Closed
Description
I get the following error when trying to install pysam with pip in Python 3.8.0 ( I also posted this on the user group):
(python38) yoursham-linux:~$ pip3 install pysam
Collecting pysam
Using cached https://files.pythonhosted.org/packages/15/e7/2dab8bb0ac739555e69586f1492f0ff6bc4a1f8312992a83001d3deb77ac/pysam-0.15.3.tar.gz
Building wheels for collected packages: pysam
Building wheel for pysam (setup.py) ... error
ERROR: Command errored out with exit status 1:
command: /home/myourshaw/.virtualenvs/python38/bin/python3 -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-install-2vtoq395/pysam/setup.py'"'"'; __file__='"'"'/tmp/pip-install-2vtoq395/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/pip-wheel-warpx6kv --python-tag cp38
cwd: /tmp/pip-install-2vtoq395/pysam/
Complete output (382 lines):
# pysam: cython is available - using cythonize if necessary
# pysam: htslib mode is shared
# pysam: HTSLIB_CONFIGURE_OPTIONS=None
# pysam: (sysconfig) CC=gcc -pthread
# pysam: (sysconfig) CFLAGS=-Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall
# pysam: (sysconfig) LDFLAGS=-L//home/myourshaw/.local/extlib/lib -Wl,--rpath=//home/myourshaw/.local/lib -Wl,--rpath=//home/myourshaw/.local/extlib/lib
checking for gcc... gcc -pthread
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 -pthread accepts -g... yes
checking for gcc -pthread 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... unknown
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 -pthread -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... 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 libdeflate.h... no
checking for libdeflate_deflate_compress in -ldeflate... no
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 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_64-3.8
creating build/lib.linux-x86_64-3.8/pysam
copying pysam/Pileup.py -> build/lib.linux-x86_64-3.8/pysam
copying pysam/__init__.py -> build/lib.linux-x86_64-3.8/pysam
copying pysam/bcftools.py -> build/lib.linux-x86_64-3.8/pysam
copying pysam/config.py -> build/lib.linux-x86_64-3.8/pysam
copying pysam/samtools.py -> build/lib.linux-x86_64-3.8/pysam
copying pysam/utils.py -> build/lib.linux-x86_64-3.8/pysam
copying pysam/version.py -> build/lib.linux-x86_64-3.8/pysam
creating build/lib.linux-x86_64-3.8/pysam/include
copying pysam/include/__init__.py -> build/lib.linux-x86_64-3.8/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.linux-x86_64-3.8/pysam
copying pysam/libcalignmentfile.pxd -> build/lib.linux-x86_64-3.8/pysam
copying pysam/libcbcf.pxd -> build/lib.linux-x86_64-3.8/pysam
copying pysam/libcbcftools.pxd -> build/lib.linux-x86_64-3.8/pysam
copying pysam/libcfaidx.pxd -> build/lib.linux-x86_64-3.8/pysam
copying pysam/libchtslib.pxd -> build/lib.linux-x86_64-3.8/pysam
copying pysam/libcsamfile.pxd -> build/lib.linux-x86_64-3.8/pysam
copying pysam/libcsamtools.pxd -> build/lib.linux-x86_64-3.8/pysam
copying pysam/libctabix.pxd -> build/lib.linux-x86_64-3.8/pysam
copying pysam/libctabixproxies.pxd -> build/lib.linux-x86_64-3.8/pysam
copying pysam/libcutils.pxd -> build/lib.linux-x86_64-3.8/pysam
copying pysam/libcvcf.pxd -> build/lib.linux-x86_64-3.8/pysam
copying pysam/cbcftools_util.h -> build/lib.linux-x86_64-3.8/pysam
copying pysam/csamtools_util.h -> build/lib.linux-x86_64-3.8/pysam
copying pysam/htslib_util.h -> build/lib.linux-x86_64-3.8/pysam
copying pysam/pysam_stream.h -> build/lib.linux-x86_64-3.8/pysam
copying pysam/pysam_util.h -> build/lib.linux-x86_64-3.8/pysam
creating build/lib.linux-x86_64-3.8/pysam/include/samtools
copying samtools/bam.h -> build/lib.linux-x86_64-3.8/pysam/include/samtools
copying samtools/bam2bcf.h -> build/lib.linux-x86_64-3.8/pysam/include/samtools
copying samtools/bam_endian.h -> build/lib.linux-x86_64-3.8/pysam/include/samtools
copying samtools/bam_lpileup.h -> build/lib.linux-x86_64-3.8/pysam/include/samtools
copying samtools/bam_plbuf.h -> build/lib.linux-x86_64-3.8/pysam/include/samtools
copying samtools/bedidx.h -> build/lib.linux-x86_64-3.8/pysam/include/samtools
copying samtools/sam.h -> build/lib.linux-x86_64-3.8/pysam/include/samtools
copying samtools/sam_header.h -> build/lib.linux-x86_64-3.8/pysam/include/samtools
copying samtools/sam_opts.h -> build/lib.linux-x86_64-3.8/pysam/include/samtools
copying samtools/sample.h -> build/lib.linux-x86_64-3.8/pysam/include/samtools
copying samtools/samtools.h -> build/lib.linux-x86_64-3.8/pysam/include/samtools
copying samtools/samtools.pysam.h -> build/lib.linux-x86_64-3.8/pysam/include/samtools
copying samtools/stats_isize.h -> build/lib.linux-x86_64-3.8/pysam/include/samtools
copying samtools/tmp_file.h -> build/lib.linux-x86_64-3.8/pysam/include/samtools
copying samtools/version.h -> build/lib.linux-x86_64-3.8/pysam/include/samtools
copying samtools/config.h -> build/lib.linux-x86_64-3.8/pysam/include/samtools
creating build/lib.linux-x86_64-3.8/pysam/include/bcftools
copying bcftools/HMM.h -> build/lib.linux-x86_64-3.8/pysam/include/bcftools
copying bcftools/bam2bcf.h -> build/lib.linux-x86_64-3.8/pysam/include/bcftools
copying bcftools/bam_sample.h -> build/lib.linux-x86_64-3.8/pysam/include/bcftools
copying bcftools/bcftools.h -> build/lib.linux-x86_64-3.8/pysam/include/bcftools
copying bcftools/bcftools.pysam.h -> build/lib.linux-x86_64-3.8/pysam/include/bcftools
copying bcftools/bin.h -> build/lib.linux-x86_64-3.8/pysam/include/bcftools
copying bcftools/call.h -> build/lib.linux-x86_64-3.8/pysam/include/bcftools
copying bcftools/convert.h -> build/lib.linux-x86_64-3.8/pysam/include/bcftools
copying bcftools/filter.h -> build/lib.linux-x86_64-3.8/pysam/include/bcftools
copying bcftools/gvcf.h -> build/lib.linux-x86_64-3.8/pysam/include/bcftools
copying bcftools/hclust.h -> build/lib.linux-x86_64-3.8/pysam/include/bcftools
copying bcftools/khash_str2str.h -> build/lib.linux-x86_64-3.8/pysam/include/bcftools
copying bcftools/kheap.h -> build/lib.linux-x86_64-3.8/pysam/include/bcftools
copying bcftools/kmin.h -> build/lib.linux-x86_64-3.8/pysam/include/bcftools
copying bcftools/mw.h -> build/lib.linux-x86_64-3.8/pysam/include/bcftools
copying bcftools/ploidy.h -> build/lib.linux-x86_64-3.8/pysam/include/bcftools
copying bcftools/prob1.h -> build/lib.linux-x86_64-3.8/pysam/include/bcftools
copying bcftools/rbuf.h -> build/lib.linux-x86_64-3.8/pysam/include/bcftools
copying bcftools/regidx.h -> build/lib.linux-x86_64-3.8/pysam/include/bcftools
copying bcftools/smpl_ilist.h -> build/lib.linux-x86_64-3.8/pysam/include/bcftools
copying bcftools/tsv2vcf.h -> build/lib.linux-x86_64-3.8/pysam/include/bcftools
copying bcftools/vcfbuf.h -> build/lib.linux-x86_64-3.8/pysam/include/bcftools
copying bcftools/vcmp.h -> build/lib.linux-x86_64-3.8/pysam/include/bcftools
copying bcftools/version.h -> build/lib.linux-x86_64-3.8/pysam/include/bcftools
copying bcftools/config.h -> build/lib.linux-x86_64-3.8/pysam/include/bcftools
creating build/lib.linux-x86_64-3.8/pysam/include/samtools/win32
copying samtools/win32/xcurses.h -> build/lib.linux-x86_64-3.8/pysam/include/samtools/win32
copying samtools/win32/zconf.h -> build/lib.linux-x86_64-3.8/pysam/include/samtools/win32
copying samtools/win32/zlib.h -> build/lib.linux-x86_64-3.8/pysam/include/samtools/win32
creating build/lib.linux-x86_64-3.8/pysam/include/htslib
copying htslib/bcf_sr_sort.h -> build/lib.linux-x86_64-3.8/pysam/include/htslib
copying htslib/hfile_internal.h -> build/lib.linux-x86_64-3.8/pysam/include/htslib
copying htslib/hts_internal.h -> build/lib.linux-x86_64-3.8/pysam/include/htslib
copying htslib/textutils_internal.h -> build/lib.linux-x86_64-3.8/pysam/include/htslib
copying htslib/thread_pool_internal.h -> build/lib.linux-x86_64-3.8/pysam/include/htslib
copying htslib/version.h -> build/lib.linux-x86_64-3.8/pysam/include/htslib
copying htslib/config.h -> build/lib.linux-x86_64-3.8/pysam/include/htslib
creating build/lib.linux-x86_64-3.8/pysam/include/htslib/htslib
copying htslib/htslib/bgzf.h -> build/lib.linux-x86_64-3.8/pysam/include/htslib/htslib
copying htslib/htslib/cram.h -> build/lib.linux-x86_64-3.8/pysam/include/htslib/htslib
copying htslib/htslib/faidx.h -> build/lib.linux-x86_64-3.8/pysam/include/htslib/htslib
copying htslib/htslib/hfile.h -> build/lib.linux-x86_64-3.8/pysam/include/htslib/htslib
copying htslib/htslib/hts.h -> build/lib.linux-x86_64-3.8/pysam/include/htslib/htslib
copying htslib/htslib/hts_defs.h -> build/lib.linux-x86_64-3.8/pysam/include/htslib/htslib
copying htslib/htslib/hts_endian.h -> build/lib.linux-x86_64-3.8/pysam/include/htslib/htslib
copying htslib/htslib/hts_log.h -> build/lib.linux-x86_64-3.8/pysam/include/htslib/htslib
copying htslib/htslib/hts_os.h -> build/lib.linux-x86_64-3.8/pysam/include/htslib/htslib
copying htslib/htslib/kbitset.h -> build/lib.linux-x86_64-3.8/pysam/include/htslib/htslib
copying htslib/htslib/kfunc.h -> build/lib.linux-x86_64-3.8/pysam/include/htslib/htslib
copying htslib/htslib/khash.h -> build/lib.linux-x86_64-3.8/pysam/include/htslib/htslib
copying htslib/htslib/khash_str2int.h -> build/lib.linux-x86_64-3.8/pysam/include/htslib/htslib
copying htslib/htslib/klist.h -> build/lib.linux-x86_64-3.8/pysam/include/htslib/htslib
copying htslib/htslib/knetfile.h -> build/lib.linux-x86_64-3.8/pysam/include/htslib/htslib
copying htslib/htslib/kseq.h -> build/lib.linux-x86_64-3.8/pysam/include/htslib/htslib
copying htslib/htslib/ksort.h -> build/lib.linux-x86_64-3.8/pysam/include/htslib/htslib
copying htslib/htslib/kstring.h -> build/lib.linux-x86_64-3.8/pysam/include/htslib/htslib
copying htslib/htslib/regidx.h -> build/lib.linux-x86_64-3.8/pysam/include/htslib/htslib
copying htslib/htslib/sam.h -> build/lib.linux-x86_64-3.8/pysam/include/htslib/htslib
copying htslib/htslib/synced_bcf_reader.h -> build/lib.linux-x86_64-3.8/pysam/include/htslib/htslib
copying htslib/htslib/tbx.h -> build/lib.linux-x86_64-3.8/pysam/include/htslib/htslib
copying htslib/htslib/thread_pool.h -> build/lib.linux-x86_64-3.8/pysam/include/htslib/htslib
copying htslib/htslib/vcf.h -> build/lib.linux-x86_64-3.8/pysam/include/htslib/htslib
copying htslib/htslib/vcf_sweep.h -> build/lib.linux-x86_64-3.8/pysam/include/htslib/htslib
copying htslib/htslib/vcfutils.h -> build/lib.linux-x86_64-3.8/pysam/include/htslib/htslib
Fixing build/lib.linux-x86_64-3.8/pysam/Pileup.py build/lib.linux-x86_64-3.8/pysam/__init__.py build/lib.linux-x86_64-3.8/pysam/bcftools.py build/lib.linux-x86_64-3.8/pysam/config.py build/lib.linux-x86_64-3.8/pysam/samtools.py build/lib.linux-x86_64-3.8/pysam/utils.py build/lib.linux-x86_64-3.8/pysam/version.py build/lib.linux-x86_64-3.8/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_64-3.8/pysam/Pileup.py build/lib.linux-x86_64-3.8/pysam/__init__.py build/lib.linux-x86_64-3.8/pysam/bcftools.py build/lib.linux-x86_64-3.8/pysam/config.py build/lib.linux-x86_64-3.8/pysam/samtools.py build/lib.linux-x86_64-3.8/pysam/utils.py build/lib.linux-x86_64-3.8/pysam/version.py build/lib.linux-x86_64-3.8/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
cythoning pysam/libchtslib.pyx to pysam/libchtslib.c
/home/myourshaw/.virtualenvs/python38/lib/python3.8/site-packages/Cython/Compiler/Main.py:369: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /tmp/pip-install-2vtoq395/pysam/pysam/libchtslib.pxd
tree = Parsing.p_module(s, pxd, full_module_name)
skipping 'pysam/libcsamtools.c' Cython extension (up-to-date)
skipping 'pysam/libcbcftools.c' Cython extension (up-to-date)
cythoning pysam/libcutils.pyx to pysam/libcutils.c
/home/myourshaw/.virtualenvs/python38/lib/python3.8/site-packages/Cython/Compiler/Main.py:369: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /tmp/pip-install-2vtoq395/pysam/pysam/libcutils.pxd
tree = Parsing.p_module(s, pxd, full_module_name)
cythoning pysam/libcalignmentfile.pyx to pysam/libcalignmentfile.c
/home/myourshaw/.virtualenvs/python38/lib/python3.8/site-packages/Cython/Compiler/Main.py:369: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /tmp/pip-install-2vtoq395/pysam/pysam/libcalignmentfile.pxd
tree = Parsing.p_module(s, pxd, full_module_name)
warning: pysam/libcalignmentfile.pyx:2530:49: Casting a GIL-requiring function into a nogil function circumvents GIL validation
warning: pysam/libcalignmentfile.pyx:2535:49: Casting a GIL-requiring function into a nogil function circumvents GIL validation
warning: pysam/libcalignmentfile.pyx:2540:49: Casting a GIL-requiring function into a nogil function circumvents GIL validation
skipping 'pysam/libcsamfile.c' Cython extension (up-to-date)
skipping 'pysam/libcalignedsegment.c' Cython extension (up-to-date)
skipping 'pysam/libctabix.c' Cython extension (up-to-date)
skipping 'pysam/libcfaidx.c' Cython extension (up-to-date)
cythoning pysam/libcbcf.pyx to pysam/libcbcf.c
/home/myourshaw/.virtualenvs/python38/lib/python3.8/site-packages/Cython/Compiler/Main.py:369: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /tmp/pip-install-2vtoq395/pysam/pysam/libcbcf.pxd
tree = Parsing.p_module(s, pxd, full_module_name)
skipping 'pysam/libcbgzf.c' Cython extension (up-to-date)
skipping 'pysam/libctabixproxies.c' Cython extension (up-to-date)
skipping 'pysam/libcvcf.c' Cython extension (up-to-date)
building 'pysam.libchtslib' extension
creating build/temp.linux-x86_64-3.8
creating build/temp.linux-x86_64-3.8/pysam
creating build/temp.linux-x86_64-3.8/htslib
creating build/temp.linux-x86_64-3.8/htslib/cram
gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -fPIC -I/tmp/pip-install-2vtoq395/pysam/htslib -I/tmp/pip-install-2vtoq395/pysam/samtools -I/tmp/pip-install-2vtoq395/pysam/samtools/lz4 -I/tmp/pip-install-2vtoq395/pysam/bcftools -I/tmp/pip-install-2vtoq395/pysam/pysam -I/tmp/pip-install-2vtoq395/pysam -I/home/myourshaw/.virtualenvs/python38/include -I/home/myourshaw/.local/include/python3.8 -c pysam/libchtslib.c -o build/temp.linux-x86_64-3.8/pysam/libchtslib.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -fPIC -I/tmp/pip-install-2vtoq395/pysam/htslib -I/tmp/pip-install-2vtoq395/pysam/samtools -I/tmp/pip-install-2vtoq395/pysam/samtools/lz4 -I/tmp/pip-install-2vtoq395/pysam/bcftools -I/tmp/pip-install-2vtoq395/pysam/pysam -I/tmp/pip-install-2vtoq395/pysam -I/home/myourshaw/.virtualenvs/python38/include -I/home/myourshaw/.local/include/python3.8 -c pysam/htslib_util.c -o build/temp.linux-x86_64-3.8/pysam/htslib_util.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -fPIC -I/tmp/pip-install-2vtoq395/pysam/htslib -I/tmp/pip-install-2vtoq395/pysam/samtools -I/tmp/pip-install-2vtoq395/pysam/samtools/lz4 -I/tmp/pip-install-2vtoq395/pysam/bcftools -I/tmp/pip-install-2vtoq395/pysam/pysam -I/tmp/pip-install-2vtoq395/pysam -I/home/myourshaw/.virtualenvs/python38/include -I/home/myourshaw/.local/include/python3.8 -c htslib/kfunc.c -o build/temp.linux-x86_64-3.8/htslib/kfunc.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -fPIC -I/tmp/pip-install-2vtoq395/pysam/htslib -I/tmp/pip-install-2vtoq395/pysam/samtools -I/tmp/pip-install-2vtoq395/pysam/samtools/lz4 -I/tmp/pip-install-2vtoq395/pysam/bcftools -I/tmp/pip-install-2vtoq395/pysam/pysam -I/tmp/pip-install-2vtoq395/pysam -I/home/myourshaw/.virtualenvs/python38/include -I/home/myourshaw/.local/include/python3.8 -c htslib/knetfile.c -o build/temp.linux-x86_64-3.8/htslib/knetfile.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -fPIC -I/tmp/pip-install-2vtoq395/pysam/htslib -I/tmp/pip-install-2vtoq395/pysam/samtools -I/tmp/pip-install-2vtoq395/pysam/samtools/lz4 -I/tmp/pip-install-2vtoq395/pysam/bcftools -I/tmp/pip-install-2vtoq395/pysam/pysam -I/tmp/pip-install-2vtoq395/pysam -I/home/myourshaw/.virtualenvs/python38/include -I/home/myourshaw/.local/include/python3.8 -c htslib/kstring.c -o build/temp.linux-x86_64-3.8/htslib/kstring.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -fPIC -I/tmp/pip-install-2vtoq395/pysam/htslib -I/tmp/pip-install-2vtoq395/pysam/samtools -I/tmp/pip-install-2vtoq395/pysam/samtools/lz4 -I/tmp/pip-install-2vtoq395/pysam/bcftools -I/tmp/pip-install-2vtoq395/pysam/pysam -I/tmp/pip-install-2vtoq395/pysam -I/home/myourshaw/.virtualenvs/python38/include -I/home/myourshaw/.local/include/python3.8 -c htslib/bcf_sr_sort.c -o build/temp.linux-x86_64-3.8/htslib/bcf_sr_sort.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -fPIC -I/tmp/pip-install-2vtoq395/pysam/htslib -I/tmp/pip-install-2vtoq395/pysam/samtools -I/tmp/pip-install-2vtoq395/pysam/samtools/lz4 -I/tmp/pip-install-2vtoq395/pysam/bcftools -I/tmp/pip-install-2vtoq395/pysam/pysam -I/tmp/pip-install-2vtoq395/pysam -I/home/myourshaw/.virtualenvs/python38/include -I/home/myourshaw/.local/include/python3.8 -c htslib/bgzf.c -o build/temp.linux-x86_64-3.8/htslib/bgzf.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -fPIC -I/tmp/pip-install-2vtoq395/pysam/htslib -I/tmp/pip-install-2vtoq395/pysam/samtools -I/tmp/pip-install-2vtoq395/pysam/samtools/lz4 -I/tmp/pip-install-2vtoq395/pysam/bcftools -I/tmp/pip-install-2vtoq395/pysam/pysam -I/tmp/pip-install-2vtoq395/pysam -I/home/myourshaw/.virtualenvs/python38/include -I/home/myourshaw/.local/include/python3.8 -c htslib/errmod.c -o build/temp.linux-x86_64-3.8/htslib/errmod.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -fPIC -I/tmp/pip-install-2vtoq395/pysam/htslib -I/tmp/pip-install-2vtoq395/pysam/samtools -I/tmp/pip-install-2vtoq395/pysam/samtools/lz4 -I/tmp/pip-install-2vtoq395/pysam/bcftools -I/tmp/pip-install-2vtoq395/pysam/pysam -I/tmp/pip-install-2vtoq395/pysam -I/home/myourshaw/.virtualenvs/python38/include -I/home/myourshaw/.local/include/python3.8 -c htslib/faidx.c -o build/temp.linux-x86_64-3.8/htslib/faidx.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -fPIC -I/tmp/pip-install-2vtoq395/pysam/htslib -I/tmp/pip-install-2vtoq395/pysam/samtools -I/tmp/pip-install-2vtoq395/pysam/samtools/lz4 -I/tmp/pip-install-2vtoq395/pysam/bcftools -I/tmp/pip-install-2vtoq395/pysam/pysam -I/tmp/pip-install-2vtoq395/pysam -I/home/myourshaw/.virtualenvs/python38/include -I/home/myourshaw/.local/include/python3.8 -c htslib/hfile.c -o build/temp.linux-x86_64-3.8/htslib/hfile.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -fPIC -I/tmp/pip-install-2vtoq395/pysam/htslib -I/tmp/pip-install-2vtoq395/pysam/samtools -I/tmp/pip-install-2vtoq395/pysam/samtools/lz4 -I/tmp/pip-install-2vtoq395/pysam/bcftools -I/tmp/pip-install-2vtoq395/pysam/pysam -I/tmp/pip-install-2vtoq395/pysam -I/home/myourshaw/.virtualenvs/python38/include -I/home/myourshaw/.local/include/python3.8 -c htslib/hfile_net.c -o build/temp.linux-x86_64-3.8/htslib/hfile_net.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -fPIC -I/tmp/pip-install-2vtoq395/pysam/htslib -I/tmp/pip-install-2vtoq395/pysam/samtools -I/tmp/pip-install-2vtoq395/pysam/samtools/lz4 -I/tmp/pip-install-2vtoq395/pysam/bcftools -I/tmp/pip-install-2vtoq395/pysam/pysam -I/tmp/pip-install-2vtoq395/pysam -I/home/myourshaw/.virtualenvs/python38/include -I/home/myourshaw/.local/include/python3.8 -c htslib/hts.c -o build/temp.linux-x86_64-3.8/htslib/hts.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -fPIC -I/tmp/pip-install-2vtoq395/pysam/htslib -I/tmp/pip-install-2vtoq395/pysam/samtools -I/tmp/pip-install-2vtoq395/pysam/samtools/lz4 -I/tmp/pip-install-2vtoq395/pysam/bcftools -I/tmp/pip-install-2vtoq395/pysam/pysam -I/tmp/pip-install-2vtoq395/pysam -I/home/myourshaw/.virtualenvs/python38/include -I/home/myourshaw/.local/include/python3.8 -c htslib/hts_os.c -o build/temp.linux-x86_64-3.8/htslib/hts_os.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -fPIC -I/tmp/pip-install-2vtoq395/pysam/htslib -I/tmp/pip-install-2vtoq395/pysam/samtools -I/tmp/pip-install-2vtoq395/pysam/samtools/lz4 -I/tmp/pip-install-2vtoq395/pysam/bcftools -I/tmp/pip-install-2vtoq395/pysam/pysam -I/tmp/pip-install-2vtoq395/pysam -I/home/myourshaw/.virtualenvs/python38/include -I/home/myourshaw/.local/include/python3.8 -c htslib/md5.c -o build/temp.linux-x86_64-3.8/htslib/md5.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -fPIC -I/tmp/pip-install-2vtoq395/pysam/htslib -I/tmp/pip-install-2vtoq395/pysam/samtools -I/tmp/pip-install-2vtoq395/pysam/samtools/lz4 -I/tmp/pip-install-2vtoq395/pysam/bcftools -I/tmp/pip-install-2vtoq395/pysam/pysam -I/tmp/pip-install-2vtoq395/pysam -I/home/myourshaw/.virtualenvs/python38/include -I/home/myourshaw/.local/include/python3.8 -c htslib/multipart.c -o build/temp.linux-x86_64-3.8/htslib/multipart.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -fPIC -I/tmp/pip-install-2vtoq395/pysam/htslib -I/tmp/pip-install-2vtoq395/pysam/samtools -I/tmp/pip-install-2vtoq395/pysam/samtools/lz4 -I/tmp/pip-install-2vtoq395/pysam/bcftools -I/tmp/pip-install-2vtoq395/pysam/pysam -I/tmp/pip-install-2vtoq395/pysam -I/home/myourshaw/.virtualenvs/python38/include -I/home/myourshaw/.local/include/python3.8 -c htslib/probaln.c -o build/temp.linux-x86_64-3.8/htslib/probaln.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -fPIC -I/tmp/pip-install-2vtoq395/pysam/htslib -I/tmp/pip-install-2vtoq395/pysam/samtools -I/tmp/pip-install-2vtoq395/pysam/samtools/lz4 -I/tmp/pip-install-2vtoq395/pysam/bcftools -I/tmp/pip-install-2vtoq395/pysam/pysam -I/tmp/pip-install-2vtoq395/pysam -I/home/myourshaw/.virtualenvs/python38/include -I/home/myourshaw/.local/include/python3.8 -c htslib/realn.c -o build/temp.linux-x86_64-3.8/htslib/realn.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -fPIC -I/tmp/pip-install-2vtoq395/pysam/htslib -I/tmp/pip-install-2vtoq395/pysam/samtools -I/tmp/pip-install-2vtoq395/pysam/samtools/lz4 -I/tmp/pip-install-2vtoq395/pysam/bcftools -I/tmp/pip-install-2vtoq395/pysam/pysam -I/tmp/pip-install-2vtoq395/pysam -I/home/myourshaw/.virtualenvs/python38/include -I/home/myourshaw/.local/include/python3.8 -c htslib/regidx.c -o build/temp.linux-x86_64-3.8/htslib/regidx.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -fPIC -I/tmp/pip-install-2vtoq395/pysam/htslib -I/tmp/pip-install-2vtoq395/pysam/samtools -I/tmp/pip-install-2vtoq395/pysam/samtools/lz4 -I/tmp/pip-install-2vtoq395/pysam/bcftools -I/tmp/pip-install-2vtoq395/pysam/pysam -I/tmp/pip-install-2vtoq395/pysam -I/home/myourshaw/.virtualenvs/python38/include -I/home/myourshaw/.local/include/python3.8 -c htslib/sam.c -o build/temp.linux-x86_64-3.8/htslib/sam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -fPIC -I/tmp/pip-install-2vtoq395/pysam/htslib -I/tmp/pip-install-2vtoq395/pysam/samtools -I/tmp/pip-install-2vtoq395/pysam/samtools/lz4 -I/tmp/pip-install-2vtoq395/pysam/bcftools -I/tmp/pip-install-2vtoq395/pysam/pysam -I/tmp/pip-install-2vtoq395/pysam -I/home/myourshaw/.virtualenvs/python38/include -I/home/myourshaw/.local/include/python3.8 -c htslib/synced_bcf_reader.c -o build/temp.linux-x86_64-3.8/htslib/synced_bcf_reader.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -fPIC -I/tmp/pip-install-2vtoq395/pysam/htslib -I/tmp/pip-install-2vtoq395/pysam/samtools -I/tmp/pip-install-2vtoq395/pysam/samtools/lz4 -I/tmp/pip-install-2vtoq395/pysam/bcftools -I/tmp/pip-install-2vtoq395/pysam/pysam -I/tmp/pip-install-2vtoq395/pysam -I/home/myourshaw/.virtualenvs/python38/include -I/home/myourshaw/.local/include/python3.8 -c htslib/vcf_sweep.c -o build/temp.linux-x86_64-3.8/htslib/vcf_sweep.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -fPIC -I/tmp/pip-install-2vtoq395/pysam/htslib -I/tmp/pip-install-2vtoq395/pysam/samtools -I/tmp/pip-install-2vtoq395/pysam/samtools/lz4 -I/tmp/pip-install-2vtoq395/pysam/bcftools -I/tmp/pip-install-2vtoq395/pysam/pysam -I/tmp/pip-install-2vtoq395/pysam -I/home/myourshaw/.virtualenvs/python38/include -I/home/myourshaw/.local/include/python3.8 -c htslib/tbx.c -o build/temp.linux-x86_64-3.8/htslib/tbx.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -fPIC -I/tmp/pip-install-2vtoq395/pysam/htslib -I/tmp/pip-install-2vtoq395/pysam/samtools -I/tmp/pip-install-2vtoq395/pysam/samtools/lz4 -I/tmp/pip-install-2vtoq395/pysam/bcftools -I/tmp/pip-install-2vtoq395/pysam/pysam -I/tmp/pip-install-2vtoq395/pysam -I/home/myourshaw/.virtualenvs/python38/include -I/home/myourshaw/.local/include/python3.8 -c htslib/textutils.c -o build/temp.linux-x86_64-3.8/htslib/textutils.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -fPIC -I/tmp/pip-install-2vtoq395/pysam/htslib -I/tmp/pip-install-2vtoq395/pysam/samtools -I/tmp/pip-install-2vtoq395/pysam/samtools/lz4 -I/tmp/pip-install-2vtoq395/pysam/bcftools -I/tmp/pip-install-2vtoq395/pysam/pysam -I/tmp/pip-install-2vtoq395/pysam -I/home/myourshaw/.virtualenvs/python38/include -I/home/myourshaw/.local/include/python3.8 -c htslib/thread_pool.c -o build/temp.linux-x86_64-3.8/htslib/thread_pool.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -fPIC -I/tmp/pip-install-2vtoq395/pysam/htslib -I/tmp/pip-install-2vtoq395/pysam/samtools -I/tmp/pip-install-2vtoq395/pysam/samtools/lz4 -I/tmp/pip-install-2vtoq395/pysam/bcftools -I/tmp/pip-install-2vtoq395/pysam/pysam -I/tmp/pip-install-2vtoq395/pysam -I/home/myourshaw/.virtualenvs/python38/include -I/home/myourshaw/.local/include/python3.8 -c htslib/vcf.c -o build/temp.linux-x86_64-3.8/htslib/vcf.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -fPIC -I/tmp/pip-install-2vtoq395/pysam/htslib -I/tmp/pip-install-2vtoq395/pysam/samtools -I/tmp/pip-install-2vtoq395/pysam/samtools/lz4 -I/tmp/pip-install-2vtoq395/pysam/bcftools -I/tmp/pip-install-2vtoq395/pysam/pysam -I/tmp/pip-install-2vtoq395/pysam -I/home/myourshaw/.virtualenvs/python38/include -I/home/myourshaw/.local/include/python3.8 -c htslib/vcfutils.c -o build/temp.linux-x86_64-3.8/htslib/vcfutils.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -fPIC -I/tmp/pip-install-2vtoq395/pysam/htslib -I/tmp/pip-install-2vtoq395/pysam/samtools -I/tmp/pip-install-2vtoq395/pysam/samtools/lz4 -I/tmp/pip-install-2vtoq395/pysam/bcftools -I/tmp/pip-install-2vtoq395/pysam/pysam -I/tmp/pip-install-2vtoq395/pysam -I/home/myourshaw/.virtualenvs/python38/include -I/home/myourshaw/.local/include/python3.8 -c htslib/cram/cram_codecs.c -o build/temp.linux-x86_64-3.8/htslib/cram/cram_codecs.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -fPIC -I/tmp/pip-install-2vtoq395/pysam/htslib -I/tmp/pip-install-2vtoq395/pysam/samtools -I/tmp/pip-install-2vtoq395/pysam/samtools/lz4 -I/tmp/pip-install-2vtoq395/pysam/bcftools -I/tmp/pip-install-2vtoq395/pysam/pysam -I/tmp/pip-install-2vtoq395/pysam -I/home/myourshaw/.virtualenvs/python38/include -I/home/myourshaw/.local/include/python3.8 -c htslib/cram/cram_decode.c -o build/temp.linux-x86_64-3.8/htslib/cram/cram_decode.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -fPIC -I/tmp/pip-install-2vtoq395/pysam/htslib -I/tmp/pip-install-2vtoq395/pysam/samtools -I/tmp/pip-install-2vtoq395/pysam/samtools/lz4 -I/tmp/pip-install-2vtoq395/pysam/bcftools -I/tmp/pip-install-2vtoq395/pysam/pysam -I/tmp/pip-install-2vtoq395/pysam -I/home/myourshaw/.virtualenvs/python38/include -I/home/myourshaw/.local/include/python3.8 -c htslib/cram/cram_encode.c -o build/temp.linux-x86_64-3.8/htslib/cram/cram_encode.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -fPIC -I/tmp/pip-install-2vtoq395/pysam/htslib -I/tmp/pip-install-2vtoq395/pysam/samtools -I/tmp/pip-install-2vtoq395/pysam/samtools/lz4 -I/tmp/pip-install-2vtoq395/pysam/bcftools -I/tmp/pip-install-2vtoq395/pysam/pysam -I/tmp/pip-install-2vtoq395/pysam -I/home/myourshaw/.virtualenvs/python38/include -I/home/myourshaw/.local/include/python3.8 -c htslib/cram/cram_external.c -o build/temp.linux-x86_64-3.8/htslib/cram/cram_external.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -fPIC -I/tmp/pip-install-2vtoq395/pysam/htslib -I/tmp/pip-install-2vtoq395/pysam/samtools -I/tmp/pip-install-2vtoq395/pysam/samtools/lz4 -I/tmp/pip-install-2vtoq395/pysam/bcftools -I/tmp/pip-install-2vtoq395/pysam/pysam -I/tmp/pip-install-2vtoq395/pysam -I/home/myourshaw/.virtualenvs/python38/include -I/home/myourshaw/.local/include/python3.8 -c htslib/cram/cram_index.c -o build/temp.linux-x86_64-3.8/htslib/cram/cram_index.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -fPIC -I/tmp/pip-install-2vtoq395/pysam/htslib -I/tmp/pip-install-2vtoq395/pysam/samtools -I/tmp/pip-install-2vtoq395/pysam/samtools/lz4 -I/tmp/pip-install-2vtoq395/pysam/bcftools -I/tmp/pip-install-2vtoq395/pysam/pysam -I/tmp/pip-install-2vtoq395/pysam -I/home/myourshaw/.virtualenvs/python38/include -I/home/myourshaw/.local/include/python3.8 -c htslib/cram/cram_io.c -o build/temp.linux-x86_64-3.8/htslib/cram/cram_io.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
In function ‘full_path’,
inlined from ‘cram_write_SAM_hdr’ at htslib/cram/cram_io.c:3823:17:
htslib/cram/cram_io.c:3748:13: warning: ‘strncpy’ specified bound 4096 equals destination size [-Wstringop-truncation]
strncpy(out, in, PATH_MAX);
^~~~~~~~~~~~~~~~~~~~~~~~~~
htslib/cram/cram_io.c:3740:9: warning: ‘strncpy’ specified bound 4096 equals destination size [-Wstringop-truncation]
strncpy(out, in, PATH_MAX);
^~~~~~~~~~~~~~~~~~~~~~~~~~
gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -fPIC -I/tmp/pip-install-2vtoq395/pysam/htslib -I/tmp/pip-install-2vtoq395/pysam/samtools -I/tmp/pip-install-2vtoq395/pysam/samtools/lz4 -I/tmp/pip-install-2vtoq395/pysam/bcftools -I/tmp/pip-install-2vtoq395/pysam/pysam -I/tmp/pip-install-2vtoq395/pysam -I/home/myourshaw/.virtualenvs/python38/include -I/home/myourshaw/.local/include/python3.8 -c htslib/cram/cram_samtools.c -o build/temp.linux-x86_64-3.8/htslib/cram/cram_samtools.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -fPIC -I/tmp/pip-install-2vtoq395/pysam/htslib -I/tmp/pip-install-2vtoq395/pysam/samtools -I/tmp/pip-install-2vtoq395/pysam/samtools/lz4 -I/tmp/pip-install-2vtoq395/pysam/bcftools -I/tmp/pip-install-2vtoq395/pysam/pysam -I/tmp/pip-install-2vtoq395/pysam -I/home/myourshaw/.virtualenvs/python38/include -I/home/myourshaw/.local/include/python3.8 -c htslib/cram/cram_stats.c -o build/temp.linux-x86_64-3.8/htslib/cram/cram_stats.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -fPIC -I/tmp/pip-install-2vtoq395/pysam/htslib -I/tmp/pip-install-2vtoq395/pysam/samtools -I/tmp/pip-install-2vtoq395/pysam/samtools/lz4 -I/tmp/pip-install-2vtoq395/pysam/bcftools -I/tmp/pip-install-2vtoq395/pysam/pysam -I/tmp/pip-install-2vtoq395/pysam -I/home/myourshaw/.virtualenvs/python38/include -I/home/myourshaw/.local/include/python3.8 -c htslib/cram/files.c -o build/temp.linux-x86_64-3.8/htslib/cram/files.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -fPIC -I/tmp/pip-install-2vtoq395/pysam/htslib -I/tmp/pip-install-2vtoq395/pysam/samtools -I/tmp/pip-install-2vtoq395/pysam/samtools/lz4 -I/tmp/pip-install-2vtoq395/pysam/bcftools -I/tmp/pip-install-2vtoq395/pysam/pysam -I/tmp/pip-install-2vtoq395/pysam -I/home/myourshaw/.virtualenvs/python38/include -I/home/myourshaw/.local/include/python3.8 -c htslib/cram/mFILE.c -o build/temp.linux-x86_64-3.8/htslib/cram/mFILE.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -fPIC -I/tmp/pip-install-2vtoq395/pysam/htslib -I/tmp/pip-install-2vtoq395/pysam/samtools -I/tmp/pip-install-2vtoq395/pysam/samtools/lz4 -I/tmp/pip-install-2vtoq395/pysam/bcftools -I/tmp/pip-install-2vtoq395/pysam/pysam -I/tmp/pip-install-2vtoq395/pysam -I/home/myourshaw/.virtualenvs/python38/include -I/home/myourshaw/.local/include/python3.8 -c htslib/cram/open_trace_file.c -o build/temp.linux-x86_64-3.8/htslib/cram/open_trace_file.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -fPIC -I/tmp/pip-install-2vtoq395/pysam/htslib -I/tmp/pip-install-2vtoq395/pysam/samtools -I/tmp/pip-install-2vtoq395/pysam/samtools/lz4 -I/tmp/pip-install-2vtoq395/pysam/bcftools -I/tmp/pip-install-2vtoq395/pysam/pysam -I/tmp/pip-install-2vtoq395/pysam -I/home/myourshaw/.virtualenvs/python38/include -I/home/myourshaw/.local/include/python3.8 -c htslib/cram/pooled_alloc.c -o build/temp.linux-x86_64-3.8/htslib/cram/pooled_alloc.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -fPIC -I/tmp/pip-install-2vtoq395/pysam/htslib -I/tmp/pip-install-2vtoq395/pysam/samtools -I/tmp/pip-install-2vtoq395/pysam/samtools/lz4 -I/tmp/pip-install-2vtoq395/pysam/bcftools -I/tmp/pip-install-2vtoq395/pysam/pysam -I/tmp/pip-install-2vtoq395/pysam -I/home/myourshaw/.virtualenvs/python38/include -I/home/myourshaw/.local/include/python3.8 -c htslib/cram/rANS_static.c -o build/temp.linux-x86_64-3.8/htslib/cram/rANS_static.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -fPIC -I/tmp/pip-install-2vtoq395/pysam/htslib -I/tmp/pip-install-2vtoq395/pysam/samtools -I/tmp/pip-install-2vtoq395/pysam/samtools/lz4 -I/tmp/pip-install-2vtoq395/pysam/bcftools -I/tmp/pip-install-2vtoq395/pysam/pysam -I/tmp/pip-install-2vtoq395/pysam -I/home/myourshaw/.virtualenvs/python38/include -I/home/myourshaw/.local/include/python3.8 -c htslib/cram/sam_header.c -o build/temp.linux-x86_64-3.8/htslib/cram/sam_header.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -fPIC -I/tmp/pip-install-2vtoq395/pysam/htslib -I/tmp/pip-install-2vtoq395/pysam/samtools -I/tmp/pip-install-2vtoq395/pysam/samtools/lz4 -I/tmp/pip-install-2vtoq395/pysam/bcftools -I/tmp/pip-install-2vtoq395/pysam/pysam -I/tmp/pip-install-2vtoq395/pysam -I/home/myourshaw/.virtualenvs/python38/include -I/home/myourshaw/.local/include/python3.8 -c htslib/cram/string_alloc.c -o build/temp.linux-x86_64-3.8/htslib/cram/string_alloc.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -fPIC -I/tmp/pip-install-2vtoq395/pysam/htslib -I/tmp/pip-install-2vtoq395/pysam/samtools -I/tmp/pip-install-2vtoq395/pysam/samtools/lz4 -I/tmp/pip-install-2vtoq395/pysam/bcftools -I/tmp/pip-install-2vtoq395/pysam/pysam -I/tmp/pip-install-2vtoq395/pysam -I/home/myourshaw/.virtualenvs/python38/include -I/home/myourshaw/.local/include/python3.8 -c htslib/hfile_libcurl.c -o build/temp.linux-x86_64-3.8/htslib/hfile_libcurl.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -fPIC -I/tmp/pip-install-2vtoq395/pysam/htslib -I/tmp/pip-install-2vtoq395/pysam/samtools -I/tmp/pip-install-2vtoq395/pysam/samtools/lz4 -I/tmp/pip-install-2vtoq395/pysam/bcftools -I/tmp/pip-install-2vtoq395/pysam/pysam -I/tmp/pip-install-2vtoq395/pysam -I/home/myourshaw/.virtualenvs/python38/include -I/home/myourshaw/.local/include/python3.8 -c htslib/hfile_gcs.c -o build/temp.linux-x86_64-3.8/htslib/hfile_gcs.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -fPIC -I/tmp/pip-install-2vtoq395/pysam/htslib -I/tmp/pip-install-2vtoq395/pysam/samtools -I/tmp/pip-install-2vtoq395/pysam/samtools/lz4 -I/tmp/pip-install-2vtoq395/pysam/bcftools -I/tmp/pip-install-2vtoq395/pysam/pysam -I/tmp/pip-install-2vtoq395/pysam -I/home/myourshaw/.virtualenvs/python38/include -I/home/myourshaw/.local/include/python3.8 -c htslib/hfile_s3.c -o build/temp.linux-x86_64-3.8/htslib/hfile_s3.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
gcc -pthread -shared -L//home/myourshaw/.local/extlib/lib -Wl,--rpath=//home/myourshaw/.local/lib -Wl,--rpath=//home/myourshaw/.local/extlib/lib build/temp.linux-x86_64-3.8/pysam/libchtslib.o build/temp.linux-x86_64-3.8/pysam/htslib_util.o build/temp.linux-x86_64-3.8/htslib/kfunc.o build/temp.linux-x86_64-3.8/htslib/knetfile.o build/temp.linux-x86_64-3.8/htslib/kstring.o build/temp.linux-x86_64-3.8/htslib/bcf_sr_sort.o build/temp.linux-x86_64-3.8/htslib/bgzf.o build/temp.linux-x86_64-3.8/htslib/errmod.o build/temp.linux-x86_64-3.8/htslib/faidx.o build/temp.linux-x86_64-3.8/htslib/hfile.o build/temp.linux-x86_64-3.8/htslib/hfile_net.o build/temp.linux-x86_64-3.8/htslib/hts.o build/temp.linux-x86_64-3.8/htslib/hts_os.o build/temp.linux-x86_64-3.8/htslib/md5.o build/temp.linux-x86_64-3.8/htslib/multipart.o build/temp.linux-x86_64-3.8/htslib/probaln.o build/temp.linux-x86_64-3.8/htslib/realn.o build/temp.linux-x86_64-3.8/htslib/regidx.o build/temp.linux-x86_64-3.8/htslib/sam.o build/temp.linux-x86_64-3.8/htslib/synced_bcf_reader.o build/temp.linux-x86_64-3.8/htslib/vcf_sweep.o build/temp.linux-x86_64-3.8/htslib/tbx.o build/temp.linux-x86_64-3.8/htslib/textutils.o build/temp.linux-x86_64-3.8/htslib/thread_pool.o build/temp.linux-x86_64-3.8/htslib/vcf.o build/temp.linux-x86_64-3.8/htslib/vcfutils.o build/temp.linux-x86_64-3.8/htslib/cram/cram_codecs.o build/temp.linux-x86_64-3.8/htslib/cram/cram_decode.o build/temp.linux-x86_64-3.8/htslib/cram/cram_encode.o build/temp.linux-x86_64-3.8/htslib/cram/cram_external.o build/temp.linux-x86_64-3.8/htslib/cram/cram_index.o build/temp.linux-x86_64-3.8/htslib/cram/cram_io.o build/temp.linux-x86_64-3.8/htslib/cram/cram_samtools.o build/temp.linux-x86_64-3.8/htslib/cram/cram_stats.o build/temp.linux-x86_64-3.8/htslib/cram/files.o build/temp.linux-x86_64-3.8/htslib/cram/mFILE.o build/temp.linux-x86_64-3.8/htslib/cram/open_trace_file.o build/temp.linux-x86_64-3.8/htslib/cram/pooled_alloc.o build/temp.linux-x86_64-3.8/htslib/cram/rANS_static.o build/temp.linux-x86_64-3.8/htslib/cram/sam_header.o build/temp.linux-x86_64-3.8/htslib/cram/string_alloc.o build/temp.linux-x86_64-3.8/htslib/hfile_libcurl.o build/temp.linux-x86_64-3.8/htslib/hfile_gcs.o build/temp.linux-x86_64-3.8/htslib/hfile_s3.o -L/tmp/pip-install-2vtoq395/pysam/pysam -L/tmp/pip-install-2vtoq395/pysam/pysam -L/tmp/pip-install-2vtoq395/pysam -L/tmp/pip-install-2vtoq395/pysam/build/lib.linux-x86_64-3.8/pysam -Lbuild/lib.linux-x86_64-3.8/pysam -L//home/myourshaw/.local/lib -lz -llzma -lbz2 -lz -lm -lcurl -lcrypto -o build/lib.linux-x86_64-3.8/pysam/libchtslib.cpython-38-x86_64-linux-gnu.so -Wl,-rpath,$ORIGIN
building 'pysam.libcsamtools' extension
creating build/temp.linux-x86_64-3.8/samtools
creating build/temp.linux-x86_64-3.8/samtools/lz4
gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -fPIC -I/tmp/pip-install-2vtoq395/pysam/htslib -I/tmp/pip-install-2vtoq395/pysam/samtools -I/tmp/pip-install-2vtoq395/pysam/samtools/lz4 -I/tmp/pip-install-2vtoq395/pysam/bcftools -I/tmp/pip-install-2vtoq395/pysam/pysam -I/tmp/pip-install-2vtoq395/pysam -I/home/myourshaw/.virtualenvs/python38/include -I/home/myourshaw/.local/include/python3.8 -c pysam/libcsamtools.c -o build/temp.linux-x86_64-3.8/pysam/libcsamtools.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
pysam/libcsamtools.c: In function ‘__Pyx_InitCachedConstants’:
/home/myourshaw/.local/include/python3.8/code.h:72:25: warning: passing argument 6 of ‘PyCode_New’ makes pointer from integer without a cast [-Wint-conversion]
#define CO_OPTIMIZED 0x0001
^
pysam/libcsamtools.c:318:37: note: in definition of macro ‘__Pyx_PyCode_New’
PyCode_New(a, 0, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos)
^
pysam/libcsamtools.c:1120:60: note: in expansion of macro ‘CO_OPTIMIZED’
__pyx_codeobj_ = (PyObject*)__Pyx_PyCode_New(0, 0, 0, 0, CO_OPTIMIZED|CO_NEWLOCALS, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_pysam_libcsamtools_pyx, __pyx_n_s_py_samtools, 1, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj_)) __PYX_ERR(0, 1, __pyx_L1_error)
^~~~~~~~~~~~
In file included from /home/myourshaw/.local/include/python3.8/compile.h:5,
from /home/myourshaw/.local/include/python3.8/Python.h:138,
from pysam/libcsamtools.c:4:
/home/myourshaw/.local/include/python3.8/code.h:122:28: note: expected ‘PyObject *’ {aka ‘struct _object *’} but argument is of type ‘int’
PyAPI_FUNC(PyCodeObject *) PyCode_New(
^~~~~~~~~~
pysam/libcsamtools.c:1120:236: warning: passing argument 14 of ‘PyCode_New’ makes integer from pointer without a cast [-Wint-conversion]
__pyx_codeobj_ = (PyObject*)__Pyx_PyCode_New(0, 0, 0, 0, CO_OPTIMIZED|CO_NEWLOCALS, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_pysam_libcsamtools_pyx, __pyx_n_s_py_samtools, 1, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj_)) __PYX_ERR(0, 1, __pyx_L1_error)
^~~~~~~~~~~~~~~~~~~~~
pysam/libcsamtools.c:318:69: note: in definition of macro ‘__Pyx_PyCode_New’
PyCode_New(a, 0, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos)
^~~~
In file included from /home/myourshaw/.local/include/python3.8/compile.h:5,
from /home/myourshaw/.local/include/python3.8/Python.h:138,
from pysam/libcsamtools.c:4:
/home/myourshaw/.local/include/python3.8/code.h:122:28: note: expected ‘int’ but argument is of type ‘PyObject *’ {aka ‘struct _object *’}
PyAPI_FUNC(PyCodeObject *) PyCode_New(
^~~~~~~~~~
pysam/libcsamtools.c:1120:259: warning: passing argument 15 of ‘PyCode_New’ makes pointer from integer without a cast [-Wint-conversion]
__pyx_codeobj_ = (PyObject*)__Pyx_PyCode_New(0, 0, 0, 0, CO_OPTIMIZED|CO_NEWLOCALS, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_pysam_libcsamtools_pyx, __pyx_n_s_py_samtools, 1, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj_)) __PYX_ERR(0, 1, __pyx_L1_error)
^
pysam/libcsamtools.c:318:75: note: in definition of macro ‘__Pyx_PyCode_New’
PyCode_New(a, 0, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos)
^~~~~
In file included from /home/myourshaw/.local/include/python3.8/compile.h:5,
from /home/myourshaw/.local/include/python3.8/Python.h:138,
from pysam/libcsamtools.c:4:
/home/myourshaw/.local/include/python3.8/code.h:122:28: note: expected ‘PyObject *’ {aka ‘struct _object *’} but argument is of type ‘int’
PyAPI_FUNC(PyCodeObject *) PyCode_New(
^~~~~~~~~~
pysam/libcsamtools.c:318:11: error: too many arguments to function ‘PyCode_New’
PyCode_New(a, 0, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos)
^~~~~~~~~~
pysam/libcsamtools.c:1120:31: note: in expansion of macro ‘__Pyx_PyCode_New’
__pyx_codeobj_ = (PyObject*)__Pyx_PyCode_New(0, 0, 0, 0, CO_OPTIMIZED|CO_NEWLOCALS, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_pysam_libcsamtools_pyx, __pyx_n_s_py_samtools, 1, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj_)) __PYX_ERR(0, 1, __pyx_L1_error)
^~~~~~~~~~~~~~~~
In file included from /home/myourshaw/.local/include/python3.8/compile.h:5,
from /home/myourshaw/.local/include/python3.8/Python.h:138,
from pysam/libcsamtools.c:4:
/home/myourshaw/.local/include/python3.8/code.h:122:28: note: declared here
PyAPI_FUNC(PyCodeObject *) PyCode_New(
^~~~~~~~~~
pysam/libcsamtools.c: In function ‘__Pyx_CreateCodeObjectForTraceback’:
pysam/libcsamtools.c:1681:9: warning: passing argument 14 of ‘PyCode_New’ makes integer from pointer without a cast [-Wint-conversion]
py_funcname, /*PyObject *name,*/
^~~~~~~~~~~
pysam/libcsamtools.c:318:69: note: in definition of macro ‘__Pyx_PyCode_New’
PyCode_New(a, 0, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos)
^~~~
In file included from /home/myourshaw/.local/include/python3.8/compile.h:5,
from /home/myourshaw/.local/include/python3.8/Python.h:138,
from pysam/libcsamtools.c:4:
/home/myourshaw/.local/include/python3.8/code.h:122:28: note: expected ‘int’ but argument is of type ‘PyObject *’ {aka ‘struct _object *’}
PyAPI_FUNC(PyCodeObject *) PyCode_New(
^~~~~~~~~~
pysam/libcsamtools.c:1682:9: warning: passing argument 15 of ‘PyCode_New’ makes pointer from integer without a cast [-Wint-conversion]
py_line,
^~~~~~~
pysam/libcsamtools.c:318:75: note: in definition of macro ‘__Pyx_PyCode_New’
PyCode_New(a, 0, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos)
^~~~~
In file included from /home/myourshaw/.local/include/python3.8/compile.h:5,
from /home/myourshaw/.local/include/python3.8/Python.h:138,
from pysam/libcsamtools.c:4:
/home/myourshaw/.local/include/python3.8/code.h:122:28: note: expected ‘PyObject *’ {aka ‘struct _object *’} but argument is of type ‘int’
PyAPI_FUNC(PyCodeObject *) PyCode_New(
^~~~~~~~~~
pysam/libcsamtools.c:318:11: error: too many arguments to function ‘PyCode_New’
PyCode_New(a, 0, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos)
^~~~~~~~~~
pysam/libcsamtools.c:1668:15: note: in expansion of macro ‘__Pyx_PyCode_New’
py_code = __Pyx_PyCode_New(
^~~~~~~~~~~~~~~~
In file included from /home/myourshaw/.local/include/python3.8/compile.h:5,
from /home/myourshaw/.local/include/python3.8/Python.h:138,
from pysam/libcsamtools.c:4:
/home/myourshaw/.local/include/python3.8/code.h:122:28: note: declared here
PyAPI_FUNC(PyCodeObject *) PyCode_New(
^~~~~~~~~~
error: command 'gcc' failed with exit status 1
----------------------------------------
ERROR: Failed building wheel for pysam
Running setup.py clean for pysam
Failed to build pysam
Installing collected packages: pysam
Running setup.py install for pysam ... error
ERROR: Command errored out with exit status 1:
command: /home/myourshaw/.virtualenvs/python38/bin/python3 -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-install-2vtoq395/pysam/setup.py'"'"'; __file__='"'"'/tmp/pip-install-2vtoq395/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-record-576yoxir/install-record.txt --single-version-externally-managed --compile --install-headers /home/myourshaw/.virtualenvs/python38/include/site/python3.8/pysam
cwd: /tmp/pip-install-2vtoq395/pysam/
Complete output (371 lines):
# pysam: cython is available - using cythonize if necessary
# pysam: htslib mode is shared
# pysam: HTSLIB_CONFIGURE_OPTIONS=None
# pysam: (sysconfig) CC=gcc -pthread
# pysam: (sysconfig) CFLAGS=-Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall
# pysam: (sysconfig) LDFLAGS=-L//home/myourshaw/.local/extlib/lib -Wl,--rpath=//home/myourshaw/.local/lib -Wl,--rpath=//home/myourshaw/.local/extlib/lib
checking for gcc... gcc -pthread
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 -pthread accepts -g... yes
checking for gcc -pthread 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... unknown
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 -pthread -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... 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 libdeflate.h... no
checking for libdeflate_deflate_compress in -ldeflate... no
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 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_64-3.8
creating build/lib.linux-x86_64-3.8/pysam
copying pysam/Pileup.py -> build/lib.linux-x86_64-3.8/pysam
copying pysam/__init__.py -> build/lib.linux-x86_64-3.8/pysam
copying pysam/bcftools.py -> build/lib.linux-x86_64-3.8/pysam
copying pysam/config.py -> build/lib.linux-x86_64-3.8/pysam
copying pysam/samtools.py -> build/lib.linux-x86_64-3.8/pysam
copying pysam/utils.py -> build/lib.linux-x86_64-3.8/pysam
copying pysam/version.py -> build/lib.linux-x86_64-3.8/pysam
creating build/lib.linux-x86_64-3.8/pysam/include
copying pysam/include/__init__.py -> build/lib.linux-x86_64-3.8/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.linux-x86_64-3.8/pysam
copying pysam/libcalignmentfile.pxd -> build/lib.linux-x86_64-3.8/pysam
copying pysam/libcbcf.pxd -> build/lib.linux-x86_64-3.8/pysam
copying pysam/libcbcftools.pxd -> build/lib.linux-x86_64-3.8/pysam
copying pysam/libcfaidx.pxd -> build/lib.linux-x86_64-3.8/pysam
copying pysam/libchtslib.pxd -> build/lib.linux-x86_64-3.8/pysam
copying pysam/libcsamfile.pxd -> build/lib.linux-x86_64-3.8/pysam
copying pysam/libcsamtools.pxd -> build/lib.linux-x86_64-3.8/pysam
copying pysam/libctabix.pxd -> build/lib.linux-x86_64-3.8/pysam
copying pysam/libctabixproxies.pxd -> build/lib.linux-x86_64-3.8/pysam
copying pysam/libcutils.pxd -> build/lib.linux-x86_64-3.8/pysam
copying pysam/libcvcf.pxd -> build/lib.linux-x86_64-3.8/pysam
copying pysam/cbcftools_util.h -> build/lib.linux-x86_64-3.8/pysam
copying pysam/csamtools_util.h -> build/lib.linux-x86_64-3.8/pysam
copying pysam/htslib_util.h -> build/lib.linux-x86_64-3.8/pysam
copying pysam/pysam_stream.h -> build/lib.linux-x86_64-3.8/pysam
copying pysam/pysam_util.h -> build/lib.linux-x86_64-3.8/pysam
creating build/lib.linux-x86_64-3.8/pysam/include/samtools
copying samtools/bam.h -> build/lib.linux-x86_64-3.8/pysam/include/samtools
copying samtools/bam2bcf.h -> build/lib.linux-x86_64-3.8/pysam/include/samtools
copying samtools/bam_endian.h -> build/lib.linux-x86_64-3.8/pysam/include/samtools
copying samtools/bam_lpileup.h -> build/lib.linux-x86_64-3.8/pysam/include/samtools
copying samtools/bam_plbuf.h -> build/lib.linux-x86_64-3.8/pysam/include/samtools
copying samtools/bedidx.h -> build/lib.linux-x86_64-3.8/pysam/include/samtools
copying samtools/sam.h -> build/lib.linux-x86_64-3.8/pysam/include/samtools
copying samtools/sam_header.h -> build/lib.linux-x86_64-3.8/pysam/include/samtools
copying samtools/sam_opts.h -> build/lib.linux-x86_64-3.8/pysam/include/samtools
copying samtools/sample.h -> build/lib.linux-x86_64-3.8/pysam/include/samtools
copying samtools/samtools.h -> build/lib.linux-x86_64-3.8/pysam/include/samtools
copying samtools/samtools.pysam.h -> build/lib.linux-x86_64-3.8/pysam/include/samtools
copying samtools/stats_isize.h -> build/lib.linux-x86_64-3.8/pysam/include/samtools
copying samtools/tmp_file.h -> build/lib.linux-x86_64-3.8/pysam/include/samtools
copying samtools/version.h -> build/lib.linux-x86_64-3.8/pysam/include/samtools
copying samtools/config.h -> build/lib.linux-x86_64-3.8/pysam/include/samtools
creating build/lib.linux-x86_64-3.8/pysam/include/bcftools
copying bcftools/HMM.h -> build/lib.linux-x86_64-3.8/pysam/include/bcftools
copying bcftools/bam2bcf.h -> build/lib.linux-x86_64-3.8/pysam/include/bcftools
copying bcftools/bam_sample.h -> build/lib.linux-x86_64-3.8/pysam/include/bcftools
copying bcftools/bcftools.h -> build/lib.linux-x86_64-3.8/pysam/include/bcftools
copying bcftools/bcftools.pysam.h -> build/lib.linux-x86_64-3.8/pysam/include/bcftools
copying bcftools/bin.h -> build/lib.linux-x86_64-3.8/pysam/include/bcftools
copying bcftools/call.h -> build/lib.linux-x86_64-3.8/pysam/include/bcftools
copying bcftools/convert.h -> build/lib.linux-x86_64-3.8/pysam/include/bcftools
copying bcftools/filter.h -> build/lib.linux-x86_64-3.8/pysam/include/bcftools
copying bcftools/gvcf.h -> build/lib.linux-x86_64-3.8/pysam/include/bcftools
copying bcftools/hclust.h -> build/lib.linux-x86_64-3.8/pysam/include/bcftools
copying bcftools/khash_str2str.h -> build/lib.linux-x86_64-3.8/pysam/include/bcftools
copying bcftools/kheap.h -> build/lib.linux-x86_64-3.8/pysam/include/bcftools
copying bcftools/kmin.h -> build/lib.linux-x86_64-3.8/pysam/include/bcftools
copying bcftools/mw.h -> build/lib.linux-x86_64-3.8/pysam/include/bcftools
copying bcftools/ploidy.h -> build/lib.linux-x86_64-3.8/pysam/include/bcftools
copying bcftools/prob1.h -> build/lib.linux-x86_64-3.8/pysam/include/bcftools
copying bcftools/rbuf.h -> build/lib.linux-x86_64-3.8/pysam/include/bcftools
copying bcftools/regidx.h -> build/lib.linux-x86_64-3.8/pysam/include/bcftools
copying bcftools/smpl_ilist.h -> build/lib.linux-x86_64-3.8/pysam/include/bcftools
copying bcftools/tsv2vcf.h -> build/lib.linux-x86_64-3.8/pysam/include/bcftools
copying bcftools/vcfbuf.h -> build/lib.linux-x86_64-3.8/pysam/include/bcftools
copying bcftools/vcmp.h -> build/lib.linux-x86_64-3.8/pysam/include/bcftools
copying bcftools/version.h -> build/lib.linux-x86_64-3.8/pysam/include/bcftools
copying bcftools/config.h -> build/lib.linux-x86_64-3.8/pysam/include/bcftools
creating build/lib.linux-x86_64-3.8/pysam/include/samtools/win32
copying samtools/win32/xcurses.h -> build/lib.linux-x86_64-3.8/pysam/include/samtools/win32
copying samtools/win32/zconf.h -> build/lib.linux-x86_64-3.8/pysam/include/samtools/win32
copying samtools/win32/zlib.h -> build/lib.linux-x86_64-3.8/pysam/include/samtools/win32
creating build/lib.linux-x86_64-3.8/pysam/include/htslib
copying htslib/bcf_sr_sort.h -> build/lib.linux-x86_64-3.8/pysam/include/htslib
copying htslib/hfile_internal.h -> build/lib.linux-x86_64-3.8/pysam/include/htslib
copying htslib/hts_internal.h -> build/lib.linux-x86_64-3.8/pysam/include/htslib
copying htslib/textutils_internal.h -> build/lib.linux-x86_64-3.8/pysam/include/htslib
copying htslib/thread_pool_internal.h -> build/lib.linux-x86_64-3.8/pysam/include/htslib
copying htslib/version.h -> build/lib.linux-x86_64-3.8/pysam/include/htslib
copying htslib/config.h -> build/lib.linux-x86_64-3.8/pysam/include/htslib
creating build/lib.linux-x86_64-3.8/pysam/include/htslib/htslib
copying htslib/htslib/bgzf.h -> build/lib.linux-x86_64-3.8/pysam/include/htslib/htslib
copying htslib/htslib/cram.h -> build/lib.linux-x86_64-3.8/pysam/include/htslib/htslib
copying htslib/htslib/faidx.h -> build/lib.linux-x86_64-3.8/pysam/include/htslib/htslib
copying htslib/htslib/hfile.h -> build/lib.linux-x86_64-3.8/pysam/include/htslib/htslib
copying htslib/htslib/hts.h -> build/lib.linux-x86_64-3.8/pysam/include/htslib/htslib
copying htslib/htslib/hts_defs.h -> build/lib.linux-x86_64-3.8/pysam/include/htslib/htslib
copying htslib/htslib/hts_endian.h -> build/lib.linux-x86_64-3.8/pysam/include/htslib/htslib
copying htslib/htslib/hts_log.h -> build/lib.linux-x86_64-3.8/pysam/include/htslib/htslib
copying htslib/htslib/hts_os.h -> build/lib.linux-x86_64-3.8/pysam/include/htslib/htslib
copying htslib/htslib/kbitset.h -> build/lib.linux-x86_64-3.8/pysam/include/htslib/htslib
copying htslib/htslib/kfunc.h -> build/lib.linux-x86_64-3.8/pysam/include/htslib/htslib
copying htslib/htslib/khash.h -> build/lib.linux-x86_64-3.8/pysam/include/htslib/htslib
copying htslib/htslib/khash_str2int.h -> build/lib.linux-x86_64-3.8/pysam/include/htslib/htslib
copying htslib/htslib/klist.h -> build/lib.linux-x86_64-3.8/pysam/include/htslib/htslib
copying htslib/htslib/knetfile.h -> build/lib.linux-x86_64-3.8/pysam/include/htslib/htslib
copying htslib/htslib/kseq.h -> build/lib.linux-x86_64-3.8/pysam/include/htslib/htslib
copying htslib/htslib/ksort.h -> build/lib.linux-x86_64-3.8/pysam/include/htslib/htslib
copying htslib/htslib/kstring.h -> build/lib.linux-x86_64-3.8/pysam/include/htslib/htslib
copying htslib/htslib/regidx.h -> build/lib.linux-x86_64-3.8/pysam/include/htslib/htslib
copying htslib/htslib/sam.h -> build/lib.linux-x86_64-3.8/pysam/include/htslib/htslib
copying htslib/htslib/synced_bcf_reader.h -> build/lib.linux-x86_64-3.8/pysam/include/htslib/htslib
copying htslib/htslib/tbx.h -> build/lib.linux-x86_64-3.8/pysam/include/htslib/htslib
copying htslib/htslib/thread_pool.h -> build/lib.linux-x86_64-3.8/pysam/include/htslib/htslib
copying htslib/htslib/vcf.h -> build/lib.linux-x86_64-3.8/pysam/include/htslib/htslib
copying htslib/htslib/vcf_sweep.h -> build/lib.linux-x86_64-3.8/pysam/include/htslib/htslib
copying htslib/htslib/vcfutils.h -> build/lib.linux-x86_64-3.8/pysam/include/htslib/htslib
Fixing build/lib.linux-x86_64-3.8/pysam/Pileup.py build/lib.linux-x86_64-3.8/pysam/__init__.py build/lib.linux-x86_64-3.8/pysam/bcftools.py build/lib.linux-x86_64-3.8/pysam/config.py build/lib.linux-x86_64-3.8/pysam/samtools.py build/lib.linux-x86_64-3.8/pysam/utils.py build/lib.linux-x86_64-3.8/pysam/version.py build/lib.linux-x86_64-3.8/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_64-3.8/pysam/Pileup.py build/lib.linux-x86_64-3.8/pysam/__init__.py build/lib.linux-x86_64-3.8/pysam/bcftools.py build/lib.linux-x86_64-3.8/pysam/config.py build/lib.linux-x86_64-3.8/pysam/samtools.py build/lib.linux-x86_64-3.8/pysam/utils.py build/lib.linux-x86_64-3.8/pysam/version.py build/lib.linux-x86_64-3.8/pysam/include/__init__.py
Skipping optional fixer: buffer
Skipping optional fixer: idioms
Skipping optional fixer: set_literal
Skipping optional fixer: ws_comma
running build_ext
skipping 'pysam/libchtslib.c' Cython extension (up-to-date)
skipping 'pysam/libcsamtools.c' Cython extension (up-to-date)
skipping 'pysam/libcbcftools.c' Cython extension (up-to-date)
skipping 'pysam/libcutils.c' Cython extension (up-to-date)
skipping 'pysam/libcalignmentfile.c' Cython extension (up-to-date)
skipping 'pysam/libcsamfile.c' Cython extension (up-to-date)
skipping 'pysam/libcalignedsegment.c' Cython extension (up-to-date)
skipping 'pysam/libctabix.c' Cython extension (up-to-date)
skipping 'pysam/libcfaidx.c' Cython extension (up-to-date)
skipping 'pysam/libcbcf.c' Cython extension (up-to-date)
skipping 'pysam/libcbgzf.c' Cython extension (up-to-date)
skipping 'pysam/libctabixproxies.c' Cython extension (up-to-date)
skipping 'pysam/libcvcf.c' Cython extension (up-to-date)
building 'pysam.libchtslib' extension
creating build/temp.linux-x86_64-3.8
creating build/temp.linux-x86_64-3.8/pysam
creating build/temp.linux-x86_64-3.8/htslib
creating build/temp.linux-x86_64-3.8/htslib/cram
gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -fPIC -I/tmp/pip-install-2vtoq395/pysam/htslib -I/tmp/pip-install-2vtoq395/pysam/samtools -I/tmp/pip-install-2vtoq395/pysam/samtools/lz4 -I/tmp/pip-install-2vtoq395/pysam/bcftools -I/tmp/pip-install-2vtoq395/pysam/pysam -I/tmp/pip-install-2vtoq395/pysam -I/home/myourshaw/.virtualenvs/python38/include -I/home/myourshaw/.local/include/python3.8 -c pysam/libchtslib.c -o build/temp.linux-x86_64-3.8/pysam/libchtslib.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -fPIC -I/tmp/pip-install-2vtoq395/pysam/htslib -I/tmp/pip-install-2vtoq395/pysam/samtools -I/tmp/pip-install-2vtoq395/pysam/samtools/lz4 -I/tmp/pip-install-2vtoq395/pysam/bcftools -I/tmp/pip-install-2vtoq395/pysam/pysam -I/tmp/pip-install-2vtoq395/pysam -I/home/myourshaw/.virtualenvs/python38/include -I/home/myourshaw/.local/include/python3.8 -c pysam/htslib_util.c -o build/temp.linux-x86_64-3.8/pysam/htslib_util.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -fPIC -I/tmp/pip-install-2vtoq395/pysam/htslib -I/tmp/pip-install-2vtoq395/pysam/samtools -I/tmp/pip-install-2vtoq395/pysam/samtools/lz4 -I/tmp/pip-install-2vtoq395/pysam/bcftools -I/tmp/pip-install-2vtoq395/pysam/pysam -I/tmp/pip-install-2vtoq395/pysam -I/home/myourshaw/.virtualenvs/python38/include -I/home/myourshaw/.local/include/python3.8 -c htslib/kfunc.c -o build/temp.linux-x86_64-3.8/htslib/kfunc.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -fPIC -I/tmp/pip-install-2vtoq395/pysam/htslib -I/tmp/pip-install-2vtoq395/pysam/samtools -I/tmp/pip-install-2vtoq395/pysam/samtools/lz4 -I/tmp/pip-install-2vtoq395/pysam/bcftools -I/tmp/pip-install-2vtoq395/pysam/pysam -I/tmp/pip-install-2vtoq395/pysam -I/home/myourshaw/.virtualenvs/python38/include -I/home/myourshaw/.local/include/python3.8 -c htslib/knetfile.c -o build/temp.linux-x86_64-3.8/htslib/knetfile.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -fPIC -I/tmp/pip-install-2vtoq395/pysam/htslib -I/tmp/pip-install-2vtoq395/pysam/samtools -I/tmp/pip-install-2vtoq395/pysam/samtools/lz4 -I/tmp/pip-install-2vtoq395/pysam/bcftools -I/tmp/pip-install-2vtoq395/pysam/pysam -I/tmp/pip-install-2vtoq395/pysam -I/home/myourshaw/.virtualenvs/python38/include -I/home/myourshaw/.local/include/python3.8 -c htslib/kstring.c -o build/temp.linux-x86_64-3.8/htslib/kstring.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -fPIC -I/tmp/pip-install-2vtoq395/pysam/htslib -I/tmp/pip-install-2vtoq395/pysam/samtools -I/tmp/pip-install-2vtoq395/pysam/samtools/lz4 -I/tmp/pip-install-2vtoq395/pysam/bcftools -I/tmp/pip-install-2vtoq395/pysam/pysam -I/tmp/pip-install-2vtoq395/pysam -I/home/myourshaw/.virtualenvs/python38/include -I/home/myourshaw/.local/include/python3.8 -c htslib/bcf_sr_sort.c -o build/temp.linux-x86_64-3.8/htslib/bcf_sr_sort.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -fPIC -I/tmp/pip-install-2vtoq395/pysam/htslib -I/tmp/pip-install-2vtoq395/pysam/samtools -I/tmp/pip-install-2vtoq395/pysam/samtools/lz4 -I/tmp/pip-install-2vtoq395/pysam/bcftools -I/tmp/pip-install-2vtoq395/pysam/pysam -I/tmp/pip-install-2vtoq395/pysam -I/home/myourshaw/.virtualenvs/python38/include -I/home/myourshaw/.local/include/python3.8 -c htslib/bgzf.c -o build/temp.linux-x86_64-3.8/htslib/bgzf.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -fPIC -I/tmp/pip-install-2vtoq395/pysam/htslib -I/tmp/pip-install-2vtoq395/pysam/samtools -I/tmp/pip-install-2vtoq395/pysam/samtools/lz4 -I/tmp/pip-install-2vtoq395/pysam/bcftools -I/tmp/pip-install-2vtoq395/pysam/pysam -I/tmp/pip-install-2vtoq395/pysam -I/home/myourshaw/.virtualenvs/python38/include -I/home/myourshaw/.local/include/python3.8 -c htslib/errmod.c -o build/temp.linux-x86_64-3.8/htslib/errmod.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -fPIC -I/tmp/pip-install-2vtoq395/pysam/htslib -I/tmp/pip-install-2vtoq395/pysam/samtools -I/tmp/pip-install-2vtoq395/pysam/samtools/lz4 -I/tmp/pip-install-2vtoq395/pysam/bcftools -I/tmp/pip-install-2vtoq395/pysam/pysam -I/tmp/pip-install-2vtoq395/pysam -I/home/myourshaw/.virtualenvs/python38/include -I/home/myourshaw/.local/include/python3.8 -c htslib/faidx.c -o build/temp.linux-x86_64-3.8/htslib/faidx.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -fPIC -I/tmp/pip-install-2vtoq395/pysam/htslib -I/tmp/pip-install-2vtoq395/pysam/samtools -I/tmp/pip-install-2vtoq395/pysam/samtools/lz4 -I/tmp/pip-install-2vtoq395/pysam/bcftools -I/tmp/pip-install-2vtoq395/pysam/pysam -I/tmp/pip-install-2vtoq395/pysam -I/home/myourshaw/.virtualenvs/python38/include -I/home/myourshaw/.local/include/python3.8 -c htslib/hfile.c -o build/temp.linux-x86_64-3.8/htslib/hfile.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -fPIC -I/tmp/pip-install-2vtoq395/pysam/htslib -I/tmp/pip-install-2vtoq395/pysam/samtools -I/tmp/pip-install-2vtoq395/pysam/samtools/lz4 -I/tmp/pip-install-2vtoq395/pysam/bcftools -I/tmp/pip-install-2vtoq395/pysam/pysam -I/tmp/pip-install-2vtoq395/pysam -I/home/myourshaw/.virtualenvs/python38/include -I/home/myourshaw/.local/include/python3.8 -c htslib/hfile_net.c -o build/temp.linux-x86_64-3.8/htslib/hfile_net.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -fPIC -I/tmp/pip-install-2vtoq395/pysam/htslib -I/tmp/pip-install-2vtoq395/pysam/samtools -I/tmp/pip-install-2vtoq395/pysam/samtools/lz4 -I/tmp/pip-install-2vtoq395/pysam/bcftools -I/tmp/pip-install-2vtoq395/pysam/pysam -I/tmp/pip-install-2vtoq395/pysam -I/home/myourshaw/.virtualenvs/python38/include -I/home/myourshaw/.local/include/python3.8 -c htslib/hts.c -o build/temp.linux-x86_64-3.8/htslib/hts.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -fPIC -I/tmp/pip-install-2vtoq395/pysam/htslib -I/tmp/pip-install-2vtoq395/pysam/samtools -I/tmp/pip-install-2vtoq395/pysam/samtools/lz4 -I/tmp/pip-install-2vtoq395/pysam/bcftools -I/tmp/pip-install-2vtoq395/pysam/pysam -I/tmp/pip-install-2vtoq395/pysam -I/home/myourshaw/.virtualenvs/python38/include -I/home/myourshaw/.local/include/python3.8 -c htslib/hts_os.c -o build/temp.linux-x86_64-3.8/htslib/hts_os.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -fPIC -I/tmp/pip-install-2vtoq395/pysam/htslib -I/tmp/pip-install-2vtoq395/pysam/samtools -I/tmp/pip-install-2vtoq395/pysam/samtools/lz4 -I/tmp/pip-install-2vtoq395/pysam/bcftools -I/tmp/pip-install-2vtoq395/pysam/pysam -I/tmp/pip-install-2vtoq395/pysam -I/home/myourshaw/.virtualenvs/python38/include -I/home/myourshaw/.local/include/python3.8 -c htslib/md5.c -o build/temp.linux-x86_64-3.8/htslib/md5.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -fPIC -I/tmp/pip-install-2vtoq395/pysam/htslib -I/tmp/pip-install-2vtoq395/pysam/samtools -I/tmp/pip-install-2vtoq395/pysam/samtools/lz4 -I/tmp/pip-install-2vtoq395/pysam/bcftools -I/tmp/pip-install-2vtoq395/pysam/pysam -I/tmp/pip-install-2vtoq395/pysam -I/home/myourshaw/.virtualenvs/python38/include -I/home/myourshaw/.local/include/python3.8 -c htslib/multipart.c -o build/temp.linux-x86_64-3.8/htslib/multipart.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -fPIC -I/tmp/pip-install-2vtoq395/pysam/htslib -I/tmp/pip-install-2vtoq395/pysam/samtools -I/tmp/pip-install-2vtoq395/pysam/samtools/lz4 -I/tmp/pip-install-2vtoq395/pysam/bcftools -I/tmp/pip-install-2vtoq395/pysam/pysam -I/tmp/pip-install-2vtoq395/pysam -I/home/myourshaw/.virtualenvs/python38/include -I/home/myourshaw/.local/include/python3.8 -c htslib/probaln.c -o build/temp.linux-x86_64-3.8/htslib/probaln.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -fPIC -I/tmp/pip-install-2vtoq395/pysam/htslib -I/tmp/pip-install-2vtoq395/pysam/samtools -I/tmp/pip-install-2vtoq395/pysam/samtools/lz4 -I/tmp/pip-install-2vtoq395/pysam/bcftools -I/tmp/pip-install-2vtoq395/pysam/pysam -I/tmp/pip-install-2vtoq395/pysam -I/home/myourshaw/.virtualenvs/python38/include -I/home/myourshaw/.local/include/python3.8 -c htslib/realn.c -o build/temp.linux-x86_64-3.8/htslib/realn.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -fPIC -I/tmp/pip-install-2vtoq395/pysam/htslib -I/tmp/pip-install-2vtoq395/pysam/samtools -I/tmp/pip-install-2vtoq395/pysam/samtools/lz4 -I/tmp/pip-install-2vtoq395/pysam/bcftools -I/tmp/pip-install-2vtoq395/pysam/pysam -I/tmp/pip-install-2vtoq395/pysam -I/home/myourshaw/.virtualenvs/python38/include -I/home/myourshaw/.local/include/python3.8 -c htslib/regidx.c -o build/temp.linux-x86_64-3.8/htslib/regidx.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -fPIC -I/tmp/pip-install-2vtoq395/pysam/htslib -I/tmp/pip-install-2vtoq395/pysam/samtools -I/tmp/pip-install-2vtoq395/pysam/samtools/lz4 -I/tmp/pip-install-2vtoq395/pysam/bcftools -I/tmp/pip-install-2vtoq395/pysam/pysam -I/tmp/pip-install-2vtoq395/pysam -I/home/myourshaw/.virtualenvs/python38/include -I/home/myourshaw/.local/include/python3.8 -c htslib/sam.c -o build/temp.linux-x86_64-3.8/htslib/sam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -fPIC -I/tmp/pip-install-2vtoq395/pysam/htslib -I/tmp/pip-install-2vtoq395/pysam/samtools -I/tmp/pip-install-2vtoq395/pysam/samtools/lz4 -I/tmp/pip-install-2vtoq395/pysam/bcftools -I/tmp/pip-install-2vtoq395/pysam/pysam -I/tmp/pip-install-2vtoq395/pysam -I/home/myourshaw/.virtualenvs/python38/include -I/home/myourshaw/.local/include/python3.8 -c htslib/synced_bcf_reader.c -o build/temp.linux-x86_64-3.8/htslib/synced_bcf_reader.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -fPIC -I/tmp/pip-install-2vtoq395/pysam/htslib -I/tmp/pip-install-2vtoq395/pysam/samtools -I/tmp/pip-install-2vtoq395/pysam/samtools/lz4 -I/tmp/pip-install-2vtoq395/pysam/bcftools -I/tmp/pip-install-2vtoq395/pysam/pysam -I/tmp/pip-install-2vtoq395/pysam -I/home/myourshaw/.virtualenvs/python38/include -I/home/myourshaw/.local/include/python3.8 -c htslib/vcf_sweep.c -o build/temp.linux-x86_64-3.8/htslib/vcf_sweep.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -fPIC -I/tmp/pip-install-2vtoq395/pysam/htslib -I/tmp/pip-install-2vtoq395/pysam/samtools -I/tmp/pip-install-2vtoq395/pysam/samtools/lz4 -I/tmp/pip-install-2vtoq395/pysam/bcftools -I/tmp/pip-install-2vtoq395/pysam/pysam -I/tmp/pip-install-2vtoq395/pysam -I/home/myourshaw/.virtualenvs/python38/include -I/home/myourshaw/.local/include/python3.8 -c htslib/tbx.c -o build/temp.linux-x86_64-3.8/htslib/tbx.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -fPIC -I/tmp/pip-install-2vtoq395/pysam/htslib -I/tmp/pip-install-2vtoq395/pysam/samtools -I/tmp/pip-install-2vtoq395/pysam/samtools/lz4 -I/tmp/pip-install-2vtoq395/pysam/bcftools -I/tmp/pip-install-2vtoq395/pysam/pysam -I/tmp/pip-install-2vtoq395/pysam -I/home/myourshaw/.virtualenvs/python38/include -I/home/myourshaw/.local/include/python3.8 -c htslib/textutils.c -o build/temp.linux-x86_64-3.8/htslib/textutils.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -fPIC -I/tmp/pip-install-2vtoq395/pysam/htslib -I/tmp/pip-install-2vtoq395/pysam/samtools -I/tmp/pip-install-2vtoq395/pysam/samtools/lz4 -I/tmp/pip-install-2vtoq395/pysam/bcftools -I/tmp/pip-install-2vtoq395/pysam/pysam -I/tmp/pip-install-2vtoq395/pysam -I/home/myourshaw/.virtualenvs/python38/include -I/home/myourshaw/.local/include/python3.8 -c htslib/thread_pool.c -o build/temp.linux-x86_64-3.8/htslib/thread_pool.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -fPIC -I/tmp/pip-install-2vtoq395/pysam/htslib -I/tmp/pip-install-2vtoq395/pysam/samtools -I/tmp/pip-install-2vtoq395/pysam/samtools/lz4 -I/tmp/pip-install-2vtoq395/pysam/bcftools -I/tmp/pip-install-2vtoq395/pysam/pysam -I/tmp/pip-install-2vtoq395/pysam -I/home/myourshaw/.virtualenvs/python38/include -I/home/myourshaw/.local/include/python3.8 -c htslib/vcf.c -o build/temp.linux-x86_64-3.8/htslib/vcf.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -fPIC -I/tmp/pip-install-2vtoq395/pysam/htslib -I/tmp/pip-install-2vtoq395/pysam/samtools -I/tmp/pip-install-2vtoq395/pysam/samtools/lz4 -I/tmp/pip-install-2vtoq395/pysam/bcftools -I/tmp/pip-install-2vtoq395/pysam/pysam -I/tmp/pip-install-2vtoq395/pysam -I/home/myourshaw/.virtualenvs/python38/include -I/home/myourshaw/.local/include/python3.8 -c htslib/vcfutils.c -o build/temp.linux-x86_64-3.8/htslib/vcfutils.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -fPIC -I/tmp/pip-install-2vtoq395/pysam/htslib -I/tmp/pip-install-2vtoq395/pysam/samtools -I/tmp/pip-install-2vtoq395/pysam/samtools/lz4 -I/tmp/pip-install-2vtoq395/pysam/bcftools -I/tmp/pip-install-2vtoq395/pysam/pysam -I/tmp/pip-install-2vtoq395/pysam -I/home/myourshaw/.virtualenvs/python38/include -I/home/myourshaw/.local/include/python3.8 -c htslib/cram/cram_codecs.c -o build/temp.linux-x86_64-3.8/htslib/cram/cram_codecs.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -fPIC -I/tmp/pip-install-2vtoq395/pysam/htslib -I/tmp/pip-install-2vtoq395/pysam/samtools -I/tmp/pip-install-2vtoq395/pysam/samtools/lz4 -I/tmp/pip-install-2vtoq395/pysam/bcftools -I/tmp/pip-install-2vtoq395/pysam/pysam -I/tmp/pip-install-2vtoq395/pysam -I/home/myourshaw/.virtualenvs/python38/include -I/home/myourshaw/.local/include/python3.8 -c htslib/cram/cram_decode.c -o build/temp.linux-x86_64-3.8/htslib/cram/cram_decode.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -fPIC -I/tmp/pip-install-2vtoq395/pysam/htslib -I/tmp/pip-install-2vtoq395/pysam/samtools -I/tmp/pip-install-2vtoq395/pysam/samtools/lz4 -I/tmp/pip-install-2vtoq395/pysam/bcftools -I/tmp/pip-install-2vtoq395/pysam/pysam -I/tmp/pip-install-2vtoq395/pysam -I/home/myourshaw/.virtualenvs/python38/include -I/home/myourshaw/.local/include/python3.8 -c htslib/cram/cram_encode.c -o build/temp.linux-x86_64-3.8/htslib/cram/cram_encode.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -fPIC -I/tmp/pip-install-2vtoq395/pysam/htslib -I/tmp/pip-install-2vtoq395/pysam/samtools -I/tmp/pip-install-2vtoq395/pysam/samtools/lz4 -I/tmp/pip-install-2vtoq395/pysam/bcftools -I/tmp/pip-install-2vtoq395/pysam/pysam -I/tmp/pip-install-2vtoq395/pysam -I/home/myourshaw/.virtualenvs/python38/include -I/home/myourshaw/.local/include/python3.8 -c htslib/cram/cram_external.c -o build/temp.linux-x86_64-3.8/htslib/cram/cram_external.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -fPIC -I/tmp/pip-install-2vtoq395/pysam/htslib -I/tmp/pip-install-2vtoq395/pysam/samtools -I/tmp/pip-install-2vtoq395/pysam/samtools/lz4 -I/tmp/pip-install-2vtoq395/pysam/bcftools -I/tmp/pip-install-2vtoq395/pysam/pysam -I/tmp/pip-install-2vtoq395/pysam -I/home/myourshaw/.virtualenvs/python38/include -I/home/myourshaw/.local/include/python3.8 -c htslib/cram/cram_index.c -o build/temp.linux-x86_64-3.8/htslib/cram/cram_index.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -fPIC -I/tmp/pip-install-2vtoq395/pysam/htslib -I/tmp/pip-install-2vtoq395/pysam/samtools -I/tmp/pip-install-2vtoq395/pysam/samtools/lz4 -I/tmp/pip-install-2vtoq395/pysam/bcftools -I/tmp/pip-install-2vtoq395/pysam/pysam -I/tmp/pip-install-2vtoq395/pysam -I/home/myourshaw/.virtualenvs/python38/include -I/home/myourshaw/.local/include/python3.8 -c htslib/cram/cram_io.c -o build/temp.linux-x86_64-3.8/htslib/cram/cram_io.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
In function ‘full_path’,
inlined from ‘cram_write_SAM_hdr’ at htslib/cram/cram_io.c:3823:17:
htslib/cram/cram_io.c:3748:13: warning: ‘strncpy’ specified bound 4096 equals destination size [-Wstringop-truncation]
strncpy(out, in, PATH_MAX);
^~~~~~~~~~~~~~~~~~~~~~~~~~
htslib/cram/cram_io.c:3740:9: warning: ‘strncpy’ specified bound 4096 equals destination size [-Wstringop-truncation]
strncpy(out, in, PATH_MAX);
^~~~~~~~~~~~~~~~~~~~~~~~~~
gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -fPIC -I/tmp/pip-install-2vtoq395/pysam/htslib -I/tmp/pip-install-2vtoq395/pysam/samtools -I/tmp/pip-install-2vtoq395/pysam/samtools/lz4 -I/tmp/pip-install-2vtoq395/pysam/bcftools -I/tmp/pip-install-2vtoq395/pysam/pysam -I/tmp/pip-install-2vtoq395/pysam -I/home/myourshaw/.virtualenvs/python38/include -I/home/myourshaw/.local/include/python3.8 -c htslib/cram/cram_samtools.c -o build/temp.linux-x86_64-3.8/htslib/cram/cram_samtools.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -fPIC -I/tmp/pip-install-2vtoq395/pysam/htslib -I/tmp/pip-install-2vtoq395/pysam/samtools -I/tmp/pip-install-2vtoq395/pysam/samtools/lz4 -I/tmp/pip-install-2vtoq395/pysam/bcftools -I/tmp/pip-install-2vtoq395/pysam/pysam -I/tmp/pip-install-2vtoq395/pysam -I/home/myourshaw/.virtualenvs/python38/include -I/home/myourshaw/.local/include/python3.8 -c htslib/cram/cram_stats.c -o build/temp.linux-x86_64-3.8/htslib/cram/cram_stats.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -fPIC -I/tmp/pip-install-2vtoq395/pysam/htslib -I/tmp/pip-install-2vtoq395/pysam/samtools -I/tmp/pip-install-2vtoq395/pysam/samtools/lz4 -I/tmp/pip-install-2vtoq395/pysam/bcftools -I/tmp/pip-install-2vtoq395/pysam/pysam -I/tmp/pip-install-2vtoq395/pysam -I/home/myourshaw/.virtualenvs/python38/include -I/home/myourshaw/.local/include/python3.8 -c htslib/cram/files.c -o build/temp.linux-x86_64-3.8/htslib/cram/files.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -fPIC -I/tmp/pip-install-2vtoq395/pysam/htslib -I/tmp/pip-install-2vtoq395/pysam/samtools -I/tmp/pip-install-2vtoq395/pysam/samtools/lz4 -I/tmp/pip-install-2vtoq395/pysam/bcftools -I/tmp/pip-install-2vtoq395/pysam/pysam -I/tmp/pip-install-2vtoq395/pysam -I/home/myourshaw/.virtualenvs/python38/include -I/home/myourshaw/.local/include/python3.8 -c htslib/cram/mFILE.c -o build/temp.linux-x86_64-3.8/htslib/cram/mFILE.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -fPIC -I/tmp/pip-install-2vtoq395/pysam/htslib -I/tmp/pip-install-2vtoq395/pysam/samtools -I/tmp/pip-install-2vtoq395/pysam/samtools/lz4 -I/tmp/pip-install-2vtoq395/pysam/bcftools -I/tmp/pip-install-2vtoq395/pysam/pysam -I/tmp/pip-install-2vtoq395/pysam -I/home/myourshaw/.virtualenvs/python38/include -I/home/myourshaw/.local/include/python3.8 -c htslib/cram/open_trace_file.c -o build/temp.linux-x86_64-3.8/htslib/cram/open_trace_file.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -fPIC -I/tmp/pip-install-2vtoq395/pysam/htslib -I/tmp/pip-install-2vtoq395/pysam/samtools -I/tmp/pip-install-2vtoq395/pysam/samtools/lz4 -I/tmp/pip-install-2vtoq395/pysam/bcftools -I/tmp/pip-install-2vtoq395/pysam/pysam -I/tmp/pip-install-2vtoq395/pysam -I/home/myourshaw/.virtualenvs/python38/include -I/home/myourshaw/.local/include/python3.8 -c htslib/cram/pooled_alloc.c -o build/temp.linux-x86_64-3.8/htslib/cram/pooled_alloc.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -fPIC -I/tmp/pip-install-2vtoq395/pysam/htslib -I/tmp/pip-install-2vtoq395/pysam/samtools -I/tmp/pip-install-2vtoq395/pysam/samtools/lz4 -I/tmp/pip-install-2vtoq395/pysam/bcftools -I/tmp/pip-install-2vtoq395/pysam/pysam -I/tmp/pip-install-2vtoq395/pysam -I/home/myourshaw/.virtualenvs/python38/include -I/home/myourshaw/.local/include/python3.8 -c htslib/cram/rANS_static.c -o build/temp.linux-x86_64-3.8/htslib/cram/rANS_static.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -fPIC -I/tmp/pip-install-2vtoq395/pysam/htslib -I/tmp/pip-install-2vtoq395/pysam/samtools -I/tmp/pip-install-2vtoq395/pysam/samtools/lz4 -I/tmp/pip-install-2vtoq395/pysam/bcftools -I/tmp/pip-install-2vtoq395/pysam/pysam -I/tmp/pip-install-2vtoq395/pysam -I/home/myourshaw/.virtualenvs/python38/include -I/home/myourshaw/.local/include/python3.8 -c htslib/cram/sam_header.c -o build/temp.linux-x86_64-3.8/htslib/cram/sam_header.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -fPIC -I/tmp/pip-install-2vtoq395/pysam/htslib -I/tmp/pip-install-2vtoq395/pysam/samtools -I/tmp/pip-install-2vtoq395/pysam/samtools/lz4 -I/tmp/pip-install-2vtoq395/pysam/bcftools -I/tmp/pip-install-2vtoq395/pysam/pysam -I/tmp/pip-install-2vtoq395/pysam -I/home/myourshaw/.virtualenvs/python38/include -I/home/myourshaw/.local/include/python3.8 -c htslib/cram/string_alloc.c -o build/temp.linux-x86_64-3.8/htslib/cram/string_alloc.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -fPIC -I/tmp/pip-install-2vtoq395/pysam/htslib -I/tmp/pip-install-2vtoq395/pysam/samtools -I/tmp/pip-install-2vtoq395/pysam/samtools/lz4 -I/tmp/pip-install-2vtoq395/pysam/bcftools -I/tmp/pip-install-2vtoq395/pysam/pysam -I/tmp/pip-install-2vtoq395/pysam -I/home/myourshaw/.virtualenvs/python38/include -I/home/myourshaw/.local/include/python3.8 -c htslib/hfile_libcurl.c -o build/temp.linux-x86_64-3.8/htslib/hfile_libcurl.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -fPIC -I/tmp/pip-install-2vtoq395/pysam/htslib -I/tmp/pip-install-2vtoq395/pysam/samtools -I/tmp/pip-install-2vtoq395/pysam/samtools/lz4 -I/tmp/pip-install-2vtoq395/pysam/bcftools -I/tmp/pip-install-2vtoq395/pysam/pysam -I/tmp/pip-install-2vtoq395/pysam -I/home/myourshaw/.virtualenvs/python38/include -I/home/myourshaw/.local/include/python3.8 -c htslib/hfile_gcs.c -o build/temp.linux-x86_64-3.8/htslib/hfile_gcs.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -fPIC -I/tmp/pip-install-2vtoq395/pysam/htslib -I/tmp/pip-install-2vtoq395/pysam/samtools -I/tmp/pip-install-2vtoq395/pysam/samtools/lz4 -I/tmp/pip-install-2vtoq395/pysam/bcftools -I/tmp/pip-install-2vtoq395/pysam/pysam -I/tmp/pip-install-2vtoq395/pysam -I/home/myourshaw/.virtualenvs/python38/include -I/home/myourshaw/.local/include/python3.8 -c htslib/hfile_s3.c -o build/temp.linux-x86_64-3.8/htslib/hfile_s3.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
gcc -pthread -shared -L//home/myourshaw/.local/extlib/lib -Wl,--rpath=//home/myourshaw/.local/lib -Wl,--rpath=//home/myourshaw/.local/extlib/lib build/temp.linux-x86_64-3.8/pysam/libchtslib.o build/temp.linux-x86_64-3.8/pysam/htslib_util.o build/temp.linux-x86_64-3.8/htslib/kfunc.o build/temp.linux-x86_64-3.8/htslib/knetfile.o build/temp.linux-x86_64-3.8/htslib/kstring.o build/temp.linux-x86_64-3.8/htslib/bcf_sr_sort.o build/temp.linux-x86_64-3.8/htslib/bgzf.o build/temp.linux-x86_64-3.8/htslib/errmod.o build/temp.linux-x86_64-3.8/htslib/faidx.o build/temp.linux-x86_64-3.8/htslib/hfile.o build/temp.linux-x86_64-3.8/htslib/hfile_net.o build/temp.linux-x86_64-3.8/htslib/hts.o build/temp.linux-x86_64-3.8/htslib/hts_os.o build/temp.linux-x86_64-3.8/htslib/md5.o build/temp.linux-x86_64-3.8/htslib/multipart.o build/temp.linux-x86_64-3.8/htslib/probaln.o build/temp.linux-x86_64-3.8/htslib/realn.o build/temp.linux-x86_64-3.8/htslib/regidx.o build/temp.linux-x86_64-3.8/htslib/sam.o build/temp.linux-x86_64-3.8/htslib/synced_bcf_reader.o build/temp.linux-x86_64-3.8/htslib/vcf_sweep.o build/temp.linux-x86_64-3.8/htslib/tbx.o build/temp.linux-x86_64-3.8/htslib/textutils.o build/temp.linux-x86_64-3.8/htslib/thread_pool.o build/temp.linux-x86_64-3.8/htslib/vcf.o build/temp.linux-x86_64-3.8/htslib/vcfutils.o build/temp.linux-x86_64-3.8/htslib/cram/cram_codecs.o build/temp.linux-x86_64-3.8/htslib/cram/cram_decode.o build/temp.linux-x86_64-3.8/htslib/cram/cram_encode.o build/temp.linux-x86_64-3.8/htslib/cram/cram_external.o build/temp.linux-x86_64-3.8/htslib/cram/cram_index.o build/temp.linux-x86_64-3.8/htslib/cram/cram_io.o build/temp.linux-x86_64-3.8/htslib/cram/cram_samtools.o build/temp.linux-x86_64-3.8/htslib/cram/cram_stats.o build/temp.linux-x86_64-3.8/htslib/cram/files.o build/temp.linux-x86_64-3.8/htslib/cram/mFILE.o build/temp.linux-x86_64-3.8/htslib/cram/open_trace_file.o build/temp.linux-x86_64-3.8/htslib/cram/pooled_alloc.o build/temp.linux-x86_64-3.8/htslib/cram/rANS_static.o build/temp.linux-x86_64-3.8/htslib/cram/sam_header.o build/temp.linux-x86_64-3.8/htslib/cram/string_alloc.o build/temp.linux-x86_64-3.8/htslib/hfile_libcurl.o build/temp.linux-x86_64-3.8/htslib/hfile_gcs.o build/temp.linux-x86_64-3.8/htslib/hfile_s3.o -L/tmp/pip-install-2vtoq395/pysam/pysam -L/tmp/pip-install-2vtoq395/pysam/pysam -L/tmp/pip-install-2vtoq395/pysam -L/tmp/pip-install-2vtoq395/pysam/build/lib.linux-x86_64-3.8/pysam -Lbuild/lib.linux-x86_64-3.8/pysam -L//home/myourshaw/.local/lib -lz -llzma -lbz2 -lz -lm -lcurl -lcrypto -o build/lib.linux-x86_64-3.8/pysam/libchtslib.cpython-38-x86_64-linux-gnu.so -Wl,-rpath,$ORIGIN
building 'pysam.libcsamtools' extension
creating build/temp.linux-x86_64-3.8/samtools
creating build/temp.linux-x86_64-3.8/samtools/lz4
gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -fPIC -I/tmp/pip-install-2vtoq395/pysam/htslib -I/tmp/pip-install-2vtoq395/pysam/samtools -I/tmp/pip-install-2vtoq395/pysam/samtools/lz4 -I/tmp/pip-install-2vtoq395/pysam/bcftools -I/tmp/pip-install-2vtoq395/pysam/pysam -I/tmp/pip-install-2vtoq395/pysam -I/home/myourshaw/.virtualenvs/python38/include -I/home/myourshaw/.local/include/python3.8 -c pysam/libcsamtools.c -o build/temp.linux-x86_64-3.8/pysam/libcsamtools.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
pysam/libcsamtools.c: In function ‘__Pyx_InitCachedConstants’:
/home/myourshaw/.local/include/python3.8/code.h:72:25: warning: passing argument 6 of ‘PyCode_New’ makes pointer from integer without a cast [-Wint-conversion]
#define CO_OPTIMIZED 0x0001
^
pysam/libcsamtools.c:318:37: note: in definition of macro ‘__Pyx_PyCode_New’
PyCode_New(a, 0, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos)
^
pysam/libcsamtools.c:1120:60: note: in expansion of macro ‘CO_OPTIMIZED’
__pyx_codeobj_ = (PyObject*)__Pyx_PyCode_New(0, 0, 0, 0, CO_OPTIMIZED|CO_NEWLOCALS, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_pysam_libcsamtools_pyx, __pyx_n_s_py_samtools, 1, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj_)) __PYX_ERR(0, 1, __pyx_L1_error)
^~~~~~~~~~~~
In file included from /home/myourshaw/.local/include/python3.8/compile.h:5,
from /home/myourshaw/.local/include/python3.8/Python.h:138,
from pysam/libcsamtools.c:4:
/home/myourshaw/.local/include/python3.8/code.h:122:28: note: expected ‘PyObject *’ {aka ‘struct _object *’} but argument is of type ‘int’
PyAPI_FUNC(PyCodeObject *) PyCode_New(
^~~~~~~~~~
pysam/libcsamtools.c:1120:236: warning: passing argument 14 of ‘PyCode_New’ makes integer from pointer without a cast [-Wint-conversion]
__pyx_codeobj_ = (PyObject*)__Pyx_PyCode_New(0, 0, 0, 0, CO_OPTIMIZED|CO_NEWLOCALS, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_pysam_libcsamtools_pyx, __pyx_n_s_py_samtools, 1, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj_)) __PYX_ERR(0, 1, __pyx_L1_error)
^~~~~~~~~~~~~~~~~~~~~
pysam/libcsamtools.c:318:69: note: in definition of macro ‘__Pyx_PyCode_New’
PyCode_New(a, 0, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos)
^~~~
In file included from /home/myourshaw/.local/include/python3.8/compile.h:5,
from /home/myourshaw/.local/include/python3.8/Python.h:138,
from pysam/libcsamtools.c:4:
/home/myourshaw/.local/include/python3.8/code.h:122:28: note: expected ‘int’ but argument is of type ‘PyObject *’ {aka ‘struct _object *’}
PyAPI_FUNC(PyCodeObject *) PyCode_New(
^~~~~~~~~~
pysam/libcsamtools.c:1120:259: warning: passing argument 15 of ‘PyCode_New’ makes pointer from integer without a cast [-Wint-conversion]
__pyx_codeobj_ = (PyObject*)__Pyx_PyCode_New(0, 0, 0, 0, CO_OPTIMIZED|CO_NEWLOCALS, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_pysam_libcsamtools_pyx, __pyx_n_s_py_samtools, 1, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj_)) __PYX_ERR(0, 1, __pyx_L1_error)
^
pysam/libcsamtools.c:318:75: note: in definition of macro ‘__Pyx_PyCode_New’
PyCode_New(a, 0, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos)
^~~~~
In file included from /home/myourshaw/.local/include/python3.8/compile.h:5,
from /home/myourshaw/.local/include/python3.8/Python.h:138,
from pysam/libcsamtools.c:4:
/home/myourshaw/.local/include/python3.8/code.h:122:28: note: expected ‘PyObject *’ {aka ‘struct _object *’} but argument is of type ‘int’
PyAPI_FUNC(PyCodeObject *) PyCode_New(
^~~~~~~~~~
pysam/libcsamtools.c:318:11: error: too many arguments to function ‘PyCode_New’
PyCode_New(a, 0, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos)
^~~~~~~~~~
pysam/libcsamtools.c:1120:31: note: in expansion of macro ‘__Pyx_PyCode_New’
__pyx_codeobj_ = (PyObject*)__Pyx_PyCode_New(0, 0, 0, 0, CO_OPTIMIZED|CO_NEWLOCALS, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_pysam_libcsamtools_pyx, __pyx_n_s_py_samtools, 1, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj_)) __PYX_ERR(0, 1, __pyx_L1_error)
^~~~~~~~~~~~~~~~
In file included from /home/myourshaw/.local/include/python3.8/compile.h:5,
from /home/myourshaw/.local/include/python3.8/Python.h:138,
from pysam/libcsamtools.c:4:
/home/myourshaw/.local/include/python3.8/code.h:122:28: note: declared here
PyAPI_FUNC(PyCodeObject *) PyCode_New(
^~~~~~~~~~
pysam/libcsamtools.c: In function ‘__Pyx_CreateCodeObjectForTraceback’:
pysam/libcsamtools.c:1681:9: warning: passing argument 14 of ‘PyCode_New’ makes integer from pointer without a cast [-Wint-conversion]
py_funcname, /*PyObject *name,*/
^~~~~~~~~~~
pysam/libcsamtools.c:318:69: note: in definition of macro ‘__Pyx_PyCode_New’
PyCode_New(a, 0, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos)
^~~~
In file included from /home/myourshaw/.local/include/python3.8/compile.h:5,
from /home/myourshaw/.local/include/python3.8/Python.h:138,
from pysam/libcsamtools.c:4:
/home/myourshaw/.local/include/python3.8/code.h:122:28: note: expected ‘int’ but argument is of type ‘PyObject *’ {aka ‘struct _object *’}
PyAPI_FUNC(PyCodeObject *) PyCode_New(
^~~~~~~~~~
pysam/libcsamtools.c:1682:9: warning: passing argument 15 of ‘PyCode_New’ makes pointer from integer without a cast [-Wint-conversion]
py_line,
^~~~~~~
pysam/libcsamtools.c:318:75: note: in definition of macro ‘__Pyx_PyCode_New’
PyCode_New(a, 0, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos)
^~~~~
In file included from /home/myourshaw/.local/include/python3.8/compile.h:5,
from /home/myourshaw/.local/include/python3.8/Python.h:138,
from pysam/libcsamtools.c:4:
/home/myourshaw/.local/include/python3.8/code.h:122:28: note: expected ‘PyObject *’ {aka ‘struct _object *’} but argument is of type ‘int’
PyAPI_FUNC(PyCodeObject *) PyCode_New(
^~~~~~~~~~
pysam/libcsamtools.c:318:11: error: too many arguments to function ‘PyCode_New’
PyCode_New(a, 0, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos)
^~~~~~~~~~
pysam/libcsamtools.c:1668:15: note: in expansion of macro ‘__Pyx_PyCode_New’
py_code = __Pyx_PyCode_New(
^~~~~~~~~~~~~~~~
In file included from /home/myourshaw/.local/include/python3.8/compile.h:5,
from /home/myourshaw/.local/include/python3.8/Python.h:138,
from pysam/libcsamtools.c:4:
/home/myourshaw/.local/include/python3.8/code.h:122:28: note: declared here
PyAPI_FUNC(PyCodeObject *) PyCode_New(
^~~~~~~~~~
error: command 'gcc' failed with exit status 1
----------------------------------------
ERROR: Command errored out with exit status 1: /home/myourshaw/.virtualenvs/python38/bin/python3 -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-install-2vtoq395/pysam/setup.py'"'"'; __file__='"'"'/tmp/pip-install-2vtoq395/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-record-576yoxir/install-record.txt --single-version-externally-managed --compile --install-headers /home/myourshaw/.virtualenvs/python38/include/site/python3.8/pysam Check the logs for full command output.
(python38) yoursham-linux:~$
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