Unable to install pysam (Failed building wheel for pysam)

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Adarsh Singh

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Dec 8, 2019, 4:25:26 AM12/8/19

to Pysam User group

I have tried all the solutions provided by users and experts in different threads, and I keep getting this error. Earlier, pysam was working fine, but suddenly few days it stopped (is used in checkm). Please provide me detailed solution. Really thankful!!!

Collecting pysam

Using cached https://files.pythonhosted.org/packages/15/e7/2dab8bb0ac739555e69586f1492f0ff6bc4a1f8312992a83001d3deb77ac/pysam-0.15.3.tar.gz

Building wheels for collected packages: pysam

Running setup.py bdist_wheel for pysam ... error

Complete output from command /usr/bin/python3 -u -c "import setuptools, tokenize;__file__='/tmp/pip-build-bkca2rmp/pysam/setup.py';f=getattr(tokenize, 'open', open)(__file__);code=f.read().replace('\r\n', '\n');f.close();exec(compile(code, __file__, 'exec'))" bdist_wheel -d /tmp/tmpq3pk9fynpip-wheel- --python-tag cp36:

# pysam: no cython available - using pre-compiled C

# pysam: htslib mode is shared

# pysam: HTSLIB_CONFIGURE_OPTIONS=None

# pysam: (env) CC=/home/ciralab/miniconda3/bin/x86_64-conda_cos6-linux-gnu-cc

# pysam: (env) CFLAGS=-march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /home/ciralab/miniconda3/include

# pysam: (env) LDFLAGS=-Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,-rpath,/home/ciralab/miniconda3/lib -Wl,-rpath-link,/home/ciralab/miniconda3/lib -L/home/ciralab/miniconda3/lib

checking for gcc... /home/ciralab/miniconda3/bin/x86_64-conda_cos6-linux-gnu-cc

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 /home/ciralab/miniconda3/bin/x86_64-conda_cos6-linux-gnu-cc accepts -g... yes

checking for /home/ciralab/miniconda3/bin/x86_64-conda_cos6-linux-gnu-cc option to accept ISO C89... none needed

checking for ranlib... /home/ciralab/miniconda3/bin/x86_64-conda_cos6-linux-gnu-ranlib

checking for grep that handles long lines and -e... /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-Linux... plain .so

checking how to run the C preprocessor... /home/ciralab/miniconda3/bin/x86_64-conda_cos6-linux-gnu-cpp

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

checking for ANSI C header files... yes

checking for sys/types.h... yes

checking for sys/stat.h... yes

checking for stdlib.h... yes

checking for string.h... yes

checking for memory.h... yes

checking for strings.h... yes

checking for inttypes.h... yes

checking for stdint.h... yes

checking for unistd.h... yes

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

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

checking for sys/param.h... yes

checking for getpagesize... yes

checking for working mmap... yes

checking for gmtime_r... yes

checking for fsync... yes

checking for drand48... yes

checking whether fdatasync is declared... yes

checking for fdatasync... yes

checking for library containing log... -lm

checking for zlib.h... yes

checking for inflate in -lz... yes

checking for library containing recv... none required

checking for bzlib.h... yes

checking for BZ2_bzBuffToBuffCompress in -lbz2... yes

checking for lzma.h... yes

checking for lzma_easy_buffer_encode in -llzma... yes

checking for libdeflate.h... yes

checking for libdeflate_deflate_compress in -ldeflate... yes

checking for curl_easy_pause in -lcurl... yes

checking for CCHmac... no

checking for library containing HMAC... -lcrypto

checking whether PTHREAD_MUTEX_RECURSIVE is declared... yes

configure: creating ./config.status

config.status: creating config.mk

config.status: creating htslib.pc.tmp

config.status: creating config.h

config.status: config.h is unchanged

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

make: ./version.sh: Command not found

# pysam: htslib_config LDFLAGS=-Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,-rpath,/home/ciralab/miniconda3/lib -Wl,-rpath-link,/home/ciralab/miniconda3/lib -L/home/ciralab/miniconda3/lib

# 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=-ldeflate -llzma -lbz2 -lz -lm -lcurl -lcrypto

# pysam: htslib_config PLATFORM=default

# pysam: config_option: ENABLE_PLUGINS=0

# pysam: config_option: HAVE_COMMONCRYPTO=0

# pysam: config_option: HAVE_GMTIME_R=1

# pysam: config_option: HAVE_HMAC=1

# pysam: config_option: HAVE_IRODS=0

# pysam: config_option: HAVE_LIBCURL=1

# pysam: config_option: HAVE_MMAP=1

running bdist_wheel

running build

running build_py

creating build

creating build/lib.linux-x86_64-3.6

creating build/lib.linux-x86_64-3.6/pysam

copying pysam/samtools.py -> build/lib.linux-x86_64-3.6/pysam

copying pysam/Pileup.py -> build/lib.linux-x86_64-3.6/pysam

copying pysam/version.py -> build/lib.linux-x86_64-3.6/pysam

copying pysam/config.py -> build/lib.linux-x86_64-3.6/pysam

copying pysam/__init__.py -> build/lib.linux-x86_64-3.6/pysam

copying pysam/utils.py -> build/lib.linux-x86_64-3.6/pysam

copying pysam/bcftools.py -> build/lib.linux-x86_64-3.6/pysam

creating build/lib.linux-x86_64-3.6/pysam/include

copying pysam/include/__init__.py -> build/lib.linux-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/libcvcf.pxd -> build/lib.linux-x86_64-3.6/pysam

copying pysam/libcsamtools.pxd -> build/lib.linux-x86_64-3.6/pysam

copying pysam/libchtslib.pxd -> build/lib.linux-x86_64-3.6/pysam

copying pysam/libcbcftools.pxd -> build/lib.linux-x86_64-3.6/pysam

copying pysam/libcbcf.pxd -> build/lib.linux-x86_64-3.6/pysam

copying pysam/libcutils.pxd -> build/lib.linux-x86_64-3.6/pysam

copying pysam/libcsamfile.pxd -> build/lib.linux-x86_64-3.6/pysam

copying pysam/libctabix.pxd -> build/lib.linux-x86_64-3.6/pysam

copying pysam/libcalignedsegment.pxd -> build/lib.linux-x86_64-3.6/pysam

copying pysam/libcfaidx.pxd -> build/lib.linux-x86_64-3.6/pysam

copying pysam/libctabixproxies.pxd -> build/lib.linux-x86_64-3.6/pysam

copying pysam/libcalignmentfile.pxd -> build/lib.linux-x86_64-3.6/pysam

copying pysam/pysam_util.h -> build/lib.linux-x86_64-3.6/pysam

copying pysam/htslib_util.h -> build/lib.linux-x86_64-3.6/pysam

copying pysam/cbcftools_util.h -> build/lib.linux-x86_64-3.6/pysam

copying pysam/pysam_stream.h -> build/lib.linux-x86_64-3.6/pysam

copying pysam/csamtools_util.h -> build/lib.linux-x86_64-3.6/pysam

creating build/lib.linux-x86_64-3.6/pysam/include/samtools

copying samtools/bam_plbuf.h -> build/lib.linux-x86_64-3.6/pysam/include/samtools

copying samtools/sam_opts.h -> build/lib.linux-x86_64-3.6/pysam/include/samtools

copying samtools/bam_endian.h -> build/lib.linux-x86_64-3.6/pysam/include/samtools

copying samtools/sample.h -> build/lib.linux-x86_64-3.6/pysam/include/samtools

copying samtools/bam.h -> build/lib.linux-x86_64-3.6/pysam/include/samtools

copying samtools/sam.h -> build/lib.linux-x86_64-3.6/pysam/include/samtools

copying samtools/stats_isize.h -> build/lib.linux-x86_64-3.6/pysam/include/samtools

copying samtools/sam_header.h -> build/lib.linux-x86_64-3.6/pysam/include/samtools

copying samtools/bedidx.h -> build/lib.linux-x86_64-3.6/pysam/include/samtools

copying samtools/samtools.h -> build/lib.linux-x86_64-3.6/pysam/include/samtools

copying samtools/bam_lpileup.h -> build/lib.linux-x86_64-3.6/pysam/include/samtools

copying samtools/bam2bcf.h -> build/lib.linux-x86_64-3.6/pysam/include/samtools

copying samtools/tmp_file.h -> build/lib.linux-x86_64-3.6/pysam/include/samtools

copying samtools/version.h -> build/lib.linux-x86_64-3.6/pysam/include/samtools

copying samtools/samtools.pysam.h -> build/lib.linux-x86_64-3.6/pysam/include/samtools

copying samtools/config.h -> build/lib.linux-x86_64-3.6/pysam/include/samtools

creating build/lib.linux-x86_64-3.6/pysam/include/bcftools

copying bcftools/vcfbuf.h -> build/lib.linux-x86_64-3.6/pysam/include/bcftools

copying bcftools/regidx.h -> build/lib.linux-x86_64-3.6/pysam/include/bcftools

copying bcftools/bam_sample.h -> build/lib.linux-x86_64-3.6/pysam/include/bcftools

copying bcftools/kheap.h -> build/lib.linux-x86_64-3.6/pysam/include/bcftools

copying bcftools/mw.h -> build/lib.linux-x86_64-3.6/pysam/include/bcftools

copying bcftools/call.h -> build/lib.linux-x86_64-3.6/pysam/include/bcftools

copying bcftools/khash_str2str.h -> build/lib.linux-x86_64-3.6/pysam/include/bcftools

copying bcftools/bin.h -> build/lib.linux-x86_64-3.6/pysam/include/bcftools

copying bcftools/hclust.h -> build/lib.linux-x86_64-3.6/pysam/include/bcftools

copying bcftools/rbuf.h -> build/lib.linux-x86_64-3.6/pysam/include/bcftools

copying bcftools/vcmp.h -> build/lib.linux-x86_64-3.6/pysam/include/bcftools

copying bcftools/kmin.h -> build/lib.linux-x86_64-3.6/pysam/include/bcftools

copying bcftools/bcftools.h -> build/lib.linux-x86_64-3.6/pysam/include/bcftools

copying bcftools/bcftools.pysam.h -> build/lib.linux-x86_64-3.6/pysam/include/bcftools

copying bcftools/convert.h -> build/lib.linux-x86_64-3.6/pysam/include/bcftools

copying bcftools/HMM.h -> build/lib.linux-x86_64-3.6/pysam/include/bcftools

copying bcftools/prob1.h -> build/lib.linux-x86_64-3.6/pysam/include/bcftools

copying bcftools/tsv2vcf.h -> build/lib.linux-x86_64-3.6/pysam/include/bcftools

copying bcftools/smpl_ilist.h -> build/lib.linux-x86_64-3.6/pysam/include/bcftools

copying bcftools/ploidy.h -> build/lib.linux-x86_64-3.6/pysam/include/bcftools

copying bcftools/bam2bcf.h -> build/lib.linux-x86_64-3.6/pysam/include/bcftools

copying bcftools/version.h -> build/lib.linux-x86_64-3.6/pysam/include/bcftools

copying bcftools/filter.h -> build/lib.linux-x86_64-3.6/pysam/include/bcftools

copying bcftools/gvcf.h -> build/lib.linux-x86_64-3.6/pysam/include/bcftools

copying bcftools/config.h -> build/lib.linux-x86_64-3.6/pysam/include/bcftools

creating build/lib.linux-x86_64-3.6/pysam/include/samtools/win32

copying samtools/win32/zconf.h -> build/lib.linux-x86_64-3.6/pysam/include/samtools/win32

copying samtools/win32/xcurses.h -> build/lib.linux-x86_64-3.6/pysam/include/samtools/win32

copying samtools/win32/zlib.h -> build/lib.linux-x86_64-3.6/pysam/include/samtools/win32

creating build/lib.linux-x86_64-3.6/pysam/include/htslib

copying htslib/textutils_internal.h -> build/lib.linux-x86_64-3.6/pysam/include/htslib

copying htslib/hts_internal.h -> build/lib.linux-x86_64-3.6/pysam/include/htslib

copying htslib/bcf_sr_sort.h -> build/lib.linux-x86_64-3.6/pysam/include/htslib

copying htslib/version.h -> build/lib.linux-x86_64-3.6/pysam/include/htslib

copying htslib/hfile_internal.h -> build/lib.linux-x86_64-3.6/pysam/include/htslib

copying htslib/thread_pool_internal.h -> build/lib.linux-x86_64-3.6/pysam/include/htslib

copying htslib/config.h -> build/lib.linux-x86_64-3.6/pysam/include/htslib

creating build/lib.linux-x86_64-3.6/pysam/include/htslib/htslib

copying htslib/htslib/regidx.h -> build/lib.linux-x86_64-3.6/pysam/include/htslib/htslib

copying htslib/htslib/hts_defs.h -> build/lib.linux-x86_64-3.6/pysam/include/htslib/htslib

copying htslib/htslib/thread_pool.h -> build/lib.linux-x86_64-3.6/pysam/include/htslib/htslib

copying htslib/htslib/cram.h -> build/lib.linux-x86_64-3.6/pysam/include/htslib/htslib

copying htslib/htslib/hfile.h -> build/lib.linux-x86_64-3.6/pysam/include/htslib/htslib

copying htslib/htslib/vcf.h -> build/lib.linux-x86_64-3.6/pysam/include/htslib/htslib

copying htslib/htslib/kseq.h -> build/lib.linux-x86_64-3.6/pysam/include/htslib/htslib

copying htslib/htslib/sam.h -> build/lib.linux-x86_64-3.6/pysam/include/htslib/htslib

copying htslib/htslib/bgzf.h -> build/lib.linux-x86_64-3.6/pysam/include/htslib/htslib

copying htslib/htslib/ksort.h -> build/lib.linux-x86_64-3.6/pysam/include/htslib/htslib

copying htslib/htslib/kstring.h -> build/lib.linux-x86_64-3.6/pysam/include/htslib/htslib

copying htslib/htslib/faidx.h -> build/lib.linux-x86_64-3.6/pysam/include/htslib/htslib

copying htslib/htslib/tbx.h -> build/lib.linux-x86_64-3.6/pysam/include/htslib/htslib

copying htslib/htslib/hts_log.h -> build/lib.linux-x86_64-3.6/pysam/include/htslib/htslib

copying htslib/htslib/kfunc.h -> build/lib.linux-x86_64-3.6/pysam/include/htslib/htslib

copying htslib/htslib/hts_endian.h -> build/lib.linux-x86_64-3.6/pysam/include/htslib/htslib

copying htslib/htslib/khash.h -> build/lib.linux-x86_64-3.6/pysam/include/htslib/htslib

copying htslib/htslib/knetfile.h -> build/lib.linux-x86_64-3.6/pysam/include/htslib/htslib

copying htslib/htslib/kbitset.h -> build/lib.linux-x86_64-3.6/pysam/include/htslib/htslib

copying htslib/htslib/klist.h -> build/lib.linux-x86_64-3.6/pysam/include/htslib/htslib

copying htslib/htslib/vcf_sweep.h -> build/lib.linux-x86_64-3.6/pysam/include/htslib/htslib

copying htslib/htslib/khash_str2int.h -> build/lib.linux-x86_64-3.6/pysam/include/htslib/htslib

copying htslib/htslib/hts_os.h -> build/lib.linux-x86_64-3.6/pysam/include/htslib/htslib

copying htslib/htslib/hts.h -> build/lib.linux-x86_64-3.6/pysam/include/htslib/htslib

copying htslib/htslib/synced_bcf_reader.h -> build/lib.linux-x86_64-3.6/pysam/include/htslib/htslib

copying htslib/htslib/vcfutils.h -> build/lib.linux-x86_64-3.6/pysam/include/htslib/htslib

Fixing build/lib.linux-x86_64-3.6/pysam/samtools.py build/lib.linux-x86_64-3.6/pysam/Pileup.py build/lib.linux-x86_64-3.6/pysam/version.py build/lib.linux-x86_64-3.6/pysam/config.py build/lib.linux-x86_64-3.6/pysam/__init__.py build/lib.linux-x86_64-3.6/pysam/utils.py build/lib.linux-x86_64-3.6/pysam/bcftools.py build/lib.linux-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

Skipping optional fixer: buffer

Skipping optional fixer: idioms

Skipping optional fixer: set_literal

Skipping optional fixer: ws_comma

running build_ext

building 'pysam.libchtslib' extension

creating build/temp.linux-x86_64-3.6

creating build/temp.linux-x86_64-3.6/pysam

/home/ciralab/miniconda3/bin/x86_64-conda_cos6-linux-gnu-cc -DNDEBUG -g -fwrapv -O2 -Wall -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /home/ciralab/miniconda3/include -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /home/ciralab/miniconda3/include -fPIC -I/usr/local/include -I/tmp/pip-build-bkca2rmp/pysam/samtools -I/tmp/pip-build-bkca2rmp/pysam/samtools/lz4 -I/tmp/pip-build-bkca2rmp/pysam/bcftools -I/tmp/pip-build-bkca2rmp/pysam/pysam -I/tmp/pip-build-bkca2rmp/pysam -I/usr/include/python3.6m -c pysam/libchtslib.c -o build/temp.linux-x86_64-3.6/pysam/libchtslib.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement

In file included from /usr/include/python3.6m/Python.h:8:0,

from pysam/libchtslib.c:4:

/usr/include/python3.6m/pyconfig.h:3:12: fatal error: x86_64-linux-gnu/python3.6m/pyconfig.h: No such file or directory

# include <x86_64-linux-gnu/python3.6m/pyconfig.h>

^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

compilation terminated.

error: command '/home/ciralab/miniconda3/bin/x86_64-conda_cos6-linux-gnu-cc' failed with exit status 1

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

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 /usr/bin/python3 -u -c "import setuptools, tokenize;__file__='/tmp/pip-build-bkca2rmp/pysam/setup.py';f=getattr(tokenize, 'open', open)(__file__);code=f.read().replace('\r\n', '\n');f.close();exec(compile(code, __file__, 'exec'))" install --record /tmp/pip-0y6mfzu9-record/install-record.txt --single-version-externally-managed --compile --user --prefix=:

# pysam: no cython available - using pre-compiled C

# pysam: htslib mode is shared

# pysam: HTSLIB_CONFIGURE_OPTIONS=None

# pysam: (env) CC=/home/ciralab/miniconda3/bin/x86_64-conda_cos6-linux-gnu-cc

# pysam: (env) CFLAGS=-march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /home/ciralab/miniconda3/include

checking for gcc... /home/ciralab/miniconda3/bin/x86_64-conda_cos6-linux-gnu-cc

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 /home/ciralab/miniconda3/bin/x86_64-conda_cos6-linux-gnu-cc accepts -g... yes

checking for /home/ciralab/miniconda3/bin/x86_64-conda_cos6-linux-gnu-cc option to accept ISO C89... none needed

checking for ranlib... /home/ciralab/miniconda3/bin/x86_64-conda_cos6-linux-gnu-ranlib

checking for grep that handles long lines and -e... /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-Linux... plain .so

checking how to run the C preprocessor... /home/ciralab/miniconda3/bin/x86_64-conda_cos6-linux-gnu-cpp

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

checking for ANSI C header files... yes

checking for sys/types.h... yes

checking for sys/stat.h... yes

checking for stdlib.h... yes

checking for string.h... yes

checking for memory.h... yes

checking for strings.h... yes

checking for inttypes.h... yes

checking for stdint.h... yes

checking for unistd.h... yes

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

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

checking for sys/param.h... yes

checking for getpagesize... yes

checking for working mmap... yes

checking for gmtime_r... yes

checking for fsync... yes

checking for drand48... yes

checking whether fdatasync is declared... yes

checking for fdatasync... yes

checking for library containing log... -lm

checking for zlib.h... yes

checking for inflate in -lz... yes

checking for library containing recv... none required

checking for bzlib.h... yes

checking for BZ2_bzBuffToBuffCompress in -lbz2... yes

checking for lzma.h... yes

checking for lzma_easy_buffer_encode in -llzma... yes

checking for libdeflate.h... yes

checking for libdeflate_deflate_compress in -ldeflate... yes

checking for curl_easy_pause in -lcurl... yes

checking for CCHmac... no

checking for library containing HMAC... -lcrypto

checking whether PTHREAD_MUTEX_RECURSIVE is declared... yes

configure: creating ./config.status

config.status: creating config.mk

config.status: creating htslib.pc.tmp

config.status: creating config.h

config.status: config.h is unchanged

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

make: ./version.sh: Command not found

# pysam: htslib_config LIBS=-ldeflate -llzma -lbz2 -lz -lm -lcurl -lcrypto

# pysam: htslib_config PLATFORM=default

# pysam: config_option: ENABLE_PLUGINS=0

# pysam: config_option: HAVE_COMMONCRYPTO=0

# pysam: config_option: HAVE_GMTIME_R=1

# pysam: config_option: HAVE_HMAC=1

# pysam: config_option: HAVE_IRODS=0

# pysam: config_option: HAVE_LIBCURL=1

# pysam: config_option: HAVE_MMAP=1

running install