pysam upgrade error

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Han Fang

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Mar 24, 2016, 11:16:48 PM3/24/16

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Hi there,

I was trying to upgrade pysam to v0.9.0 from v0.8.3 and got the below errors. Can you help me with this? Thank you.

$ pip list | egrep "Cython|pysam"

Cython (0.23.4)

pysam (0.8.3)

$ pip install pysam --upgrade

Collecting pysam

Using cached pysam-0.9.0.tar.gz

Building wheels for collected packages: pysam

Running setup.py bdist_wheel for pysam ... error

Complete output from command /sonas-hs/lyon/hpc/home/hfang/miniconda3/bin/python -u -c "import setuptools, tokenize;__file__='/tmp/pip-build-48jgbesk/pysam/setup.py';exec(compile(getattr(tokenize, 'open', open)(__file__).read().replace('\r\n', '\n'), __file__, 'exec'))" bdist_wheel -d /tmp/tmpjdzcd8mapip-wheel- --python-tag cp34:

# pysam: htslib mode is shared

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 how to run the C preprocessor... gcc -E

checking for grep that handles long lines and -e... /opt/hpc/bin/grep

checking for egrep... /opt/hpc/bin/grep -E

checking for ANSI C header files... yes

checking for sys/types.h... yes

checking for sys/stat.h... yes

checking for stdlib.h... yes

checking for string.h... yes

checking for memory.h... yes

checking for strings.h... yes

checking for inttypes.h... yes

checking for stdint.h... yes

checking for unistd.h... yes

checking for stdlib.h... (cached) yes

checking for unistd.h... (cached) yes

checking for sys/param.h... yes

checking for getpagesize... yes

checking for working mmap... yes

checking for gmtime_r... yes

checking for zlib.h... yes

checking for inflate in -lz... yes

checking for curl_easy_pause in -lcurl... yes

checking for CCHmac... no

checking for library containing HMAC... -lcrypto

configure: creating ./config.status

config.status: creating config.mk

config.status: creating config.h

config.status: config.h is unchanged

# pysam: htslib configure options: --enable-libcurl

# pysam: libcurl of builtin htslib has been enabled, adding shared libcurl and libcrypto

running bdist_wheel

running build

running build_py

creating build

creating build/lib.linux-x86_64-3.4

creating build/lib.linux-x86_64-3.4/pysam

copying pysam/Pileup.py -> build/lib.linux-x86_64-3.4/pysam

copying pysam/version.py -> build/lib.linux-x86_64-3.4/pysam

copying pysam/__init__.py -> build/lib.linux-x86_64-3.4/pysam

copying pysam/bcftools.py -> build/lib.linux-x86_64-3.4/pysam

copying pysam/namedtuple.py -> build/lib.linux-x86_64-3.4/pysam

copying pysam/utils.py -> build/lib.linux-x86_64-3.4/pysam

copying pysam/samtools.py -> build/lib.linux-x86_64-3.4/pysam

copying pysam/config.py -> build/lib.linux-x86_64-3.4/pysam

creating build/lib.linux-x86_64-3.4/pysam/include

copying pysam/include/__init__.py -> build/lib.linux-x86_64-3.4/pysam/include

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)

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)

copying pysam/calignmentfile.pxd -> build/lib.linux-x86_64-3.4/pysam

copying pysam/calignedsegment.pxd -> build/lib.linux-x86_64-3.4/pysam

copying pysam/ctabix.pxd -> build/lib.linux-x86_64-3.4/pysam

copying pysam/csamfile.pxd -> build/lib.linux-x86_64-3.4/pysam

copying pysam/cvcf.pxd -> build/lib.linux-x86_64-3.4/pysam

copying pysam/cbcf.pxd -> build/lib.linux-x86_64-3.4/pysam

copying pysam/cutils.pxd -> build/lib.linux-x86_64-3.4/pysam

copying pysam/chtslib.pxd -> build/lib.linux-x86_64-3.4/pysam

copying pysam/ctabixproxies.pxd -> build/lib.linux-x86_64-3.4/pysam

copying pysam/cfaidx.pxd -> build/lib.linux-x86_64-3.4/pysam

copying pysam/htslib_util.h -> build/lib.linux-x86_64-3.4/pysam

copying pysam/samfile_util.h -> build/lib.linux-x86_64-3.4/pysam

copying pysam/tabix_util.h -> build/lib.linux-x86_64-3.4/pysam

copying pysam/pysam_util.h -> build/lib.linux-x86_64-3.4/pysam

copying pysam/pysam_stream.h -> build/lib.linux-x86_64-3.4/pysam

creating build/lib.linux-x86_64-3.4/pysam/include/htslib

copying htslib/hts_internal.h -> build/lib.linux-x86_64-3.4/pysam/include/htslib

copying htslib/hfile_internal.h -> build/lib.linux-x86_64-3.4/pysam/include/htslib

copying htslib/config.h -> build/lib.linux-x86_64-3.4/pysam/include/htslib

copying htslib/version.h -> build/lib.linux-x86_64-3.4/pysam/include/htslib

creating build/lib.linux-x86_64-3.4/pysam/include/htslib/htslib

copying htslib/htslib/kstring.h -> build/lib.linux-x86_64-3.4/pysam/include/htslib/htslib

copying htslib/htslib/kseq.h -> build/lib.linux-x86_64-3.4/pysam/include/htslib/htslib

copying htslib/htslib/kfunc.h -> build/lib.linux-x86_64-3.4/pysam/include/htslib/htslib

copying htslib/htslib/knetfile.h -> build/lib.linux-x86_64-3.4/pysam/include/htslib/htslib

copying htslib/htslib/khash_str2int.h -> build/lib.linux-x86_64-3.4/pysam/include/htslib/htslib

copying htslib/htslib/vcf_sweep.h -> build/lib.linux-x86_64-3.4/pysam/include/htslib/htslib

copying htslib/htslib/cram.h -> build/lib.linux-x86_64-3.4/pysam/include/htslib/htslib

copying htslib/htslib/regidx.h -> build/lib.linux-x86_64-3.4/pysam/include/htslib/htslib

copying htslib/htslib/bgzf.h -> build/lib.linux-x86_64-3.4/pysam/include/htslib/htslib

copying htslib/htslib/hts_defs.h -> build/lib.linux-x86_64-3.4/pysam/include/htslib/htslib

copying htslib/htslib/tbx.h -> build/lib.linux-x86_64-3.4/pysam/include/htslib/htslib

copying htslib/htslib/faidx.h -> build/lib.linux-x86_64-3.4/pysam/include/htslib/htslib

copying htslib/htslib/ksort.h -> build/lib.linux-x86_64-3.4/pysam/include/htslib/htslib

copying htslib/htslib/synced_bcf_reader.h -> build/lib.linux-x86_64-3.4/pysam/include/htslib/htslib

copying htslib/htslib/khash.h -> build/lib.linux-x86_64-3.4/pysam/include/htslib/htslib

copying htslib/htslib/kbitset.h -> build/lib.linux-x86_64-3.4/pysam/include/htslib/htslib

copying htslib/htslib/vcf.h -> build/lib.linux-x86_64-3.4/pysam/include/htslib/htslib

copying htslib/htslib/sam.h -> build/lib.linux-x86_64-3.4/pysam/include/htslib/htslib

copying htslib/htslib/hfile.h -> build/lib.linux-x86_64-3.4/pysam/include/htslib/htslib

copying htslib/htslib/vcfutils.h -> build/lib.linux-x86_64-3.4/pysam/include/htslib/htslib

copying htslib/htslib/hts.h -> build/lib.linux-x86_64-3.4/pysam/include/htslib/htslib

copying htslib/htslib/klist.h -> build/lib.linux-x86_64-3.4/pysam/include/htslib/htslib

creating build/lib.linux-x86_64-3.4/pysam/include/samtools

copying samtools/stats_isize.h -> build/lib.linux-x86_64-3.4/pysam/include/samtools

copying samtools/kprobaln.h -> build/lib.linux-x86_64-3.4/pysam/include/samtools

copying samtools/errmod.h -> build/lib.linux-x86_64-3.4/pysam/include/samtools

copying samtools/bam_endian.h -> build/lib.linux-x86_64-3.4/pysam/include/samtools

copying samtools/bam_plbuf.h -> build/lib.linux-x86_64-3.4/pysam/include/samtools

copying samtools/bam_lpileup.h -> build/lib.linux-x86_64-3.4/pysam/include/samtools

copying samtools/bam2bcf.h -> build/lib.linux-x86_64-3.4/pysam/include/samtools

copying samtools/sam_header.h -> build/lib.linux-x86_64-3.4/pysam/include/samtools

copying samtools/bam.h -> build/lib.linux-x86_64-3.4/pysam/include/samtools

copying samtools/bam_tview.h -> build/lib.linux-x86_64-3.4/pysam/include/samtools

copying samtools/pysam.h -> build/lib.linux-x86_64-3.4/pysam/include/samtools

copying samtools/sample.h -> build/lib.linux-x86_64-3.4/pysam/include/samtools

copying samtools/sam.h -> build/lib.linux-x86_64-3.4/pysam/include/samtools

copying samtools/version.h -> build/lib.linux-x86_64-3.4/pysam/include/samtools

copying samtools/sam_opts.h -> build/lib.linux-x86_64-3.4/pysam/include/samtools

copying samtools/samtools.h -> build/lib.linux-x86_64-3.4/pysam/include/samtools

creating build/lib.linux-x86_64-3.4/pysam/include/bcftools

copying bcftools/call.h -> build/lib.linux-x86_64-3.4/pysam/include/bcftools

copying bcftools/gvcf.h -> build/lib.linux-x86_64-3.4/pysam/include/bcftools

copying bcftools/convert.h -> build/lib.linux-x86_64-3.4/pysam/include/bcftools

copying bcftools/khash_str2str.h -> build/lib.linux-x86_64-3.4/pysam/include/bcftools

copying bcftools/prob1.h -> build/lib.linux-x86_64-3.4/pysam/include/bcftools

copying bcftools/filter.h -> build/lib.linux-x86_64-3.4/pysam/include/bcftools

copying bcftools/kmin.h -> build/lib.linux-x86_64-3.4/pysam/include/bcftools

copying bcftools/vcmp.h -> build/lib.linux-x86_64-3.4/pysam/include/bcftools

copying bcftools/rbuf.h -> build/lib.linux-x86_64-3.4/pysam/include/bcftools

copying bcftools/ploidy.h -> build/lib.linux-x86_64-3.4/pysam/include/bcftools

copying bcftools/pysam.h -> build/lib.linux-x86_64-3.4/pysam/include/bcftools

copying bcftools/bcftools.h -> build/lib.linux-x86_64-3.4/pysam/include/bcftools

copying bcftools/HMM.h -> build/lib.linux-x86_64-3.4/pysam/include/bcftools

copying bcftools/version.h -> build/lib.linux-x86_64-3.4/pysam/include/bcftools

copying bcftools/tsv2vcf.h -> build/lib.linux-x86_64-3.4/pysam/include/bcftools

creating build/lib.linux-x86_64-3.4/pysam/include/samtools/win32

copying samtools/win32/xcurses.h -> build/lib.linux-x86_64-3.4/pysam/include/samtools/win32

copying samtools/win32/zlib.h -> build/lib.linux-x86_64-3.4/pysam/include/samtools/win32

copying samtools/win32/zconf.h -> build/lib.linux-x86_64-3.4/pysam/include/samtools/win32

Fixing build/lib.linux-x86_64-3.4/pysam/Pileup.py build/lib.linux-x86_64-3.4/pysam/version.py build/lib.linux-x86_64-3.4/pysam/__init__.py build/lib.linux-x86_64-3.4/pysam/bcftools.py build/lib.linux-x86_64-3.4/pysam/namedtuple.py build/lib.linux-x86_64-3.4/pysam/utils.py build/lib.linux-x86_64-3.4/pysam/samtools.py build/lib.linux-x86_64-3.4/pysam/config.py build/lib.linux-x86_64-3.4/pysam/include/__init__.py

Skipping optional fixer: buffer

Skipping optional fixer: idioms

Skipping optional fixer: set_literal

Skipping optional fixer: ws_comma

Skipping optional fixer: buffer

Skipping optional fixer: idioms

Skipping optional fixer: set_literal

Skipping optional fixer: ws_comma

running build_ext

cythoning pysam/chtslib.pyx to pysam/chtslib.c

building 'pysam.libchtslib' extension

creating build/temp.linux-x86_64-3.4

creating build/temp.linux-x86_64-3.4/pysam

creating build/temp.linux-x86_64-3.4/htslib

creating build/temp.linux-x86_64-3.4/htslib/cram

gcc -pthread -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -Ipysam -I. -Ihtslib -I/sonas-hs/lyon/hpc/home/hfang/miniconda3/include/python3.4m -c pysam/chtslib.c -o build/temp.linux-x86_64-3.4/pysam/chtslib.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement

gcc -pthread -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -Ipysam -I. -Ihtslib -I/sonas-hs/lyon/hpc/home/hfang/miniconda3/include/python3.4m -c pysam/htslib_util.c -o build/temp.linux-x86_64-3.4/pysam/htslib_util.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement

gcc -pthread -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -Ipysam -I. -Ihtslib -I/sonas-hs/lyon/hpc/home/hfang/miniconda3/include/python3.4m -c htslib/faidx.c -o build/temp.linux-x86_64-3.4/htslib/faidx.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement

gcc -pthread -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -Ipysam -I. -Ihtslib -I/sonas-hs/lyon/hpc/home/hfang/miniconda3/include/python3.4m -c htslib/vcf.c -o build/temp.linux-x86_64-3.4/htslib/vcf.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement

gcc -pthread -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -Ipysam -I. -Ihtslib -I/sonas-hs/lyon/hpc/home/hfang/miniconda3/include/python3.4m -c htslib/hfile.c -o build/temp.linux-x86_64-3.4/htslib/hfile.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement

gcc -pthread -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -Ipysam -I. -Ihtslib -I/sonas-hs/lyon/hpc/home/hfang/miniconda3/include/python3.4m -c htslib/kstring.c -o build/temp.linux-x86_64-3.4/htslib/kstring.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement

gcc -pthread -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -Ipysam -I. -Ihtslib -I/sonas-hs/lyon/hpc/home/hfang/miniconda3/include/python3.4m -c htslib/md5.c -o build/temp.linux-x86_64-3.4/htslib/md5.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement

gcc -pthread -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -Ipysam -I. -Ihtslib -I/sonas-hs/lyon/hpc/home/hfang/miniconda3/include/python3.4m -c htslib/knetfile.c -o build/temp.linux-x86_64-3.4/htslib/knetfile.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement

gcc -pthread -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -Ipysam -I. -Ihtslib -I/sonas-hs/lyon/hpc/home/hfang/miniconda3/include/python3.4m -c htslib/hfile_libcurl.c -o build/temp.linux-x86_64-3.4/htslib/hfile_libcurl.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement

htslib/hfile_libcurl.c: In function ‘easy_errno’:

htslib/hfile_libcurl.c:93: error: ‘CURLE_NOT_BUILT_IN’ undeclared (first use in this function)

htslib/hfile_libcurl.c:93: error: (Each undeclared identifier is reported only once

htslib/hfile_libcurl.c:93: error: for each function it appears in.)

error: command 'gcc' failed with exit status 1

----------------------------------------

Failed building wheel for pysam

Running setup.py clean for pysam

Failed to build pysam

Installing collected packages: pysam

Found existing installation: pysam 0.8.3

Uninstalling pysam-0.8.3:

Successfully uninstalled pysam-0.8.3

Running setup.py install for pysam ... error

Complete output from command /sonas-hs/lyon/hpc/home/hfang/miniconda3/bin/python -u -c "import setuptools, tokenize;__file__='/tmp/pip-build-48jgbesk/pysam/setup.py';exec(compile(getattr(tokenize, 'open', open)(__file__).read().replace('\r\n', '\n'), __file__, 'exec'))" install --record /tmp/pip-3im_uvn1-record/install-record.txt --single-version-externally-managed --compile: