can not install hivtrace using command line : "pip3 install hivtrace"
Closed this issue · 6 comments
libexec/gcc/x86_64-apple-darwin17.5.0/8.1.0/cc1
Reason: image not found
gcc: internal compiler error: Abort trap: 6 signal terminated program cc1
Please submit a full bug report,
with preprocessed source if appropriate.
See https://gcc.gnu.org/bugs/ for instructions.
error: command 'gcc' failed with exit status 4
----------------------------------------
Command "/anaconda3/bin/python -u -c "import setuptools, tokenize;file='/private/var/folders/q4/gvrdsnj94vl527nfhj25rxh40000gn/T/pip-install-fj234sxj/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/q4/gvrdsnj94vl527nfhj25rxh40000gn/T/pip-record-k_n9iuce/install-record.txt --single-version-externally-managed --compile" failed with error code 1 in /private/var/folders/q4/gvrdsnj94vl527nfhj25rxh40000gn/T/pip-install-fj234sxj/pysam/
Dear @LIXINGGUANG,
Apologies for the delay. Can you please try installing pysam independently and see if the issue persists?
Best,
Steven
Last login: Sat Jan 12 09:21:29 on ttys003
lixingguangtekiMacBook-puro:~ lixingguang$ pip3 install pysam
Collecting pysam
Using cached https://files.pythonhosted.org/packages/15/f6/ce0611aaa1865a616f7dc164fbf046eaf38f2b17c6d404403c56250beb93/pysam-0.15.2.tar.gz
Building wheels for collected packages: pysam
Running setup.py bdist_wheel for pysam ... error
Complete output from command /anaconda3/bin/python -u -c "import setuptools, tokenize;file='/private/var/folders/q4/gvrdsnj94vl527nfhj25rxh40000gn/T/pip-install-d8cyw9ql/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/q4/gvrdsnj94vl527nfhj25rxh40000gn/T/pip-wheel-do4016jo --python-tag cp36:
pysam: cython is available - using cythonize if necessary
pysam: htslib mode is shared
pysam: HTSLIB_CONFIGURE_OPTIONS=None
checking for gcc... gcc
checking whether the C compiler works... no
configure: error: in /private/var/folders/q4/gvrdsnj94vl527nfhj25rxh40000gn/T/pip-install-d8cyw9ql/pysam/htslib': configure: error: C compiler cannot create executables See config.log' for more details
checking for gcc... gcc
checking whether the C compiler works... no
configure: error: in /private/var/folders/q4/gvrdsnj94vl527nfhj25rxh40000gn/T/pip-install-d8cyw9ql/pysam/htslib': configure: error: C compiler cannot create executables See config.log' for more details
pysam: htslib configure options: None
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
pysam: htslib_config LIBS=-lz -lm -lbz2 -llzma
pysam: htslib_config PLATFORM=Darwin
pysam: config_option: ENABLE_PLUGINS=0
pysam: config_option: HAVE_COMMONCRYPTO=0
pysam: config_option: HAVE_GMTIME_R=0
pysam: config_option: HAVE_HMAC=0
pysam: config_option: HAVE_IRODS=0
pysam: config_option: HAVE_LIBCURL=0
pysam: config_option: HAVE_MMAP=0
running bdist_wheel
running build
running build_py
creating build
creating build/lib.macosx-10.7-x86_64-3.6
creating build/lib.macosx-10.7-x86_64-3.6/pysam
copying pysam/bcftools.py -> build/lib.macosx-10.7-x86_64-3.6/pysam
copying pysam/config.py -> build/lib.macosx-10.7-x86_64-3.6/pysam
copying pysam/version.py -> build/lib.macosx-10.7-x86_64-3.6/pysam
copying pysam/samtools.py -> build/lib.macosx-10.7-x86_64-3.6/pysam
copying pysam/init.py -> build/lib.macosx-10.7-x86_64-3.6/pysam
copying pysam/Pileup.py -> build/lib.macosx-10.7-x86_64-3.6/pysam
copying pysam/utils.py -> build/lib.macosx-10.7-x86_64-3.6/pysam
creating build/lib.macosx-10.7-x86_64-3.6/pysam/include
copying pysam/include/init.py -> build/lib.macosx-10.7-x86_64-3.6/pysam/include
package init file 'samtools/init.py' not found (or not a regular file)
package init file 'bcftools/init.py' not found (or not a regular file)
package init file 'samtools/win32/init.py' not found (or not a regular file)
package init file 'htslib/init.py' not found (or not a regular file)
package init file 'htslib/htslib/init.py' not found (or not a regular file)
copying pysam/libcsamtools.pxd -> build/lib.macosx-10.7-x86_64-3.6/pysam
copying pysam/libcalignedsegment.pxd -> build/lib.macosx-10.7-x86_64-3.6/pysam
copying pysam/libcbcf.pxd -> build/lib.macosx-10.7-x86_64-3.6/pysam
copying pysam/libctabixproxies.pxd -> build/lib.macosx-10.7-x86_64-3.6/pysam
copying pysam/libcutils.pxd -> build/lib.macosx-10.7-x86_64-3.6/pysam
copying pysam/libchtslib.pxd -> build/lib.macosx-10.7-x86_64-3.6/pysam
copying pysam/libcalignmentfile.pxd -> build/lib.macosx-10.7-x86_64-3.6/pysam
copying pysam/libcvcf.pxd -> build/lib.macosx-10.7-x86_64-3.6/pysam
copying pysam/libctabix.pxd -> build/lib.macosx-10.7-x86_64-3.6/pysam
copying pysam/libcsamfile.pxd -> build/lib.macosx-10.7-x86_64-3.6/pysam
copying pysam/libcbcftools.pxd -> build/lib.macosx-10.7-x86_64-3.6/pysam
copying pysam/libcfaidx.pxd -> build/lib.macosx-10.7-x86_64-3.6/pysam
copying pysam/pysam_stream.h -> build/lib.macosx-10.7-x86_64-3.6/pysam
copying pysam/htslib_util.h -> build/lib.macosx-10.7-x86_64-3.6/pysam
copying pysam/pysam_util.h -> build/lib.macosx-10.7-x86_64-3.6/pysam
copying pysam/csamtools_util.h -> build/lib.macosx-10.7-x86_64-3.6/pysam
copying pysam/cbcftools_util.h -> build/lib.macosx-10.7-x86_64-3.6/pysam
creating build/lib.macosx-10.7-x86_64-3.6/pysam/include/samtools
copying samtools/sam.h -> build/lib.macosx-10.7-x86_64-3.6/pysam/include/samtools
copying samtools/tmp_file.h -> build/lib.macosx-10.7-x86_64-3.6/pysam/include/samtools
copying samtools/sam_opts.h -> build/lib.macosx-10.7-x86_64-3.6/pysam/include/samtools
copying samtools/bedidx.h -> build/lib.macosx-10.7-x86_64-3.6/pysam/include/samtools
copying samtools/version.h -> build/lib.macosx-10.7-x86_64-3.6/pysam/include/samtools
copying samtools/bam.h -> build/lib.macosx-10.7-x86_64-3.6/pysam/include/samtools
copying samtools/config.h -> build/lib.macosx-10.7-x86_64-3.6/pysam/include/samtools
copying samtools/samtools.h -> build/lib.macosx-10.7-x86_64-3.6/pysam/include/samtools
copying samtools/bam2bcf.h -> build/lib.macosx-10.7-x86_64-3.6/pysam/include/samtools
copying samtools/bam_plbuf.h -> build/lib.macosx-10.7-x86_64-3.6/pysam/include/samtools
copying samtools/sam_header.h -> build/lib.macosx-10.7-x86_64-3.6/pysam/include/samtools
copying samtools/bam_endian.h -> build/lib.macosx-10.7-x86_64-3.6/pysam/include/samtools
copying samtools/stats_isize.h -> build/lib.macosx-10.7-x86_64-3.6/pysam/include/samtools
copying samtools/bam_lpileup.h -> build/lib.macosx-10.7-x86_64-3.6/pysam/include/samtools
copying samtools/sample.h -> build/lib.macosx-10.7-x86_64-3.6/pysam/include/samtools
copying samtools/samtools.pysam.h -> build/lib.macosx-10.7-x86_64-3.6/pysam/include/samtools
creating build/lib.macosx-10.7-x86_64-3.6/pysam/include/bcftools
copying bcftools/bam_sample.h -> build/lib.macosx-10.7-x86_64-3.6/pysam/include/bcftools
copying bcftools/bcftools.h -> build/lib.macosx-10.7-x86_64-3.6/pysam/include/bcftools
copying bcftools/version.h -> build/lib.macosx-10.7-x86_64-3.6/pysam/include/bcftools
copying bcftools/smpl_ilist.h -> build/lib.macosx-10.7-x86_64-3.6/pysam/include/bcftools
copying bcftools/vcfbuf.h -> build/lib.macosx-10.7-x86_64-3.6/pysam/include/bcftools
copying bcftools/config.h -> build/lib.macosx-10.7-x86_64-3.6/pysam/include/bcftools
copying bcftools/prob1.h -> build/lib.macosx-10.7-x86_64-3.6/pysam/include/bcftools
copying bcftools/ploidy.h -> build/lib.macosx-10.7-x86_64-3.6/pysam/include/bcftools
copying bcftools/vcmp.h -> build/lib.macosx-10.7-x86_64-3.6/pysam/include/bcftools
copying bcftools/tsv2vcf.h -> build/lib.macosx-10.7-x86_64-3.6/pysam/include/bcftools
copying bcftools/call.h -> build/lib.macosx-10.7-x86_64-3.6/pysam/include/bcftools
copying bcftools/HMM.h -> build/lib.macosx-10.7-x86_64-3.6/pysam/include/bcftools
copying bcftools/bam2bcf.h -> build/lib.macosx-10.7-x86_64-3.6/pysam/include/bcftools
copying bcftools/gvcf.h -> build/lib.macosx-10.7-x86_64-3.6/pysam/include/bcftools
copying bcftools/regidx.h -> build/lib.macosx-10.7-x86_64-3.6/pysam/include/bcftools
copying bcftools/mw.h -> build/lib.macosx-10.7-x86_64-3.6/pysam/include/bcftools
copying bcftools/khash_str2str.h -> build/lib.macosx-10.7-x86_64-3.6/pysam/include/bcftools
copying bcftools/kmin.h -> build/lib.macosx-10.7-x86_64-3.6/pysam/include/bcftools
copying bcftools/rbuf.h -> build/lib.macosx-10.7-x86_64-3.6/pysam/include/bcftools
copying bcftools/hclust.h -> build/lib.macosx-10.7-x86_64-3.6/pysam/include/bcftools
copying bcftools/kheap.h -> build/lib.macosx-10.7-x86_64-3.6/pysam/include/bcftools
copying bcftools/convert.h -> build/lib.macosx-10.7-x86_64-3.6/pysam/include/bcftools
copying bcftools/filter.h -> build/lib.macosx-10.7-x86_64-3.6/pysam/include/bcftools
copying bcftools/bcftools.pysam.h -> build/lib.macosx-10.7-x86_64-3.6/pysam/include/bcftools
copying bcftools/bin.h -> build/lib.macosx-10.7-x86_64-3.6/pysam/include/bcftools
creating build/lib.macosx-10.7-x86_64-3.6/pysam/include/samtools/win32
copying samtools/win32/zlib.h -> build/lib.macosx-10.7-x86_64-3.6/pysam/include/samtools/win32
copying samtools/win32/xcurses.h -> build/lib.macosx-10.7-x86_64-3.6/pysam/include/samtools/win32
copying samtools/win32/zconf.h -> build/lib.macosx-10.7-x86_64-3.6/pysam/include/samtools/win32
creating build/lib.macosx-10.7-x86_64-3.6/pysam/include/htslib
copying htslib/bcf_sr_sort.h -> build/lib.macosx-10.7-x86_64-3.6/pysam/include/htslib
copying htslib/version.h -> build/lib.macosx-10.7-x86_64-3.6/pysam/include/htslib
copying htslib/config.h -> build/lib.macosx-10.7-x86_64-3.6/pysam/include/htslib
copying htslib/hfile_internal.h -> build/lib.macosx-10.7-x86_64-3.6/pysam/include/htslib
copying htslib/hts_internal.h -> build/lib.macosx-10.7-x86_64-3.6/pysam/include/htslib
copying htslib/textutils_internal.h -> build/lib.macosx-10.7-x86_64-3.6/pysam/include/htslib
copying htslib/thread_pool_internal.h -> build/lib.macosx-10.7-x86_64-3.6/pysam/include/htslib
creating build/lib.macosx-10.7-x86_64-3.6/pysam/include/htslib/htslib
copying htslib/htslib/sam.h -> build/lib.macosx-10.7-x86_64-3.6/pysam/include/htslib/htslib
copying htslib/htslib/synced_bcf_reader.h -> build/lib.macosx-10.7-x86_64-3.6/pysam/include/htslib/htslib
copying htslib/htslib/vcf_sweep.h -> build/lib.macosx-10.7-x86_64-3.6/pysam/include/htslib/htslib
copying htslib/htslib/vcf.h -> build/lib.macosx-10.7-x86_64-3.6/pysam/include/htslib/htslib
copying htslib/htslib/khash_str2int.h -> build/lib.macosx-10.7-x86_64-3.6/pysam/include/htslib/htslib
copying htslib/htslib/bgzf.h -> build/lib.macosx-10.7-x86_64-3.6/pysam/include/htslib/htslib
copying htslib/htslib/cram.h -> build/lib.macosx-10.7-x86_64-3.6/pysam/include/htslib/htslib
copying htslib/htslib/kstring.h -> build/lib.macosx-10.7-x86_64-3.6/pysam/include/htslib/htslib
copying htslib/htslib/knetfile.h -> build/lib.macosx-10.7-x86_64-3.6/pysam/include/htslib/htslib
copying htslib/htslib/hts_log.h -> build/lib.macosx-10.7-x86_64-3.6/pysam/include/htslib/htslib
copying htslib/htslib/hfile.h -> build/lib.macosx-10.7-x86_64-3.6/pysam/include/htslib/htslib
copying htslib/htslib/thread_pool.h -> build/lib.macosx-10.7-x86_64-3.6/pysam/include/htslib/htslib
copying htslib/htslib/hts_defs.h -> build/lib.macosx-10.7-x86_64-3.6/pysam/include/htslib/htslib
copying htslib/htslib/khash.h -> build/lib.macosx-10.7-x86_64-3.6/pysam/include/htslib/htslib
copying htslib/htslib/regidx.h -> build/lib.macosx-10.7-x86_64-3.6/pysam/include/htslib/htslib
copying htslib/htslib/faidx.h -> build/lib.macosx-10.7-x86_64-3.6/pysam/include/htslib/htslib
copying htslib/htslib/vcfutils.h -> build/lib.macosx-10.7-x86_64-3.6/pysam/include/htslib/htslib
copying htslib/htslib/kseq.h -> build/lib.macosx-10.7-x86_64-3.6/pysam/include/htslib/htslib
copying htslib/htslib/kfunc.h -> build/lib.macosx-10.7-x86_64-3.6/pysam/include/htslib/htslib
copying htslib/htslib/tbx.h -> build/lib.macosx-10.7-x86_64-3.6/pysam/include/htslib/htslib
copying htslib/htslib/ksort.h -> build/lib.macosx-10.7-x86_64-3.6/pysam/include/htslib/htslib
copying htslib/htslib/kbitset.h -> build/lib.macosx-10.7-x86_64-3.6/pysam/include/htslib/htslib
copying htslib/htslib/hts_os.h -> build/lib.macosx-10.7-x86_64-3.6/pysam/include/htslib/htslib
copying htslib/htslib/klist.h -> build/lib.macosx-10.7-x86_64-3.6/pysam/include/htslib/htslib
copying htslib/htslib/hts.h -> build/lib.macosx-10.7-x86_64-3.6/pysam/include/htslib/htslib
copying htslib/htslib/hts_endian.h -> build/lib.macosx-10.7-x86_64-3.6/pysam/include/htslib/htslib
Fixing build/lib.macosx-10.7-x86_64-3.6/pysam/bcftools.py build/lib.macosx-10.7-x86_64-3.6/pysam/config.py build/lib.macosx-10.7-x86_64-3.6/pysam/version.py build/lib.macosx-10.7-x86_64-3.6/pysam/samtools.py build/lib.macosx-10.7-x86_64-3.6/pysam/init.py build/lib.macosx-10.7-x86_64-3.6/pysam/Pileup.py build/lib.macosx-10.7-x86_64-3.6/pysam/utils.py build/lib.macosx-10.7-x86_64-3.6/pysam/include/init.py
Skipping optional fixer: buffer
Skipping optional fixer: idioms
Skipping optional fixer: set_literal
Skipping optional fixer: ws_comma
Fixing build/lib.macosx-10.7-x86_64-3.6/pysam/bcftools.py build/lib.macosx-10.7-x86_64-3.6/pysam/config.py build/lib.macosx-10.7-x86_64-3.6/pysam/version.py build/lib.macosx-10.7-x86_64-3.6/pysam/samtools.py build/lib.macosx-10.7-x86_64-3.6/pysam/init.py build/lib.macosx-10.7-x86_64-3.6/pysam/Pileup.py build/lib.macosx-10.7-x86_64-3.6/pysam/utils.py build/lib.macosx-10.7-x86_64-3.6/pysam/include/init.py
Skipping optional fixer: buffer
Skipping optional fixer: idioms
Skipping optional fixer: set_literal
Skipping optional fixer: ws_comma
running build_ext
skipping 'pysam/libchtslib.c' Cython extension (up-to-date)
building 'pysam.libchtslib' extension
creating build/temp.macosx-10.7-x86_64-3.6
creating build/temp.macosx-10.7-x86_64-3.6/pysam
creating build/temp.macosx-10.7-x86_64-3.6/htslib
creating build/temp.macosx-10.7-x86_64-3.6/htslib/cram
gcc -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/anaconda3/include -arch x86_64 -I/anaconda3/include -arch x86_64 -I/private/var/folders/q4/gvrdsnj94vl527nfhj25rxh40000gn/T/pip-install-d8cyw9ql/pysam/htslib -I/private/var/folders/q4/gvrdsnj94vl527nfhj25rxh40000gn/T/pip-install-d8cyw9ql/pysam/samtools -I/private/var/folders/q4/gvrdsnj94vl527nfhj25rxh40000gn/T/pip-install-d8cyw9ql/pysam/samtools/lz4 -I/private/var/folders/q4/gvrdsnj94vl527nfhj25rxh40000gn/T/pip-install-d8cyw9ql/pysam/bcftools -I/private/var/folders/q4/gvrdsnj94vl527nfhj25rxh40000gn/T/pip-install-d8cyw9ql/pysam/pysam -I/private/var/folders/q4/gvrdsnj94vl527nfhj25rxh40000gn/T/pip-install-d8cyw9ql/pysam -I/anaconda3/include/python3.6m -c pysam/libchtslib.c -o build/temp.macosx-10.7-x86_64-3.6/pysam/libchtslib.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
dyld: Library not loaded: /usr/local/lib/libmpfr.4.dylib
Referenced from: /Users/lixingguang/Downloads/1-HIVtrace/usr/local/bin/../libexec/gcc/x86_64-apple-darwin17.5.0/8.1.0/cc1
Reason: image not found
gcc: internal compiler error: Abort trap: 6 signal terminated program cc1
Please submit a full bug report,
with preprocessed source if appropriate.
See https://gcc.gnu.org/bugs/ for instructions.
error: command 'gcc' failed with exit status 4
Failed building wheel for pysam
Running setup.py clean for pysam
Failed to build pysam
Installing collected packages: pysam
Running setup.py install for pysam ... error
Complete output from command /anaconda3/bin/python -u -c "import setuptools, tokenize;file='/private/var/folders/q4/gvrdsnj94vl527nfhj25rxh40000gn/T/pip-install-d8cyw9ql/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/q4/gvrdsnj94vl527nfhj25rxh40000gn/T/pip-record-irqo4g_g/install-record.txt --single-version-externally-managed --compile:
# pysam: cython is available - using cythonize if necessary
# pysam: htslib mode is shared
# pysam: HTSLIB_CONFIGURE_OPTIONS=None
checking for gcc... gcc
checking whether the C compiler works... no
configure: error: in /private/var/folders/q4/gvrdsnj94vl527nfhj25rxh40000gn/T/pip-install-d8cyw9ql/pysam/htslib': configure: error: C compiler cannot create executables See config.log' for more details
checking for gcc... gcc
checking whether the C compiler works... no
configure: error: in /private/var/folders/q4/gvrdsnj94vl527nfhj25rxh40000gn/T/pip-install-d8cyw9ql/pysam/htslib': configure: error: C compiler cannot create executables See config.log' for more details
# pysam: htslib configure options: None
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
# pysam: htslib_config LIBS=-lz -lm -lbz2 -llzma
# pysam: htslib_config PLATFORM=Darwin
# pysam: config_option: ENABLE_PLUGINS=0
# pysam: config_option: HAVE_COMMONCRYPTO=0
# pysam: config_option: HAVE_GMTIME_R=0
# pysam: config_option: HAVE_HMAC=0
# pysam: config_option: HAVE_IRODS=0
# pysam: config_option: HAVE_LIBCURL=0
# pysam: config_option: HAVE_MMAP=0
running install
running build
running build_py
creating build
creating build/lib.macosx-10.7-x86_64-3.6
creating build/lib.macosx-10.7-x86_64-3.6/pysam
copying pysam/bcftools.py -> build/lib.macosx-10.7-x86_64-3.6/pysam
copying pysam/config.py -> build/lib.macosx-10.7-x86_64-3.6/pysam
copying pysam/version.py -> build/lib.macosx-10.7-x86_64-3.6/pysam
copying pysam/samtools.py -> build/lib.macosx-10.7-x86_64-3.6/pysam
copying pysam/init.py -> build/lib.macosx-10.7-x86_64-3.6/pysam
copying pysam/Pileup.py -> build/lib.macosx-10.7-x86_64-3.6/pysam
copying pysam/utils.py -> build/lib.macosx-10.7-x86_64-3.6/pysam
creating build/lib.macosx-10.7-x86_64-3.6/pysam/include
copying pysam/include/init.py -> build/lib.macosx-10.7-x86_64-3.6/pysam/include
package init file 'samtools/init.py' not found (or not a regular file)
package init file 'bcftools/init.py' not found (or not a regular file)
package init file 'samtools/win32/init.py' not found (or not a regular file)
package init file 'htslib/init.py' not found (or not a regular file)
package init file 'htslib/htslib/init.py' not found (or not a regular file)
copying pysam/libcsamtools.pxd -> build/lib.macosx-10.7-x86_64-3.6/pysam
copying pysam/libcalignedsegment.pxd -> build/lib.macosx-10.7-x86_64-3.6/pysam
copying pysam/libcbcf.pxd -> build/lib.macosx-10.7-x86_64-3.6/pysam
copying pysam/libctabixproxies.pxd -> build/lib.macosx-10.7-x86_64-3.6/pysam
copying pysam/libcutils.pxd -> build/lib.macosx-10.7-x86_64-3.6/pysam
copying pysam/libchtslib.pxd -> build/lib.macosx-10.7-x86_64-3.6/pysam
copying pysam/libcalignmentfile.pxd -> build/lib.macosx-10.7-x86_64-3.6/pysam
copying pysam/libcvcf.pxd -> build/lib.macosx-10.7-x86_64-3.6/pysam
copying pysam/libctabix.pxd -> build/lib.macosx-10.7-x86_64-3.6/pysam
copying pysam/libcsamfile.pxd -> build/lib.macosx-10.7-x86_64-3.6/pysam
copying pysam/libcbcftools.pxd -> build/lib.macosx-10.7-x86_64-3.6/pysam
copying pysam/libcfaidx.pxd -> build/lib.macosx-10.7-x86_64-3.6/pysam
copying pysam/pysam_stream.h -> build/lib.macosx-10.7-x86_64-3.6/pysam
copying pysam/htslib_util.h -> build/lib.macosx-10.7-x86_64-3.6/pysam
copying pysam/pysam_util.h -> build/lib.macosx-10.7-x86_64-3.6/pysam
copying pysam/csamtools_util.h -> build/lib.macosx-10.7-x86_64-3.6/pysam
copying pysam/cbcftools_util.h -> build/lib.macosx-10.7-x86_64-3.6/pysam
creating build/lib.macosx-10.7-x86_64-3.6/pysam/include/samtools
copying samtools/sam.h -> build/lib.macosx-10.7-x86_64-3.6/pysam/include/samtools
copying samtools/tmp_file.h -> build/lib.macosx-10.7-x86_64-3.6/pysam/include/samtools
copying samtools/sam_opts.h -> build/lib.macosx-10.7-x86_64-3.6/pysam/include/samtools
copying samtools/bedidx.h -> build/lib.macosx-10.7-x86_64-3.6/pysam/include/samtools
copying samtools/version.h -> build/lib.macosx-10.7-x86_64-3.6/pysam/include/samtools
copying samtools/bam.h -> build/lib.macosx-10.7-x86_64-3.6/pysam/include/samtools
copying samtools/config.h -> build/lib.macosx-10.7-x86_64-3.6/pysam/include/samtools
copying samtools/samtools.h -> build/lib.macosx-10.7-x86_64-3.6/pysam/include/samtools
copying samtools/bam2bcf.h -> build/lib.macosx-10.7-x86_64-3.6/pysam/include/samtools
copying samtools/bam_plbuf.h -> build/lib.macosx-10.7-x86_64-3.6/pysam/include/samtools
copying samtools/sam_header.h -> build/lib.macosx-10.7-x86_64-3.6/pysam/include/samtools
copying samtools/bam_endian.h -> build/lib.macosx-10.7-x86_64-3.6/pysam/include/samtools
copying samtools/stats_isize.h -> build/lib.macosx-10.7-x86_64-3.6/pysam/include/samtools
copying samtools/bam_lpileup.h -> build/lib.macosx-10.7-x86_64-3.6/pysam/include/samtools
copying samtools/sample.h -> build/lib.macosx-10.7-x86_64-3.6/pysam/include/samtools
copying samtools/samtools.pysam.h -> build/lib.macosx-10.7-x86_64-3.6/pysam/include/samtools
creating build/lib.macosx-10.7-x86_64-3.6/pysam/include/bcftools
copying bcftools/bam_sample.h -> build/lib.macosx-10.7-x86_64-3.6/pysam/include/bcftools
copying bcftools/bcftools.h -> build/lib.macosx-10.7-x86_64-3.6/pysam/include/bcftools
copying bcftools/version.h -> build/lib.macosx-10.7-x86_64-3.6/pysam/include/bcftools
copying bcftools/smpl_ilist.h -> build/lib.macosx-10.7-x86_64-3.6/pysam/include/bcftools
copying bcftools/vcfbuf.h -> build/lib.macosx-10.7-x86_64-3.6/pysam/include/bcftools
copying bcftools/config.h -> build/lib.macosx-10.7-x86_64-3.6/pysam/include/bcftools
copying bcftools/prob1.h -> build/lib.macosx-10.7-x86_64-3.6/pysam/include/bcftools
copying bcftools/ploidy.h -> build/lib.macosx-10.7-x86_64-3.6/pysam/include/bcftools
copying bcftools/vcmp.h -> build/lib.macosx-10.7-x86_64-3.6/pysam/include/bcftools
copying bcftools/tsv2vcf.h -> build/lib.macosx-10.7-x86_64-3.6/pysam/include/bcftools
copying bcftools/call.h -> build/lib.macosx-10.7-x86_64-3.6/pysam/include/bcftools
copying bcftools/HMM.h -> build/lib.macosx-10.7-x86_64-3.6/pysam/include/bcftools
copying bcftools/bam2bcf.h -> build/lib.macosx-10.7-x86_64-3.6/pysam/include/bcftools
copying bcftools/gvcf.h -> build/lib.macosx-10.7-x86_64-3.6/pysam/include/bcftools
copying bcftools/regidx.h -> build/lib.macosx-10.7-x86_64-3.6/pysam/include/bcftools
copying bcftools/mw.h -> build/lib.macosx-10.7-x86_64-3.6/pysam/include/bcftools
copying bcftools/khash_str2str.h -> build/lib.macosx-10.7-x86_64-3.6/pysam/include/bcftools
copying bcftools/kmin.h -> build/lib.macosx-10.7-x86_64-3.6/pysam/include/bcftools
copying bcftools/rbuf.h -> build/lib.macosx-10.7-x86_64-3.6/pysam/include/bcftools
copying bcftools/hclust.h -> build/lib.macosx-10.7-x86_64-3.6/pysam/include/bcftools
copying bcftools/kheap.h -> build/lib.macosx-10.7-x86_64-3.6/pysam/include/bcftools
copying bcftools/convert.h -> build/lib.macosx-10.7-x86_64-3.6/pysam/include/bcftools
copying bcftools/filter.h -> build/lib.macosx-10.7-x86_64-3.6/pysam/include/bcftools
copying bcftools/bcftools.pysam.h -> build/lib.macosx-10.7-x86_64-3.6/pysam/include/bcftools
copying bcftools/bin.h -> build/lib.macosx-10.7-x86_64-3.6/pysam/include/bcftools
creating build/lib.macosx-10.7-x86_64-3.6/pysam/include/samtools/win32
copying samtools/win32/zlib.h -> build/lib.macosx-10.7-x86_64-3.6/pysam/include/samtools/win32
copying samtools/win32/xcurses.h -> build/lib.macosx-10.7-x86_64-3.6/pysam/include/samtools/win32
copying samtools/win32/zconf.h -> build/lib.macosx-10.7-x86_64-3.6/pysam/include/samtools/win32
creating build/lib.macosx-10.7-x86_64-3.6/pysam/include/htslib
copying htslib/bcf_sr_sort.h -> build/lib.macosx-10.7-x86_64-3.6/pysam/include/htslib
copying htslib/version.h -> build/lib.macosx-10.7-x86_64-3.6/pysam/include/htslib
copying htslib/config.h -> build/lib.macosx-10.7-x86_64-3.6/pysam/include/htslib
copying htslib/hfile_internal.h -> build/lib.macosx-10.7-x86_64-3.6/pysam/include/htslib
copying htslib/hts_internal.h -> build/lib.macosx-10.7-x86_64-3.6/pysam/include/htslib
copying htslib/textutils_internal.h -> build/lib.macosx-10.7-x86_64-3.6/pysam/include/htslib
copying htslib/thread_pool_internal.h -> build/lib.macosx-10.7-x86_64-3.6/pysam/include/htslib
creating build/lib.macosx-10.7-x86_64-3.6/pysam/include/htslib/htslib
copying htslib/htslib/sam.h -> build/lib.macosx-10.7-x86_64-3.6/pysam/include/htslib/htslib
copying htslib/htslib/synced_bcf_reader.h -> build/lib.macosx-10.7-x86_64-3.6/pysam/include/htslib/htslib
copying htslib/htslib/vcf_sweep.h -> build/lib.macosx-10.7-x86_64-3.6/pysam/include/htslib/htslib
copying htslib/htslib/vcf.h -> build/lib.macosx-10.7-x86_64-3.6/pysam/include/htslib/htslib
copying htslib/htslib/khash_str2int.h -> build/lib.macosx-10.7-x86_64-3.6/pysam/include/htslib/htslib
copying htslib/htslib/bgzf.h -> build/lib.macosx-10.7-x86_64-3.6/pysam/include/htslib/htslib
copying htslib/htslib/cram.h -> build/lib.macosx-10.7-x86_64-3.6/pysam/include/htslib/htslib
copying htslib/htslib/kstring.h -> build/lib.macosx-10.7-x86_64-3.6/pysam/include/htslib/htslib
copying htslib/htslib/knetfile.h -> build/lib.macosx-10.7-x86_64-3.6/pysam/include/htslib/htslib
copying htslib/htslib/hts_log.h -> build/lib.macosx-10.7-x86_64-3.6/pysam/include/htslib/htslib
copying htslib/htslib/hfile.h -> build/lib.macosx-10.7-x86_64-3.6/pysam/include/htslib/htslib
copying htslib/htslib/thread_pool.h -> build/lib.macosx-10.7-x86_64-3.6/pysam/include/htslib/htslib
copying htslib/htslib/hts_defs.h -> build/lib.macosx-10.7-x86_64-3.6/pysam/include/htslib/htslib
copying htslib/htslib/khash.h -> build/lib.macosx-10.7-x86_64-3.6/pysam/include/htslib/htslib
copying htslib/htslib/regidx.h -> build/lib.macosx-10.7-x86_64-3.6/pysam/include/htslib/htslib
copying htslib/htslib/faidx.h -> build/lib.macosx-10.7-x86_64-3.6/pysam/include/htslib/htslib
copying htslib/htslib/vcfutils.h -> build/lib.macosx-10.7-x86_64-3.6/pysam/include/htslib/htslib
copying htslib/htslib/kseq.h -> build/lib.macosx-10.7-x86_64-3.6/pysam/include/htslib/htslib
copying htslib/htslib/kfunc.h -> build/lib.macosx-10.7-x86_64-3.6/pysam/include/htslib/htslib
copying htslib/htslib/tbx.h -> build/lib.macosx-10.7-x86_64-3.6/pysam/include/htslib/htslib
copying htslib/htslib/ksort.h -> build/lib.macosx-10.7-x86_64-3.6/pysam/include/htslib/htslib
copying htslib/htslib/kbitset.h -> build/lib.macosx-10.7-x86_64-3.6/pysam/include/htslib/htslib
copying htslib/htslib/hts_os.h -> build/lib.macosx-10.7-x86_64-3.6/pysam/include/htslib/htslib
copying htslib/htslib/klist.h -> build/lib.macosx-10.7-x86_64-3.6/pysam/include/htslib/htslib
copying htslib/htslib/hts.h -> build/lib.macosx-10.7-x86_64-3.6/pysam/include/htslib/htslib
copying htslib/htslib/hts_endian.h -> build/lib.macosx-10.7-x86_64-3.6/pysam/include/htslib/htslib
Fixing build/lib.macosx-10.7-x86_64-3.6/pysam/bcftools.py build/lib.macosx-10.7-x86_64-3.6/pysam/config.py build/lib.macosx-10.7-x86_64-3.6/pysam/version.py build/lib.macosx-10.7-x86_64-3.6/pysam/samtools.py build/lib.macosx-10.7-x86_64-3.6/pysam/init.py build/lib.macosx-10.7-x86_64-3.6/pysam/Pileup.py build/lib.macosx-10.7-x86_64-3.6/pysam/utils.py build/lib.macosx-10.7-x86_64-3.6/pysam/include/init.py
Skipping optional fixer: buffer
Skipping optional fixer: idioms
Skipping optional fixer: set_literal
Skipping optional fixer: ws_comma
Fixing build/lib.macosx-10.7-x86_64-3.6/pysam/bcftools.py build/lib.macosx-10.7-x86_64-3.6/pysam/config.py build/lib.macosx-10.7-x86_64-3.6/pysam/version.py build/lib.macosx-10.7-x86_64-3.6/pysam/samtools.py build/lib.macosx-10.7-x86_64-3.6/pysam/init.py build/lib.macosx-10.7-x86_64-3.6/pysam/Pileup.py build/lib.macosx-10.7-x86_64-3.6/pysam/utils.py build/lib.macosx-10.7-x86_64-3.6/pysam/include/init.py
Skipping optional fixer: buffer
Skipping optional fixer: idioms
Skipping optional fixer: set_literal
Skipping optional fixer: ws_comma
running build_ext
skipping 'pysam/libchtslib.c' Cython extension (up-to-date)
building 'pysam.libchtslib' extension
creating build/temp.macosx-10.7-x86_64-3.6
creating build/temp.macosx-10.7-x86_64-3.6/pysam
creating build/temp.macosx-10.7-x86_64-3.6/htslib
creating build/temp.macosx-10.7-x86_64-3.6/htslib/cram
gcc -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/anaconda3/include -arch x86_64 -I/anaconda3/include -arch x86_64 -I/private/var/folders/q4/gvrdsnj94vl527nfhj25rxh40000gn/T/pip-install-d8cyw9ql/pysam/htslib -I/private/var/folders/q4/gvrdsnj94vl527nfhj25rxh40000gn/T/pip-install-d8cyw9ql/pysam/samtools -I/private/var/folders/q4/gvrdsnj94vl527nfhj25rxh40000gn/T/pip-install-d8cyw9ql/pysam/samtools/lz4 -I/private/var/folders/q4/gvrdsnj94vl527nfhj25rxh40000gn/T/pip-install-d8cyw9ql/pysam/bcftools -I/private/var/folders/q4/gvrdsnj94vl527nfhj25rxh40000gn/T/pip-install-d8cyw9ql/pysam/pysam -I/private/var/folders/q4/gvrdsnj94vl527nfhj25rxh40000gn/T/pip-install-d8cyw9ql/pysam -I/anaconda3/include/python3.6m -c pysam/libchtslib.c -o build/temp.macosx-10.7-x86_64-3.6/pysam/libchtslib.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
dyld: Library not loaded: /usr/local/lib/libmpfr.4.dylib
Referenced from: /Users/lixingguang/Downloads/1-HIVtrace/usr/local/bin/../libexec/gcc/x86_64-apple-darwin17.5.0/8.1.0/cc1
Reason: image not found
gcc: internal compiler error: Abort trap: 6 signal terminated program cc1
Please submit a full bug report,
with preprocessed source if appropriate.
See https://gcc.gnu.org/bugs/ for instructions.
error: command 'gcc' failed with exit status 4
----------------------------------------
Command "/anaconda3/bin/python -u -c "import setuptools, tokenize;file='/private/var/folders/q4/gvrdsnj94vl527nfhj25rxh40000gn/T/pip-install-d8cyw9ql/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/q4/gvrdsnj94vl527nfhj25rxh40000gn/T/pip-record-irqo4g_g/install-record.txt --single-version-externally-managed --compile" failed with error code 1 in /private/var/folders/q4/gvrdsnj94vl527nfhj25rxh40000gn/T/pip-install-d8cyw9ql/pysam/
lixingguangtekiMacBook-puro:~ lixingguang$ conda install pysam
Solving environment: done
Package Plan
environment location: /anaconda3
added / updated specs:
- pysam
The following packages will be downloaded:
package | build
---------------------------|-----------------
pysam-0.15.2 | py36h0380709_0 2.0 MB bioconda
htslib-1.9 | hc238db4_4 1.2 MB bioconda
libdeflate-1.0 | h470a237_0 44 KB bioconda
samtools-1.9 | h8ee4bcc_1 526 KB bioconda
bcftools-1.9 | h4da6232_0 789 KB bioconda
------------------------------------------------------------
Total: 4.5 MB
The following NEW packages will be INSTALLED:
bcftools: 1.9-h4da6232_0 bioconda
htslib: 1.9-hc238db4_4 bioconda
libdeflate: 1.0-h470a237_0 bioconda
pysam: 0.15.2-py36h0380709_0 bioconda
samtools: 1.9-h8ee4bcc_1 bioconda
The following packages will be UPDATED:
conda: 4.5.11-py36_0 --> 4.5.12-py36_0
Proceed ([y]/n)? n
CondaSystemExit: Exiting.
lixingguangtekiMacBook-puro:~ lixingguang$ conda install pysam
Solving environment: done
Package Plan
environment location: /anaconda3
added / updated specs:
- pysam
The following packages will be downloaded:
package | build
---------------------------|-----------------
htslib-1.9 | hc238db4_4 1.2 MB bioconda
samtools-1.9 | h8ee4bcc_1 526 KB bioconda
libdeflate-1.0 | h470a237_0 44 KB bioconda
bcftools-1.9 | h4da6232_0 789 KB bioconda
pysam-0.15.2 | py36h0380709_0 2.0 MB bioconda
------------------------------------------------------------
Total: 4.5 MB
The following NEW packages will be INSTALLED:
bcftools: 1.9-h4da6232_0 bioconda
htslib: 1.9-hc238db4_4 bioconda
libdeflate: 1.0-h470a237_0 bioconda
pysam: 0.15.2-py36h0380709_0 bioconda
samtools: 1.9-h8ee4bcc_1 bioconda
The following packages will be UPDATED:
conda: 4.5.11-py36_0 --> 4.5.12-py36_0
Proceed ([y]/n)? y
Downloading and Extracting Packages
htslib-1.9 | 1.2 MB | | 0%
samtools-1.9 | 526 KB | | 0%
libdeflate-1.0 | 44 KB | | 0%
bcftools-1.9 | 789 KB | ##2 | 6%
pysam-0.15.2 | 2.0 MB | #7 | 5%
CondaHTTPError: HTTP 000 CONNECTION FAILED for url https://conda.anaconda.org/bioconda/osx-64/htslib-1.9-hc238db4_4.tar.bz2
Elapsed: -
An HTTP error occurred when trying to retrieve this URL.
HTTP errors are often intermittent, and a simple retry will get you on your way.
CondaHTTPError: HTTP 000 CONNECTION FAILED for url https://conda.anaconda.org/bioconda/osx-64/samtools-1.9-h8ee4bcc_1.tar.bz2
Elapsed: -
An HTTP error occurred when trying to retrieve this URL.
HTTP errors are often intermittent, and a simple retry will get you on your way.
CondaHTTPError: HTTP 000 CONNECTION FAILED for url https://conda.anaconda.org/bioconda/osx-64/libdeflate-1.0-h470a237_0.tar.bz2
Elapsed: -
An HTTP error occurred when trying to retrieve this URL.
HTTP errors are often intermittent, and a simple retry will get you on your way.
CondaHTTPError: HTTP 000 CONNECTION FAILED for url https://conda.anaconda.org/bioconda/osx-64/bcftools-1.9-h4da6232_0.tar.bz2
Elapsed: -
An HTTP error occurred when trying to retrieve this URL.
HTTP errors are often intermittent, and a simple retry will get you on your way.
CondaHTTPError: HTTP 000 CONNECTION FAILED for url https://conda.anaconda.org/bioconda/osx-64/pysam-0.15.2-py36h0380709_0.tar.bz2
Elapsed: -
An HTTP error occurred when trying to retrieve this URL.
HTTP errors are often intermittent, and a simple retry will get you on your way.
@stevenweaver can not install pysam, still have error.
pysam is a dependency of hivtrace, and it looks like there is either some sort of path issue, permissions issue, or compiler issue associated with your environment. I cannot replicate it with ours.
The people over at https://github.com/pysam-developers/pysam/issues might be able to provide better assistance.
Best,
Steven
lixingguangtekiMacBook-puro:~ lixingguang$ pip3 install hivtrace
Requirement already satisfied: hivtrace in /anaconda3/lib/python3.6/site-packages (0.1.6)
Requirement already satisfied: biopython>=1.58 in /anaconda3/lib/python3.6/site-packages (from hivtrace) (1.72)
Collecting BioExt>=0.17.2 (from hivtrace)
Downloading https://files.pythonhosted.org/packages/c4/f0/779ed11ff3ce38d9a317a7988ec607202e8124d57e01b3f9b2d566860720/bioext-0.19.5.tar.gz (1.8MB)
100% |████████████████████████████████| 1.8MB 28kB/s
Collecting HyPhy>=0.1.1 (from hivtrace)
Could not find a version that satisfies the requirement HyPhy>=0.1.1 (from hivtrace) (from versions: )
No matching distribution found for HyPhy>=0.1.1 (from hivtrace)
@stevenweaver why hivtrace can not include hyphy?