2021-07-15T11:04:48,464 Created temporary directory: /tmp/pip-ephem-wheel-cache-pegxtibu 2021-07-15T11:04:48,467 Created temporary directory: /tmp/pip-req-tracker-lfjvlokv 2021-07-15T11:04:48,468 Initialized build tracking at /tmp/pip-req-tracker-lfjvlokv 2021-07-15T11:04:48,468 Created build tracker: /tmp/pip-req-tracker-lfjvlokv 2021-07-15T11:04:48,468 Entered build tracker: /tmp/pip-req-tracker-lfjvlokv 2021-07-15T11:04:48,469 Created temporary directory: /tmp/pip-wheel-aps2kmfz 2021-07-15T11:04:48,501 1 location(s) to search for versions of pysam-cabbage: 2021-07-15T11:04:48,501 * https://pypi.org/simple/pysam-cabbage/ 2021-07-15T11:04:48,501 Fetching project page and analyzing links: https://pypi.org/simple/pysam-cabbage/ 2021-07-15T11:04:48,502 Getting page https://pypi.org/simple/pysam-cabbage/ 2021-07-15T11:04:48,503 Found index url https://pypi.org/simple 2021-07-15T11:04:48,717 Found link https://files.pythonhosted.org/packages/20/ee/0a784b6bebbda418a284f9787edfcdf2477a93c9f2f7f2ccb3bc9e882297/pysam-cabbage-0.15.3.tar.gz#sha256=172364a01c2c4eaf469e68a1d4774a4851e1eb43be2573a7f747d0ccd8458b49 (from https://pypi.org/simple/pysam-cabbage/), version: 0.15.3 2021-07-15T11:04:48,718 Skipping link: not a file: https://pypi.org/simple/pysam-cabbage/ 2021-07-15T11:04:48,736 Given no hashes to check 1 links for project 'pysam-cabbage': discarding no candidates 2021-07-15T11:04:48,755 Collecting pysam-cabbage==0.15.3 2021-07-15T11:04:48,756 Created temporary directory: /tmp/pip-unpack-29an5yhg 2021-07-15T11:04:49,097 Downloading pysam-cabbage-0.15.3.tar.gz (1.6 MB) 2021-07-15T11:04:50,538 Added pysam-cabbage==0.15.3 from https://files.pythonhosted.org/packages/20/ee/0a784b6bebbda418a284f9787edfcdf2477a93c9f2f7f2ccb3bc9e882297/pysam-cabbage-0.15.3.tar.gz#sha256=172364a01c2c4eaf469e68a1d4774a4851e1eb43be2573a7f747d0ccd8458b49 to build tracker '/tmp/pip-req-tracker-lfjvlokv' 2021-07-15T11:04:50,538 Running setup.py (path:/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/setup.py) egg_info for package pysam-cabbage 2021-07-15T11:04:50,539 Created temporary directory: /tmp/pip-pip-egg-info-bjf1ac3m 2021-07-15T11:04:50,540 Running command python setup.py egg_info 2021-07-15T11:04:51,732 # pysam: cython is available - using cythonize if necessary 2021-07-15T11:04:51,732 # pysam: htslib mode is shared 2021-07-15T11:04:51,732 # pysam: HTSLIB_CONFIGURE_OPTIONS=None 2021-07-15T11:04:51,732 # pysam: (sysconfig) CC=arm-linux-gnueabihf-gcc -pthread 2021-07-15T11:04:51,733 # pysam: (sysconfig) CFLAGS=-Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 2021-07-15T11:04:51,733 # pysam: (sysconfig) LDFLAGS= -Wl,-z,relro -g -fwrapv -O2 2021-07-15T11:04:52,196 checking for gcc... arm-linux-gnueabihf-gcc -pthread 2021-07-15T11:04:52,539 checking whether the C compiler works... yes 2021-07-15T11:04:52,541 checking for C compiler default output file name... a.out 2021-07-15T11:04:52,734 checking for suffix of executables... 2021-07-15T11:04:52,964 checking whether we are cross compiling... no 2021-07-15T11:04:53,078 checking for suffix of object files... o 2021-07-15T11:04:53,181 checking whether we are using the GNU C compiler... yes 2021-07-15T11:04:53,279 checking whether arm-linux-gnueabihf-gcc -pthread accepts -g... yes 2021-07-15T11:04:53,448 checking for arm-linux-gnueabihf-gcc -pthread option to accept ISO C89... none needed 2021-07-15T11:04:53,451 checking for ranlib... ranlib 2021-07-15T11:04:53,462 checking for grep that handles long lines and -e... /usr/bin/grep 2021-07-15T11:04:53,547 checking for C compiler warning flags... unknown 2021-07-15T11:04:53,550 checking for special C compiler options needed for large files... no 2021-07-15T11:04:53,788 checking for _FILE_OFFSET_BITS value needed for large files... 64 2021-07-15T11:04:54,036 checking for _LARGEFILE_SOURCE value needed for large files... no 2021-07-15T11:04:54,052 checking shared library type for unknown-Linux... plain .so 2021-07-15T11:04:54,194 checking how to run the C preprocessor... arm-linux-gnueabihf-gcc -pthread -E 2021-07-15T11:04:54,352 checking for egrep... /usr/bin/grep -E 2021-07-15T11:04:54,905 checking for ANSI C header files... yes 2021-07-15T11:04:55,057 checking for sys/types.h... yes 2021-07-15T11:04:55,231 checking for sys/stat.h... yes 2021-07-15T11:04:55,404 checking for stdlib.h... yes 2021-07-15T11:04:55,584 checking for string.h... yes 2021-07-15T11:04:55,766 checking for memory.h... yes 2021-07-15T11:04:55,945 checking for strings.h... yes 2021-07-15T11:04:56,129 checking for inttypes.h... yes 2021-07-15T11:04:56,314 checking for stdint.h... yes 2021-07-15T11:04:56,509 checking for unistd.h... yes 2021-07-15T11:04:56,547 checking for stdlib.h... (cached) yes 2021-07-15T11:04:56,584 checking for unistd.h... (cached) yes 2021-07-15T11:04:56,807 checking for sys/param.h... yes 2021-07-15T11:04:57,045 checking for getpagesize... yes 2021-07-15T11:04:57,414 checking for working mmap... yes 2021-07-15T11:04:57,650 checking for gmtime_r... yes 2021-07-15T11:04:57,897 checking for fsync... yes 2021-07-15T11:04:58,144 checking for drand48... yes 2021-07-15T11:04:58,381 checking whether fdatasync is declared... yes 2021-07-15T11:04:58,591 checking for fdatasync... yes 2021-07-15T11:04:59,078 checking for library containing log... -lm 2021-07-15T11:04:59,215 checking for zlib.h... yes 2021-07-15T11:04:59,426 checking for inflate in -lz... yes 2021-07-15T11:04:59,652 checking for library containing recv... none required 2021-07-15T11:04:59,765 checking for bzlib.h... yes 2021-07-15T11:04:59,982 checking for BZ2_bzBuffToBuffCompress in -lbz2... yes 2021-07-15T11:05:00,128 checking for lzma.h... yes 2021-07-15T11:05:00,354 checking for lzma_easy_buffer_encode in -llzma... yes 2021-07-15T11:05:00,472 checking for libdeflate.h... yes 2021-07-15T11:05:00,683 checking for libdeflate_deflate_compress in -ldeflate... yes 2021-07-15T11:05:01,093 checking for curl_easy_pause in -lcurl... yes 2021-07-15T11:05:01,350 checking for CCHmac... no 2021-07-15T11:05:02,005 checking for library containing HMAC... -lcrypto 2021-07-15T11:05:02,150 checking whether PTHREAD_MUTEX_RECURSIVE is declared... yes 2021-07-15T11:05:02,217 configure: creating ./config.status 2021-07-15T11:05:02,661 config.status: creating config.mk 2021-07-15T11:05:02,725 config.status: creating htslib.pc.tmp 2021-07-15T11:05:02,795 config.status: creating config.h 2021-07-15T11:05:02,955 make: ./version.sh: No such file or directory 2021-07-15T11:05:02,956 make: ./version.sh: No such file or directory 2021-07-15T11:05:03,253 # pysam: htslib configure options: --enable-libcurl 2021-07-15T11:05:03,253 # pysam: htslib_config LDFLAGS=-Wl,-z,relro -g -fwrapv -O2 2021-07-15T11:05:03,254 # 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 2021-07-15T11:05:03,254 # pysam: htslib_config LIBS=-ldeflate -llzma -lbz2 -lz -lm -lcurl -lcrypto 2021-07-15T11:05:03,254 # pysam: htslib_config PLATFORM=default 2021-07-15T11:05:03,254 # pysam: config_option: ENABLE_PLUGINS=0 2021-07-15T11:05:03,254 # pysam: config_option: HAVE_COMMONCRYPTO=0 2021-07-15T11:05:03,254 # pysam: config_option: HAVE_GMTIME_R=1 2021-07-15T11:05:03,254 # pysam: config_option: HAVE_HMAC=1 2021-07-15T11:05:03,254 # pysam: config_option: HAVE_IRODS=0 2021-07-15T11:05:03,255 # pysam: config_option: HAVE_LIBCURL=1 2021-07-15T11:05:03,255 # pysam: config_option: HAVE_MMAP=1 2021-07-15T11:05:03,255 running egg_info 2021-07-15T11:05:03,258 creating /tmp/pip-pip-egg-info-bjf1ac3m/pysam_cabbage.egg-info 2021-07-15T11:05:03,259 writing /tmp/pip-pip-egg-info-bjf1ac3m/pysam_cabbage.egg-info/PKG-INFO 2021-07-15T11:05:03,262 writing dependency_links to /tmp/pip-pip-egg-info-bjf1ac3m/pysam_cabbage.egg-info/dependency_links.txt 2021-07-15T11:05:03,265 writing top-level names to /tmp/pip-pip-egg-info-bjf1ac3m/pysam_cabbage.egg-info/top_level.txt 2021-07-15T11:05:03,267 writing manifest file '/tmp/pip-pip-egg-info-bjf1ac3m/pysam_cabbage.egg-info/SOURCES.txt' 2021-07-15T11:05:03,420 package init file 'samtools/__init__.py' not found (or not a regular file) 2021-07-15T11:05:03,422 package init file 'bcftools/__init__.py' not found (or not a regular file) 2021-07-15T11:05:03,423 package init file 'samtools/win32/__init__.py' not found (or not a regular file) 2021-07-15T11:05:03,424 package init file 'htslib/__init__.py' not found (or not a regular file) 2021-07-15T11:05:03,425 package init file 'htslib/htslib/__init__.py' not found (or not a regular file) 2021-07-15T11:05:03,479 reading manifest file '/tmp/pip-pip-egg-info-bjf1ac3m/pysam_cabbage.egg-info/SOURCES.txt' 2021-07-15T11:05:03,481 reading manifest template 'MANIFEST.in' 2021-07-15T11:05:03,484 warning: no files found matching 'KNOWN_BUGS' 2021-07-15T11:05:03,485 warning: no files found matching 'THANKS' 2021-07-15T11:05:03,490 warning: no files found matching 'pysam/libc*.c' 2021-07-15T11:05:03,494 no previously-included directories found matching 'tests/' 2021-07-15T11:05:03,495 warning: no files found matching 'samtools/configure' 2021-07-15T11:05:03,495 warning: no files found matching 'samtools/config.mk.in' 2021-07-15T11:05:03,496 warning: no files found matching 'samtools/config.h.in' 2021-07-15T11:05:03,543 adding license file 'COPYING' 2021-07-15T11:05:03,562 writing manifest file '/tmp/pip-pip-egg-info-bjf1ac3m/pysam_cabbage.egg-info/SOURCES.txt' 2021-07-15T11:05:03,640 Source in /tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27 has version 0.15.3, which satisfies requirement pysam-cabbage==0.15.3 from https://files.pythonhosted.org/packages/20/ee/0a784b6bebbda418a284f9787edfcdf2477a93c9f2f7f2ccb3bc9e882297/pysam-cabbage-0.15.3.tar.gz#sha256=172364a01c2c4eaf469e68a1d4774a4851e1eb43be2573a7f747d0ccd8458b49 2021-07-15T11:05:03,641 Removed pysam-cabbage==0.15.3 from https://files.pythonhosted.org/packages/20/ee/0a784b6bebbda418a284f9787edfcdf2477a93c9f2f7f2ccb3bc9e882297/pysam-cabbage-0.15.3.tar.gz#sha256=172364a01c2c4eaf469e68a1d4774a4851e1eb43be2573a7f747d0ccd8458b49 from build tracker '/tmp/pip-req-tracker-lfjvlokv' 2021-07-15T11:05:03,645 Created temporary directory: /tmp/pip-unpack-g3ab7fdn 2021-07-15T11:05:03,645 Building wheels for collected packages: pysam-cabbage 2021-07-15T11:05:03,649 Created temporary directory: /tmp/pip-wheel-3m5bkvge 2021-07-15T11:05:03,650 Building wheel for pysam-cabbage (setup.py): started 2021-07-15T11:05:03,650 Destination directory: /tmp/pip-wheel-3m5bkvge 2021-07-15T11:05:03,650 Running command /usr/bin/python3 -u -c 'import io, os, sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/setup.py'"'"'; __file__='"'"'/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/setup.py'"'"';f = getattr(tokenize, '"'"'open'"'"', open)(__file__) if os.path.exists(__file__) else io.StringIO('"'"'from setuptools import setup; setup()'"'"');code = f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' bdist_wheel -d /tmp/pip-wheel-3m5bkvge 2021-07-15T11:05:05,062 # pysam: cython is available - using cythonize if necessary 2021-07-15T11:05:05,062 # pysam: htslib mode is shared 2021-07-15T11:05:05,063 # pysam: HTSLIB_CONFIGURE_OPTIONS=None 2021-07-15T11:05:05,063 # pysam: (sysconfig) CC=arm-linux-gnueabihf-gcc -pthread 2021-07-15T11:05:05,063 # pysam: (sysconfig) CFLAGS=-Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 2021-07-15T11:05:05,063 # pysam: (sysconfig) LDFLAGS= -Wl,-z,relro -g -fwrapv -O2 2021-07-15T11:05:05,531 checking for gcc... arm-linux-gnueabihf-gcc -pthread 2021-07-15T11:05:05,883 checking whether the C compiler works... yes 2021-07-15T11:05:05,884 checking for C compiler default output file name... a.out 2021-07-15T11:05:06,076 checking for suffix of executables... 2021-07-15T11:05:06,312 checking whether we are cross compiling... no 2021-07-15T11:05:06,427 checking for suffix of object files... o 2021-07-15T11:05:06,533 checking whether we are using the GNU C compiler... yes 2021-07-15T11:05:06,633 checking whether arm-linux-gnueabihf-gcc -pthread accepts -g... yes 2021-07-15T11:05:06,802 checking for arm-linux-gnueabihf-gcc -pthread option to accept ISO C89... none needed 2021-07-15T11:05:06,804 checking for ranlib... ranlib 2021-07-15T11:05:06,815 checking for grep that handles long lines and -e... /usr/bin/grep 2021-07-15T11:05:06,904 checking for C compiler warning flags... unknown 2021-07-15T11:05:06,907 checking for special C compiler options needed for large files... no 2021-07-15T11:05:07,151 checking for _FILE_OFFSET_BITS value needed for large files... 64 2021-07-15T11:05:07,407 checking for _LARGEFILE_SOURCE value needed for large files... no 2021-07-15T11:05:07,421 checking shared library type for unknown-Linux... plain .so 2021-07-15T11:05:07,570 checking how to run the C preprocessor... arm-linux-gnueabihf-gcc -pthread -E 2021-07-15T11:05:07,723 checking for egrep... /usr/bin/grep -E 2021-07-15T11:05:08,273 checking for ANSI C header files... yes 2021-07-15T11:05:08,432 checking for sys/types.h... yes 2021-07-15T11:05:08,613 checking for sys/stat.h... yes 2021-07-15T11:05:08,790 checking for stdlib.h... yes 2021-07-15T11:05:08,977 checking for string.h... yes 2021-07-15T11:05:09,163 checking for memory.h... yes 2021-07-15T11:05:09,350 checking for strings.h... yes 2021-07-15T11:05:09,538 checking for inttypes.h... yes 2021-07-15T11:05:09,728 checking for stdint.h... yes 2021-07-15T11:05:09,921 checking for unistd.h... yes 2021-07-15T11:05:09,956 checking for stdlib.h... (cached) yes 2021-07-15T11:05:09,995 checking for unistd.h... (cached) yes 2021-07-15T11:05:10,223 checking for sys/param.h... yes 2021-07-15T11:05:10,463 checking for getpagesize... yes 2021-07-15T11:05:10,825 checking for working mmap... yes 2021-07-15T11:05:11,065 checking for gmtime_r... yes 2021-07-15T11:05:11,327 checking for fsync... yes 2021-07-15T11:05:11,595 checking for drand48... yes 2021-07-15T11:05:11,839 checking whether fdatasync is declared... yes 2021-07-15T11:05:12,057 checking for fdatasync... yes 2021-07-15T11:05:12,553 checking for library containing log... -lm 2021-07-15T11:05:12,693 checking for zlib.h... yes 2021-07-15T11:05:12,900 checking for inflate in -lz... yes 2021-07-15T11:05:13,127 checking for library containing recv... none required 2021-07-15T11:05:13,264 checking for bzlib.h... yes 2021-07-15T11:05:13,498 checking for BZ2_bzBuffToBuffCompress in -lbz2... yes 2021-07-15T11:05:13,624 checking for lzma.h... yes 2021-07-15T11:05:13,840 checking for lzma_easy_buffer_encode in -llzma... yes 2021-07-15T11:05:13,954 checking for libdeflate.h... yes 2021-07-15T11:05:14,172 checking for libdeflate_deflate_compress in -ldeflate... yes 2021-07-15T11:05:14,575 checking for curl_easy_pause in -lcurl... yes 2021-07-15T11:05:14,843 checking for CCHmac... no 2021-07-15T11:05:15,500 checking for library containing HMAC... -lcrypto 2021-07-15T11:05:15,656 checking whether PTHREAD_MUTEX_RECURSIVE is declared... yes 2021-07-15T11:05:15,744 configure: creating ./config.status 2021-07-15T11:05:16,449 config.status: creating config.mk 2021-07-15T11:05:16,521 config.status: creating htslib.pc.tmp 2021-07-15T11:05:16,594 config.status: creating config.h 2021-07-15T11:05:16,623 config.status: config.h is unchanged 2021-07-15T11:05:16,738 # pysam: htslib configure options: --enable-libcurl 2021-07-15T11:05:16,755 make: ./version.sh: No such file or directory 2021-07-15T11:05:16,755 make: ./version.sh: No such file or directory 2021-07-15T11:05:16,796 # pysam: htslib_config LDFLAGS=-Wl,-z,relro -g -fwrapv -O2 2021-07-15T11:05:16,797 # 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 2021-07-15T11:05:16,797 # pysam: htslib_config LIBS=-ldeflate -llzma -lbz2 -lz -lm -lcurl -lcrypto 2021-07-15T11:05:16,797 # pysam: htslib_config PLATFORM=default 2021-07-15T11:05:16,802 # pysam: config_option: ENABLE_PLUGINS=0 2021-07-15T11:05:16,803 # pysam: config_option: HAVE_COMMONCRYPTO=0 2021-07-15T11:05:16,803 # pysam: config_option: HAVE_GMTIME_R=1 2021-07-15T11:05:16,804 # pysam: config_option: HAVE_HMAC=1 2021-07-15T11:05:16,804 # pysam: config_option: HAVE_IRODS=0 2021-07-15T11:05:16,804 # pysam: config_option: HAVE_LIBCURL=1 2021-07-15T11:05:16,804 # pysam: config_option: HAVE_MMAP=1 2021-07-15T11:05:17,040 running bdist_wheel 2021-07-15T11:05:17,046 running build 2021-07-15T11:05:17,047 running build_py 2021-07-15T11:05:17,189 creating build 2021-07-15T11:05:17,189 creating build/lib.linux-armv7l-3.9 2021-07-15T11:05:17,190 creating build/lib.linux-armv7l-3.9/pysam 2021-07-15T11:05:17,192 copying pysam/__init__.py -> build/lib.linux-armv7l-3.9/pysam 2021-07-15T11:05:17,195 copying pysam/samtools.py -> build/lib.linux-armv7l-3.9/pysam 2021-07-15T11:05:17,197 copying pysam/config.py -> build/lib.linux-armv7l-3.9/pysam 2021-07-15T11:05:17,199 copying pysam/utils.py -> build/lib.linux-armv7l-3.9/pysam 2021-07-15T11:05:17,201 copying pysam/bcftools.py -> build/lib.linux-armv7l-3.9/pysam 2021-07-15T11:05:17,203 copying pysam/version.py -> build/lib.linux-armv7l-3.9/pysam 2021-07-15T11:05:17,205 copying pysam/Pileup.py -> build/lib.linux-armv7l-3.9/pysam 2021-07-15T11:05:17,208 creating build/lib.linux-armv7l-3.9/pysam/include 2021-07-15T11:05:17,209 copying pysam/include/__init__.py -> build/lib.linux-armv7l-3.9/pysam/include 2021-07-15T11:05:17,211 package init file 'samtools/__init__.py' not found (or not a regular file) 2021-07-15T11:05:17,212 package init file 'bcftools/__init__.py' not found (or not a regular file) 2021-07-15T11:05:17,213 package init file 'samtools/win32/__init__.py' not found (or not a regular file) 2021-07-15T11:05:17,214 package init file 'htslib/__init__.py' not found (or not a regular file) 2021-07-15T11:05:17,215 package init file 'htslib/htslib/__init__.py' not found (or not a regular file) 2021-07-15T11:05:17,257 copying pysam/libcsamtools.pxd -> build/lib.linux-armv7l-3.9/pysam 2021-07-15T11:05:17,260 copying pysam/libcutils.pxd -> build/lib.linux-armv7l-3.9/pysam 2021-07-15T11:05:17,262 copying pysam/libctabix.pxd -> build/lib.linux-armv7l-3.9/pysam 2021-07-15T11:05:17,264 copying pysam/libcsamfile.pxd -> build/lib.linux-armv7l-3.9/pysam 2021-07-15T11:05:17,267 copying pysam/libcbcftools.pxd -> build/lib.linux-armv7l-3.9/pysam 2021-07-15T11:05:17,269 copying pysam/libcalignedsegment.pxd -> build/lib.linux-armv7l-3.9/pysam 2021-07-15T11:05:17,272 copying pysam/libcbcf.pxd -> build/lib.linux-armv7l-3.9/pysam 2021-07-15T11:05:17,274 copying pysam/libcalignmentfile.pxd -> build/lib.linux-armv7l-3.9/pysam 2021-07-15T11:05:17,277 copying pysam/libchtslib.pxd -> build/lib.linux-armv7l-3.9/pysam 2021-07-15T11:05:17,282 copying pysam/libctabixproxies.pxd -> build/lib.linux-armv7l-3.9/pysam 2021-07-15T11:05:17,284 copying pysam/libcfaidx.pxd -> build/lib.linux-armv7l-3.9/pysam 2021-07-15T11:05:17,287 copying pysam/libcvcf.pxd -> build/lib.linux-armv7l-3.9/pysam 2021-07-15T11:05:17,289 copying pysam/htslib_util.h -> build/lib.linux-armv7l-3.9/pysam 2021-07-15T11:05:17,292 copying pysam/csamtools_util.h -> build/lib.linux-armv7l-3.9/pysam 2021-07-15T11:05:17,294 copying pysam/pysam_util.h -> build/lib.linux-armv7l-3.9/pysam 2021-07-15T11:05:17,296 copying pysam/pysam_stream.h -> build/lib.linux-armv7l-3.9/pysam 2021-07-15T11:05:17,298 copying pysam/cbcftools_util.h -> build/lib.linux-armv7l-3.9/pysam 2021-07-15T11:05:17,300 creating build/lib.linux-armv7l-3.9/pysam/include/samtools 2021-07-15T11:05:17,301 copying samtools/bam_plbuf.h -> build/lib.linux-armv7l-3.9/pysam/include/samtools 2021-07-15T11:05:17,303 copying samtools/sam.h -> build/lib.linux-armv7l-3.9/pysam/include/samtools 2021-07-15T11:05:17,306 copying samtools/sample.h -> build/lib.linux-armv7l-3.9/pysam/include/samtools 2021-07-15T11:05:17,308 copying samtools/config.h -> build/lib.linux-armv7l-3.9/pysam/include/samtools 2021-07-15T11:05:17,310 copying samtools/sam_opts.h -> build/lib.linux-armv7l-3.9/pysam/include/samtools 2021-07-15T11:05:17,313 copying samtools/samtools.h -> build/lib.linux-armv7l-3.9/pysam/include/samtools 2021-07-15T11:05:17,315 copying samtools/version.h -> build/lib.linux-armv7l-3.9/pysam/include/samtools 2021-07-15T11:05:17,317 copying samtools/bam_lpileup.h -> build/lib.linux-armv7l-3.9/pysam/include/samtools 2021-07-15T11:05:17,319 copying samtools/stats_isize.h -> build/lib.linux-armv7l-3.9/pysam/include/samtools 2021-07-15T11:05:17,322 copying samtools/bam2bcf.h -> build/lib.linux-armv7l-3.9/pysam/include/samtools 2021-07-15T11:05:17,324 copying samtools/sam_header.h -> build/lib.linux-armv7l-3.9/pysam/include/samtools 2021-07-15T11:05:17,326 copying samtools/bam_endian.h -> build/lib.linux-armv7l-3.9/pysam/include/samtools 2021-07-15T11:05:17,329 copying samtools/tmp_file.h -> build/lib.linux-armv7l-3.9/pysam/include/samtools 2021-07-15T11:05:17,331 copying samtools/samtools.pysam.h -> build/lib.linux-armv7l-3.9/pysam/include/samtools 2021-07-15T11:05:17,334 copying samtools/bedidx.h -> build/lib.linux-armv7l-3.9/pysam/include/samtools 2021-07-15T11:05:17,338 copying samtools/bam.h -> build/lib.linux-armv7l-3.9/pysam/include/samtools 2021-07-15T11:05:17,342 creating build/lib.linux-armv7l-3.9/pysam/include/bcftools 2021-07-15T11:05:17,343 copying bcftools/smpl_ilist.h -> build/lib.linux-armv7l-3.9/pysam/include/bcftools 2021-07-15T11:05:17,346 copying bcftools/gvcf.h -> build/lib.linux-armv7l-3.9/pysam/include/bcftools 2021-07-15T11:05:17,349 copying bcftools/tsv2vcf.h -> build/lib.linux-armv7l-3.9/pysam/include/bcftools 2021-07-15T11:05:17,353 copying bcftools/vcmp.h -> build/lib.linux-armv7l-3.9/pysam/include/bcftools 2021-07-15T11:05:17,356 copying bcftools/convert.h -> build/lib.linux-armv7l-3.9/pysam/include/bcftools 2021-07-15T11:05:17,358 copying bcftools/rbuf.h -> build/lib.linux-armv7l-3.9/pysam/include/bcftools 2021-07-15T11:05:17,362 copying bcftools/config.h -> build/lib.linux-armv7l-3.9/pysam/include/bcftools 2021-07-15T11:05:17,364 copying bcftools/filter.h -> build/lib.linux-armv7l-3.9/pysam/include/bcftools 2021-07-15T11:05:17,367 copying bcftools/mw.h -> build/lib.linux-armv7l-3.9/pysam/include/bcftools 2021-07-15T11:05:17,373 copying bcftools/version.h -> build/lib.linux-armv7l-3.9/pysam/include/bcftools 2021-07-15T11:05:17,377 copying bcftools/HMM.h -> build/lib.linux-armv7l-3.9/pysam/include/bcftools 2021-07-15T11:05:17,381 copying bcftools/hclust.h -> build/lib.linux-armv7l-3.9/pysam/include/bcftools 2021-07-15T11:05:17,384 copying bcftools/kheap.h -> build/lib.linux-armv7l-3.9/pysam/include/bcftools 2021-07-15T11:05:17,387 copying bcftools/call.h -> build/lib.linux-armv7l-3.9/pysam/include/bcftools 2021-07-15T11:05:17,391 copying bcftools/kmin.h -> build/lib.linux-armv7l-3.9/pysam/include/bcftools 2021-07-15T11:05:17,394 copying bcftools/bcftools.pysam.h -> build/lib.linux-armv7l-3.9/pysam/include/bcftools 2021-07-15T11:05:17,396 copying bcftools/bin.h -> build/lib.linux-armv7l-3.9/pysam/include/bcftools 2021-07-15T11:05:17,399 copying bcftools/prob1.h -> build/lib.linux-armv7l-3.9/pysam/include/bcftools 2021-07-15T11:05:17,402 copying bcftools/bam2bcf.h -> build/lib.linux-armv7l-3.9/pysam/include/bcftools 2021-07-15T11:05:17,405 copying bcftools/bcftools.h -> build/lib.linux-armv7l-3.9/pysam/include/bcftools 2021-07-15T11:05:17,408 copying bcftools/vcfbuf.h -> build/lib.linux-armv7l-3.9/pysam/include/bcftools 2021-07-15T11:05:17,412 copying bcftools/khash_str2str.h -> build/lib.linux-armv7l-3.9/pysam/include/bcftools 2021-07-15T11:05:17,415 copying bcftools/bam_sample.h -> build/lib.linux-armv7l-3.9/pysam/include/bcftools 2021-07-15T11:05:17,418 copying bcftools/regidx.h -> build/lib.linux-armv7l-3.9/pysam/include/bcftools 2021-07-15T11:05:17,421 copying bcftools/ploidy.h -> build/lib.linux-armv7l-3.9/pysam/include/bcftools 2021-07-15T11:05:17,424 creating build/lib.linux-armv7l-3.9/pysam/include/samtools/win32 2021-07-15T11:05:17,425 copying samtools/win32/zlib.h -> build/lib.linux-armv7l-3.9/pysam/include/samtools/win32 2021-07-15T11:05:17,430 copying samtools/win32/xcurses.h -> build/lib.linux-armv7l-3.9/pysam/include/samtools/win32 2021-07-15T11:05:17,435 copying samtools/win32/zconf.h -> build/lib.linux-armv7l-3.9/pysam/include/samtools/win32 2021-07-15T11:05:17,439 creating build/lib.linux-armv7l-3.9/pysam/include/htslib 2021-07-15T11:05:17,440 copying htslib/thread_pool_internal.h -> build/lib.linux-armv7l-3.9/pysam/include/htslib 2021-07-15T11:05:17,443 copying htslib/bcf_sr_sort.h -> build/lib.linux-armv7l-3.9/pysam/include/htslib 2021-07-15T11:05:17,447 copying htslib/config.h -> build/lib.linux-armv7l-3.9/pysam/include/htslib 2021-07-15T11:05:17,450 copying htslib/version.h -> build/lib.linux-armv7l-3.9/pysam/include/htslib 2021-07-15T11:05:17,452 copying htslib/hts_internal.h -> build/lib.linux-armv7l-3.9/pysam/include/htslib 2021-07-15T11:05:17,455 copying htslib/hfile_internal.h -> build/lib.linux-armv7l-3.9/pysam/include/htslib 2021-07-15T11:05:17,457 copying htslib/textutils_internal.h -> build/lib.linux-armv7l-3.9/pysam/include/htslib 2021-07-15T11:05:17,460 creating build/lib.linux-armv7l-3.9/pysam/include/htslib/htslib 2021-07-15T11:05:17,461 copying htslib/htslib/sam.h -> build/lib.linux-armv7l-3.9/pysam/include/htslib/htslib 2021-07-15T11:05:17,465 copying htslib/htslib/ksort.h -> build/lib.linux-armv7l-3.9/pysam/include/htslib/htslib 2021-07-15T11:05:17,468 copying htslib/htslib/cram.h -> build/lib.linux-armv7l-3.9/pysam/include/htslib/htslib 2021-07-15T11:05:17,472 copying htslib/htslib/faidx.h -> build/lib.linux-armv7l-3.9/pysam/include/htslib/htslib 2021-07-15T11:05:17,475 copying htslib/htslib/hts_log.h -> build/lib.linux-armv7l-3.9/pysam/include/htslib/htslib 2021-07-15T11:05:17,477 copying htslib/htslib/khash_str2int.h -> build/lib.linux-armv7l-3.9/pysam/include/htslib/htslib 2021-07-15T11:05:17,479 copying htslib/htslib/kfunc.h -> build/lib.linux-armv7l-3.9/pysam/include/htslib/htslib 2021-07-15T11:05:17,482 copying htslib/htslib/vcf.h -> build/lib.linux-armv7l-3.9/pysam/include/htslib/htslib 2021-07-15T11:05:17,485 copying htslib/htslib/hfile.h -> build/lib.linux-armv7l-3.9/pysam/include/htslib/htslib 2021-07-15T11:05:17,488 copying htslib/htslib/khash.h -> build/lib.linux-armv7l-3.9/pysam/include/htslib/htslib 2021-07-15T11:05:17,491 copying htslib/htslib/hts.h -> build/lib.linux-armv7l-3.9/pysam/include/htslib/htslib 2021-07-15T11:05:17,494 copying htslib/htslib/kseq.h -> build/lib.linux-armv7l-3.9/pysam/include/htslib/htslib 2021-07-15T11:05:17,497 copying htslib/htslib/hts_defs.h -> build/lib.linux-armv7l-3.9/pysam/include/htslib/htslib 2021-07-15T11:05:17,499 copying htslib/htslib/tbx.h -> build/lib.linux-armv7l-3.9/pysam/include/htslib/htslib 2021-07-15T11:05:17,502 copying htslib/htslib/thread_pool.h -> build/lib.linux-armv7l-3.9/pysam/include/htslib/htslib 2021-07-15T11:05:17,505 copying htslib/htslib/synced_bcf_reader.h -> build/lib.linux-armv7l-3.9/pysam/include/htslib/htslib 2021-07-15T11:05:17,508 copying htslib/htslib/hts_os.h -> build/lib.linux-armv7l-3.9/pysam/include/htslib/htslib 2021-07-15T11:05:17,510 copying htslib/htslib/kbitset.h -> build/lib.linux-armv7l-3.9/pysam/include/htslib/htslib 2021-07-15T11:05:17,513 copying htslib/htslib/kstring.h -> build/lib.linux-armv7l-3.9/pysam/include/htslib/htslib 2021-07-15T11:05:17,516 copying htslib/htslib/bgzf.h -> build/lib.linux-armv7l-3.9/pysam/include/htslib/htslib 2021-07-15T11:05:17,519 copying htslib/htslib/hts_endian.h -> build/lib.linux-armv7l-3.9/pysam/include/htslib/htslib 2021-07-15T11:05:17,522 copying htslib/htslib/klist.h -> build/lib.linux-armv7l-3.9/pysam/include/htslib/htslib 2021-07-15T11:05:17,524 copying htslib/htslib/knetfile.h -> build/lib.linux-armv7l-3.9/pysam/include/htslib/htslib 2021-07-15T11:05:17,527 copying htslib/htslib/vcf_sweep.h -> build/lib.linux-armv7l-3.9/pysam/include/htslib/htslib 2021-07-15T11:05:17,529 copying htslib/htslib/regidx.h -> build/lib.linux-armv7l-3.9/pysam/include/htslib/htslib 2021-07-15T11:05:17,532 copying htslib/htslib/vcfutils.h -> build/lib.linux-armv7l-3.9/pysam/include/htslib/htslib 2021-07-15T11:05:17,535 /usr/local/lib/python3.9/dist-packages/setuptools/lib2to3_ex.py:36: SetuptoolsDeprecationWarning: 2to3 support is deprecated. If the project still requires Python 2 support, please migrate to a single-codebase solution or employ an independent conversion process. 2021-07-15T11:05:17,535 warnings.warn( 2021-07-15T11:05:17,535 Fixing build/lib.linux-armv7l-3.9/pysam/__init__.py build/lib.linux-armv7l-3.9/pysam/samtools.py build/lib.linux-armv7l-3.9/pysam/config.py build/lib.linux-armv7l-3.9/pysam/utils.py build/lib.linux-armv7l-3.9/pysam/bcftools.py build/lib.linux-armv7l-3.9/pysam/version.py build/lib.linux-armv7l-3.9/pysam/Pileup.py build/lib.linux-armv7l-3.9/pysam/include/__init__.py 2021-07-15T11:05:17,560 Skipping optional fixer: buffer 2021-07-15T11:05:17,626 Skipping optional fixer: idioms 2021-07-15T11:05:17,792 Skipping optional fixer: set_literal 2021-07-15T11:05:17,917 Skipping optional fixer: ws_comma 2021-07-15T11:05:18,571 Fixing build/lib.linux-armv7l-3.9/pysam/__init__.py build/lib.linux-armv7l-3.9/pysam/samtools.py build/lib.linux-armv7l-3.9/pysam/config.py build/lib.linux-armv7l-3.9/pysam/utils.py build/lib.linux-armv7l-3.9/pysam/bcftools.py build/lib.linux-armv7l-3.9/pysam/version.py build/lib.linux-armv7l-3.9/pysam/Pileup.py build/lib.linux-armv7l-3.9/pysam/include/__init__.py 2021-07-15T11:05:18,580 Skipping optional fixer: buffer 2021-07-15T11:05:18,626 Skipping optional fixer: idioms 2021-07-15T11:05:18,759 Skipping optional fixer: set_literal 2021-07-15T11:05:18,847 Skipping optional fixer: ws_comma 2021-07-15T11:05:18,997 running build_ext 2021-07-15T11:05:19,061 cythoning pysam/libchtslib.pyx to pysam/libchtslib.c 2021-07-15T11:05:19,732 /usr/local/lib/python3.9/dist-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-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/pysam/libchtslib.pxd 2021-07-15T11:05:19,732 tree = Parsing.p_module(s, pxd, full_module_name) 2021-07-15T11:05:24,531 cythoning pysam/libcsamtools.pyx to pysam/libcsamtools.c 2021-07-15T11:05:24,538 /usr/local/lib/python3.9/dist-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-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/pysam/libcsamtools.pxd 2021-07-15T11:05:24,539 tree = Parsing.p_module(s, pxd, full_module_name) 2021-07-15T11:05:24,579 cythoning pysam/libcbcftools.pyx to pysam/libcbcftools.c 2021-07-15T11:05:24,586 /usr/local/lib/python3.9/dist-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-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/pysam/libcbcftools.pxd 2021-07-15T11:05:24,586 tree = Parsing.p_module(s, pxd, full_module_name) 2021-07-15T11:05:24,622 cythoning pysam/libcutils.pyx to pysam/libcutils.c 2021-07-15T11:05:24,629 /usr/local/lib/python3.9/dist-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-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/pysam/libcutils.pxd 2021-07-15T11:05:24,630 tree = Parsing.p_module(s, pxd, full_module_name) 2021-07-15T11:05:27,526 cythoning pysam/libcalignmentfile.pyx to pysam/libcalignmentfile.c 2021-07-15T11:05:27,548 /usr/local/lib/python3.9/dist-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-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/pysam/libcalignmentfile.pxd 2021-07-15T11:05:27,548 tree = Parsing.p_module(s, pxd, full_module_name) 2021-07-15T11:05:33,311 warning: pysam/libcalignmentfile.pyx:2528:49: Casting a GIL-requiring function into a nogil function circumvents GIL validation 2021-07-15T11:05:33,312 warning: pysam/libcalignmentfile.pyx:2533:49: Casting a GIL-requiring function into a nogil function circumvents GIL validation 2021-07-15T11:05:33,312 warning: pysam/libcalignmentfile.pyx:2538:49: Casting a GIL-requiring function into a nogil function circumvents GIL validation 2021-07-15T11:05:35,003 cythoning pysam/libcsamfile.pyx to pysam/libcsamfile.c 2021-07-15T11:05:35,010 /usr/local/lib/python3.9/dist-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-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/pysam/libcsamfile.pxd 2021-07-15T11:05:35,010 tree = Parsing.p_module(s, pxd, full_module_name) 2021-07-15T11:05:38,460 cythoning pysam/libcalignedsegment.pyx to pysam/libcalignedsegment.c 2021-07-15T11:05:38,467 /usr/local/lib/python3.9/dist-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-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/pysam/libcalignedsegment.pxd 2021-07-15T11:05:38,467 tree = Parsing.p_module(s, pxd, full_module_name) 2021-07-15T11:05:52,236 cythoning pysam/libctabix.pyx to pysam/libctabix.c 2021-07-15T11:05:52,245 /usr/local/lib/python3.9/dist-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-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/pysam/libctabix.pxd 2021-07-15T11:05:52,245 tree = Parsing.p_module(s, pxd, full_module_name) 2021-07-15T11:05:57,978 cythoning pysam/libcfaidx.pyx to pysam/libcfaidx.c 2021-07-15T11:05:57,985 /usr/local/lib/python3.9/dist-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-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/pysam/libcfaidx.pxd 2021-07-15T11:05:57,986 tree = Parsing.p_module(s, pxd, full_module_name) 2021-07-15T11:06:02,599 cythoning pysam/libcbcf.pyx to pysam/libcbcf.c 2021-07-15T11:06:02,613 /usr/local/lib/python3.9/dist-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-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/pysam/libcbcf.pxd 2021-07-15T11:06:02,614 tree = Parsing.p_module(s, pxd, full_module_name) 2021-07-15T11:06:16,175 cythoning pysam/libcbgzf.pyx to pysam/libcbgzf.c 2021-07-15T11:06:16,184 /usr/local/lib/python3.9/dist-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-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/pysam/libcbgzf.pyx 2021-07-15T11:06:16,184 tree = Parsing.p_module(s, pxd, full_module_name) 2021-07-15T11:06:20,101 cythoning pysam/libctabixproxies.pyx to pysam/libctabixproxies.c 2021-07-15T11:06:20,108 /usr/local/lib/python3.9/dist-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-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/pysam/libctabixproxies.pxd 2021-07-15T11:06:20,108 tree = Parsing.p_module(s, pxd, full_module_name) 2021-07-15T11:06:23,958 cythoning pysam/libcvcf.pyx to pysam/libcvcf.c 2021-07-15T11:06:23,966 /usr/local/lib/python3.9/dist-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-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/pysam/libcvcf.pxd 2021-07-15T11:06:23,966 tree = Parsing.p_module(s, pxd, full_module_name) 2021-07-15T11:06:25,105 warning: pysam/libcvcf.pyx:1083:27: Unreachable code 2021-07-15T11:06:30,944 building 'pysam.libchtslib' extension 2021-07-15T11:06:30,946 creating build/temp.linux-armv7l-3.9 2021-07-15T11:06:30,947 creating build/temp.linux-armv7l-3.9/htslib 2021-07-15T11:06:30,948 creating build/temp.linux-armv7l-3.9/htslib/cram 2021-07-15T11:06:30,951 creating build/temp.linux-armv7l-3.9/pysam 2021-07-15T11:06:30,951 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/htslib -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/samtools -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/samtools/lz4 -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/bcftools -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/pysam -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27 -I/usr/include/python3.9 -c htslib/bcf_sr_sort.c -o build/temp.linux-armv7l-3.9/htslib/bcf_sr_sort.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 2021-07-15T11:06:32,872 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/htslib -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/samtools -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/samtools/lz4 -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/bcftools -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/pysam -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27 -I/usr/include/python3.9 -c htslib/bgzf.c -o build/temp.linux-armv7l-3.9/htslib/bgzf.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 2021-07-15T11:06:35,299 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/htslib -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/samtools -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/samtools/lz4 -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/bcftools -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/pysam -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27 -I/usr/include/python3.9 -c htslib/cram/cram_codecs.c -o build/temp.linux-armv7l-3.9/htslib/cram/cram_codecs.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 2021-07-15T11:06:38,098 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/htslib -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/samtools -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/samtools/lz4 -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/bcftools -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/pysam -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27 -I/usr/include/python3.9 -c htslib/cram/cram_decode.c -o build/temp.linux-armv7l-3.9/htslib/cram/cram_decode.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 2021-07-15T11:06:44,252 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/htslib -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/samtools -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/samtools/lz4 -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/bcftools -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/pysam -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27 -I/usr/include/python3.9 -c htslib/cram/cram_encode.c -o build/temp.linux-armv7l-3.9/htslib/cram/cram_encode.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 2021-07-15T11:06:49,794 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/htslib -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/samtools -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/samtools/lz4 -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/bcftools -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/pysam -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27 -I/usr/include/python3.9 -c htslib/cram/cram_external.c -o build/temp.linux-armv7l-3.9/htslib/cram/cram_external.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 2021-07-15T11:06:50,392 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/htslib -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/samtools -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/samtools/lz4 -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/bcftools -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/pysam -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27 -I/usr/include/python3.9 -c htslib/cram/cram_index.c -o build/temp.linux-armv7l-3.9/htslib/cram/cram_index.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 2021-07-15T11:06:51,452 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/htslib -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/samtools -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/samtools/lz4 -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/bcftools -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/pysam -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27 -I/usr/include/python3.9 -c htslib/cram/cram_io.c -o build/temp.linux-armv7l-3.9/htslib/cram/cram_io.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 2021-07-15T11:06:56,040 In file included from /usr/include/string.h:495, 2021-07-15T11:06:56,040 from htslib/cram/cram_io.c:53: 2021-07-15T11:06:56,040 In function ‘strncpy’, 2021-07-15T11:06:56,040 inlined from ‘full_path’ at htslib/cram/cram_io.c:3748:13, 2021-07-15T11:06:56,041 inlined from ‘cram_write_SAM_hdr’ at htslib/cram/cram_io.c:3823:17: 2021-07-15T11:06:56,041 /usr/include/arm-linux-gnueabihf/bits/string_fortified.h:106:10: warning: ‘__builtin_strncpy’ specified bound 4096 equals destination size [-Wstringop-truncation] 2021-07-15T11:06:56,041 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); 2021-07-15T11:06:56,041 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-15T11:06:56,041 In function ‘strncpy’, 2021-07-15T11:06:56,041 inlined from ‘full_path’ at htslib/cram/cram_io.c:3740:9, 2021-07-15T11:06:56,041 inlined from ‘cram_write_SAM_hdr’ at htslib/cram/cram_io.c:3823:17: 2021-07-15T11:06:56,041 /usr/include/arm-linux-gnueabihf/bits/string_fortified.h:106:10: warning: ‘__builtin_strncpy’ specified bound 4096 equals destination size [-Wstringop-truncation] 2021-07-15T11:06:56,042 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); 2021-07-15T11:06:56,042 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-15T11:06:56,313 In function ‘strncpy’, 2021-07-15T11:06:56,313 inlined from ‘cram_dopen’ at htslib/cram/cram_io.c:4126:9: 2021-07-15T11:06:56,313 /usr/include/arm-linux-gnueabihf/bits/string_fortified.h:106:10: warning: ‘__builtin_strncpy’ specified bound 20 equals destination size [-Wstringop-truncation] 2021-07-15T11:06:56,314 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); 2021-07-15T11:06:56,314 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-15T11:06:57,157 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/htslib -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/samtools -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/samtools/lz4 -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/bcftools -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/pysam -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27 -I/usr/include/python3.9 -c htslib/cram/cram_samtools.c -o build/temp.linux-armv7l-3.9/htslib/cram/cram_samtools.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 2021-07-15T11:06:57,561 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/htslib -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/samtools -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/samtools/lz4 -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/bcftools -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/pysam -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27 -I/usr/include/python3.9 -c htslib/cram/cram_stats.c -o build/temp.linux-armv7l-3.9/htslib/cram/cram_stats.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 2021-07-15T11:06:58,180 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/htslib -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/samtools -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/samtools/lz4 -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/bcftools -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/pysam -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27 -I/usr/include/python3.9 -c htslib/cram/files.c -o build/temp.linux-armv7l-3.9/htslib/cram/files.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 2021-07-15T11:06:58,376 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/htslib -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/samtools -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/samtools/lz4 -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/bcftools -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/pysam -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27 -I/usr/include/python3.9 -c htslib/cram/mFILE.c -o build/temp.linux-armv7l-3.9/htslib/cram/mFILE.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 2021-07-15T11:06:58,992 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/htslib -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/samtools -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/samtools/lz4 -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/bcftools -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/pysam -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27 -I/usr/include/python3.9 -c htslib/cram/open_trace_file.c -o build/temp.linux-armv7l-3.9/htslib/cram/open_trace_file.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 2021-07-15T11:06:59,536 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/htslib -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/samtools -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/samtools/lz4 -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/bcftools -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/pysam -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27 -I/usr/include/python3.9 -c htslib/cram/pooled_alloc.c -o build/temp.linux-armv7l-3.9/htslib/cram/pooled_alloc.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 2021-07-15T11:06:59,758 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/htslib -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/samtools -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/samtools/lz4 -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/bcftools -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/pysam -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27 -I/usr/include/python3.9 -c htslib/cram/rANS_static.c -o build/temp.linux-armv7l-3.9/htslib/cram/rANS_static.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 2021-07-15T11:07:01,250 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/htslib -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/samtools -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/samtools/lz4 -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/bcftools -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/pysam -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27 -I/usr/include/python3.9 -c htslib/cram/sam_header.c -o build/temp.linux-armv7l-3.9/htslib/cram/sam_header.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 2021-07-15T11:07:03,495 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/htslib -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/samtools -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/samtools/lz4 -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/bcftools -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/pysam -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27 -I/usr/include/python3.9 -c htslib/cram/string_alloc.c -o build/temp.linux-armv7l-3.9/htslib/cram/string_alloc.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 2021-07-15T11:07:03,724 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/htslib -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/samtools -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/samtools/lz4 -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/bcftools -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/pysam -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27 -I/usr/include/python3.9 -c htslib/errmod.c -o build/temp.linux-armv7l-3.9/htslib/errmod.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 2021-07-15T11:07:04,477 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/htslib -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/samtools -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/samtools/lz4 -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/bcftools -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/pysam -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27 -I/usr/include/python3.9 -c htslib/faidx.c -o build/temp.linux-armv7l-3.9/htslib/faidx.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 2021-07-15T11:07:06,160 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/htslib -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/samtools -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/samtools/lz4 -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/bcftools -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/pysam -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27 -I/usr/include/python3.9 -c htslib/hfile.c -o build/temp.linux-armv7l-3.9/htslib/hfile.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 2021-07-15T11:07:07,656 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/htslib -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/samtools -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/samtools/lz4 -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/bcftools -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/pysam -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27 -I/usr/include/python3.9 -c htslib/hfile_gcs.c -o build/temp.linux-armv7l-3.9/htslib/hfile_gcs.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 2021-07-15T11:07:08,137 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/htslib -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/samtools -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/samtools/lz4 -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/bcftools -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/pysam -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27 -I/usr/include/python3.9 -c htslib/hfile_libcurl.c -o build/temp.linux-armv7l-3.9/htslib/hfile_libcurl.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 2021-07-15T11:07:10,166 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/htslib -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/samtools -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/samtools/lz4 -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/bcftools -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/pysam -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27 -I/usr/include/python3.9 -c htslib/hfile_net.c -o build/temp.linux-armv7l-3.9/htslib/hfile_net.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 2021-07-15T11:07:10,401 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/htslib -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/samtools -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/samtools/lz4 -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/bcftools -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/pysam -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27 -I/usr/include/python3.9 -c htslib/hfile_s3.c -o build/temp.linux-armv7l-3.9/htslib/hfile_s3.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 2021-07-15T11:07:11,644 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/htslib -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/samtools -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/samtools/lz4 -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/bcftools -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/pysam -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27 -I/usr/include/python3.9 -c htslib/hts.c -o build/temp.linux-armv7l-3.9/htslib/hts.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 2021-07-15T11:07:11,987 htslib/hts.c: In function ‘hts_idx_init’: 2021-07-15T11:07:11,987 htslib/hts.c:1386:59: warning: overflow in conversion from ‘uint32_t’ {aka ‘unsigned int’} to ‘int’ changes value from ‘idx->z.last_bin = 4294967295’ to ‘-1’ [-Woverflow] 2021-07-15T11:07:11,987 1386 | idx->z.save_bin = idx->z.save_tid = idx->z.last_tid = idx->z.last_bin = 0xffffffffu; 2021-07-15T11:07:11,987 | ^~~ 2021-07-15T11:07:17,493 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/htslib -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/samtools -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/samtools/lz4 -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/bcftools -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/pysam -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27 -I/usr/include/python3.9 -c htslib/hts_os.c -o build/temp.linux-armv7l-3.9/htslib/hts_os.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 2021-07-15T11:07:17,638 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/htslib -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/samtools -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/samtools/lz4 -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/bcftools -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/pysam -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27 -I/usr/include/python3.9 -c htslib/kfunc.c -o build/temp.linux-armv7l-3.9/htslib/kfunc.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 2021-07-15T11:07:18,076 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/htslib -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/samtools -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/samtools/lz4 -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/bcftools -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/pysam -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27 -I/usr/include/python3.9 -c htslib/knetfile.c -o build/temp.linux-armv7l-3.9/htslib/knetfile.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 2021-07-15T11:07:18,855 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/htslib -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/samtools -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/samtools/lz4 -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/bcftools -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/pysam -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27 -I/usr/include/python3.9 -c htslib/kstring.c -o build/temp.linux-armv7l-3.9/htslib/kstring.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 2021-07-15T11:07:19,585 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/htslib -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/samtools -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/samtools/lz4 -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/bcftools -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/pysam -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27 -I/usr/include/python3.9 -c htslib/md5.c -o build/temp.linux-armv7l-3.9/htslib/md5.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 2021-07-15T11:07:20,159 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/htslib -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/samtools -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/samtools/lz4 -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/bcftools -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/pysam -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27 -I/usr/include/python3.9 -c htslib/multipart.c -o build/temp.linux-armv7l-3.9/htslib/multipart.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 2021-07-15T11:07:20,693 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/htslib -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/samtools -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/samtools/lz4 -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/bcftools -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/pysam -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27 -I/usr/include/python3.9 -c htslib/probaln.c -o build/temp.linux-armv7l-3.9/htslib/probaln.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 2021-07-15T11:07:21,386 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/htslib -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/samtools -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/samtools/lz4 -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/bcftools -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/pysam -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27 -I/usr/include/python3.9 -c htslib/realn.c -o build/temp.linux-armv7l-3.9/htslib/realn.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 2021-07-15T11:07:22,152 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/htslib -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/samtools -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/samtools/lz4 -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/bcftools -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/pysam -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27 -I/usr/include/python3.9 -c htslib/regidx.c -o build/temp.linux-armv7l-3.9/htslib/regidx.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 2021-07-15T11:07:23,052 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/htslib -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/samtools -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/samtools/lz4 -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/bcftools -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/pysam -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27 -I/usr/include/python3.9 -c htslib/sam.c -o build/temp.linux-armv7l-3.9/htslib/sam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 2021-07-15T11:07:29,852 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/htslib -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/samtools -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/samtools/lz4 -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/bcftools -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/pysam -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27 -I/usr/include/python3.9 -c htslib/synced_bcf_reader.c -o build/temp.linux-armv7l-3.9/htslib/synced_bcf_reader.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 2021-07-15T11:07:31,878 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/htslib -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/samtools -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/samtools/lz4 -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/bcftools -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/pysam -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27 -I/usr/include/python3.9 -c htslib/tbx.c -o build/temp.linux-armv7l-3.9/htslib/tbx.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 2021-07-15T11:07:32,570 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/htslib -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/samtools -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/samtools/lz4 -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/bcftools -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/pysam -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27 -I/usr/include/python3.9 -c htslib/textutils.c -o build/temp.linux-armv7l-3.9/htslib/textutils.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 2021-07-15T11:07:33,332 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/htslib -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/samtools -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/samtools/lz4 -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/bcftools -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/pysam -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27 -I/usr/include/python3.9 -c htslib/thread_pool.c -o build/temp.linux-armv7l-3.9/htslib/thread_pool.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 2021-07-15T11:07:34,082 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/htslib -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/samtools -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/samtools/lz4 -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/bcftools -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/pysam -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27 -I/usr/include/python3.9 -c htslib/vcf.c -o build/temp.linux-armv7l-3.9/htslib/vcf.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 2021-07-15T11:07:43,315 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/htslib -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/samtools -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/samtools/lz4 -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/bcftools -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/pysam -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27 -I/usr/include/python3.9 -c htslib/vcf_sweep.c -o build/temp.linux-armv7l-3.9/htslib/vcf_sweep.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 2021-07-15T11:07:43,690 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/htslib -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/samtools -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/samtools/lz4 -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/bcftools -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/pysam -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27 -I/usr/include/python3.9 -c htslib/vcfutils.c -o build/temp.linux-armv7l-3.9/htslib/vcfutils.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 2021-07-15T11:07:46,142 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/htslib -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/samtools -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/samtools/lz4 -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/bcftools -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/pysam -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27 -I/usr/include/python3.9 -c pysam/htslib_util.c -o build/temp.linux-armv7l-3.9/pysam/htslib_util.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 2021-07-15T11:07:46,435 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/htslib -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/samtools -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/samtools/lz4 -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/bcftools -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/pysam -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27 -I/usr/include/python3.9 -c pysam/libchtslib.c -o build/temp.linux-armv7l-3.9/pysam/libchtslib.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 2021-07-15T11:07:59,424 arm-linux-gnueabihf-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -g -fwrapv -O2 -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-armv7l-3.9/htslib/bcf_sr_sort.o build/temp.linux-armv7l-3.9/htslib/bgzf.o build/temp.linux-armv7l-3.9/htslib/cram/cram_codecs.o build/temp.linux-armv7l-3.9/htslib/cram/cram_decode.o build/temp.linux-armv7l-3.9/htslib/cram/cram_encode.o build/temp.linux-armv7l-3.9/htslib/cram/cram_external.o build/temp.linux-armv7l-3.9/htslib/cram/cram_index.o build/temp.linux-armv7l-3.9/htslib/cram/cram_io.o build/temp.linux-armv7l-3.9/htslib/cram/cram_samtools.o build/temp.linux-armv7l-3.9/htslib/cram/cram_stats.o build/temp.linux-armv7l-3.9/htslib/cram/files.o build/temp.linux-armv7l-3.9/htslib/cram/mFILE.o build/temp.linux-armv7l-3.9/htslib/cram/open_trace_file.o build/temp.linux-armv7l-3.9/htslib/cram/pooled_alloc.o build/temp.linux-armv7l-3.9/htslib/cram/rANS_static.o build/temp.linux-armv7l-3.9/htslib/cram/sam_header.o build/temp.linux-armv7l-3.9/htslib/cram/string_alloc.o build/temp.linux-armv7l-3.9/htslib/errmod.o build/temp.linux-armv7l-3.9/htslib/faidx.o build/temp.linux-armv7l-3.9/htslib/hfile.o build/temp.linux-armv7l-3.9/htslib/hfile_gcs.o build/temp.linux-armv7l-3.9/htslib/hfile_libcurl.o build/temp.linux-armv7l-3.9/htslib/hfile_net.o build/temp.linux-armv7l-3.9/htslib/hfile_s3.o build/temp.linux-armv7l-3.9/htslib/hts.o build/temp.linux-armv7l-3.9/htslib/hts_os.o build/temp.linux-armv7l-3.9/htslib/kfunc.o build/temp.linux-armv7l-3.9/htslib/knetfile.o build/temp.linux-armv7l-3.9/htslib/kstring.o build/temp.linux-armv7l-3.9/htslib/md5.o build/temp.linux-armv7l-3.9/htslib/multipart.o build/temp.linux-armv7l-3.9/htslib/probaln.o build/temp.linux-armv7l-3.9/htslib/realn.o build/temp.linux-armv7l-3.9/htslib/regidx.o build/temp.linux-armv7l-3.9/htslib/sam.o build/temp.linux-armv7l-3.9/htslib/synced_bcf_reader.o build/temp.linux-armv7l-3.9/htslib/tbx.o build/temp.linux-armv7l-3.9/htslib/textutils.o build/temp.linux-armv7l-3.9/htslib/thread_pool.o build/temp.linux-armv7l-3.9/htslib/vcf.o build/temp.linux-armv7l-3.9/htslib/vcf_sweep.o build/temp.linux-armv7l-3.9/htslib/vcfutils.o build/temp.linux-armv7l-3.9/pysam/htslib_util.o build/temp.linux-armv7l-3.9/pysam/libchtslib.o -L/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/pysam -L/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/pysam -L/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27 -L/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/build/lib.linux-armv7l-3.9/pysam -Lbuild/lib.linux-armv7l-3.9/pysam -lz -ldeflate -llzma -lbz2 -lz -lm -lcurl -lcrypto -o build/lib.linux-armv7l-3.9/pysam/libchtslib.cpython-39-arm-linux-gnueabihf.so -Wl,-rpath,$ORIGIN 2021-07-15T11:08:00,103 building 'pysam.libcsamtools' extension 2021-07-15T11:08:00,104 creating build/temp.linux-armv7l-3.9/samtools 2021-07-15T11:08:00,106 creating build/temp.linux-armv7l-3.9/samtools/lz4 2021-07-15T11:08:00,107 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/htslib -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/samtools -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/samtools/lz4 -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/bcftools -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/pysam -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27 -I/usr/include/python3.9 -c pysam/libcsamtools.c -o build/temp.linux-armv7l-3.9/pysam/libcsamtools.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 2021-07-15T11:08:00,934 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/htslib -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/samtools -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/samtools/lz4 -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/bcftools -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/pysam -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27 -I/usr/include/python3.9 -c samtools/bam.c.pysam.c -o build/temp.linux-armv7l-3.9/samtools/bam.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 2021-07-15T11:08:01,490 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/htslib -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/samtools -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/samtools/lz4 -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/bcftools -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/pysam -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27 -I/usr/include/python3.9 -c samtools/bam2bcf.c.pysam.c -o build/temp.linux-armv7l-3.9/samtools/bam2bcf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 2021-07-15T11:08:03,082 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/htslib -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/samtools -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/samtools/lz4 -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/bcftools -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/pysam -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27 -I/usr/include/python3.9 -c samtools/bam2bcf_indel.c.pysam.c -o build/temp.linux-armv7l-3.9/samtools/bam2bcf_indel.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 2021-07-15T11:08:05,433 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/htslib -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/samtools -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/samtools/lz4 -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/bcftools -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/pysam -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27 -I/usr/include/python3.9 -c samtools/bam2depth.c.pysam.c -o build/temp.linux-armv7l-3.9/samtools/bam2depth.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 2021-07-15T11:08:06,073 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/htslib -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/samtools -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/samtools/lz4 -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/bcftools -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/pysam -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27 -I/usr/include/python3.9 -c samtools/bam_addrprg.c.pysam.c -o build/temp.linux-armv7l-3.9/samtools/bam_addrprg.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 2021-07-15T11:08:06,772 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/htslib -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/samtools -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/samtools/lz4 -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/bcftools -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/pysam -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27 -I/usr/include/python3.9 -c samtools/bam_aux.c.pysam.c -o build/temp.linux-armv7l-3.9/samtools/bam_aux.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 2021-07-15T11:08:07,054 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/htslib -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/samtools -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/samtools/lz4 -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/bcftools -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/pysam -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27 -I/usr/include/python3.9 -c samtools/bam_cat.c.pysam.c -o build/temp.linux-armv7l-3.9/samtools/bam_cat.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 2021-07-15T11:08:07,997 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/htslib -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/samtools -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/samtools/lz4 -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/bcftools -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/pysam -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27 -I/usr/include/python3.9 -c samtools/bam_color.c.pysam.c -o build/temp.linux-armv7l-3.9/samtools/bam_color.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 2021-07-15T11:08:08,311 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/htslib -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/samtools -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/samtools/lz4 -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/bcftools -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/pysam -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27 -I/usr/include/python3.9 -c samtools/bam_flags.c.pysam.c -o build/temp.linux-armv7l-3.9/samtools/bam_flags.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 2021-07-15T11:08:08,558 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/htslib -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/samtools -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/samtools/lz4 -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/bcftools -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/pysam -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27 -I/usr/include/python3.9 -c samtools/bam_import.c.pysam.c -o build/temp.linux-armv7l-3.9/samtools/bam_import.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 2021-07-15T11:08:08,942 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/htslib -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/samtools -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/samtools/lz4 -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/bcftools -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/pysam -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27 -I/usr/include/python3.9 -c samtools/bam_index.c.pysam.c -o build/temp.linux-armv7l-3.9/samtools/bam_index.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 2021-07-15T11:08:09,337 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/htslib -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/samtools -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/samtools/lz4 -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/bcftools -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/pysam -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27 -I/usr/include/python3.9 -c samtools/bam_lpileup.c.pysam.c -o build/temp.linux-armv7l-3.9/samtools/bam_lpileup.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 2021-07-15T11:08:10,220 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/htslib -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/samtools -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/samtools/lz4 -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/bcftools -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/pysam -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27 -I/usr/include/python3.9 -c samtools/bam_markdup.c.pysam.c -o build/temp.linux-armv7l-3.9/samtools/bam_markdup.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 2021-07-15T11:08:12,290 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/htslib -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/samtools -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/samtools/lz4 -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/bcftools -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/pysam -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27 -I/usr/include/python3.9 -c samtools/bam_mate.c.pysam.c -o build/temp.linux-armv7l-3.9/samtools/bam_mate.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 2021-07-15T11:08:13,378 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/htslib -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/samtools -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/samtools/lz4 -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/bcftools -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/pysam -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27 -I/usr/include/python3.9 -c samtools/bam_md.c.pysam.c -o build/temp.linux-armv7l-3.9/samtools/bam_md.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 2021-07-15T11:08:14,229 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/htslib -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/samtools -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/samtools/lz4 -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/bcftools -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/pysam -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27 -I/usr/include/python3.9 -c samtools/bam_plbuf.c.pysam.c -o build/temp.linux-armv7l-3.9/samtools/bam_plbuf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 2021-07-15T11:08:14,430 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/htslib -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/samtools -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/samtools/lz4 -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/bcftools -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/pysam -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27 -I/usr/include/python3.9 -c samtools/bam_plcmd.c.pysam.c -o build/temp.linux-armv7l-3.9/samtools/bam_plcmd.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 2021-07-15T11:08:16,895 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/htslib -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/samtools -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/samtools/lz4 -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/bcftools -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/pysam -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27 -I/usr/include/python3.9 -c samtools/bam_quickcheck.c.pysam.c -o build/temp.linux-armv7l-3.9/samtools/bam_quickcheck.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 2021-07-15T11:08:17,239 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/htslib -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/samtools -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/samtools/lz4 -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/bcftools -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/pysam -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27 -I/usr/include/python3.9 -c samtools/bam_reheader.c.pysam.c -o build/temp.linux-armv7l-3.9/samtools/bam_reheader.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 2021-07-15T11:08:17,866 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/htslib -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/samtools -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/samtools/lz4 -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/bcftools -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/pysam -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27 -I/usr/include/python3.9 -c samtools/bam_rmdup.c.pysam.c -o build/temp.linux-armv7l-3.9/samtools/bam_rmdup.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 2021-07-15T11:08:19,124 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/htslib -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/samtools -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/samtools/lz4 -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/bcftools -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/pysam -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27 -I/usr/include/python3.9 -c samtools/bam_rmdupse.c.pysam.c -o build/temp.linux-armv7l-3.9/samtools/bam_rmdupse.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 2021-07-15T11:08:20,210 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/htslib -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/samtools -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/samtools/lz4 -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/bcftools -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/pysam -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27 -I/usr/include/python3.9 -c samtools/bam_sort.c.pysam.c -o build/temp.linux-armv7l-3.9/samtools/bam_sort.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 2021-07-15T11:08:26,137 In file included from /usr/include/string.h:495, 2021-07-15T11:08:26,138 from samtools/bam_sort.c.pysam.c:36: 2021-07-15T11:08:26,138 In function ‘strncpy’, 2021-07-15T11:08:26,138 inlined from ‘bam_sort_core_ext’ at samtools/bam_sort.c.pysam.c:2144:9: 2021-07-15T11:08:26,138 /usr/include/arm-linux-gnueabihf/bits/string_fortified.h:106:10: warning: ‘__builtin_strncpy’ specified bound 2 equals destination size [-Wstringop-truncation] 2021-07-15T11:08:26,138 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); 2021-07-15T11:08:26,139 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-15T11:08:26,985 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/htslib -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/samtools -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/samtools/lz4 -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/bcftools -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/pysam -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27 -I/usr/include/python3.9 -c samtools/bam_split.c.pysam.c -o build/temp.linux-armv7l-3.9/samtools/bam_split.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 2021-07-15T11:08:28,271 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/htslib -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/samtools -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/samtools/lz4 -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/bcftools -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/pysam -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27 -I/usr/include/python3.9 -c samtools/bam_stat.c.pysam.c -o build/temp.linux-armv7l-3.9/samtools/bam_stat.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 2021-07-15T11:08:28,727 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/htslib -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/samtools -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/samtools/lz4 -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/bcftools -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/pysam -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27 -I/usr/include/python3.9 -c samtools/bamshuf.c.pysam.c -o build/temp.linux-armv7l-3.9/samtools/bamshuf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 2021-07-15T11:08:30,717 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/htslib -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/samtools -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/samtools/lz4 -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/bcftools -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/pysam -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27 -I/usr/include/python3.9 -c samtools/bamtk.c.pysam.c -o build/temp.linux-armv7l-3.9/samtools/bamtk.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 2021-07-15T11:08:31,056 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/htslib -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/samtools -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/samtools/lz4 -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/bcftools -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/pysam -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27 -I/usr/include/python3.9 -c samtools/bedcov.c.pysam.c -o build/temp.linux-armv7l-3.9/samtools/bedcov.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 2021-07-15T11:08:31,748 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/htslib -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/samtools -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/samtools/lz4 -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/bcftools -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/pysam -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27 -I/usr/include/python3.9 -c samtools/bedidx.c.pysam.c -o build/temp.linux-armv7l-3.9/samtools/bedidx.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 2021-07-15T11:08:33,385 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/htslib -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/samtools -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/samtools/lz4 -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/bcftools -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/pysam -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27 -I/usr/include/python3.9 -c samtools/cut_target.c.pysam.c -o build/temp.linux-armv7l-3.9/samtools/cut_target.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 2021-07-15T11:08:33,937 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/htslib -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/samtools -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/samtools/lz4 -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/bcftools -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/pysam -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27 -I/usr/include/python3.9 -c samtools/dict.c.pysam.c -o build/temp.linux-armv7l-3.9/samtools/dict.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 2021-07-15T11:08:34,537 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/htslib -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/samtools -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/samtools/lz4 -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/bcftools -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/pysam -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27 -I/usr/include/python3.9 -c samtools/faidx.c.pysam.c -o build/temp.linux-armv7l-3.9/samtools/faidx.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 2021-07-15T11:08:35,071 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/htslib -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/samtools -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/samtools/lz4 -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/bcftools -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/pysam -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27 -I/usr/include/python3.9 -c samtools/lz4/lz4.c -o build/temp.linux-armv7l-3.9/samtools/lz4/lz4.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 2021-07-15T11:08:40,375 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/htslib -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/samtools -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/samtools/lz4 -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/bcftools -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/pysam -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27 -I/usr/include/python3.9 -c samtools/padding.c.pysam.c -o build/temp.linux-armv7l-3.9/samtools/padding.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 2021-07-15T11:08:41,580 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/htslib -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/samtools -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/samtools/lz4 -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/bcftools -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/pysam -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27 -I/usr/include/python3.9 -c samtools/phase.c.pysam.c -o build/temp.linux-armv7l-3.9/samtools/phase.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 2021-07-15T11:08:44,178 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/htslib -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/samtools -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/samtools/lz4 -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/bcftools -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/pysam -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27 -I/usr/include/python3.9 -c samtools/sam.c.pysam.c -o build/temp.linux-armv7l-3.9/samtools/sam.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 2021-07-15T11:08:44,521 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/htslib -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/samtools -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/samtools/lz4 -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/bcftools -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/pysam -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27 -I/usr/include/python3.9 -c samtools/sam_header.c.pysam.c -o build/temp.linux-armv7l-3.9/samtools/sam_header.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 2021-07-15T11:08:45,745 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/htslib -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/samtools -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/samtools/lz4 -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/bcftools -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/pysam -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27 -I/usr/include/python3.9 -c samtools/sam_opts.c.pysam.c -o build/temp.linux-armv7l-3.9/samtools/sam_opts.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 2021-07-15T11:08:45,916 In file included from /usr/include/stdio.h:867, 2021-07-15T11:08:45,916 from samtools/samtools.pysam.h:4, 2021-07-15T11:08:45,916 from samtools/sam_opts.c.pysam.c:1: 2021-07-15T11:08:45,916 In function ‘fprintf’, 2021-07-15T11:08:45,916 inlined from ‘parse_sam_global_opt’ at samtools/sam_opts.c.pysam.c:87:9: 2021-07-15T11:08:45,917 /usr/include/arm-linux-gnueabihf/bits/stdio2.h:100:10: warning: ‘%s’ directive argument is null [-Wformat-overflow=] 2021-07-15T11:08:45,917 100 | return __fprintf_chk (__stream, __USE_FORTIFY_LEVEL - 1, __fmt, 2021-07-15T11:08:45,917 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-15T11:08:45,917 101 | __va_arg_pack ()); 2021-07-15T11:08:45,917 | ~~~~~~~~~~~~~~~~~ 2021-07-15T11:08:46,043 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/htslib -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/samtools -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/samtools/lz4 -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/bcftools -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/pysam -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27 -I/usr/include/python3.9 -c samtools/sam_utils.c.pysam.c -o build/temp.linux-armv7l-3.9/samtools/sam_utils.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 2021-07-15T11:08:46,221 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/htslib -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/samtools -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/samtools/lz4 -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/bcftools -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/pysam -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27 -I/usr/include/python3.9 -c samtools/sam_view.c.pysam.c -o build/temp.linux-armv7l-3.9/samtools/sam_view.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 2021-07-15T11:08:49,553 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/htslib -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/samtools -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/samtools/lz4 -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/bcftools -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/pysam -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27 -I/usr/include/python3.9 -c samtools/sample.c.pysam.c -o build/temp.linux-armv7l-3.9/samtools/sample.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 2021-07-15T11:08:50,289 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/htslib -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/samtools -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/samtools/lz4 -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/bcftools -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/pysam -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27 -I/usr/include/python3.9 -c samtools/samtools.pysam.c -o build/temp.linux-armv7l-3.9/samtools/samtools.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 2021-07-15T11:08:50,521 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/htslib -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/samtools -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/samtools/lz4 -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/bcftools -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/pysam -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27 -I/usr/include/python3.9 -c samtools/stats.c.pysam.c -o build/temp.linux-armv7l-3.9/samtools/stats.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 2021-07-15T11:08:54,128 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/htslib -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/samtools -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/samtools/lz4 -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/bcftools -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/pysam -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27 -I/usr/include/python3.9 -c samtools/stats_isize.c.pysam.c -o build/temp.linux-armv7l-3.9/samtools/stats_isize.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 2021-07-15T11:08:54,692 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/htslib -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/samtools -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/samtools/lz4 -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/bcftools -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/pysam -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27 -I/usr/include/python3.9 -c samtools/tmp_file.c.pysam.c -o build/temp.linux-armv7l-3.9/samtools/tmp_file.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 2021-07-15T11:08:55,190 arm-linux-gnueabihf-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -g -fwrapv -O2 -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-armv7l-3.9/pysam/libcsamtools.o build/temp.linux-armv7l-3.9/samtools/bam.c.pysam.o build/temp.linux-armv7l-3.9/samtools/bam2bcf.c.pysam.o build/temp.linux-armv7l-3.9/samtools/bam2bcf_indel.c.pysam.o build/temp.linux-armv7l-3.9/samtools/bam2depth.c.pysam.o build/temp.linux-armv7l-3.9/samtools/bam_addrprg.c.pysam.o build/temp.linux-armv7l-3.9/samtools/bam_aux.c.pysam.o build/temp.linux-armv7l-3.9/samtools/bam_cat.c.pysam.o build/temp.linux-armv7l-3.9/samtools/bam_color.c.pysam.o build/temp.linux-armv7l-3.9/samtools/bam_flags.c.pysam.o build/temp.linux-armv7l-3.9/samtools/bam_import.c.pysam.o build/temp.linux-armv7l-3.9/samtools/bam_index.c.pysam.o build/temp.linux-armv7l-3.9/samtools/bam_lpileup.c.pysam.o build/temp.linux-armv7l-3.9/samtools/bam_markdup.c.pysam.o build/temp.linux-armv7l-3.9/samtools/bam_mate.c.pysam.o build/temp.linux-armv7l-3.9/samtools/bam_md.c.pysam.o build/temp.linux-armv7l-3.9/samtools/bam_plbuf.c.pysam.o build/temp.linux-armv7l-3.9/samtools/bam_plcmd.c.pysam.o build/temp.linux-armv7l-3.9/samtools/bam_quickcheck.c.pysam.o build/temp.linux-armv7l-3.9/samtools/bam_reheader.c.pysam.o build/temp.linux-armv7l-3.9/samtools/bam_rmdup.c.pysam.o build/temp.linux-armv7l-3.9/samtools/bam_rmdupse.c.pysam.o build/temp.linux-armv7l-3.9/samtools/bam_sort.c.pysam.o build/temp.linux-armv7l-3.9/samtools/bam_split.c.pysam.o build/temp.linux-armv7l-3.9/samtools/bam_stat.c.pysam.o build/temp.linux-armv7l-3.9/samtools/bamshuf.c.pysam.o build/temp.linux-armv7l-3.9/samtools/bamtk.c.pysam.o build/temp.linux-armv7l-3.9/samtools/bedcov.c.pysam.o build/temp.linux-armv7l-3.9/samtools/bedidx.c.pysam.o build/temp.linux-armv7l-3.9/samtools/cut_target.c.pysam.o build/temp.linux-armv7l-3.9/samtools/dict.c.pysam.o build/temp.linux-armv7l-3.9/samtools/faidx.c.pysam.o build/temp.linux-armv7l-3.9/samtools/lz4/lz4.o build/temp.linux-armv7l-3.9/samtools/padding.c.pysam.o build/temp.linux-armv7l-3.9/samtools/phase.c.pysam.o build/temp.linux-armv7l-3.9/samtools/sam.c.pysam.o build/temp.linux-armv7l-3.9/samtools/sam_header.c.pysam.o build/temp.linux-armv7l-3.9/samtools/sam_opts.c.pysam.o build/temp.linux-armv7l-3.9/samtools/sam_utils.c.pysam.o build/temp.linux-armv7l-3.9/samtools/sam_view.c.pysam.o build/temp.linux-armv7l-3.9/samtools/sample.c.pysam.o build/temp.linux-armv7l-3.9/samtools/samtools.pysam.o build/temp.linux-armv7l-3.9/samtools/stats.c.pysam.o build/temp.linux-armv7l-3.9/samtools/stats_isize.c.pysam.o build/temp.linux-armv7l-3.9/samtools/tmp_file.c.pysam.o -L/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/pysam -L/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/pysam -L/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27 -L/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/build/lib.linux-armv7l-3.9/pysam -Lbuild/lib.linux-armv7l-3.9/pysam -Lbuild/lib.linux-armv7l-3.9/pysam -lz -ldeflate -llzma -lbz2 -lz -lm -lcurl -lcrypto -lchtslib.cpython-39-arm-linux-gnueabihf -o build/lib.linux-armv7l-3.9/pysam/libcsamtools.cpython-39-arm-linux-gnueabihf.so -Wl,-rpath,$ORIGIN 2021-07-15T11:08:55,663 building 'pysam.libcbcftools' extension 2021-07-15T11:08:55,670 creating build/temp.linux-armv7l-3.9/bcftools 2021-07-15T11:08:55,672 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/htslib -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/samtools -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/samtools/lz4 -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/bcftools -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/pysam -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27 -I/usr/include/python3.9 -c bcftools/HMM.c.pysam.c -o build/temp.linux-armv7l-3.9/bcftools/HMM.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 2021-07-15T11:08:56,589 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/htslib -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/samtools -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/samtools/lz4 -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/bcftools -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/pysam -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27 -I/usr/include/python3.9 -c bcftools/bam2bcf.c.pysam.c -o build/temp.linux-armv7l-3.9/bcftools/bam2bcf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 2021-07-15T11:08:58,200 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/htslib -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/samtools -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/samtools/lz4 -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/bcftools -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/pysam -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27 -I/usr/include/python3.9 -c bcftools/bam2bcf_indel.c.pysam.c -o build/temp.linux-armv7l-3.9/bcftools/bam2bcf_indel.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 2021-07-15T11:09:00,160 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/htslib -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/samtools -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/samtools/lz4 -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/bcftools -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/pysam -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27 -I/usr/include/python3.9 -c bcftools/bam_sample.c.pysam.c -o build/temp.linux-armv7l-3.9/bcftools/bam_sample.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 2021-07-15T11:09:01,856 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/htslib -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/samtools -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/samtools/lz4 -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/bcftools -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/pysam -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27 -I/usr/include/python3.9 -c bcftools/bcftools.pysam.c -o build/temp.linux-armv7l-3.9/bcftools/bcftools.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 2021-07-15T11:09:02,099 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/htslib -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/samtools -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/samtools/lz4 -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/bcftools -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/pysam -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27 -I/usr/include/python3.9 -c bcftools/bin.c.pysam.c -o build/temp.linux-armv7l-3.9/bcftools/bin.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 2021-07-15T11:09:02,416 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/htslib -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/samtools -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/samtools/lz4 -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/bcftools -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/pysam -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27 -I/usr/include/python3.9 -c bcftools/ccall.c.pysam.c -o build/temp.linux-armv7l-3.9/bcftools/ccall.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 2021-07-15T11:09:03,118 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/htslib -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/samtools -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/samtools/lz4 -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/bcftools -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/pysam -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27 -I/usr/include/python3.9 -c bcftools/consensus.c.pysam.c -o build/temp.linux-armv7l-3.9/bcftools/consensus.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 2021-07-15T11:09:04,460 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/htslib -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/samtools -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/samtools/lz4 -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/bcftools -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/pysam -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27 -I/usr/include/python3.9 -c bcftools/convert.c.pysam.c -o build/temp.linux-armv7l-3.9/bcftools/convert.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 2021-07-15T11:09:09,550 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/htslib -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/samtools -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/samtools/lz4 -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/bcftools -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/pysam -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27 -I/usr/include/python3.9 -c bcftools/csq.c.pysam.c -o build/temp.linux-armv7l-3.9/bcftools/csq.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 2021-07-15T11:09:16,774 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/htslib -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/samtools -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/samtools/lz4 -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/bcftools -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/pysam -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27 -I/usr/include/python3.9 -c bcftools/em.c.pysam.c -o build/temp.linux-armv7l-3.9/bcftools/em.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 2021-07-15T11:09:17,364 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/htslib -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/samtools -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/samtools/lz4 -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/bcftools -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/pysam -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27 -I/usr/include/python3.9 -c bcftools/filter.c.pysam.c -o build/temp.linux-armv7l-3.9/bcftools/filter.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 2021-07-15T11:09:25,936 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/htslib -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/samtools -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/samtools/lz4 -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/bcftools -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/pysam -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27 -I/usr/include/python3.9 -c bcftools/gvcf.c.pysam.c -o build/temp.linux-armv7l-3.9/bcftools/gvcf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 2021-07-15T11:09:26,472 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/htslib -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/samtools -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/samtools/lz4 -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/bcftools -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/pysam -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27 -I/usr/include/python3.9 -c bcftools/hclust.c.pysam.c -o build/temp.linux-armv7l-3.9/bcftools/hclust.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 2021-07-15T11:09:27,057 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/htslib -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/samtools -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/samtools/lz4 -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/bcftools -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/pysam -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27 -I/usr/include/python3.9 -c bcftools/kmin.c.pysam.c -o build/temp.linux-armv7l-3.9/bcftools/kmin.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 2021-07-15T11:09:27,505 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/htslib -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/samtools -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/samtools/lz4 -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/bcftools -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/pysam -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27 -I/usr/include/python3.9 -c bcftools/main.c.pysam.c -o build/temp.linux-armv7l-3.9/bcftools/main.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 2021-07-15T11:09:27,860 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/htslib -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/samtools -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/samtools/lz4 -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/bcftools -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/pysam -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27 -I/usr/include/python3.9 -c bcftools/mcall.c.pysam.c -o build/temp.linux-armv7l-3.9/bcftools/mcall.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 2021-07-15T11:09:30,892 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/htslib -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/samtools -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/samtools/lz4 -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/bcftools -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/pysam -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27 -I/usr/include/python3.9 -c bcftools/mpileup.c.pysam.c -o build/temp.linux-armv7l-3.9/bcftools/mpileup.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 2021-07-15T11:09:32,470 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/htslib -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/samtools -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/samtools/lz4 -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/bcftools -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/pysam -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27 -I/usr/include/python3.9 -c bcftools/ploidy.c.pysam.c -o build/temp.linux-armv7l-3.9/bcftools/ploidy.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 2021-07-15T11:09:33,401 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/htslib -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/samtools -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/samtools/lz4 -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/bcftools -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/pysam -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27 -I/usr/include/python3.9 -c bcftools/prob1.c.pysam.c -o build/temp.linux-armv7l-3.9/bcftools/prob1.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 2021-07-15T11:09:34,843 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/htslib -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/samtools -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/samtools/lz4 -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/bcftools -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/pysam -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27 -I/usr/include/python3.9 -c bcftools/regidx.c.pysam.c -o build/temp.linux-armv7l-3.9/bcftools/regidx.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 2021-07-15T11:09:36,077 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/htslib -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/samtools -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/samtools/lz4 -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/bcftools -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/pysam -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27 -I/usr/include/python3.9 -c bcftools/reheader.c.pysam.c -o build/temp.linux-armv7l-3.9/bcftools/reheader.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 2021-07-15T11:09:37,785 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/htslib -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/samtools -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/samtools/lz4 -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/bcftools -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/pysam -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27 -I/usr/include/python3.9 -c bcftools/smpl_ilist.c.pysam.c -o build/temp.linux-armv7l-3.9/bcftools/smpl_ilist.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 2021-07-15T11:09:38,123 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/htslib -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/samtools -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/samtools/lz4 -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/bcftools -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/pysam -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27 -I/usr/include/python3.9 -c bcftools/tabix.c.pysam.c -o build/temp.linux-armv7l-3.9/bcftools/tabix.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 2021-07-15T11:09:38,526 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/htslib -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/samtools -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/samtools/lz4 -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/bcftools -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/pysam -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27 -I/usr/include/python3.9 -c bcftools/tsv2vcf.c.pysam.c -o build/temp.linux-armv7l-3.9/bcftools/tsv2vcf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 2021-07-15T11:09:38,882 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/htslib -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/samtools -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/samtools/lz4 -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/bcftools -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/pysam -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27 -I/usr/include/python3.9 -c bcftools/vcfannotate.c.pysam.c -o build/temp.linux-armv7l-3.9/bcftools/vcfannotate.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 2021-07-15T11:09:44,117 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/htslib -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/samtools -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/samtools/lz4 -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/bcftools -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/pysam -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27 -I/usr/include/python3.9 -c bcftools/vcfbuf.c.pysam.c -o build/temp.linux-armv7l-3.9/bcftools/vcfbuf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 2021-07-15T11:09:44,983 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/htslib -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/samtools -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/samtools/lz4 -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/bcftools -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/pysam -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27 -I/usr/include/python3.9 -c bcftools/vcfcall.c.pysam.c -o build/temp.linux-armv7l-3.9/bcftools/vcfcall.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 2021-07-15T11:09:46,892 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/htslib -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/samtools -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/samtools/lz4 -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/bcftools -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/pysam -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27 -I/usr/include/python3.9 -c bcftools/vcfcnv.c.pysam.c -o build/temp.linux-armv7l-3.9/bcftools/vcfcnv.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 2021-07-15T11:09:48,716 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/htslib -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/samtools -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/samtools/lz4 -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/bcftools -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/pysam -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27 -I/usr/include/python3.9 -c bcftools/vcfconcat.c.pysam.c -o build/temp.linux-armv7l-3.9/bcftools/vcfconcat.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 2021-07-15T11:09:50,375 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/htslib -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/samtools -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/samtools/lz4 -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/bcftools -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/pysam -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27 -I/usr/include/python3.9 -c bcftools/vcfconvert.c.pysam.c -o build/temp.linux-armv7l-3.9/bcftools/vcfconvert.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 2021-07-15T11:09:53,398 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/htslib -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/samtools -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/samtools/lz4 -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/bcftools -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/pysam -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27 -I/usr/include/python3.9 -c bcftools/vcffilter.c.pysam.c -o build/temp.linux-armv7l-3.9/bcftools/vcffilter.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 2021-07-15T11:09:54,557 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/htslib -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/samtools -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/samtools/lz4 -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/bcftools -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/pysam -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27 -I/usr/include/python3.9 -c bcftools/vcfgtcheck.c.pysam.c -o build/temp.linux-armv7l-3.9/bcftools/vcfgtcheck.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 2021-07-15T11:09:55,863 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/htslib -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/samtools -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/samtools/lz4 -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/bcftools -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/pysam -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27 -I/usr/include/python3.9 -c bcftools/vcfindex.c.pysam.c -o build/temp.linux-armv7l-3.9/bcftools/vcfindex.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 2021-07-15T11:09:56,369 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/htslib -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/samtools -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/samtools/lz4 -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/bcftools -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/pysam -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27 -I/usr/include/python3.9 -c bcftools/vcfisec.c.pysam.c -o build/temp.linux-armv7l-3.9/bcftools/vcfisec.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 2021-07-15T11:09:57,824 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/htslib -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/samtools -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/samtools/lz4 -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/bcftools -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/pysam -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27 -I/usr/include/python3.9 -c bcftools/vcfmerge.c.pysam.c -o build/temp.linux-armv7l-3.9/bcftools/vcfmerge.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 2021-07-15T11:09:59,382 bcftools/vcfmerge.c.pysam.c: In function ‘maux_init’: 2021-07-15T11:09:59,382 bcftools/vcfmerge.c.pysam.c:684:34: warning: argument 1 range [2147483648, 4294967295] exceeds maximum object size 2147483647 [-Walloc-size-larger-than=] 2021-07-15T11:09:59,382 684 | ma->gvcf = (gvcf_aux_t*) calloc(ma->n,sizeof(gvcf_aux_t)); 2021-07-15T11:09:59,383 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-15T11:09:59,383 In file included from /tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/htslib/htslib/kstring.h:29, 2021-07-15T11:09:59,383 from /tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/htslib/htslib/vcf.h:40, 2021-07-15T11:09:59,383 from bcftools/vcfmerge.c.pysam.c:33: 2021-07-15T11:09:59,383 /usr/include/stdlib.h:542:14: note: in a call to allocation function ‘calloc’ declared here 2021-07-15T11:09:59,383 542 | extern void *calloc (size_t __nmemb, size_t __size) 2021-07-15T11:09:59,383 | ^~~~~~ 2021-07-15T11:10:05,277 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/htslib -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/samtools -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/samtools/lz4 -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/bcftools -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/pysam -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27 -I/usr/include/python3.9 -c bcftools/vcfnorm.c.pysam.c -o build/temp.linux-armv7l-3.9/bcftools/vcfnorm.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 2021-07-15T11:10:09,010 In function ‘realign’, 2021-07-15T11:10:09,010 inlined from ‘normalize_line’ at bcftools/vcfnorm.c.pysam.c:1719:23: 2021-07-15T11:10:09,010 bcftools/vcfnorm.c.pysam.c:347:17: warning: ‘%s’ directive argument is null [-Wformat-overflow=] 2021-07-15T11:10:09,010 347 | error("Non-ACGTN alternate allele at %s:%d .. REF_SEQ:'%s' vs VCF:'%s'\n", bcf_seqname(args->hdr,line),line->pos+1,ref,line->d.allele[i]); 2021-07-15T11:10:09,011 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-15T11:10:11,851 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/htslib -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/samtools -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/samtools/lz4 -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/bcftools -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/pysam -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27 -I/usr/include/python3.9 -c bcftools/vcfplugin.c.pysam.c -o build/temp.linux-armv7l-3.9/bcftools/vcfplugin.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 2021-07-15T11:10:12,140 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/htslib -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/samtools -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/samtools/lz4 -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/bcftools -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/pysam -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27 -I/usr/include/python3.9 -c bcftools/vcfquery.c.pysam.c -o build/temp.linux-armv7l-3.9/bcftools/vcfquery.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 2021-07-15T11:10:13,203 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/htslib -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/samtools -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/samtools/lz4 -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/bcftools -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/pysam -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27 -I/usr/include/python3.9 -c bcftools/vcfroh.c.pysam.c -o build/temp.linux-armv7l-3.9/bcftools/vcfroh.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 2021-07-15T11:10:15,444 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/htslib -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/samtools -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/samtools/lz4 -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/bcftools -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/pysam -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27 -I/usr/include/python3.9 -c bcftools/vcfsom.c.pysam.c -o build/temp.linux-armv7l-3.9/bcftools/vcfsom.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 2021-07-15T11:10:16,683 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/htslib -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/samtools -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/samtools/lz4 -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/bcftools -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/pysam -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27 -I/usr/include/python3.9 -c bcftools/vcfsort.c.pysam.c -o build/temp.linux-armv7l-3.9/bcftools/vcfsort.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 2021-07-15T11:10:17,277 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/htslib -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/samtools -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/samtools/lz4 -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/bcftools -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/pysam -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27 -I/usr/include/python3.9 -c bcftools/vcfstats.c.pysam.c -o build/temp.linux-armv7l-3.9/bcftools/vcfstats.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 2021-07-15T11:10:20,576 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/htslib -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/samtools -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/samtools/lz4 -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/bcftools -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/pysam -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27 -I/usr/include/python3.9 -c bcftools/vcfview.c.pysam.c -o build/temp.linux-armv7l-3.9/bcftools/vcfview.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 2021-07-15T11:10:22,303 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/htslib -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/samtools -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/samtools/lz4 -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/bcftools -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/pysam -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27 -I/usr/include/python3.9 -c bcftools/vcmp.c.pysam.c -o build/temp.linux-armv7l-3.9/bcftools/vcmp.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 2021-07-15T11:10:22,714 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/htslib -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/samtools -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/samtools/lz4 -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/bcftools -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/pysam -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27 -I/usr/include/python3.9 -c bcftools/version.c.pysam.c -o build/temp.linux-armv7l-3.9/bcftools/version.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 2021-07-15T11:10:22,958 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/htslib -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/samtools -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/samtools/lz4 -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/bcftools -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/pysam -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27 -I/usr/include/python3.9 -c pysam/libcbcftools.c -o build/temp.linux-armv7l-3.9/pysam/libcbcftools.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 2021-07-15T11:10:23,794 arm-linux-gnueabihf-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -g -fwrapv -O2 -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-armv7l-3.9/bcftools/HMM.c.pysam.o build/temp.linux-armv7l-3.9/bcftools/bam2bcf.c.pysam.o build/temp.linux-armv7l-3.9/bcftools/bam2bcf_indel.c.pysam.o build/temp.linux-armv7l-3.9/bcftools/bam_sample.c.pysam.o build/temp.linux-armv7l-3.9/bcftools/bcftools.pysam.o build/temp.linux-armv7l-3.9/bcftools/bin.c.pysam.o build/temp.linux-armv7l-3.9/bcftools/ccall.c.pysam.o build/temp.linux-armv7l-3.9/bcftools/consensus.c.pysam.o build/temp.linux-armv7l-3.9/bcftools/convert.c.pysam.o build/temp.linux-armv7l-3.9/bcftools/csq.c.pysam.o build/temp.linux-armv7l-3.9/bcftools/em.c.pysam.o build/temp.linux-armv7l-3.9/bcftools/filter.c.pysam.o build/temp.linux-armv7l-3.9/bcftools/gvcf.c.pysam.o build/temp.linux-armv7l-3.9/bcftools/hclust.c.pysam.o build/temp.linux-armv7l-3.9/bcftools/kmin.c.pysam.o build/temp.linux-armv7l-3.9/bcftools/main.c.pysam.o build/temp.linux-armv7l-3.9/bcftools/mcall.c.pysam.o build/temp.linux-armv7l-3.9/bcftools/mpileup.c.pysam.o build/temp.linux-armv7l-3.9/bcftools/ploidy.c.pysam.o build/temp.linux-armv7l-3.9/bcftools/prob1.c.pysam.o build/temp.linux-armv7l-3.9/bcftools/regidx.c.pysam.o build/temp.linux-armv7l-3.9/bcftools/reheader.c.pysam.o build/temp.linux-armv7l-3.9/bcftools/smpl_ilist.c.pysam.o build/temp.linux-armv7l-3.9/bcftools/tabix.c.pysam.o build/temp.linux-armv7l-3.9/bcftools/tsv2vcf.c.pysam.o build/temp.linux-armv7l-3.9/bcftools/vcfannotate.c.pysam.o build/temp.linux-armv7l-3.9/bcftools/vcfbuf.c.pysam.o build/temp.linux-armv7l-3.9/bcftools/vcfcall.c.pysam.o build/temp.linux-armv7l-3.9/bcftools/vcfcnv.c.pysam.o build/temp.linux-armv7l-3.9/bcftools/vcfconcat.c.pysam.o build/temp.linux-armv7l-3.9/bcftools/vcfconvert.c.pysam.o build/temp.linux-armv7l-3.9/bcftools/vcffilter.c.pysam.o build/temp.linux-armv7l-3.9/bcftools/vcfgtcheck.c.pysam.o build/temp.linux-armv7l-3.9/bcftools/vcfindex.c.pysam.o build/temp.linux-armv7l-3.9/bcftools/vcfisec.c.pysam.o build/temp.linux-armv7l-3.9/bcftools/vcfmerge.c.pysam.o build/temp.linux-armv7l-3.9/bcftools/vcfnorm.c.pysam.o build/temp.linux-armv7l-3.9/bcftools/vcfplugin.c.pysam.o build/temp.linux-armv7l-3.9/bcftools/vcfquery.c.pysam.o build/temp.linux-armv7l-3.9/bcftools/vcfroh.c.pysam.o build/temp.linux-armv7l-3.9/bcftools/vcfsom.c.pysam.o build/temp.linux-armv7l-3.9/bcftools/vcfsort.c.pysam.o build/temp.linux-armv7l-3.9/bcftools/vcfstats.c.pysam.o build/temp.linux-armv7l-3.9/bcftools/vcfview.c.pysam.o build/temp.linux-armv7l-3.9/bcftools/vcmp.c.pysam.o build/temp.linux-armv7l-3.9/bcftools/version.c.pysam.o build/temp.linux-armv7l-3.9/pysam/libcbcftools.o -L/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/pysam -L/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/pysam -L/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27 -L/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/build/lib.linux-armv7l-3.9/pysam -Lbuild/lib.linux-armv7l-3.9/pysam -Lbuild/lib.linux-armv7l-3.9/pysam -Lbuild/lib.linux-armv7l-3.9/pysam -lz -ldeflate -llzma -lbz2 -lz -lm -lcurl -lcrypto -lchtslib.cpython-39-arm-linux-gnueabihf -o build/lib.linux-armv7l-3.9/pysam/libcbcftools.cpython-39-arm-linux-gnueabihf.so -Wl,-rpath,$ORIGIN 2021-07-15T11:10:24,329 building 'pysam.libcutils' extension 2021-07-15T11:10:24,329 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/htslib -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/samtools -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/samtools/lz4 -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/bcftools -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/pysam -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27 -I/usr/include/python3.9 -c pysam/libcutils.c -o build/temp.linux-armv7l-3.9/pysam/libcutils.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 2021-07-15T11:10:31,589 pysam/libcutils.c: In function ‘__pyx_pw_5pysam_9libcutils_9_pysam_dispatch’: 2021-07-15T11:10:31,589 pysam/libcutils.c:526:40: warning: ‘__pyx_v_retval’ may be used uninitialized in this function [-Wmaybe-uninitialized] 2021-07-15T11:10:31,589 526 | #define PyInt_FromLong PyLong_FromLong 2021-07-15T11:10:31,589 | ^~~~~~~~~~~~~~~ 2021-07-15T11:10:31,592 pysam/libcutils.c:5973:7: note: ‘__pyx_v_retval’ was declared here 2021-07-15T11:10:31,592 5973 | int __pyx_v_retval; 2021-07-15T11:10:31,593 | ^~~~~~~~~~~~~~ 2021-07-15T11:10:34,196 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/htslib -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/samtools -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/samtools/lz4 -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/bcftools -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/pysam -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27 -I/usr/include/python3.9 -c pysam/pysam_util.c -o build/temp.linux-armv7l-3.9/pysam/pysam_util.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 2021-07-15T11:10:34,387 arm-linux-gnueabihf-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -g -fwrapv -O2 -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-armv7l-3.9/pysam/libcutils.o build/temp.linux-armv7l-3.9/pysam/pysam_util.o -L/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/pysam -L/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/pysam -L/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27 -L/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/build/lib.linux-armv7l-3.9/pysam -Lbuild/lib.linux-armv7l-3.9/pysam -Lbuild/lib.linux-armv7l-3.9/pysam -Lbuild/lib.linux-armv7l-3.9/pysam -Lbuild/lib.linux-armv7l-3.9/pysam -lz -ldeflate -llzma -lbz2 -lz -lm -lcurl -lcrypto -lchtslib.cpython-39-arm-linux-gnueabihf -lcsamtools.cpython-39-arm-linux-gnueabihf -lcbcftools.cpython-39-arm-linux-gnueabihf -o build/lib.linux-armv7l-3.9/pysam/libcutils.cpython-39-arm-linux-gnueabihf.so -Wl,-rpath,$ORIGIN 2021-07-15T11:10:34,588 building 'pysam.libcalignmentfile' extension 2021-07-15T11:10:34,588 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/htslib -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/samtools -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/samtools/lz4 -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/bcftools -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/pysam -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27 -I/usr/include/python3.9 -c pysam/libcalignmentfile.c -o build/temp.linux-armv7l-3.9/pysam/libcalignmentfile.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 2021-07-15T11:10:35,699 pysam/libcalignmentfile.c: In function ‘__pyx_f_5pysam_17libcalignmentfile_14IteratorColumn_cnext’: 2021-07-15T11:10:35,715 pysam/libcalignmentfile.c:29774:127: warning: passing argument 5 of ‘bam_mplp_auto’ from incompatible pointer type [-Wincompatible-pointer-types] 2021-07-15T11:10:35,715 29774 | __pyx_v_ret = bam_mplp_auto(__pyx_v_self->pileup_iter, (&__pyx_v_self->tid), (&__pyx_v_self->pos), (&__pyx_v_self->n_plp), (&__pyx_v_self->plp)); 2021-07-15T11:10:35,715 | ~^~~~~~~~~~~~~~~~~~~ 2021-07-15T11:10:35,715 | | 2021-07-15T11:10:35,715 | bam_pileup1_t ** 2021-07-15T11:10:35,716 In file included from pysam/htslib_util.h:4, 2021-07-15T11:10:35,716 from pysam/libcalignmentfile.c:618: 2021-07-15T11:10:35,717 /tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/htslib/htslib/sam.h:686:96: note: expected ‘const bam_pileup1_t **’ but argument is of type ‘bam_pileup1_t **’ 2021-07-15T11:10:35,717 686 | int bam_mplp_auto(bam_mplp_t iter, int *_tid, int *_pos, int *n_plp, const bam_pileup1_t **plp); 2021-07-15T11:10:35,717 | ~~~~~~~~~~~~~~~~~~~~~~^~~ 2021-07-15T11:11:14,900 arm-linux-gnueabihf-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -g -fwrapv -O2 -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-armv7l-3.9/pysam/libcalignmentfile.o -L/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/pysam -L/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/pysam -L/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27 -L/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/build/lib.linux-armv7l-3.9/pysam -Lbuild/lib.linux-armv7l-3.9/pysam -Lbuild/lib.linux-armv7l-3.9/pysam -Lbuild/lib.linux-armv7l-3.9/pysam -Lbuild/lib.linux-armv7l-3.9/pysam -Lbuild/lib.linux-armv7l-3.9/pysam -lz -ldeflate -llzma -lbz2 -lz -lm -lcurl -lcrypto -lchtslib.cpython-39-arm-linux-gnueabihf -lcutils.cpython-39-arm-linux-gnueabihf -o build/lib.linux-armv7l-3.9/pysam/libcalignmentfile.cpython-39-arm-linux-gnueabihf.so -Wl,-rpath,$ORIGIN 2021-07-15T11:11:15,216 building 'pysam.libcsamfile' extension 2021-07-15T11:11:15,216 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/htslib -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/samtools -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/samtools/lz4 -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/bcftools -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/pysam -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27 -I/usr/include/python3.9 -c pysam/libcsamfile.c -o build/temp.linux-armv7l-3.9/pysam/libcsamfile.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 2021-07-15T11:11:17,291 arm-linux-gnueabihf-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -g -fwrapv -O2 -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-armv7l-3.9/pysam/libcsamfile.o -L/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/pysam -L/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/pysam -L/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27 -L/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/build/lib.linux-armv7l-3.9/pysam -Lbuild/lib.linux-armv7l-3.9/pysam -Lbuild/lib.linux-armv7l-3.9/pysam -Lbuild/lib.linux-armv7l-3.9/pysam -Lbuild/lib.linux-armv7l-3.9/pysam -Lbuild/lib.linux-armv7l-3.9/pysam -Lbuild/lib.linux-armv7l-3.9/pysam -lz -ldeflate -llzma -lbz2 -lz -lm -lcurl -lcrypto -lchtslib.cpython-39-arm-linux-gnueabihf -lcutils.cpython-39-arm-linux-gnueabihf -o build/lib.linux-armv7l-3.9/pysam/libcsamfile.cpython-39-arm-linux-gnueabihf.so -Wl,-rpath,$ORIGIN 2021-07-15T11:11:17,461 building 'pysam.libcalignedsegment' extension 2021-07-15T11:11:17,462 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/htslib -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/samtools -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/samtools/lz4 -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/bcftools -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/pysam -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27 -I/usr/include/python3.9 -c pysam/libcalignedsegment.c -o build/temp.linux-armv7l-3.9/pysam/libcalignedsegment.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 2021-07-15T11:12:10,585 arm-linux-gnueabihf-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -g -fwrapv -O2 -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-armv7l-3.9/pysam/libcalignedsegment.o -L/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/pysam -L/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/pysam -L/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27 -L/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/build/lib.linux-armv7l-3.9/pysam -Lbuild/lib.linux-armv7l-3.9/pysam -Lbuild/lib.linux-armv7l-3.9/pysam -Lbuild/lib.linux-armv7l-3.9/pysam -Lbuild/lib.linux-armv7l-3.9/pysam -Lbuild/lib.linux-armv7l-3.9/pysam -Lbuild/lib.linux-armv7l-3.9/pysam -Lbuild/lib.linux-armv7l-3.9/pysam -lz -ldeflate -llzma -lbz2 -lz -lm -lcurl -lcrypto -lchtslib.cpython-39-arm-linux-gnueabihf -lcutils.cpython-39-arm-linux-gnueabihf -o build/lib.linux-armv7l-3.9/pysam/libcalignedsegment.cpython-39-arm-linux-gnueabihf.so -Wl,-rpath,$ORIGIN 2021-07-15T11:12:10,963 building 'pysam.libctabix' extension 2021-07-15T11:12:10,964 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/htslib -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/samtools -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/samtools/lz4 -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/bcftools -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/pysam -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27 -I/usr/include/python3.9 -c pysam/libctabix.c -o build/temp.linux-armv7l-3.9/pysam/libctabix.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 2021-07-15T11:12:11,538 pysam/libctabix.c: In function ‘__pyx_pf_5pysam_9libctabix_9TabixFile_7contigs___get__’: 2021-07-15T11:12:11,542 pysam/libctabix.c:8775:27: warning: assignment to ‘char **’ from incompatible pointer type ‘const char **’ [-Wincompatible-pointer-types] 2021-07-15T11:12:11,542 8775 | __pyx_v_sequences = tbx_seqnames(__pyx_v_self->index, (&__pyx_v_nsequences)); 2021-07-15T11:12:11,542 | ^ 2021-07-15T11:12:11,642 In file included from pysam/libctabix.c:625: 2021-07-15T11:12:11,642 pysam/libctabix.c: In function ‘__pyx_pf_5pysam_9libctabix_4tabix_index’: 2021-07-15T11:12:11,649 /tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/htslib/htslib/tbx.h:41:21: warning: overflow in conversion from ‘int’ to ‘int8_t’ {aka ‘signed char’} changes value from ‘65536’ to ‘0’ [-Woverflow] 2021-07-15T11:12:11,649 41 | #define TBX_UCSC 0x10000 2021-07-15T11:12:11,649 | ^~~~~~~ 2021-07-15T11:12:11,649 pysam/libctabix.c:13970:39: note: in expansion of macro ‘TBX_UCSC’ 2021-07-15T11:12:11,650 13970 | __pyx_t_1 = __Pyx_PyInt_From_int8_t(TBX_UCSC); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 975, __pyx_L1_error) 2021-07-15T11:12:11,650 | ^~~~~~~~ 2021-07-15T11:12:11,657 /tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/htslib/htslib/tbx.h:41:21: warning: overflow in conversion from ‘int’ to ‘int8_t’ {aka ‘signed char’} changes value from ‘65536’ to ‘0’ [-Woverflow] 2021-07-15T11:12:11,657 41 | #define TBX_UCSC 0x10000 2021-07-15T11:12:11,657 | ^~~~~~~ 2021-07-15T11:12:11,657 pysam/libctabix.c:14002:39: note: in expansion of macro ‘TBX_UCSC’ 2021-07-15T11:12:11,657 14002 | __pyx_t_3 = __Pyx_PyInt_From_int8_t(TBX_UCSC); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 976, __pyx_L1_error) 2021-07-15T11:12:11,657 | ^~~~~~~~ 2021-07-15T11:12:11,671 /tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/htslib/htslib/tbx.h:41:21: warning: overflow in conversion from ‘int’ to ‘int8_t’ {aka ‘signed char’} changes value from ‘65536’ to ‘0’ [-Woverflow] 2021-07-15T11:12:11,671 41 | #define TBX_UCSC 0x10000 2021-07-15T11:12:11,672 | ^~~~~~~ 2021-07-15T11:12:11,672 pysam/libctabix.c:14372:43: note: in expansion of macro ‘TBX_UCSC’ 2021-07-15T11:12:11,672 14372 | __pyx_t_3 = __Pyx_PyInt_From_int8_t(TBX_UCSC); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 1005, __pyx_L1_error) 2021-07-15T11:12:11,672 | ^~~~~~~~ 2021-07-15T11:12:31,142 arm-linux-gnueabihf-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -g -fwrapv -O2 -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-armv7l-3.9/pysam/libctabix.o -L/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/pysam -L/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/pysam -L/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27 -L/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/build/lib.linux-armv7l-3.9/pysam -Lbuild/lib.linux-armv7l-3.9/pysam -Lbuild/lib.linux-armv7l-3.9/pysam -Lbuild/lib.linux-armv7l-3.9/pysam -Lbuild/lib.linux-armv7l-3.9/pysam -Lbuild/lib.linux-armv7l-3.9/pysam -Lbuild/lib.linux-armv7l-3.9/pysam -Lbuild/lib.linux-armv7l-3.9/pysam -Lbuild/lib.linux-armv7l-3.9/pysam -lz -ldeflate -llzma -lbz2 -lz -lm -lcurl -lcrypto -lchtslib.cpython-39-arm-linux-gnueabihf -lcutils.cpython-39-arm-linux-gnueabihf -o build/lib.linux-armv7l-3.9/pysam/libctabix.cpython-39-arm-linux-gnueabihf.so -Wl,-rpath,$ORIGIN 2021-07-15T11:12:31,397 building 'pysam.libcfaidx' extension 2021-07-15T11:12:31,397 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/htslib -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/samtools -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/samtools/lz4 -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/bcftools -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/pysam -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27 -I/usr/include/python3.9 -c pysam/libcfaidx.c -o build/temp.linux-armv7l-3.9/pysam/libcfaidx.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 2021-07-15T11:12:43,021 arm-linux-gnueabihf-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -g -fwrapv -O2 -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-armv7l-3.9/pysam/libcfaidx.o -L/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/pysam -L/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/pysam -L/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27 -L/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/build/lib.linux-armv7l-3.9/pysam -Lbuild/lib.linux-armv7l-3.9/pysam -Lbuild/lib.linux-armv7l-3.9/pysam -Lbuild/lib.linux-armv7l-3.9/pysam -Lbuild/lib.linux-armv7l-3.9/pysam -Lbuild/lib.linux-armv7l-3.9/pysam -Lbuild/lib.linux-armv7l-3.9/pysam -Lbuild/lib.linux-armv7l-3.9/pysam -Lbuild/lib.linux-armv7l-3.9/pysam -Lbuild/lib.linux-armv7l-3.9/pysam -lz -ldeflate -llzma -lbz2 -lz -lm -lcurl -lcrypto -lchtslib.cpython-39-arm-linux-gnueabihf -lcutils.cpython-39-arm-linux-gnueabihf -o build/lib.linux-armv7l-3.9/pysam/libcfaidx.cpython-39-arm-linux-gnueabihf.so -Wl,-rpath,$ORIGIN 2021-07-15T11:12:43,240 building 'pysam.libcbcf' extension 2021-07-15T11:12:43,240 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/htslib -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/samtools -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/samtools/lz4 -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/bcftools -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/pysam -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27 -I/usr/include/python3.9 -c pysam/libcbcf.c -o build/temp.linux-armv7l-3.9/pysam/libcbcf.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 2021-07-15T11:13:56,117 arm-linux-gnueabihf-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -g -fwrapv -O2 -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-armv7l-3.9/pysam/libcbcf.o -L/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/pysam -L/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/pysam -L/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27 -L/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/build/lib.linux-armv7l-3.9/pysam -Lbuild/lib.linux-armv7l-3.9/pysam -Lbuild/lib.linux-armv7l-3.9/pysam -Lbuild/lib.linux-armv7l-3.9/pysam -Lbuild/lib.linux-armv7l-3.9/pysam -Lbuild/lib.linux-armv7l-3.9/pysam -Lbuild/lib.linux-armv7l-3.9/pysam -Lbuild/lib.linux-armv7l-3.9/pysam -Lbuild/lib.linux-armv7l-3.9/pysam -Lbuild/lib.linux-armv7l-3.9/pysam -Lbuild/lib.linux-armv7l-3.9/pysam -lz -ldeflate -llzma -lbz2 -lz -lm -lcurl -lcrypto -lchtslib.cpython-39-arm-linux-gnueabihf -lcutils.cpython-39-arm-linux-gnueabihf -o build/lib.linux-armv7l-3.9/pysam/libcbcf.cpython-39-arm-linux-gnueabihf.so -Wl,-rpath,$ORIGIN 2021-07-15T11:13:56,574 building 'pysam.libcbgzf' extension 2021-07-15T11:13:56,574 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/htslib -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/samtools -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/samtools/lz4 -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/bcftools -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/pysam -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27 -I/usr/include/python3.9 -c pysam/libcbgzf.c -o build/temp.linux-armv7l-3.9/pysam/libcbgzf.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 2021-07-15T11:14:01,649 arm-linux-gnueabihf-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -g -fwrapv -O2 -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-armv7l-3.9/pysam/libcbgzf.o -L/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/pysam -L/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/pysam -L/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27 -L/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/build/lib.linux-armv7l-3.9/pysam -Lbuild/lib.linux-armv7l-3.9/pysam -Lbuild/lib.linux-armv7l-3.9/pysam -Lbuild/lib.linux-armv7l-3.9/pysam -Lbuild/lib.linux-armv7l-3.9/pysam -Lbuild/lib.linux-armv7l-3.9/pysam -Lbuild/lib.linux-armv7l-3.9/pysam -Lbuild/lib.linux-armv7l-3.9/pysam -Lbuild/lib.linux-armv7l-3.9/pysam -Lbuild/lib.linux-armv7l-3.9/pysam -Lbuild/lib.linux-armv7l-3.9/pysam -Lbuild/lib.linux-armv7l-3.9/pysam -lz -ldeflate -llzma -lbz2 -lz -lm -lcurl -lcrypto -lchtslib.cpython-39-arm-linux-gnueabihf -lcutils.cpython-39-arm-linux-gnueabihf -o build/lib.linux-armv7l-3.9/pysam/libcbgzf.cpython-39-arm-linux-gnueabihf.so -Wl,-rpath,$ORIGIN 2021-07-15T11:14:01,840 building 'pysam.libctabixproxies' extension 2021-07-15T11:14:01,841 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/htslib -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/samtools -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/samtools/lz4 -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/bcftools -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/pysam -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27 -I/usr/include/python3.9 -c pysam/libctabixproxies.c -o build/temp.linux-armv7l-3.9/pysam/libctabixproxies.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 2021-07-15T11:14:18,955 arm-linux-gnueabihf-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -g -fwrapv -O2 -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-armv7l-3.9/pysam/libctabixproxies.o -L/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/pysam -L/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/pysam -L/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27 -L/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/build/lib.linux-armv7l-3.9/pysam -Lbuild/lib.linux-armv7l-3.9/pysam -Lbuild/lib.linux-armv7l-3.9/pysam -Lbuild/lib.linux-armv7l-3.9/pysam -Lbuild/lib.linux-armv7l-3.9/pysam -Lbuild/lib.linux-armv7l-3.9/pysam -Lbuild/lib.linux-armv7l-3.9/pysam -Lbuild/lib.linux-armv7l-3.9/pysam -Lbuild/lib.linux-armv7l-3.9/pysam -Lbuild/lib.linux-armv7l-3.9/pysam -Lbuild/lib.linux-armv7l-3.9/pysam -Lbuild/lib.linux-armv7l-3.9/pysam -Lbuild/lib.linux-armv7l-3.9/pysam -lz -ldeflate -llzma -lbz2 -lz -lm -lcurl -lcrypto -lchtslib.cpython-39-arm-linux-gnueabihf -lcutils.cpython-39-arm-linux-gnueabihf -o build/lib.linux-armv7l-3.9/pysam/libctabixproxies.cpython-39-arm-linux-gnueabihf.so -Wl,-rpath,$ORIGIN 2021-07-15T11:14:19,183 building 'pysam.libcvcf' extension 2021-07-15T11:14:19,184 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/htslib -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/samtools -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/samtools/lz4 -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/bcftools -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/pysam -I/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27 -I/usr/include/python3.9 -c pysam/libcvcf.c -o build/temp.linux-armv7l-3.9/pysam/libcvcf.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 2021-07-15T11:15:02,326 pysam/libcvcf.c: In function ‘__pyx_pf_5pysam_7libcvcf_3VCF_32parse_data.constprop’: 2021-07-15T11:15:02,342 pysam/libcvcf.c:25048:16: warning: ‘__pyx_v_qual’ may be used uninitialized in this function [-Wmaybe-uninitialized] 2021-07-15T11:15:02,342 25048 | __pyx_t_12 = PyFloat_FromDouble(__pyx_v_qual); if (unlikely(!__pyx_t_12)) __PYX_ERR(0, 873, __pyx_L1_error) 2021-07-15T11:15:02,343 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-15T11:15:20,885 arm-linux-gnueabihf-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -g -fwrapv -O2 -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-armv7l-3.9/pysam/libcvcf.o -L/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/pysam -L/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/pysam -L/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27 -L/tmp/pip-wheel-aps2kmfz/pysam-cabbage_eed640dcc6794258b4f5b2d643c14f27/build/lib.linux-armv7l-3.9/pysam -Lbuild/lib.linux-armv7l-3.9/pysam -Lbuild/lib.linux-armv7l-3.9/pysam -Lbuild/lib.linux-armv7l-3.9/pysam -Lbuild/lib.linux-armv7l-3.9/pysam -Lbuild/lib.linux-armv7l-3.9/pysam -Lbuild/lib.linux-armv7l-3.9/pysam -Lbuild/lib.linux-armv7l-3.9/pysam -Lbuild/lib.linux-armv7l-3.9/pysam -Lbuild/lib.linux-armv7l-3.9/pysam -Lbuild/lib.linux-armv7l-3.9/pysam -Lbuild/lib.linux-armv7l-3.9/pysam -Lbuild/lib.linux-armv7l-3.9/pysam -Lbuild/lib.linux-armv7l-3.9/pysam -lz -ldeflate -llzma -lbz2 -lz -lm -lcurl -lcrypto -lchtslib.cpython-39-arm-linux-gnueabihf -lcutils.cpython-39-arm-linux-gnueabihf -o build/lib.linux-armv7l-3.9/pysam/libcvcf.cpython-39-arm-linux-gnueabihf.so -Wl,-rpath,$ORIGIN 2021-07-15T11:15:21,240 installing to build/bdist.linux-armv7l/wheel 2021-07-15T11:15:21,240 running install 2021-07-15T11:15:21,243 running install_lib 2021-07-15T11:15:21,249 creating build/bdist.linux-armv7l 2021-07-15T11:15:21,250 creating build/bdist.linux-armv7l/wheel 2021-07-15T11:15:21,253 creating build/bdist.linux-armv7l/wheel/pysam 2021-07-15T11:15:21,254 copying build/lib.linux-armv7l-3.9/pysam/__init__.py -> build/bdist.linux-armv7l/wheel/pysam 2021-07-15T11:15:21,257 copying build/lib.linux-armv7l-3.9/pysam/samtools.py -> build/bdist.linux-armv7l/wheel/pysam 2021-07-15T11:15:21,259 copying build/lib.linux-armv7l-3.9/pysam/htslib_util.h -> build/bdist.linux-armv7l/wheel/pysam 2021-07-15T11:15:21,262 copying build/lib.linux-armv7l-3.9/pysam/libcbgzf.cpython-39-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/pysam 2021-07-15T11:15:21,273 copying build/lib.linux-armv7l-3.9/pysam/libchtslib.cpython-39-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/pysam 2021-07-15T11:15:21,356 copying build/lib.linux-armv7l-3.9/pysam/libcsamtools.pxd -> build/bdist.linux-armv7l/wheel/pysam 2021-07-15T11:15:21,357 copying build/lib.linux-armv7l-3.9/pysam/libcutils.pxd -> build/bdist.linux-armv7l/wheel/pysam 2021-07-15T11:15:21,359 copying build/lib.linux-armv7l-3.9/pysam/libctabix.pxd -> build/bdist.linux-armv7l/wheel/pysam 2021-07-15T11:15:21,361 copying build/lib.linux-armv7l-3.9/pysam/libcbcf.cpython-39-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/pysam 2021-07-15T11:15:21,467 copying build/lib.linux-armv7l-3.9/pysam/libcsamtools.cpython-39-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/pysam 2021-07-15T11:15:21,521 copying build/lib.linux-armv7l-3.9/pysam/libcsamfile.pxd -> build/bdist.linux-armv7l/wheel/pysam 2021-07-15T11:15:21,523 copying build/lib.linux-armv7l-3.9/pysam/libcvcf.cpython-39-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/pysam 2021-07-15T11:15:21,628 copying build/lib.linux-armv7l-3.9/pysam/libcbcftools.pxd -> build/bdist.linux-armv7l/wheel/pysam 2021-07-15T11:15:21,632 copying build/lib.linux-armv7l-3.9/pysam/config.py -> build/bdist.linux-armv7l/wheel/pysam 2021-07-15T11:15:21,634 copying build/lib.linux-armv7l-3.9/pysam/libcsamfile.cpython-39-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/pysam 2021-07-15T11:15:21,642 copying build/lib.linux-armv7l-3.9/pysam/libcalignedsegment.pxd -> build/bdist.linux-armv7l/wheel/pysam 2021-07-15T11:15:21,644 copying build/lib.linux-armv7l-3.9/pysam/utils.py -> build/bdist.linux-armv7l/wheel/pysam 2021-07-15T11:15:21,647 copying build/lib.linux-armv7l-3.9/pysam/libcalignedsegment.cpython-39-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/pysam 2021-07-15T11:15:21,717 copying build/lib.linux-armv7l-3.9/pysam/libcbcf.pxd -> build/bdist.linux-armv7l/wheel/pysam 2021-07-15T11:15:21,719 copying build/lib.linux-armv7l-3.9/pysam/libctabix.cpython-39-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/pysam 2021-07-15T11:15:21,752 copying build/lib.linux-armv7l-3.9/pysam/csamtools_util.h -> build/bdist.linux-armv7l/wheel/pysam 2021-07-15T11:15:21,754 copying build/lib.linux-armv7l-3.9/pysam/libcalignmentfile.cpython-39-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/pysam 2021-07-15T11:15:21,813 copying build/lib.linux-armv7l-3.9/pysam/libcalignmentfile.pxd -> build/bdist.linux-armv7l/wheel/pysam 2021-07-15T11:15:21,816 copying build/lib.linux-armv7l-3.9/pysam/libcbcftools.cpython-39-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/pysam 2021-07-15T11:15:21,892 copying build/lib.linux-armv7l-3.9/pysam/libcfaidx.cpython-39-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/pysam 2021-07-15T11:15:21,915 copying build/lib.linux-armv7l-3.9/pysam/libchtslib.pxd -> build/bdist.linux-armv7l/wheel/pysam 2021-07-15T11:15:21,921 copying build/lib.linux-armv7l-3.9/pysam/pysam_util.h -> build/bdist.linux-armv7l/wheel/pysam 2021-07-15T11:15:21,923 copying build/lib.linux-armv7l-3.9/pysam/libctabixproxies.pxd -> build/bdist.linux-armv7l/wheel/pysam 2021-07-15T11:15:21,925 copying build/lib.linux-armv7l-3.9/pysam/libcfaidx.pxd -> build/bdist.linux-armv7l/wheel/pysam 2021-07-15T11:15:21,927 copying build/lib.linux-armv7l-3.9/pysam/bcftools.py -> build/bdist.linux-armv7l/wheel/pysam 2021-07-15T11:15:21,929 copying build/lib.linux-armv7l-3.9/pysam/pysam_stream.h -> build/bdist.linux-armv7l/wheel/pysam 2021-07-15T11:15:21,931 copying build/lib.linux-armv7l-3.9/pysam/libcutils.cpython-39-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/pysam 2021-07-15T11:15:21,946 creating build/bdist.linux-armv7l/wheel/pysam/include 2021-07-15T11:15:21,947 copying build/lib.linux-armv7l-3.9/pysam/include/__init__.py -> build/bdist.linux-armv7l/wheel/pysam/include 2021-07-15T11:15:21,950 creating build/bdist.linux-armv7l/wheel/pysam/include/htslib 2021-07-15T11:15:21,951 copying build/lib.linux-armv7l-3.9/pysam/include/htslib/thread_pool_internal.h -> build/bdist.linux-armv7l/wheel/pysam/include/htslib 2021-07-15T11:15:21,954 creating build/bdist.linux-armv7l/wheel/pysam/include/htslib/htslib 2021-07-15T11:15:21,955 copying build/lib.linux-armv7l-3.9/pysam/include/htslib/htslib/sam.h -> build/bdist.linux-armv7l/wheel/pysam/include/htslib/htslib 2021-07-15T11:15:21,959 copying build/lib.linux-armv7l-3.9/pysam/include/htslib/htslib/ksort.h -> build/bdist.linux-armv7l/wheel/pysam/include/htslib/htslib 2021-07-15T11:15:21,962 copying build/lib.linux-armv7l-3.9/pysam/include/htslib/htslib/cram.h -> build/bdist.linux-armv7l/wheel/pysam/include/htslib/htslib 2021-07-15T11:15:21,964 copying build/lib.linux-armv7l-3.9/pysam/include/htslib/htslib/faidx.h -> build/bdist.linux-armv7l/wheel/pysam/include/htslib/htslib 2021-07-15T11:15:21,967 copying build/lib.linux-armv7l-3.9/pysam/include/htslib/htslib/hts_log.h -> build/bdist.linux-armv7l/wheel/pysam/include/htslib/htslib 2021-07-15T11:15:21,969 copying build/lib.linux-armv7l-3.9/pysam/include/htslib/htslib/khash_str2int.h -> build/bdist.linux-armv7l/wheel/pysam/include/htslib/htslib 2021-07-15T11:15:21,971 copying build/lib.linux-armv7l-3.9/pysam/include/htslib/htslib/kfunc.h -> build/bdist.linux-armv7l/wheel/pysam/include/htslib/htslib 2021-07-15T11:15:21,973 copying build/lib.linux-armv7l-3.9/pysam/include/htslib/htslib/vcf.h -> build/bdist.linux-armv7l/wheel/pysam/include/htslib/htslib 2021-07-15T11:15:21,977 copying build/lib.linux-armv7l-3.9/pysam/include/htslib/htslib/hfile.h -> build/bdist.linux-armv7l/wheel/pysam/include/htslib/htslib 2021-07-15T11:15:21,980 copying build/lib.linux-armv7l-3.9/pysam/include/htslib/htslib/khash.h -> build/bdist.linux-armv7l/wheel/pysam/include/htslib/htslib 2021-07-15T11:15:21,983 copying build/lib.linux-armv7l-3.9/pysam/include/htslib/htslib/hts.h -> build/bdist.linux-armv7l/wheel/pysam/include/htslib/htslib 2021-07-15T11:15:21,986 copying build/lib.linux-armv7l-3.9/pysam/include/htslib/htslib/kseq.h -> build/bdist.linux-armv7l/wheel/pysam/include/htslib/htslib 2021-07-15T11:15:21,989 copying build/lib.linux-armv7l-3.9/pysam/include/htslib/htslib/hts_defs.h -> build/bdist.linux-armv7l/wheel/pysam/include/htslib/htslib 2021-07-15T11:15:21,991 copying build/lib.linux-armv7l-3.9/pysam/include/htslib/htslib/tbx.h -> build/bdist.linux-armv7l/wheel/pysam/include/htslib/htslib 2021-07-15T11:15:21,993 copying build/lib.linux-armv7l-3.9/pysam/include/htslib/htslib/thread_pool.h -> build/bdist.linux-armv7l/wheel/pysam/include/htslib/htslib 2021-07-15T11:15:21,996 copying build/lib.linux-armv7l-3.9/pysam/include/htslib/htslib/synced_bcf_reader.h -> build/bdist.linux-armv7l/wheel/pysam/include/htslib/htslib 2021-07-15T11:15:21,998 copying build/lib.linux-armv7l-3.9/pysam/include/htslib/htslib/hts_os.h -> build/bdist.linux-armv7l/wheel/pysam/include/htslib/htslib 2021-07-15T11:15:22,000 copying build/lib.linux-armv7l-3.9/pysam/include/htslib/htslib/kbitset.h -> build/bdist.linux-armv7l/wheel/pysam/include/htslib/htslib 2021-07-15T11:15:22,003 copying build/lib.linux-armv7l-3.9/pysam/include/htslib/htslib/kstring.h -> build/bdist.linux-armv7l/wheel/pysam/include/htslib/htslib 2021-07-15T11:15:22,005 copying build/lib.linux-armv7l-3.9/pysam/include/htslib/htslib/bgzf.h -> build/bdist.linux-armv7l/wheel/pysam/include/htslib/htslib 2021-07-15T11:15:22,007 copying build/lib.linux-armv7l-3.9/pysam/include/htslib/htslib/hts_endian.h -> build/bdist.linux-armv7l/wheel/pysam/include/htslib/htslib 2021-07-15T11:15:22,010 copying build/lib.linux-armv7l-3.9/pysam/include/htslib/htslib/klist.h -> build/bdist.linux-armv7l/wheel/pysam/include/htslib/htslib 2021-07-15T11:15:22,012 copying build/lib.linux-armv7l-3.9/pysam/include/htslib/htslib/knetfile.h -> build/bdist.linux-armv7l/wheel/pysam/include/htslib/htslib 2021-07-15T11:15:22,014 copying build/lib.linux-armv7l-3.9/pysam/include/htslib/htslib/vcf_sweep.h -> build/bdist.linux-armv7l/wheel/pysam/include/htslib/htslib 2021-07-15T11:15:22,016 copying build/lib.linux-armv7l-3.9/pysam/include/htslib/htslib/regidx.h -> build/bdist.linux-armv7l/wheel/pysam/include/htslib/htslib 2021-07-15T11:15:22,018 copying build/lib.linux-armv7l-3.9/pysam/include/htslib/htslib/vcfutils.h -> build/bdist.linux-armv7l/wheel/pysam/include/htslib/htslib 2021-07-15T11:15:22,021 copying build/lib.linux-armv7l-3.9/pysam/include/htslib/bcf_sr_sort.h -> build/bdist.linux-armv7l/wheel/pysam/include/htslib 2021-07-15T11:15:22,023 copying build/lib.linux-armv7l-3.9/pysam/include/htslib/config.h -> build/bdist.linux-armv7l/wheel/pysam/include/htslib 2021-07-15T11:15:22,025 copying build/lib.linux-armv7l-3.9/pysam/include/htslib/version.h -> build/bdist.linux-armv7l/wheel/pysam/include/htslib 2021-07-15T11:15:22,027 copying build/lib.linux-armv7l-3.9/pysam/include/htslib/hts_internal.h -> build/bdist.linux-armv7l/wheel/pysam/include/htslib 2021-07-15T11:15:22,029 copying build/lib.linux-armv7l-3.9/pysam/include/htslib/hfile_internal.h -> build/bdist.linux-armv7l/wheel/pysam/include/htslib 2021-07-15T11:15:22,031 copying build/lib.linux-armv7l-3.9/pysam/include/htslib/textutils_internal.h -> build/bdist.linux-armv7l/wheel/pysam/include/htslib 2021-07-15T11:15:22,035 creating build/bdist.linux-armv7l/wheel/pysam/include/bcftools 2021-07-15T11:15:22,035 copying build/lib.linux-armv7l-3.9/pysam/include/bcftools/smpl_ilist.h -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools 2021-07-15T11:15:22,038 copying build/lib.linux-armv7l-3.9/pysam/include/bcftools/gvcf.h -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools 2021-07-15T11:15:22,040 copying build/lib.linux-armv7l-3.9/pysam/include/bcftools/tsv2vcf.h -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools 2021-07-15T11:15:22,042 copying build/lib.linux-armv7l-3.9/pysam/include/bcftools/vcmp.h -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools 2021-07-15T11:15:22,044 copying build/lib.linux-armv7l-3.9/pysam/include/bcftools/convert.h -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools 2021-07-15T11:15:22,046 copying build/lib.linux-armv7l-3.9/pysam/include/bcftools/rbuf.h -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools 2021-07-15T11:15:22,048 copying build/lib.linux-armv7l-3.9/pysam/include/bcftools/config.h -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools 2021-07-15T11:15:22,050 copying build/lib.linux-armv7l-3.9/pysam/include/bcftools/filter.h -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools 2021-07-15T11:15:22,052 copying build/lib.linux-armv7l-3.9/pysam/include/bcftools/mw.h -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools 2021-07-15T11:15:22,057 copying build/lib.linux-armv7l-3.9/pysam/include/bcftools/version.h -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools 2021-07-15T11:15:22,059 copying build/lib.linux-armv7l-3.9/pysam/include/bcftools/HMM.h -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools 2021-07-15T11:15:22,062 copying build/lib.linux-armv7l-3.9/pysam/include/bcftools/hclust.h -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools 2021-07-15T11:15:22,064 copying build/lib.linux-armv7l-3.9/pysam/include/bcftools/kheap.h -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools 2021-07-15T11:15:22,066 copying build/lib.linux-armv7l-3.9/pysam/include/bcftools/call.h -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools 2021-07-15T11:15:22,068 copying build/lib.linux-armv7l-3.9/pysam/include/bcftools/kmin.h -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools 2021-07-15T11:15:22,070 copying build/lib.linux-armv7l-3.9/pysam/include/bcftools/bcftools.pysam.h -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools 2021-07-15T11:15:22,072 copying build/lib.linux-armv7l-3.9/pysam/include/bcftools/bin.h -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools 2021-07-15T11:15:22,074 copying build/lib.linux-armv7l-3.9/pysam/include/bcftools/prob1.h -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools 2021-07-15T11:15:22,076 copying build/lib.linux-armv7l-3.9/pysam/include/bcftools/bam2bcf.h -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools 2021-07-15T11:15:22,078 copying build/lib.linux-armv7l-3.9/pysam/include/bcftools/bcftools.h -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools 2021-07-15T11:15:22,081 copying build/lib.linux-armv7l-3.9/pysam/include/bcftools/vcfbuf.h -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools 2021-07-15T11:15:22,083 copying build/lib.linux-armv7l-3.9/pysam/include/bcftools/khash_str2str.h -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools 2021-07-15T11:15:22,085 copying build/lib.linux-armv7l-3.9/pysam/include/bcftools/bam_sample.h -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools 2021-07-15T11:15:22,087 copying build/lib.linux-armv7l-3.9/pysam/include/bcftools/regidx.h -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools 2021-07-15T11:15:22,089 copying build/lib.linux-armv7l-3.9/pysam/include/bcftools/ploidy.h -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools 2021-07-15T11:15:22,093 creating build/bdist.linux-armv7l/wheel/pysam/include/samtools 2021-07-15T11:15:22,094 copying build/lib.linux-armv7l-3.9/pysam/include/samtools/bam_plbuf.h -> build/bdist.linux-armv7l/wheel/pysam/include/samtools 2021-07-15T11:15:22,096 copying build/lib.linux-armv7l-3.9/pysam/include/samtools/sam.h -> build/bdist.linux-armv7l/wheel/pysam/include/samtools 2021-07-15T11:15:22,098 copying build/lib.linux-armv7l-3.9/pysam/include/samtools/sample.h -> build/bdist.linux-armv7l/wheel/pysam/include/samtools 2021-07-15T11:15:22,101 copying build/lib.linux-armv7l-3.9/pysam/include/samtools/config.h -> build/bdist.linux-armv7l/wheel/pysam/include/samtools 2021-07-15T11:15:22,103 copying build/lib.linux-armv7l-3.9/pysam/include/samtools/sam_opts.h -> build/bdist.linux-armv7l/wheel/pysam/include/samtools 2021-07-15T11:15:22,105 copying build/lib.linux-armv7l-3.9/pysam/include/samtools/samtools.h -> build/bdist.linux-armv7l/wheel/pysam/include/samtools 2021-07-15T11:15:22,107 copying build/lib.linux-armv7l-3.9/pysam/include/samtools/version.h -> build/bdist.linux-armv7l/wheel/pysam/include/samtools 2021-07-15T11:15:22,108 copying build/lib.linux-armv7l-3.9/pysam/include/samtools/bam_lpileup.h -> build/bdist.linux-armv7l/wheel/pysam/include/samtools 2021-07-15T11:15:22,110 copying build/lib.linux-armv7l-3.9/pysam/include/samtools/stats_isize.h -> build/bdist.linux-armv7l/wheel/pysam/include/samtools 2021-07-15T11:15:22,112 copying build/lib.linux-armv7l-3.9/pysam/include/samtools/bam2bcf.h -> build/bdist.linux-armv7l/wheel/pysam/include/samtools 2021-07-15T11:15:22,115 copying build/lib.linux-armv7l-3.9/pysam/include/samtools/sam_header.h -> build/bdist.linux-armv7l/wheel/pysam/include/samtools 2021-07-15T11:15:22,117 copying build/lib.linux-armv7l-3.9/pysam/include/samtools/bam_endian.h -> build/bdist.linux-armv7l/wheel/pysam/include/samtools 2021-07-15T11:15:22,119 copying build/lib.linux-armv7l-3.9/pysam/include/samtools/tmp_file.h -> build/bdist.linux-armv7l/wheel/pysam/include/samtools 2021-07-15T11:15:22,122 creating build/bdist.linux-armv7l/wheel/pysam/include/samtools/win32 2021-07-15T11:15:22,123 copying build/lib.linux-armv7l-3.9/pysam/include/samtools/win32/zlib.h -> build/bdist.linux-armv7l/wheel/pysam/include/samtools/win32 2021-07-15T11:15:22,128 copying build/lib.linux-armv7l-3.9/pysam/include/samtools/win32/xcurses.h -> build/bdist.linux-armv7l/wheel/pysam/include/samtools/win32 2021-07-15T11:15:22,132 copying build/lib.linux-armv7l-3.9/pysam/include/samtools/win32/zconf.h -> build/bdist.linux-armv7l/wheel/pysam/include/samtools/win32 2021-07-15T11:15:22,135 copying build/lib.linux-armv7l-3.9/pysam/include/samtools/samtools.pysam.h -> build/bdist.linux-armv7l/wheel/pysam/include/samtools 2021-07-15T11:15:22,137 copying build/lib.linux-armv7l-3.9/pysam/include/samtools/bedidx.h -> build/bdist.linux-armv7l/wheel/pysam/include/samtools 2021-07-15T11:15:22,139 copying build/lib.linux-armv7l-3.9/pysam/include/samtools/bam.h -> build/bdist.linux-armv7l/wheel/pysam/include/samtools 2021-07-15T11:15:22,142 copying build/lib.linux-armv7l-3.9/pysam/libctabixproxies.cpython-39-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/pysam 2021-07-15T11:15:22,168 copying build/lib.linux-armv7l-3.9/pysam/libcvcf.pxd -> build/bdist.linux-armv7l/wheel/pysam 2021-07-15T11:15:22,169 copying build/lib.linux-armv7l-3.9/pysam/cbcftools_util.h -> build/bdist.linux-armv7l/wheel/pysam 2021-07-15T11:15:22,171 copying build/lib.linux-armv7l-3.9/pysam/version.py -> build/bdist.linux-armv7l/wheel/pysam 2021-07-15T11:15:22,173 copying build/lib.linux-armv7l-3.9/pysam/Pileup.py -> build/bdist.linux-armv7l/wheel/pysam 2021-07-15T11:15:22,174 running install_egg_info 2021-07-15T11:15:22,218 running egg_info 2021-07-15T11:15:22,219 writing pysam_cabbage.egg-info/PKG-INFO 2021-07-15T11:15:22,221 writing dependency_links to pysam_cabbage.egg-info/dependency_links.txt 2021-07-15T11:15:22,223 writing top-level names to pysam_cabbage.egg-info/top_level.txt 2021-07-15T11:15:22,315 reading manifest file 'pysam_cabbage.egg-info/SOURCES.txt' 2021-07-15T11:15:22,352 reading manifest template 'MANIFEST.in' 2021-07-15T11:15:22,353 warning: no files found matching 'KNOWN_BUGS' 2021-07-15T11:15:22,353 warning: no files found matching 'THANKS' 2021-07-15T11:15:22,362 no previously-included directories found matching 'tests/' 2021-07-15T11:15:22,362 warning: no files found matching 'samtools/configure' 2021-07-15T11:15:22,362 warning: no files found matching 'samtools/config.mk.in' 2021-07-15T11:15:22,363 warning: no files found matching 'samtools/config.h.in' 2021-07-15T11:15:22,405 adding license file 'COPYING' 2021-07-15T11:15:22,432 writing manifest file 'pysam_cabbage.egg-info/SOURCES.txt' 2021-07-15T11:15:22,434 Copying pysam_cabbage.egg-info to build/bdist.linux-armv7l/wheel/pysam_cabbage-0.15.3-py3.9.egg-info 2021-07-15T11:15:22,445 running install_scripts 2021-07-15T11:15:22,482 adding license file "COPYING" (matched pattern "COPYING*") 2021-07-15T11:15:22,486 creating build/bdist.linux-armv7l/wheel/pysam_cabbage-0.15.3.dist-info/WHEEL 2021-07-15T11:15:22,489 creating '/tmp/pip-wheel-3m5bkvge/pysam_cabbage-0.15.3-cp39-cp39-linux_armv7l.whl' and adding 'build/bdist.linux-armv7l/wheel' to it 2021-07-15T11:15:22,493 adding 'pysam/Pileup.py' 2021-07-15T11:15:22,495 adding 'pysam/__init__.py' 2021-07-15T11:15:22,496 adding 'pysam/bcftools.py' 2021-07-15T11:15:22,497 adding 'pysam/cbcftools_util.h' 2021-07-15T11:15:22,498 adding 'pysam/config.py' 2021-07-15T11:15:22,499 adding 'pysam/csamtools_util.h' 2021-07-15T11:15:22,501 adding 'pysam/htslib_util.h' 2021-07-15T11:15:23,117 adding 'pysam/libcalignedsegment.cpython-39-arm-linux-gnueabihf.so' 2021-07-15T11:15:23,145 adding 'pysam/libcalignedsegment.pxd' 2021-07-15T11:15:23,621 adding 'pysam/libcalignmentfile.cpython-39-arm-linux-gnueabihf.so' 2021-07-15T11:15:23,643 adding 'pysam/libcalignmentfile.pxd' 2021-07-15T11:15:24,440 adding 'pysam/libcbcf.cpython-39-arm-linux-gnueabihf.so' 2021-07-15T11:15:24,479 adding 'pysam/libcbcf.pxd' 2021-07-15T11:15:25,242 adding 'pysam/libcbcftools.cpython-39-arm-linux-gnueabihf.so' 2021-07-15T11:15:25,269 adding 'pysam/libcbcftools.pxd' 2021-07-15T11:15:25,342 adding 'pysam/libcbgzf.cpython-39-arm-linux-gnueabihf.so' 2021-07-15T11:15:25,507 adding 'pysam/libcfaidx.cpython-39-arm-linux-gnueabihf.so' 2021-07-15T11:15:25,515 adding 'pysam/libcfaidx.pxd' 2021-07-15T11:15:26,391 adding 'pysam/libchtslib.cpython-39-arm-linux-gnueabihf.so' 2021-07-15T11:15:26,436 adding 'pysam/libchtslib.pxd' 2021-07-15T11:15:26,463 adding 'pysam/libcsamfile.cpython-39-arm-linux-gnueabihf.so' 2021-07-15T11:15:26,466 adding 'pysam/libcsamfile.pxd' 2021-07-15T11:15:26,983 adding 'pysam/libcsamtools.cpython-39-arm-linux-gnueabihf.so' 2021-07-15T11:15:27,003 adding 'pysam/libcsamtools.pxd' 2021-07-15T11:15:27,250 adding 'pysam/libctabix.cpython-39-arm-linux-gnueabihf.so' 2021-07-15T11:15:27,262 adding 'pysam/libctabix.pxd' 2021-07-15T11:15:27,500 adding 'pysam/libctabixproxies.cpython-39-arm-linux-gnueabihf.so' 2021-07-15T11:15:27,511 adding 'pysam/libctabixproxies.pxd' 2021-07-15T11:15:27,640 adding 'pysam/libcutils.cpython-39-arm-linux-gnueabihf.so' 2021-07-15T11:15:27,646 adding 'pysam/libcutils.pxd' 2021-07-15T11:15:28,196 adding 'pysam/libcvcf.cpython-39-arm-linux-gnueabihf.so' 2021-07-15T11:15:28,220 adding 'pysam/libcvcf.pxd' 2021-07-15T11:15:28,221 adding 'pysam/pysam_stream.h' 2021-07-15T11:15:28,223 adding 'pysam/pysam_util.h' 2021-07-15T11:15:28,224 adding 'pysam/samtools.py' 2021-07-15T11:15:28,225 adding 'pysam/utils.py' 2021-07-15T11:15:28,227 adding 'pysam/version.py' 2021-07-15T11:15:28,228 adding 'pysam/include/__init__.py' 2021-07-15T11:15:28,231 adding 'pysam/include/bcftools/HMM.h' 2021-07-15T11:15:28,232 adding 'pysam/include/bcftools/bam2bcf.h' 2021-07-15T11:15:28,234 adding 'pysam/include/bcftools/bam_sample.h' 2021-07-15T11:15:28,235 adding 'pysam/include/bcftools/bcftools.h' 2021-07-15T11:15:28,236 adding 'pysam/include/bcftools/bcftools.pysam.h' 2021-07-15T11:15:28,237 adding 'pysam/include/bcftools/bin.h' 2021-07-15T11:15:28,239 adding 'pysam/include/bcftools/call.h' 2021-07-15T11:15:28,240 adding 'pysam/include/bcftools/config.h' 2021-07-15T11:15:28,241 adding 'pysam/include/bcftools/convert.h' 2021-07-15T11:15:28,243 adding 'pysam/include/bcftools/filter.h' 2021-07-15T11:15:28,244 adding 'pysam/include/bcftools/gvcf.h' 2021-07-15T11:15:28,245 adding 'pysam/include/bcftools/hclust.h' 2021-07-15T11:15:28,247 adding 'pysam/include/bcftools/khash_str2str.h' 2021-07-15T11:15:28,249 adding 'pysam/include/bcftools/kheap.h' 2021-07-15T11:15:28,250 adding 'pysam/include/bcftools/kmin.h' 2021-07-15T11:15:28,253 adding 'pysam/include/bcftools/mw.h' 2021-07-15T11:15:28,255 adding 'pysam/include/bcftools/ploidy.h' 2021-07-15T11:15:28,257 adding 'pysam/include/bcftools/prob1.h' 2021-07-15T11:15:28,259 adding 'pysam/include/bcftools/rbuf.h' 2021-07-15T11:15:28,261 adding 'pysam/include/bcftools/regidx.h' 2021-07-15T11:15:28,262 adding 'pysam/include/bcftools/smpl_ilist.h' 2021-07-15T11:15:28,264 adding 'pysam/include/bcftools/tsv2vcf.h' 2021-07-15T11:15:28,265 adding 'pysam/include/bcftools/vcfbuf.h' 2021-07-15T11:15:28,266 adding 'pysam/include/bcftools/vcmp.h' 2021-07-15T11:15:28,267 adding 'pysam/include/bcftools/version.h' 2021-07-15T11:15:28,270 adding 'pysam/include/htslib/bcf_sr_sort.h' 2021-07-15T11:15:28,271 adding 'pysam/include/htslib/config.h' 2021-07-15T11:15:28,273 adding 'pysam/include/htslib/hfile_internal.h' 2021-07-15T11:15:28,275 adding 'pysam/include/htslib/hts_internal.h' 2021-07-15T11:15:28,276 adding 'pysam/include/htslib/textutils_internal.h' 2021-07-15T11:15:28,278 adding 'pysam/include/htslib/thread_pool_internal.h' 2021-07-15T11:15:28,279 adding 'pysam/include/htslib/version.h' 2021-07-15T11:15:28,283 adding 'pysam/include/htslib/htslib/bgzf.h' 2021-07-15T11:15:28,285 adding 'pysam/include/htslib/htslib/cram.h' 2021-07-15T11:15:28,287 adding 'pysam/include/htslib/htslib/faidx.h' 2021-07-15T11:15:28,290 adding 'pysam/include/htslib/htslib/hfile.h' 2021-07-15T11:15:28,294 adding 'pysam/include/htslib/htslib/hts.h' 2021-07-15T11:15:28,296 adding 'pysam/include/htslib/htslib/hts_defs.h' 2021-07-15T11:15:28,298 adding 'pysam/include/htslib/htslib/hts_endian.h' 2021-07-15T11:15:28,300 adding 'pysam/include/htslib/htslib/hts_log.h' 2021-07-15T11:15:28,301 adding 'pysam/include/htslib/htslib/hts_os.h' 2021-07-15T11:15:28,303 adding 'pysam/include/htslib/htslib/kbitset.h' 2021-07-15T11:15:28,304 adding 'pysam/include/htslib/htslib/kfunc.h' 2021-07-15T11:15:28,307 adding 'pysam/include/htslib/htslib/khash.h' 2021-07-15T11:15:28,309 adding 'pysam/include/htslib/htslib/khash_str2int.h' 2021-07-15T11:15:28,310 adding 'pysam/include/htslib/htslib/klist.h' 2021-07-15T11:15:28,312 adding 'pysam/include/htslib/htslib/knetfile.h' 2021-07-15T11:15:28,313 adding 'pysam/include/htslib/htslib/kseq.h' 2021-07-15T11:15:28,316 adding 'pysam/include/htslib/htslib/ksort.h' 2021-07-15T11:15:28,317 adding 'pysam/include/htslib/htslib/kstring.h' 2021-07-15T11:15:28,319 adding 'pysam/include/htslib/htslib/regidx.h' 2021-07-15T11:15:28,323 adding 'pysam/include/htslib/htslib/sam.h' 2021-07-15T11:15:28,326 adding 'pysam/include/htslib/htslib/synced_bcf_reader.h' 2021-07-15T11:15:28,328 adding 'pysam/include/htslib/htslib/tbx.h' 2021-07-15T11:15:28,330 adding 'pysam/include/htslib/htslib/thread_pool.h' 2021-07-15T11:15:28,336 adding 'pysam/include/htslib/htslib/vcf.h' 2021-07-15T11:15:28,337 adding 'pysam/include/htslib/htslib/vcf_sweep.h' 2021-07-15T11:15:28,339 adding 'pysam/include/htslib/htslib/vcfutils.h' 2021-07-15T11:15:28,343 adding 'pysam/include/samtools/bam.h' 2021-07-15T11:15:28,344 adding 'pysam/include/samtools/bam2bcf.h' 2021-07-15T11:15:28,346 adding 'pysam/include/samtools/bam_endian.h' 2021-07-15T11:15:28,347 adding 'pysam/include/samtools/bam_lpileup.h' 2021-07-15T11:15:28,348 adding 'pysam/include/samtools/bam_plbuf.h' 2021-07-15T11:15:28,350 adding 'pysam/include/samtools/bedidx.h' 2021-07-15T11:15:28,351 adding 'pysam/include/samtools/config.h' 2021-07-15T11:15:28,352 adding 'pysam/include/samtools/sam.h' 2021-07-15T11:15:28,354 adding 'pysam/include/samtools/sam_header.h' 2021-07-15T11:15:28,355 adding 'pysam/include/samtools/sam_opts.h' 2021-07-15T11:15:28,356 adding 'pysam/include/samtools/sample.h' 2021-07-15T11:15:28,358 adding 'pysam/include/samtools/samtools.h' 2021-07-15T11:15:28,359 adding 'pysam/include/samtools/samtools.pysam.h' 2021-07-15T11:15:28,360 adding 'pysam/include/samtools/stats_isize.h' 2021-07-15T11:15:28,361 adding 'pysam/include/samtools/tmp_file.h' 2021-07-15T11:15:28,363 adding 'pysam/include/samtools/version.h' 2021-07-15T11:15:28,369 adding 'pysam/include/samtools/win32/xcurses.h' 2021-07-15T11:15:28,371 adding 'pysam/include/samtools/win32/zconf.h' 2021-07-15T11:15:28,382 adding 'pysam/include/samtools/win32/zlib.h' 2021-07-15T11:15:28,385 adding 'pysam_cabbage-0.15.3.dist-info/COPYING' 2021-07-15T11:15:28,386 adding 'pysam_cabbage-0.15.3.dist-info/METADATA' 2021-07-15T11:15:28,387 adding 'pysam_cabbage-0.15.3.dist-info/WHEEL' 2021-07-15T11:15:28,388 adding 'pysam_cabbage-0.15.3.dist-info/top_level.txt' 2021-07-15T11:15:28,390 adding 'pysam_cabbage-0.15.3.dist-info/RECORD' 2021-07-15T11:15:28,548 removing build/bdist.linux-armv7l/wheel 2021-07-15T11:15:29,243 Building wheel for pysam-cabbage (setup.py): finished with status 'done' 2021-07-15T11:15:29,372 Created wheel for pysam-cabbage: filename=pysam_cabbage-0.15.3-cp39-cp39-linux_armv7l.whl size=10358484 sha256=414be6a5ad1464b611307eb8dd80d2a533b77b9e1767ff0dd4ca6541f12bae63 2021-07-15T11:15:29,373 Stored in directory: /tmp/pip-ephem-wheel-cache-pegxtibu/wheels/8b/0f/0b/53d76416671aa2c1d470f4ea38c4df6b181dbe07f9ca3b92b9 2021-07-15T11:15:29,391 Successfully built pysam-cabbage 2021-07-15T11:15:29,720 Removed build tracker: '/tmp/pip-req-tracker-lfjvlokv'