64-3.7/pysam/include/bcftools
    copying bcftools/vcfbuf.h -> build/lib.linux-x86_64-3.7/pysam/include/bcftools
    copying bcftools/gvcf.h -> build/lib.linux-x86_64-3.7/pysam/include/bcftools
    copying bcftools/bam2bcf.h -> build/lib.linux-x86_64-3.7/pysam/include/bcftools
    copying bcftools/kmin.h -> build/lib.linux-x86_64-3.7/pysam/include/bcftools
    copying bcftools/khash_str2str.h -> build/lib.linux-x86_64-3.7/pysam/include/bcftools
    copying bcftools/prob1.h -> build/lib.linux-x86_64-3.7/pysam/include/bcftools
    copying bcftools/bin.h -> build/lib.linux-x86_64-3.7/pysam/include/bcftools
    copying bcftools/bam_sample.h -> build/lib.linux-x86_64-3.7/pysam/include/bcftools
    copying bcftools/bcftools.pysam.h -> build/lib.linux-x86_64-3.7/pysam/include/bcftools
    copying bcftools/ploidy.h -> build/lib.linux-x86_64-3.7/pysam/include/bcftools
    copying bcftools/regidx.h -> build/lib.linux-x86_64-3.7/pysam/include/bcftools
    copying bcftools/kheap.h -> build/lib.linux-x86_64-3.7/pysam/include/bcftools
    copying bcftools/filter.h -> build/lib.linux-x86_64-3.7/pysam/include/bcftools
    copying bcftools/call.h -> build/lib.linux-x86_64-3.7/pysam/include/bcftools
    copying bcftools/tsv2vcf.h -> build/lib.linux-x86_64-3.7/pysam/include/bcftools
    copying bcftools/bcftools.h -> build/lib.linux-x86_64-3.7/pysam/include/bcftools
    copying bcftools/hclust.h -> build/lib.linux-x86_64-3.7/pysam/include/bcftools
    copying bcftools/vcmp.h -> build/lib.linux-x86_64-3.7/pysam/include/bcftools
    copying bcftools/rbuf.h -> build/lib.linux-x86_64-3.7/pysam/include/bcftools
    copying bcftools/convert.h -> build/lib.linux-x86_64-3.7/pysam/include/bcftools
    copying bcftools/version.h -> build/lib.linux-x86_64-3.7/pysam/include/bcftools
    copying bcftools/HMM.h -> build/lib.linux-x86_64-3.7/pysam/include/bcftools
    copying bcftools/config.h -> build/lib.linux-x86_64-3.7/pysam/include/bcftools
    creating build/lib.linux-x86_64-3.7/pysam/include/samtools/win32
    copying samtools/win32/zlib.h -> build/lib.linux-x86_64-3.7/pysam/include/samtools/win32
    copying samtools/win32/xcurses.h -> build/lib.linux-x86_64-3.7/pysam/include/samtools/win32
    copying samtools/win32/zconf.h -> build/lib.linux-x86_64-3.7/pysam/include/samtools/win32
    creating build/lib.linux-x86_64-3.7/pysam/include/htslib
    copying htslib/bcf_sr_sort.h -> build/lib.linux-x86_64-3.7/pysam/include/htslib
    copying htslib/textutils_internal.h -> build/lib.linux-x86_64-3.7/pysam/include/htslib
    copying htslib/thread_pool_internal.h -> build/lib.linux-x86_64-3.7/pysam/include/htslib
    copying htslib/hts_internal.h -> build/lib.linux-x86_64-3.7/pysam/include/htslib
    copying htslib/hfile_internal.h -> build/lib.linux-x86_64-3.7/pysam/include/htslib
    copying htslib/version.h -> build/lib.linux-x86_64-3.7/pysam/include/htslib
    copying htslib/config.h -> build/lib.linux-x86_64-3.7/pysam/include/htslib
    creating build/lib.linux-x86_64-3.7/pysam/include/htslib/htslib
    copying htslib/htslib/khash_str2int.h -> build/lib.linux-x86_64-3.7/pysam/include/htslib/htslib
    copying htslib/htslib/kfunc.h -> build/lib.linux-x86_64-3.7/pysam/include/htslib/htslib
    copying htslib/htslib/faidx.h -> build/lib.linux-x86_64-3.7/pysam/include/htslib/htslib
    copying htslib/htslib/khash.h -> build/lib.linux-x86_64-3.7/pysam/include/htslib/htslib
    copying htslib/htslib/ksort.h -> build/lib.linux-x86_64-3.7/pysam/include/htslib/htslib
    copying htslib/htslib/tbx.h -> build/lib.linux-x86_64-3.7/pysam/include/htslib/htslib
    copying htslib/htslib/vcf.h -> build/lib.linux-x86_64-3.7/pysam/include/htslib/htslib
    copying htslib/htslib/hts_endian.h -> build/lib.linux-x86_64-3.7/pysam/include/htslib/htslib
    copying htslib/htslib/regidx.h -> build/lib.linux-x86_64-3.7/pysam/include/htslib/htslib
    copying htslib/htslib/hts.h -> build/lib.linux-x86_64-3.7/pysam/include/htslib/htslib
    copying htslib/htslib/hfile.h -> build/lib.linux-x86_64-3.7/pysam/include/htslib/htslib
    copying htslib/htslib/vcfutils.h -> build/lib.linux-x86_64-3.7/pysam/include/htslib/htslib
    copying htslib/htslib/synced_bcf_reader.h -> build/lib.linux-x86_64-3.7/pysam/include/htslib/htslib
    copying htslib/htslib/hts_defs.h -> build/lib.linux-x86_64-3.7/pysam/include/htslib/htslib
    copying htslib/htslib/kstring.h -> build/lib.linux-x86_64-3.7/pysam/include/htslib/htslib
    copying htslib/htslib/kseq.h -> build/lib.linux-x86_64-3.7/pysam/include/htslib/htslib
    copying htslib/htslib/kbitset.h -> build/lib.linux-x86_64-3.7/pysam/include/htslib/htslib
    copying htslib/htslib/hts_log.h -> build/lib.linux-x86_64-3.7/pysam/include/htslib/htslib
    copying htslib/htslib/vcf_sweep.h -> build/lib.linux-x86_64-3.7/pysam/include/htslib/htslib
    copying htslib/htslib/knetfile.h -> build/lib.linux-x86_64-3.7/pysam/include/htslib/htslib
    copying htslib/htslib/hts_os.h -> build/lib.linux-x86_64-3.7/pysam/include/htslib/htslib
    copying htslib/htslib/sam.h -> build/lib.linux-x86_64-3.7/pysam/include/htslib/htslib
    copying htslib/htslib/klist.h -> build/lib.linux-x86_64-3.7/pysam/include/htslib/htslib
    copying htslib/htslib/thread_pool.h -> build/lib.linux-x86_64-3.7/pysam/include/htslib/htslib
    copying htslib/htslib/cram.h -> build/lib.linux-x86_64-3.7/pysam/include/htslib/htslib
    copying htslib/htslib/bgzf.h -> build/lib.linux-x86_64-3.7/pysam/include/htslib/htslib
    Fixing build/lib.linux-x86_64-3.7/pysam/Pileup.py build/lib.linux-x86_64-3.7/pysam/samtools.py build/lib.linux-x86_64-3.7/pysam/config.py build/lib.linux-x86_64-3.7/pysam/utils.py build/lib.linux-x86_64-3.7/pysam/version.py build/lib.linux-x86_64-3.7/pysam/__init__.py build/lib.linux-x86_64-3.7/pysam/bcftools.py build/lib.linux-x86_64-3.7/pysam/include/__init__.py
    Skipping optional fixer: buffer
    Skipping optional fixer: idioms
    Skipping optional fixer: set_literal
    Skipping optional fixer: ws_comma
    Fixing build/lib.linux-x86_64-3.7/pysam/Pileup.py build/lib.linux-x86_64-3.7/pysam/samtools.py build/lib.linux-x86_64-3.7/pysam/config.py build/lib.linux-x86_64-3.7/pysam/utils.py build/lib.linux-x86_64-3.7/pysam/version.py build/lib.linux-x86_64-3.7/pysam/__init__.py build/lib.linux-x86_64-3.7/pysam/bcftools.py build/lib.linux-x86_64-3.7/pysam/include/__init__.py
    Skipping optional fixer: buffer
    Skipping optional fixer: idioms
    Skipping optional fixer: set_literal
    Skipping optional fixer: ws_comma
    warning: build_py: byte-compiling is disabled, skipping.
    
    running build_ext
    skipping 'pysam/libchtslib.c' Cython extension (up-to-date)
    building 'pysam.libchtslib' extension
    creating build/temp.linux-x86_64-3.7
    creating build/temp.linux-x86_64-3.7/pysam
    creating build/temp.linux-x86_64-3.7/htslib
    creating build/temp.linux-x86_64-3.7/htslib/cram
    gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -g -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -fPIC -I/tmp/pip-build-_24amo_b/pysam/htslib -I/tmp/pip-build-_24amo_b/pysam/samtools -I/tmp/pip-build-_24amo_b/pysam/samtools/lz4 -I/tmp/pip-build-_24amo_b/pysam/bcftools -I/tmp/pip-build-_24amo_b/pysam/pysam -I/tmp/pip-build-_24amo_b/pysam -I/opt/python/3.7-dev/include/python3.7m -c pysam/libchtslib.c -o build/temp.linux-x86_64-3.7/pysam/libchtslib.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
    pysam/libchtslib.c: In function ‘__Pyx_PyCFunction_FastCall’:
    pysam/libchtslib.c:15077:5: error: too many arguments to function ‘(struct PyObject * (*)(struct PyObject *, struct PyObject * const*, Py_ssize_t))meth’
         return (*((__Pyx_PyCFunctionFast)meth)) (self, args, nargs, NULL);
         ^
    pysam/libchtslib.c: In function ‘__Pyx__GetException’:
    pysam/libchtslib.c:15665:22: error: ‘PyThreadState’ has no member named ‘exc_type’
         tmp_type = tstate->exc_type;
                          ^
    pysam/libchtslib.c:15666:23: error: ‘PyThreadState’ has no member named ‘exc_value’
         tmp_value = tstate->exc_value;
                           ^
    pysam/libchtslib.c:15667:20: error: ‘PyThreadState’ has no member named ‘exc_traceback’
         tmp_tb = tstate->exc_traceback;
                        ^
    pysam/libchtslib.c:15668:11: error: ‘PyThreadState’ has no member named ‘exc_type’
         tstate->exc_type = local_type;
               ^
    pysam/libchtslib.c:15669:11: error: ‘PyThreadState’ has no member named ‘exc_value’
         tstate->exc_value = local_value;
               ^
    pysam/libchtslib.c:15670:11: error: ‘PyThreadState’ has no member named ‘exc_traceback’
         tstate->exc_traceback = local_tb;
               ^
    pysam/libchtslib.c: In function ‘__Pyx__ExceptionSwap’:
    pysam/libchtslib.c:15692:22: error: ‘PyThreadState’ has no member named ‘exc_type’
         tmp_type = tstate->exc_type;
                          ^
    pysam/libchtslib.c:15693:23: error: ‘PyThreadState’ has no member named ‘exc_value’
         tmp_value = tstate->exc_value;
                           ^
    pysam/libchtslib.c:15694:20: error: ‘PyThreadState’ has no member named ‘exc_traceback’
         tmp_tb = tstate->exc_traceback;
                        ^
    pysam/libchtslib.c:15695:11: error: ‘PyThreadState’ has no member named ‘exc_type’
         tstate->exc_type = *type;
               ^
    pysam/libchtslib.c:15696:11: error: ‘PyThreadState’ has no member named ‘exc_value’
         tstate->exc_value = *value;
               ^
    pysam/libchtslib.c:15697:11: error: ‘PyThreadState’ has no member named ‘exc_traceback’
         tstate->exc_traceback = *tb;
               ^
    pysam/libchtslib.c: In function ‘__Pyx__ExceptionSave’:
    pysam/libchtslib.c:15716:19: error: ‘PyThreadState’ has no member named ‘exc_type’
         *type = tstate->exc_type;
                       ^
    pysam/libchtslib.c:15717:20: error: ‘PyThreadState’ has no member named ‘exc_value’
         *value = tstate->exc_value;
                        ^
    pysam/libchtslib.c:15718:17: error: ‘PyThreadState’ has no member named ‘exc_traceback’
         *tb = tstate->exc_traceback;
                     ^
    pysam/libchtslib.c: In function ‘__Pyx__ExceptionReset’:
    pysam/libchtslib.c:15725:22: error: ‘PyThreadState’ has no member named ‘exc_type’
         tmp_type = tstate->exc_type;
                          ^
    pysam/libchtslib.c:15726:23: error: ‘PyThreadState’ has no member named ‘exc_value’
         tmp_value = tstate->exc_value;
                           ^
    pysam/libchtslib.c:15727:20: error: ‘PyThreadState’ has no member named ‘exc_traceback’
         tmp_tb = tstate->exc_traceback;
                        ^
    pysam/libchtslib.c:15728:11: error: ‘PyThreadState’ has no member named ‘exc_type’
         tstate->exc_type = type;
               ^
    pysam/libchtslib.c:15729:11: error: ‘PyThreadState’ has no member named ‘exc_value’
         tstate->exc_value = value;
               ^
    pysam/libchtslib.c:15730:11: error: ‘PyThreadState��� has no member named ‘exc_traceback’
         tstate->exc_traceback = tb;
               ^
    error: command 'gcc' failed with exit status 1
    
    ----------------------------------------
  Failed building wheel for pysam
Command "/home/travis/virtualenv/python3.7-dev/bin/python -u -c "import setuptools, tokenize;__file__='/tmp/pip-build-_24amo_b/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-whmfjk8e-record/install-record.txt --single-version-externally-managed --compile --install-headers /home/travis/virtualenv/python3.7-dev/include/site/python3.7/pysam" failed with error code 1 in /tmp/pip-build-_24amo_b/pysam/

sjackman · 2018-08-10T00:04:11Z

Any plans to tag a stable release of pysam that works with Python 3.7? Homebrew and Linuxbrew have Python 3.7.

kyleabeauchamp · 2018-08-10T16:12:13Z

So we generally release pysam versions alongside new releases of HTSLib+samtools, so I would imagine a release in a month or two. However, we can definitely review any pull requests towards fixing py37 in the meantime.

sjackman · 2018-08-10T16:35:21Z

My understanding is that the current master branch already works with Python 3.7.
See #697 (comment)
and veg/BioExt#24 (comment)
and that tagging a new release and releasing it on PyPI would resolve this issue. Do I understand correctly?

kyleabeauchamp · 2018-08-10T16:52:07Z

AFAIK the current master branch is equivalent to the v0.15.0 source tarball on pypi, modulo pypi packaging details etc. E.g. there have been no changes to master since 13 days ago (July 28) (https://github.com/pysam-developers/pysam/commits/master).

sjackman · 2018-08-30T00:14:00Z

I believe the problem is that the pysam source archive stored on PyPI
https://files.pythonhosted.org/packages/f9/c4/f1b6963a05f415aa69c8efd64ebe460d56d03ecc75db70b0e8606b589ade/pysam-0.15.0.tar.gz

includes files that were built by cython 0.25.2. For example:

❯❯❯ head -n1 pysam/libcsamfile.c
/* Generated by Cython 0.25.2 */

These files evidently do not work with Python 3.7.

I'm hopeful that upgrading Cython to the most recent version 0.28.5 on your local development machine, bumping the version number of pysam, and releasing a new version should resolve this issue.

yhoogstrate · 2018-08-30T09:35:48Z

Hi all,

I am experiencing the same error for pysam 0.14.1 and 0.15.0 using pip on Arch linux (since August 1st python 3.7 is its systems default). Manual compilation still works 😃 .

Youri

y9c · 2018-09-08T15:16:47Z

the problem still exist.

AndreasHeger · 2018-09-10T19:47:25Z

Thanks, I will take a look this weekend.

yhoogstrate · 2018-09-14T09:40:43Z

Over here 0.15.1 seems to have solved it 👍, Thanks!

oneilep · 2018-09-18T16:43:29Z

0.15.1 installed fine for me, too.

HadrienG · 2018-09-19T04:56:38Z

0.15.1 solved it for me too. Thank you!

kyleabeauchamp · 2019-02-11T17:01:48Z

The latest version of pysam should be working on py37. Also, python 3.7 pysam is now available on bioconda: https://anaconda.org/bioconda/pysam/files?version=0.15.2

stevenweaver mentioned this issue Jul 9, 2018

Unable to install in Python 3.7 veg/BioExt#24

Closed

AndreasHeger added the INSTALL label Jul 26, 2018

AndreasHeger changed the title ~~Error installing pysam 0.14.1 with pip on OS X~~ Error installing pysam 0.14.1 with pip on OS X / python 3.7 Jul 26, 2018

HadrienG mentioned this issue Aug 1, 2018

Can't install on python3.7 HadrienG/InSilicoSeq#68

Closed

yan12125 mentioned this issue Aug 6, 2018

py-htseq: update to 0.10.0; add Python 3.6 macports/macports-ports#2340

Merged

9 tasks

suujia mentioned this issue Aug 9, 2018

circlator: import from brewsci/science brewsci/homebrew-bio#351

Closed

4 tasks

ShaiberAlon mentioned this issue Aug 14, 2018

change scikit-learn requirment merenlab/anvio#935

Closed

sjackman mentioned this issue Aug 20, 2018

tigmint: bump revision for python 3.7 brewsci/homebrew-bio#355

Closed

4 tasks

luizirber mentioned this issue Sep 2, 2018

Generate signatures from 10x single cell bam file sourmash-bio/sourmash#539

Merged

5 tasks

owainkenwayucl mentioned this issue Sep 5, 2018

Python 3.7 UCL-RITS/rcps-buildscripts#194

Closed

2 tasks

stevenweaver mentioned this issue Sep 13, 2018

BioExt does not install with Python 3.7 veg/BioExt#28

Closed

sjackman mentioned this issue Oct 29, 2018

pybedtools compilation fails on python3.7 daler/pybedtools#254

Closed

wm75 mentioned this issue Nov 8, 2018

Python 3 support. galaxyproject/galaxy#1715

Closed

14 tasks

Martinsos mentioned this issue Jan 20, 2019

gcc (GCC) 8.2.1 20181127 compile problem via pip install Martinsos/edlib#125

Closed

kyleabeauchamp closed this as completed Feb 11, 2019

Provide feedback

Saved searches

Use saved searches to filter your results more quickly

Error installing pysam 0.14.1 with pip on OS X / python 3.7 #697

Error installing pysam 0.14.1 with pip on OS X / python 3.7 #697

dancooke commented Jul 5, 2018

dancooke commented Jul 5, 2018

jmarshall commented Jul 5, 2018

dancooke commented Jul 5, 2018 •

edited

Loading

AndreasHeger commented Jul 26, 2018

andersgs commented Jul 30, 2018

HadrienG commented Aug 1, 2018 •

edited

Loading

sjackman commented Aug 10, 2018

kyleabeauchamp commented Aug 10, 2018

sjackman commented Aug 10, 2018

kyleabeauchamp commented Aug 10, 2018 •

edited

Loading

sjackman commented Aug 30, 2018

yhoogstrate commented Aug 30, 2018 •

edited

Loading

y9c commented Sep 8, 2018

AndreasHeger commented Sep 10, 2018

yhoogstrate commented Sep 14, 2018

oneilep commented Sep 18, 2018

HadrienG commented Sep 19, 2018

kyleabeauchamp commented Feb 11, 2019

Error installing pysam 0.14.1 with pip on OS X / python 3.7 #697

Error installing pysam 0.14.1 with pip on OS X / python 3.7 #697

Comments

dancooke commented Jul 5, 2018

dancooke commented Jul 5, 2018

jmarshall commented Jul 5, 2018

dancooke commented Jul 5, 2018 • edited Loading

AndreasHeger commented Jul 26, 2018

andersgs commented Jul 30, 2018

HadrienG commented Aug 1, 2018 • edited Loading

sjackman commented Aug 10, 2018

kyleabeauchamp commented Aug 10, 2018

sjackman commented Aug 10, 2018

kyleabeauchamp commented Aug 10, 2018 • edited Loading

sjackman commented Aug 30, 2018

yhoogstrate commented Aug 30, 2018 • edited Loading

y9c commented Sep 8, 2018

AndreasHeger commented Sep 10, 2018

yhoogstrate commented Sep 14, 2018

oneilep commented Sep 18, 2018

HadrienG commented Sep 19, 2018

kyleabeauchamp commented Feb 11, 2019

dancooke commented Jul 5, 2018 •

edited

Loading

HadrienG commented Aug 1, 2018 •

edited

Loading

kyleabeauchamp commented Aug 10, 2018 •

edited

Loading

yhoogstrate commented Aug 30, 2018 •

edited

Loading