I was trying to install a package. Step1: wget https://raw.githubusercontent.com/rraadd88/beditor/master/environment.yml Step2: conda env create -f environment.yml Step3: source activate beditor
Step4: pip install beditor
I got a very long error message. I am completely lost. Can anyone help me? I will really really appreciate !!
(beditor) Haoxins-MacBook-Pro:~ haoxinli$ pip install beditor
Collecting beditor
Using cached beditor-1.1.9-py3-none-any.whl (122 kB)
Collecting pysam==0.14.1
Using cached pysam-0.14.1.tar.gz (3.2 MB)
Building wheels for collected packages: pysam
Building wheel for pysam (setup.py) ... error
ERROR: Command errored out with exit status 1:
command: /Applications/Python/anaconda3/envs/beditor/bin/python3.6 -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/private/var/folders/xr/wkj0mpgx3gs2l7hm2jf77x7h0000gn/T/pip-install-1ehbautp/pysam/setup.py'"'"'; __file__='"'"'/private/var/folders/xr/wkj0mpgx3gs2l7hm2jf77x7h0000gn/T/pip-install-1ehbautp/pysam/setup.py'"'"';f=getattr(tokenize, '"'"'open'"'"', open)(__file__);code=f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' bdist_wheel -d /private/var/folders/xr/wkj0mpgx3gs2l7hm2jf77x7h0000gn/T/pip-wheel-26pal1ds*
cwd: /private/var/folders/xr/wkj0mpgx3gs2l7hm2jf77x7h0000gn/T/pip-install-1ehbautp/pysam/
Complete output (241 lines):
# pysam: cython is available - using cythonize if necessary
# pysam: htslib mode is shared
# pysam: HTSLIB_CONFIGURE_OPTIONS=None
checking for gcc... gcc
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
checking for suffix of executables...
checking whether we are cross compiling... no
checking whether PTHREAD_MUTEX_RECURSIVE is declared... yes
configure: creating ./config.status
config.status: creating config.mk
config.status: creating htslib.pc.tmp
config.status: creating config.h
config.status: config.h is unchanged
# pysam: htslib configure options: --enable-libcurl
make: ./version.sh: Command not found
make: ./version.sh: Command not found
# pysam: htslib_config LDFLAGS=
# pysam: htslib_config LIBHTS_OBJS=kfunc.o knetfile.o kstring.o bcf_sr_sort.o bgzf.o errmod.o faidx.o hfile.o hfile_net.o hts.o hts_os.o md5.o multipart.o probaln.o realn.o regidx.o sam.o synced_bcf_reader.o vcf_sweep.o tbx.o textutils.o thread_pool.o vcf.o vcfutils.o cram/cram_codecs.o cram/cram_decode.o cram/cram_encode.o cram/cram_external.o cram/cram_index.o cram/cram_io.o cram/cram_samtools.o cram/cram_stats.o cram/files.o cram/mFILE.o cram/open_trace_file.o cram/pooled_alloc.o cram/rANS_static.o cram/sam_header.o cram/string_alloc.o hfile_libcurl.o hfile_gcs.o hfile_s3.o
/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/Availability.h:577:18: error: missing binary operator before token "(" #if has_include() ^ error: command 'gcc' failed with exit status 1 ---------------------------------------- ERROR: Failed building wheel for pysam Running setup.py clean for pysam Failed to build pysam Installing collected packages: pysam, beditor Attempting uninstall: pysam Found existing installation: pysam 0.15.4 Uninstalling pysam-0.15.4: Successfully uninstalled pysam-0.15.4 Running setup.py install for pysam ... error ERROR: Command errored out with exit status 1: command: /Applications/Python/anaconda3/envs/beditor/bin/python3.6 -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/private/var/folders/xr/wkj0mpgx3gs2l7hm2jf77x7h0000gn/T/pip-install-1ehbautp/pysam/setup.py'"'"'; __file='"'"'/private/var/folders/xr/wkj0mpgx3gs2l7hm2jf77x7h0000gn/T/pip-install-1ehbautp/pysam/setup.py'"'"';f=getattr(tokenize, '"'"'open'"'"', open)(file);code=f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, file, '"'"'exec'"'"'))' install --record /private/var/folders/xr/wkj0mpgx3gs2l7hm2jf77x7h0000gn/T/pip-record-m0q8xled/install-record.txt --single-version-externally-managed --compile --install-headers /Applications/Python/anaconda3/envs/beditor/include/python3.6m/pysam cwd: /private/var/folders/xr/wkj0mpgx3gs2l7hm2jf77x7h0000gn/T/pip-install-1ehbautp/pysam/ Complete output (241 lines): # pysam: cython is available - using cythonize if necessary # pysam: htslib mode is shared # pysam: HTSLIB_CONFIGURE_OPTIONS=None checking for gcc... gcc checking whether the C compiler works... yes checking for C compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether we are using the GNU C compiler... yes checking whether gcc accepts -g... yes checking for gcc option to accept ISO C89... none needed checking for ranlib... ranlib checking for grep that handles long lines and -e... /usr/bin/grep checking for C compiler warning flags... -Wall checking for special C compiler options needed for large files... no checking for _FILE_OFFSET_BITS value needed for large files... no checking for _LARGEFILE_SOURCE value needed for large files... no checking shared library type for unknown-Darwin... Darwin dylib checking how to run the C preprocessor... gcc -E checking for egrep... /usr/bin/grep -E checking for ANSI C header files... no checking for sys/types.h... yes checking for sys/stat.h... yes checking for stdlib.h... yes checking for string.h... yes checking for memory.h... yes checking for strings.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for unistd.h... yes checking for stdlib.h... (cached) yes checking for unistd.h... (cached) yes checking for sys/param.h... yes checking for getpagesize... yes checking for working mmap... yes checking for gmtime_r... yes checking for fsync... yes checking for drand48... yes checking whether fdatasync is declared... no checking for library containing log... none required checking for zlib.h... yes checking for inflate in -lz... yes checking for library containing recv... none required checking for bzlib.h... yes checking for BZ2_bzBuffToBuffCompress in -lbz2... yes checking for lzma.h... yes checking for lzma_easy_buffer_encode in -llzma... yes checking for curl_easy_pause in -lcurl... yes checking for CCHmac... yes checking whether PTHREAD_MUTEX_RECURSIVE is declared... yes configure: creating ./config.status config.status: creating config.mk config.status: creating htslib.pc.tmp config.status: creating config.h config.status: config.h is unchanged # pysam: htslib configure options: --enable-libcurl make: ./version.sh: Command not found make: ./version.sh: Command not found # pysam: htslib_config LDFLAGS= # pysam: htslib_config LIBHTS_OBJS=kfunc.o knetfile.o kstring.o bcf_sr_sort.o bgzf.o errmod.o faidx.o hfile.o hfile_net.o hts.o hts_os.o md5.o multipart.o probaln.o realn.o regidx.o sam.o synced_bcf_reader.o vcf_sweep.o tbx.o textutils.o thread_pool.o vcf.o vcfutils.o cram/cram_codecs.o cram/cram_decode.o cram/cram_encode.o cram/cram_external.o cram/cram_index.o cram/cram_io.o cram/cram_samtools.o cram/cram_stats.o cram/files.o cram/mFILE.o cram/open_trace_file.o cram/pooled_alloc.o cram/rANS_static.o cram/sam_header.o cram/string_alloc.o hfile_libcurl.o hfile_gcs.o hfile_s3.o # pysam: htslib_config LIBS=-llzma -lbz2 -lz -lcurl # pysam: htslib_config PLATFORM=Darwin # pysam: config_option: ENABLE_PLUGINS=0 # pysam: config_option: HAVE_COMMONCRYPTO=1 # pysam: config_option: HAVE_GMTIME_R=1 # pysam: config_option: HAVE_HMAC=0 # pysam: config_option: HAVE_IRODS=0 # pysam: config_option: HAVE_LIBCURL=1 # pysam: config_option: HAVE_MMAP=1 running install running build running build_py creating build creating build/lib.macosx-10.9-x86_64-3.6 creating build/lib.macosx-10.9-x86_64-3.6/pysam
Fixing build/lib.macosx-10.9-x86_64-3.6/pysam/bcftools.py build/lib.macosx-10.9-x86_64-3.6/pysam/config.py build/lib.macosx-10.9-x86_64-3.6/pysam/version.py build/lib.macosx-10.9-x86_64-3.6/pysam/samtools.py build/lib.macosx-10.9-x86_64-3.6/pysam/__init__.py build/lib.macosx-10.9-x86_64-3.6/pysam/Pileup.py build/lib.macosx-10.9-x86_64-3.6/pysam/utils.py build/lib.macosx-10.9-x86_64-3.6/pysam/include/__init__.py
Skipping optional fixer: buffer
Skipping optional fixer: idioms
Skipping optional fixer: set_literal
Skipping optional fixer: ws_comma
Fixing build/lib.macosx-10.9-x86_64-3.6/pysam/bcftools.py build/lib.macosx-10.9-x86_64-3.6/pysam/config.py build/lib.macosx-10.9-x86_64-3.6/pysam/version.py build/lib.macosx-10.9-x86_64-3.6/pysam/samtools.py build/lib.macosx-10.9-x86_64-3.6/pysam/__init__.py build/lib.macosx-10.9-x86_64-3.6/pysam/Pileup.py build/lib.macosx-10.9-x86_64-3.6/pysam/utils.py build/lib.macosx-10.9-x86_64-3.6/pysam/include/__init__.py
Skipping optional fixer: buffer
Skipping optional fixer: idioms
Skipping optional fixer: set_literal
Skipping optional fixer: ws_comma
running build_ext
skipping 'pysam/libchtslib.c' Cython extension (up-to-date)
skipping 'pysam/libcsamtools.c' Cython extension (up-to-date)
skipping 'pysam/libcbcftools.c' Cython extension (up-to-date)
skipping 'pysam/libcutils.c' Cython extension (up-to-date)
skipping 'pysam/libcalignmentfile.c' Cython extension (up-to-date)
skipping 'pysam/libcsamfile.c' Cython extension (up-to-date)
skipping 'pysam/libcalignedsegment.c' Cython extension (up-to-date)
skipping 'pysam/libctabix.c' Cython extension (up-to-date)
skipping 'pysam/libcfaidx.c' Cython extension (up-to-date)
skipping 'pysam/libcbcf.c' Cython extension (up-to-date)
skipping 'pysam/libcbgzf.c' Cython extension (up-to-date)
skipping 'pysam/libctabixproxies.c' Cython extension (up-to-date)
skipping 'pysam/libcvcf.c' Cython extension (up-to-date)
building 'pysam.libchtslib' extension
creating build/temp.macosx-10.9-x86_64-3.6
creating build/temp.macosx-10.9-x86_64-3.6/pysam
creating build/temp.macosx-10.9-x86_64-3.6/htslib
creating build/temp.macosx-10.9-x86_64-3.6/htslib/cram
gcc -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/Applications/Python/anaconda3/envs/beditor/include -arch x86_64 -I/Applications/Python/anaconda3/envs/beditor/include -arch x86_64 -I/private/var/folders/xr/wkj0mpgx3gs2l7hm2jf77x7h0000gn/T/pip-install-1ehbautp/pysam/htslib -I/private/var/folders/xr/wkj0mpgx3gs2l7hm2jf77x7h0000gn/T/pip-install-1ehbautp/pysam/samtools -I/private/var/folders/xr/wkj0mpgx3gs2l7hm2jf77x7h0000gn/T/pip-install-1ehbautp/pysam/samtools/lz4 -I/private/var/folders/xr/wkj0mpgx3gs2l7hm2jf77x7h0000gn/T/pip-install-1ehbautp/pysam/bcftools -I/private/var/folders/xr/wkj0mpgx3gs2l7hm2jf77x7h0000gn/T/pip-install-1ehbautp/pysam/pysam -I/private/var/folders/xr/wkj0mpgx3gs2l7hm2jf77x7h0000gn/T/pip-install-1ehbautp/pysam -I/Applications/Python/anaconda3/envs/beditor/include/python3.6m -c pysam/libchtslib.c -o build/temp.macosx-10.9-x86_64-3.6/pysam/libchtslib.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
gcc -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/Applications/Python/anaconda3/envs/beditor/include -arch x86_64 -I/Applications/Python/anaconda3/envs/beditor/include -arch x86_64 -build/temp.macosx-10.9-x86_64-3.6/pysam/htslib_util.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
gcc -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/Applications/Python/anaconda3/envs/beditor/include -arch x86_64 -I/Applications/Python/anaconda3/envs/beditor/include -arch x86_64 -I/private/var/folders/xr/wkj0mpgx3gs2l7hm2jf77x7h0000gn/T/pip-install-1ehbautp/pysam/htslib -I/private/var/folders/xr/wkj0mpgx3gs2l7hm2jf77x7h0000gn/T/pip-install-1ehbautp/pysam/samtools -I/private/var/folders/xr/wkj0mpgx3gs2l7hm2jf77x7h0000gn/T/pip-install-1ehbautp/pysam/samtools/lz4 -I/private/var/folders/xr/wkj0mpgx3gs2l7hm2jf77x7h0000gn/T/pip-install-1ehbautp/pysam/bcftools -I/private/var/folders/xr/wkj0mpgx3gs2l7hm2jf77x7h0000gn/T/pip-install-1ehbautp/pysam/pysam -I/private/var/folders/xr/wkj0mpgx3gs2l7hm2jf77x7h0000gn/T/pip-install-1ehbautp/pysam -I/Applications/Python/anaconda3/envs/beditor/include/python3.6m -c htslib/kfunc.c -o build/temp.macosx-10.9-x86_64-3.6/htslib/kfunc.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
gcc -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/Applications/Python/anaconda3/envs/beditor/include -arch x86_64 -I/Applications/Python/anaconda3/envs/beditor/include -arch x86_64 -I/private/var/folders/xr/wkj0mpgx3gs2l7hm2jf77x7h0000gn/T/pip-install-1ehbautp/pysam/htslib -I/private/var/folders/xr/wkj0mpgx3gs2l7hm2jf77x7h0000gn/T/pip-install-1ehbautp/pysam/samtools -I/private/var/folders/xr/wkj0mpgx3gs2l7hm2jf77x7h0000gn/T/pip-install-1ehbautp/pysam/samtools/lz4 -I/private/var/folders/xr/wkj0mpgx3gs2l7hm2jf77x7h0000gn/T/pip-install-1ehbautp/pysam/bcftools -I/private/var/folders/xr/wkj0mpgx3gs2l7hm2jf77x7h0000gn/T/pip-install-1ehbautp/pysam/pysam -I/private/var/folders/xr/wkj0mpgx3gs2l7hm2jf77x7h0000gn/T/pip-install-1ehbautp/pysam -I/Applications/Python/anaconda3/envs/beditor/include/python3.6m -c htslib/knetfile.c -o build/temp.macosx-10.9-x86_64-3.6/htslib/knetfile.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
gcc -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/Applications/Python/anaconda3/envs/beditor/include -arch x86_64 -I/Applications/Python/anaconda3/envs/beditor/include -arch x86_64 -I/private/var/folders/xr/wkj0mpgx3gs2l7hm2jf77x7h0000gn/T/pip-install-1ehbautp/pysam/htslib -I/private/var/folders/xr/wkj0mpgx3gs2l7hm2jf77x7h0000gn/T/pip-install-1ehbautp/pysam/samtools -I/private/var/folders/xr/wkj0mpgx3gs2l7hm2jf77x7h0000gn/T/pip-install-1ehbautp/pysam/samtools/lz4 -I/private/var/folders/xr/wkj0mpgx3gs2l7hm2jf77x7h0000gn/T/pip-install-1ehbautp/pysam/bcftools -I/private/var/folders/xr/wkj0mpgx3gs2l7hm2jf77x7h0000gn/T/pip-install-1ehbautp/pysam/pysam -I/private/var/folders/xr/wkj0mpgx3gs2l7hm2jf77x7h0000gn/T/pip-install-1ehbautp/pysam -I/Applications/Python/anaconda3/envs/beditor/include/python3.6m -c htslib/kstring.c -o build/temp.macosx-10.9-x86_64-3.6/htslib/kstring.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
gcc -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/Applications/Python/anaconda3/envs/beditor/include -arch x86_64 -I/Applications/Python/anaconda3/envs/beditor/include -arch x86_64 -