Hello, I encountered the following error (see ### error log ###) when trying to install circlator on a specific server via "py3_virtualenv_circlator/bin/pip3 install "circlator==1.5.1". The installation is fine on other servers though. It appears to me the problem is the library liblzma cannot be found. But in fact this library has been installed in the system:
gilles@big-daddy:~$ /sbin/ldconfig -p|egrep liblzma
liblzma.so.5 (libc6,x86-64) => /lib/x86_64-linux-gnu/liblzma.so.5
liblzma.so.5 (libc6) => /lib/i386-linux-gnu/liblzma.so.5
Could you help to to diagnose what might be the true cause of this problem? Thx!
################# error log #############################
Downloading/unpacking circlator==1.5.1
Downloading circlator-1.5.1.tar.gz (5.3MB): 5.3MB downloaded
Running setup.py (path:/home/gilles/LRSDAY_v20170710/build/py3_virtualenv_circlator/build/circlator/setup.py) egg_info for package circlator
Downloading/unpacking openpyxl (from circlator==1.5.1)
Downloading openpyxl-2.4.8.tar.gz (156kB): 156kB downloaded
Running setup.py (path:/home/gilles/LRSDAY_v20170710/build/py3_virtualenv_circlator/build/openpyxl/setup.py) egg_info for package openpyxl
no previously-included directories found matching 'openpyxl/tests'
no previously-included directories found matching 'openpyxl/sample'
no previously-included directories found matching 'openpyxl/benchmarks'
no previously-included directories found matching 'openpyxl/develop'
no previously-included directories found matching 'scratchpad'
warning: no previously-included files matching 'test_*.py' found under directory 'openpyxl'
warning: no previously-included files matching 'tests/*.py' found under directory 'openpyxl'
Downloading/unpacking pyfastaq>=3.12.1 (from circlator==1.5.1)
Downloading pyfastaq-3.15.0.tar.gz (49kB): 49kB downloaded
Running setup.py (path:/home/gilles/LRSDAY_v20170710/build/py3_virtualenv_circlator/build/pyfastaq/setup.py) egg_info for package pyfastaq
Downloading/unpacking pysam>=0.8.1 (from circlator==1.5.1)
Downloading pysam-0.11.2.2.tar.gz (2.5MB): 2.5MB downloaded
Running setup.py (path:/home/gilles/LRSDAY_v20170710/build/py3_virtualenv_circlator/build/pysam/setup.py) egg_info for package pysam
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 special C compiler options needed for large files... no
checking for _FILE_OFFSET_BITS value needed for large files... no
checking shared library type... plain .so
checking how to run the C preprocessor... gcc -E
checking for grep that handles long lines and -e... /bin/grep
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 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 connect... none required
checking for bzlib.h... yes
checking for BZ2_bzBuffToBuffCompress in -lbz2... yes
checking for lzma.h... no
checking for lzma_easy_buffer_encode in -llzma... no
configure: error: liblzma development files not found
The CRAM format may use LZMA2 compression, which is implemented in HTSlib
by using compression routines from liblzma <http://tukaani.org/xz/>.
Building HTSlib requires liblzma development files to be installed on the
build machine; you may need to ensure a package such as liblzma-dev (on Debian
or Ubuntu Linux), xz-devel (on RPM-based Linux distributions or Cygwin), or
xz (via Homebrew on macOS) is installed; or build XZ Utils from source.
Either configure with --disable-lzma (which will make some CRAM files
produced elsewhere unreadable) or resolve this error to build HTSlib.
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 special C compiler options needed for large files... no
checking for _FILE_OFFSET_BITS value needed for large files... no
checking shared library type... plain .so
checking how to run the C preprocessor... gcc -E
checking for grep that handles long lines and -e... /bin/grep
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 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 connect... none required
checking for bzlib.h... yes
checking for BZ2_bzBuffToBuffCompress in -lbz2... yes
checking for lzma.h... no
checking for lzma_easy_buffer_encode in -llzma... no
configure: error: liblzma development files not found
The CRAM format may use LZMA2 compression, which is implemented in HTSlib
by using compression routines from liblzma <http://tukaani.org/xz/>.
Building HTSlib requires liblzma development files to be installed on the
build machine; you may need to ensure a package such as liblzma-dev (on Debian
or Ubuntu Linux), xz-devel (on RPM-based Linux distributions or Cygwin), or
xz (via Homebrew on macOS) is installed; or build XZ Utils from source.
Either configure with --disable-lzma (which will make some CRAM files
produced elsewhere unreadable) or resolve this error to build HTSlib.
# pysam: no cython available - using pre-compiled C
# pysam: htslib mode is shared
# pysam: HTSLIB_CONFIGURE_OPTIONS=None
# pysam: htslib configure options: None
# pysam: htslib_config PLATFORM=Linux
# 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 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 cram/vlen.o cram/zfio.o
# pysam: htslib_config LDFLAGS=
# pysam: htslib_config LIBS=-lz -lm -lbz2 -llzma
# 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
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)
warning: no files found matching 'KNOWN_BUGS'
warning: no files found matching 'THANKS'
warning: no files found matching 'samtools/configure'
warning: no files found matching 'samtools/config.mk.in'
warning: no files found matching 'samtools/config.h.in'
warning: no files found matching 'tests/pysam_data'
warning: no files found matching 'tests/tabix_data'
Downloading/unpacking pymummer>=0.9.0 (from circlator==1.5.1)
Downloading pymummer-0.10.2.tar.gz
Running setup.py (path:/home/gilles/LRSDAY_v20170710/build/py3_virtualenv_circlator/build/pymummer/setup.py) egg_info for package pymummer
Checking MUMmer programs found in path:
OK nucmer
OK show-coords
OK show-snps
OK delta-filter
Downloading/unpacking jdcal (from openpyxl->circlator==1.5.1)
Downloading jdcal-1.3.tar.gz
Running setup.py (path:/home/gilles/LRSDAY_v20170710/build/py3_virtualenv_circlator/build/jdcal/setup.py) egg_info for package jdcal
Downloading/unpacking et-xmlfile (from openpyxl->circlator==1.5.1)
Downloading et_xmlfile-1.0.1.tar.gz
Running setup.py (path:/home/gilles/LRSDAY_v20170710/build/py3_virtualenv_circlator/build/et-xmlfile/setup.py) egg_info for package et-xmlfile
Installing collected packages: circlator, openpyxl, pyfastaq, pysam, pymummer, jdcal, et-xmlfile
Running setup.py install for circlator
changing mode of build/scripts-3.4/circlator from 664 to 775
changing mode of /home/gilles/LRSDAY_v20170710/build/py3_virtualenv_circlator/bin/circlator to 775
Running setup.py install for openpyxl
no previously-included directories found matching 'openpyxl/tests'
no previously-included directories found matching 'openpyxl/sample'
no previously-included directories found matching 'openpyxl/benchmarks'
no previously-included directories found matching 'openpyxl/develop'
no previously-included directories found matching 'scratchpad'
warning: no previously-included files matching 'test_*.py' found under directory 'openpyxl'
warning: no previously-included files matching 'tests/*.py' found under directory 'openpyxl'
Running setup.py install for pyfastaq
changing mode of build/scripts-3.4/fastaq from 664 to 775
changing mode of /home/gilles/LRSDAY_v20170710/build/py3_virtualenv_circlator/bin/fastaq to 775
Running setup.py install for pysam
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 special C compiler options needed for large files... no
checking for _FILE_OFFSET_BITS value needed for large files... no
checking shared library type... plain .so
checking how to run the C preprocessor... gcc -E
checking for grep that handles long lines and -e... /bin/grep
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 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 connect... none required
checking for bzlib.h... yes
checking for BZ2_bzBuffToBuffCompress in -lbz2... yes
checking for lzma.h... no
checking for lzma_easy_buffer_encode in -llzma... no
configure: error: liblzma development files not found
The CRAM format may use LZMA2 compression, which is implemented in HTSlib
by using compression routines from liblzma <http://tukaani.org/xz/>.
Building HTSlib requires liblzma development files to be installed on the
build machine; you may need to ensure a package such as liblzma-dev (on Debian
or Ubuntu Linux), xz-devel (on RPM-based Linux distributions or Cygwin), or
xz (via Homebrew on macOS) is installed; or build XZ Utils from source.
Either configure with --disable-lzma (which will make some CRAM files
produced elsewhere unreadable) or resolve this error to build HTSlib.
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 special C compiler options needed for large files... no
checking for _FILE_OFFSET_BITS value needed for large files... no
checking shared library type... plain .so
checking how to run the C preprocessor... gcc -E
checking for grep that handles long lines and -e... /bin/grep
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 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 connect... none required
checking for bzlib.h... yes
checking for BZ2_bzBuffToBuffCompress in -lbz2... yes
checking for lzma.h... no
checking for lzma_easy_buffer_encode in -llzma... no
configure: error: liblzma development files not found
The CRAM format may use LZMA2 compression, which is implemented in HTSlib
by using compression routines from liblzma <http://tukaani.org/xz/>.
Building HTSlib requires liblzma development files to be installed on the
build machine; you may need to ensure a package such as liblzma-dev (on Debian
or Ubuntu Linux), xz-devel (on RPM-based Linux distributions or Cygwin), or
xz (via Homebrew on macOS) is installed; or build XZ Utils from source.
Either configure with --disable-lzma (which will make some CRAM files
produced elsewhere unreadable) or resolve this error to build HTSlib.
# pysam: no cython available - using pre-compiled C
# pysam: htslib mode is shared
# pysam: HTSLIB_CONFIGURE_OPTIONS=None
# pysam: htslib configure options: None
# pysam: htslib_config LIBS=-lz -lm -lbz2 -llzma
# 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 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 cram/vlen.o cram/zfio.o
# pysam: htslib_config PLATFORM=Linux
# pysam: htslib_config LDFLAGS=
# 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
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)
Fixing build/lib.linux-x86_64-3.4/pysam/config.py build/lib.linux-x86_64-3.4/pysam/bcftools.py build/lib.linux-x86_64-3.4/pysam/utils.py build/lib.linux-x86_64-3.4/pysam/__init__.py build/lib.linux-x86_64-3.4/pysam/version.py build/lib.linux-x86_64-3.4/pysam/Pileup.py build/lib.linux-x86_64-3.4/pysam/samtools.py build/lib.linux-x86_64-3.4/pysam/namedtuple.py build/lib.linux-x86_64-3.4/pysam/include/__init__.py
Skipping implicit fixer: buffer
Skipping implicit fixer: idioms
Skipping implicit fixer: set_literal
Skipping implicit fixer: ws_comma
Fixing build/lib.linux-x86_64-3.4/pysam/config.py build/lib.linux-x86_64-3.4/pysam/bcftools.py build/lib.linux-x86_64-3.4/pysam/utils.py build/lib.linux-x86_64-3.4/pysam/__init__.py build/lib.linux-x86_64-3.4/pysam/version.py build/lib.linux-x86_64-3.4/pysam/Pileup.py build/lib.linux-x86_64-3.4/pysam/samtools.py build/lib.linux-x86_64-3.4/pysam/namedtuple.py build/lib.linux-x86_64-3.4/pysam/include/__init__.py
Skipping implicit fixer: buffer
Skipping implicit fixer: idioms
Skipping implicit fixer: set_literal
Skipping implicit fixer: ws_comma
building 'pysam.libchtslib' extension
x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -Ipysam -I. -Ihtslib -I/usr/include/python3.4m -I/home/gilles/LRSDAY_v20170710/build/py3_virtualenv_circlator/include/python3.4m -c pysam/libchtslib.c -o build/temp.linux-x86_64-3.4/pysam/libchtslib.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
pysam/libchtslib.c:4:20: fatal error: Python.h: No such file or directory
compilation terminated.
error: command 'x86_64-linux-gnu-gcc' failed with exit status 1
Complete output from command /home/gilles/LRSDAY_v20170710/build/py3_virtualenv_circlator/bin/python3 -c "import setuptools, tokenize;__file__='/home/gilles/LRSDAY_v20170710/build/py3_virtualenv_circlator/build/pysam/setup.py';exec(compile(getattr(tokenize, 'open', open)(__file__).read().replace('\r\n', '\n'), __file__, 'exec'))" install --record /tmp/pip-diwk06nb-record/install-record.txt --single-version-externally-managed --compile --install-headers /home/gilles/LRSDAY_v20170710/build/py3_virtualenv_circlator/include/site/python3.4:
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 special C compiler options needed for large files... no
checking for _FILE_OFFSET_BITS value needed for large files... no
checking shared library type... plain .so
checking how to run the C preprocessor... gcc -E
checking for grep that handles long lines and -e... /bin/grep
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 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 connect... none required
checking for bzlib.h... yes
checking for BZ2_bzBuffToBuffCompress in -lbz2... yes
checking for lzma.h... no
checking for lzma_easy_buffer_encode in -llzma... no
configure: error: liblzma development files not found
The CRAM format may use LZMA2 compression, which is implemented in HTSlib
by using compression routines from liblzma http://tukaani.org/xz/.
Building HTSlib requires liblzma development files to be installed on the
build machine; you may need to ensure a package such as liblzma-dev (on Debian
or Ubuntu Linux), xz-devel (on RPM-based Linux distributions or Cygwin), or
xz (via Homebrew on macOS) is installed; or build XZ Utils from source.
Either configure with --disable-lzma (which will make some CRAM files
produced elsewhere unreadable) or resolve this error to build HTSlib.
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 special C compiler options needed for large files... no
checking for _FILE_OFFSET_BITS value needed for large files... no
checking shared library type... plain .so
checking how to run the C preprocessor... gcc -E
checking for grep that handles long lines and -e... /bin/grep
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 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 connect... none required
checking for bzlib.h... yes
checking for BZ2_bzBuffToBuffCompress in -lbz2... yes
checking for lzma.h... no
checking for lzma_easy_buffer_encode in -llzma... no
configure: error: liblzma development files not found
The CRAM format may use LZMA2 compression, which is implemented in HTSlib
by using compression routines from liblzma http://tukaani.org/xz/.
Building HTSlib requires liblzma development files to be installed on the
build machine; you may need to ensure a package such as liblzma-dev (on Debian
or Ubuntu Linux), xz-devel (on RPM-based Linux distributions or Cygwin), or
xz (via Homebrew on macOS) is installed; or build XZ Utils from source.
Either configure with --disable-lzma (which will make some CRAM files
produced elsewhere unreadable) or resolve this error to build HTSlib.
pysam: no cython available - using pre-compiled C
pysam: htslib mode is shared
pysam: HTSLIB_CONFIGURE_OPTIONS=None
pysam: htslib configure options: None
pysam: htslib_config LIBS=-lz -lm -lbz2 -llzma
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 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 cram/vlen.o cram/zfio.o
pysam: htslib_config PLATFORM=Linux
pysam: htslib_config LDFLAGS=
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.linux-x86_64-3.4
creating build/lib.linux-x86_64-3.4/pysam
copying pysam/config.py -> build/lib.linux-x86_64-3.4/pysam
copying pysam/bcftools.py -> build/lib.linux-x86_64-3.4/pysam
copying pysam/utils.py -> build/lib.linux-x86_64-3.4/pysam
copying pysam/init.py -> build/lib.linux-x86_64-3.4/pysam
copying pysam/version.py -> build/lib.linux-x86_64-3.4/pysam
copying pysam/Pileup.py -> build/lib.linux-x86_64-3.4/pysam
copying pysam/samtools.py -> build/lib.linux-x86_64-3.4/pysam
copying pysam/namedtuple.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 '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/libcbcf.pxd -> build/lib.linux-x86_64-3.4/pysam
copying pysam/libcfaidx.pxd -> build/lib.linux-x86_64-3.4/pysam
copying pysam/libcsamtools.pxd -> build/lib.linux-x86_64-3.4/pysam
copying pysam/libchtslib.pxd -> build/lib.linux-x86_64-3.4/pysam
copying pysam/libctabix.pxd -> build/lib.linux-x86_64-3.4/pysam
copying pysam/libctabixproxies.pxd -> build/lib.linux-x86_64-3.4/pysam
copying pysam/libcalignedsegment.pxd -> build/lib.linux-x86_64-3.4/pysam
copying pysam/libcvcf.pxd -> build/lib.linux-x86_64-3.4/pysam
copying pysam/libcbcftools.pxd -> build/lib.linux-x86_64-3.4/pysam
copying pysam/libcalignmentfile.pxd -> build/lib.linux-x86_64-3.4/pysam
copying pysam/libcutils.pxd -> build/lib.linux-x86_64-3.4/pysam
copying pysam/libcsamfile.pxd -> 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/cbcftools_util.h -> build/lib.linux-x86_64-3.4/pysam
copying pysam/csamtools_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/htslib_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/samtools
copying samtools/bam2bcf.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/config.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/sample.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/samtools.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/sam_opts.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/bam_lpileup.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/stats_isize.h -> build/lib.linux-x86_64-3.4/pysam/include/samtools
creating 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/call.h -> build/lib.linux-x86_64-3.4/pysam/include/bcftools
copying bcftools/bam2bcf.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/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/kmin.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/mw.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/filter.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
copying bcftools/gvcf.h -> build/lib.linux-x86_64-3.4/pysam/include/bcftools
copying bcftools/hclust.h -> build/lib.linux-x86_64-3.4/pysam/include/bcftools
copying bcftools/bam_sample.h -> build/lib.linux-x86_64-3.4/pysam/include/bcftools
copying bcftools/regidx.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/bcftools.h -> build/lib.linux-x86_64-3.4/pysam/include/bcftools
copying bcftools/kheap.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/bin.h -> build/lib.linux-x86_64-3.4/pysam/include/bcftools
copying bcftools/smpl_ilist.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/zconf.h -> 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
creating 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/bcf_sr_sort.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
copying htslib/hts_internal.h -> build/lib.linux-x86_64-3.4/pysam/include/htslib
copying htslib/thread_pool_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
creating 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/kstring.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/bgzf.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/tbx.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/hfile.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/hts_defs.h -> build/lib.linux-x86_64-3.4/pysam/include/htslib/htslib
copying htslib/htslib/thread_pool.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/vcf.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/hts_endian.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/kbitset.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/sam.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
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/cram.h -> build/lib.linux-x86_64-3.4/pysam/include/htslib/htslib
Fixing build/lib.linux-x86_64-3.4/pysam/config.py build/lib.linux-x86_64-3.4/pysam/bcftools.py build/lib.linux-x86_64-3.4/pysam/utils.py build/lib.linux-x86_64-3.4/pysam/init.py build/lib.linux-x86_64-3.4/pysam/version.py build/lib.linux-x86_64-3.4/pysam/Pileup.py build/lib.linux-x86_64-3.4/pysam/samtools.py build/lib.linux-x86_64-3.4/pysam/namedtuple.py build/lib.linux-x86_64-3.4/pysam/include/init.py
Skipping implicit fixer: buffer
Skipping implicit fixer: idioms
Skipping implicit fixer: set_literal
Skipping implicit fixer: ws_comma
Fixing build/lib.linux-x86_64-3.4/pysam/config.py build/lib.linux-x86_64-3.4/pysam/bcftools.py build/lib.linux-x86_64-3.4/pysam/utils.py build/lib.linux-x86_64-3.4/pysam/init.py build/lib.linux-x86_64-3.4/pysam/version.py build/lib.linux-x86_64-3.4/pysam/Pileup.py build/lib.linux-x86_64-3.4/pysam/samtools.py build/lib.linux-x86_64-3.4/pysam/namedtuple.py build/lib.linux-x86_64-3.4/pysam/include/init.py
Skipping implicit fixer: buffer
Skipping implicit fixer: idioms
Skipping implicit fixer: set_literal
Skipping implicit fixer: ws_comma
running build_ext
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
x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -Ipysam -I. -Ihtslib -I/usr/include/python3.4m -I/home/gilles/LRSDAY_v20170710/build/py3_virtualenv_circlator/include/python3.4m -c pysam/libchtslib.c -o build/temp.linux-x86_64-3.4/pysam/libchtslib.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
pysam/libchtslib.c:4:20: fatal error: Python.h: No such file or directory
compilation terminated.
error: command 'x86_64-linux-gnu-gcc' failed with exit status 1