I got a little further, but not much.
Here’s a whole new, giant error (can only paste part becaues it’s so big):
Building wheel for numpy (setup.py) ... error
ERROR: Command errored out with exit status 1:
command: /home/jyaron/galaxy/.venv/bin/python3 -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-install-ro11f7y5/numpy/setup.py'"'"'; __file__='"'"'/tmp/pip-install-ro11f7y5/numpy/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/pip-wheel-uc_uxcql
cwd: /tmp/pip-install-ro11f7y5/numpy/
Complete output (374 lines):
Running from numpy source directory.
/tmp/pip-install-ro11f7y5/numpy/numpy/distutils/misc_util.py:476: SyntaxWarning: "is" with a literal. Did you mean "=="?
return is_string(s) and ('*' in s or '?' is s)
blas_opt_info:
blas_mkl_info:
customize UnixCCompiler
libraries mkl_rt not found in ['/home/jyaron/galaxy/.venv/lib', '/usr/local/lib', '/usr/lib64', '/usr/lib', '/usr/lib/x86_64-linux-gnu']
NOT AVAILABLE
blis_info:
customize UnixCCompiler
libraries blis not found in ['/home/jyaron/galaxy/.venv/lib', '/usr/local/lib', '/usr/lib64', '/usr/lib', '/usr/lib/x86_64-linux-gnu']
NOT AVAILABLE
openblas_info:
customize UnixCCompiler
customize UnixCCompiler
libraries openblas not found in ['/home/jyaron/galaxy/.venv/lib', '/usr/local/lib', '/usr/lib64', '/usr/lib', '/usr/lib/x86_64-linux-gnu']
NOT AVAILABLE
atlas_3_10_blas_threads_info:
Setting PTATLAS=ATLAS
customize UnixCCompiler
libraries tatlas not found in ['/home/jyaron/galaxy/.venv/lib', '/usr/local/lib', '/usr/lib64', '/usr/lib', '/usr/lib/x86_64-linux-gnu']
NOT AVAILABLE
atlas_3_10_blas_info:
customize UnixCCompiler
libraries satlas not found in ['/home/jyaron/galaxy/.venv/lib', '/usr/local/lib', '/usr/lib64', '/usr/lib', '/usr/lib/x86_64-linux-gnu']
NOT AVAILABLE
atlas_blas_threads_info:
Setting PTATLAS=ATLAS
customize UnixCCompiler
libraries ptf77blas,ptcblas,atlas not found in ['/home/jyaron/galaxy/.venv/lib', '/usr/local/lib', '/usr/lib64', '/usr/lib', '/usr/lib/x86_64-linux-gnu']
NOT AVAILABLE
atlas_blas_info:
customize UnixCCompiler
libraries f77blas,cblas,atlas not found in ['/home/jyaron/galaxy/.venv/lib', '/usr/local/lib', '/usr/lib64', '/usr/lib', '/usr/lib/x86_64-linux-gnu']
NOT AVAILABLE
accelerate_info:
NOT AVAILABLE
/tmp/pip-install-ro11f7y5/numpy/numpy/distutils/system_info.py:639: UserWarning:
Atlas (http://math-atlas.sourceforge.net/) libraries not found.
Directories to search for the libraries can be specified in the
numpy/distutils/site.cfg file (section [atlas]) or by setting
the ATLAS environment variable.
self.calc_info()
blas_info:
customize UnixCCompiler
libraries blas not found in ['/home/jyaron/galaxy/.venv/lib', '/usr/local/lib', '/usr/lib64', '/usr/lib', '/usr/lib/x86_64-linux-gnu']
NOT AVAILABLE
/tmp/pip-install-ro11f7y5/numpy/numpy/distutils/system_info.py:639: UserWarning:
Blas (http://www.netlib.org/blas/) libraries not found.
Directories to search for the libraries can be specified in the
numpy/distutils/site.cfg file (section [blas]) or by setting
the BLAS environment variable.
self.calc_info()
blas_src_info:
NOT AVAILABLE
/tmp/pip-install-ro11f7y5/numpy/numpy/distutils/system_info.py:639: UserWarning:
Blas (http://www.netlib.org/blas/) sources not found.
Directories to search for the sources can be specified in the
numpy/distutils/site.cfg file (section [blas_src]) or by setting
the BLAS_SRC environment variable.
self.calc_info()
NOT AVAILABLE
/bin/sh: 1: svnversion: not found
non-existing path in 'numpy/distutils': 'site.cfg'
lapack_opt_info:
lapack_mkl_info:
customize UnixCCompiler
libraries mkl_rt not found in ['/home/jyaron/galaxy/.venv/lib', '/usr/local/lib', '/usr/lib64', '/usr/lib', '/usr/lib/x86_64-linux-gnu']
NOT AVAILABLE
openblas_lapack_info:
customize UnixCCompiler
customize UnixCCompiler
libraries openblas not found in ['/home/jyaron/galaxy/.venv/lib', '/usr/local/lib', '/usr/lib64', '/usr/lib', '/usr/lib/x86_64-linux-gnu']
NOT AVAILABLE
openblas_clapack_info:
customize UnixCCompiler
customize UnixCCompiler
libraries openblas,lapack not found in ['/home/jyaron/galaxy/.venv/lib', '/usr/local/lib', '/usr/lib64', '/usr/lib', '/usr/lib/x86_64-linux-gnu']
NOT AVAILABLE
atlas_3_10_threads_info:
Setting PTATLAS=ATLAS
customize UnixCCompiler
libraries lapack_atlas not found in /home/jyaron/galaxy/.venv/lib
customize UnixCCompiler
libraries tatlas,tatlas not found in /home/jyaron/galaxy/.venv/lib
customize UnixCCompiler
libraries lapack_atlas not found in /usr/local/lib
customize UnixCCompiler
libraries tatlas,tatlas not found in /usr/local/lib
customize UnixCCompiler
libraries lapack_atlas not found in /usr/lib64
customize UnixCCompiler
libraries tatlas,tatlas not found in /usr/lib64
customize UnixCCompiler
libraries lapack_atlas not found in /usr/lib
customize UnixCCompiler
libraries tatlas,tatlas not found in /usr/lib
customize UnixCCompiler
libraries lapack_atlas not found in /usr/lib/x86_64-linux-gnu
customize UnixCCompiler
libraries tatlas,tatlas not found in /usr/lib/x86_64-linux-gnu
<class 'numpy.distutils.system_info.atlas_3_10_threads_info'>
NOT AVAILABLE
atlas_3_10_info:
customize UnixCCompiler
libraries lapack_atlas not found in /home/jyaron/galaxy/.venv/lib
customize UnixCCompiler
libraries satlas,satlas not found in /home/jyaron/galaxy/.venv/lib
customize UnixCCompiler
libraries lapack_atlas not found in /usr/local/lib
customize UnixCCompiler
libraries satlas,satlas not found in /usr/local/lib
customize UnixCCompiler
libraries lapack_atlas not found in /usr/lib64
customize UnixCCompiler
libraries satlas,satlas not found in /usr/lib64
customize UnixCCompiler
libraries lapack_atlas not found in /usr/lib
customize UnixCCompiler
libraries satlas,satlas not found in /usr/lib
customize UnixCCompiler
libraries lapack_atlas not found in /usr/lib/x86_64-linux-gnu
customize UnixCCompiler
libraries satlas,satlas not found in /usr/lib/x86_64-linux-gnu
<class 'numpy.distutils.system_info.atlas_3_10_info'>
NOT AVAILABLE
atlas_threads_info:
Setting PTATLAS=ATLAS
customize UnixCCompiler
libraries lapack_atlas not found in /home/jyaron/galaxy/.venv/lib
customize UnixCCompiler
libraries ptf77blas,ptcblas,atlas not found in /home/jyaron/galaxy/.venv/lib
customize UnixCCompiler
libraries lapack_atlas not found in /usr/local/lib
customize UnixCCompiler
libraries ptf77blas,ptcblas,atlas not found in /usr/local/lib
customize UnixCCompiler
libraries lapack_atlas not found in /usr/lib64
customize UnixCCompiler
libraries ptf77blas,ptcblas,atlas not found in /usr/lib64
customize UnixCCompiler
libraries lapack_atlas not found in /usr/lib
customize UnixCCompiler
libraries ptf77blas,ptcblas,atlas not found in /usr/lib
customize UnixCCompiler
libraries lapack_atlas not found in /usr/lib/x86_64-linux-gnu
customize UnixCCompiler
libraries ptf77blas,ptcblas,atlas not found in /usr/lib/x86_64-linux-gnu
<class 'numpy.distutils.system_info.atlas_threads_info'>
NOT AVAILABLE
atlas_info:
customize UnixCCompiler
libraries lapack_atlas not found in /home/jyaron/galaxy/.venv/lib
customize UnixCCompiler
libraries f77blas,cblas,atlas not found in /home/jyaron/galaxy/.venv/lib
customize UnixCCompiler
libraries lapack_atlas not found in /usr/local/lib
customize UnixCCompiler
libraries f77blas,cblas,atlas not found in /usr/local/lib
customize UnixCCompiler
libraries lapack_atlas not found in /usr/lib64
customize UnixCCompiler
libraries f77blas,cblas,atlas not found in /usr/lib64
customize UnixCCompiler
libraries lapack_atlas not found in /usr/lib
customize UnixCCompiler
libraries f77blas,cblas,atlas not found in /usr/lib
customize UnixCCompiler
libraries lapack_atlas not found in /usr/lib/x86_64-linux-gnu
customize UnixCCompiler
libraries f77blas,cblas,atlas not found in /usr/lib/x86_64-linux-gnu
<class 'numpy.distutils.system_info.atlas_info'>
NOT AVAILABLE
lapack_info:
customize UnixCCompiler
libraries lapack not found in ['/home/jyaron/galaxy/.venv/lib', '/usr/local/lib', '/usr/lib64', '/usr/lib', '/usr/lib/x86_64-linux-gnu']
NOT AVAILABLE
/tmp/pip-install-ro11f7y5/numpy/numpy/distutils/system_info.py:639: UserWarning:
Lapack (http://www.netlib.org/lapack/) libraries not found.
Directories to search for the libraries can be specified in the
numpy/distutils/site.cfg file (section [lapack]) or by setting
the LAPACK environment variable.
self.calc_info()
lapack_src_info:
NOT AVAILABLE
/tmp/pip-install-ro11f7y5/numpy/numpy/distutils/system_info.py:639: UserWarning:
Lapack (http://www.netlib.org/lapack/) sources not found.
Directories to search for the sources can be specified in the
numpy/distutils/site.cfg file (section [lapack_src]) or by setting
the LAPACK_SRC environment variable.
self.calc_info()
NOT AVAILABLE
/usr/lib/python3.8/distutils/dist.py:274: UserWarning: Unknown distribution option: 'define_macros'
warnings.warn(msg)
running bdist_wheel
running build
running config_cc
unifing config_cc, config, build_clib, build_ext, build commands --compiler options
running config_fc
unifing config_fc, config, build_clib, build_ext, build commands --fcompiler options
running build_src
build_src
building py_modules sources
creating build
creating build/src.linux-x86_64-3.8
creating build/src.linux-x86_64-3.8/numpy
creating build/src.linux-x86_64-3.8/numpy/distutils
building library "npymath" sources
get_default_fcompiler: matching types: '['gnu95', 'intel', 'lahey', 'pg', 'absoft', 'nag', 'vast', 'compaq', 'intele', 'intelem', 'gnu', 'g95', 'pathf95', 'nagfor']'
customize Gnu95FCompiler
Could not locate executable gfortran
Could not locate executable f95
customize IntelFCompiler
Could not locate executable ifort
Could not locate executable ifc
customize LaheyFCompiler
Could not locate executable lf95
customize PGroupFCompiler
Could not locate executable pgfortran
customize AbsoftFCompiler
Could not locate executable f90
Could not locate executable f77
customize NAGFCompiler
customize VastFCompiler
customize CompaqFCompiler
Could not locate executable fort
customize IntelItaniumFCompiler
Could not locate executable efort
Could not locate executable efc
customize IntelEM64TFCompiler
customize GnuFCompiler
Could not locate executable g77
customize G95FCompiler
Could not locate executable g95
customize PathScaleFCompiler
Could not locate executable pathf95
customize NAGFORCompiler
Could not locate executable nagfor
don't know how to compile Fortran code on platform 'posix'
C compiler: x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC
compile options: '-Inumpy/core/src/common -Inumpy/core/src -Inumpy/core -Inumpy/core/src/npymath -Inumpy/core/src/multiarray -Inumpy/core/src/umath -Inumpy/core/src/npysort -I/usr/include/python3.8 -I/home/jyaron/galaxy/.venv/include/python3.8 -c'
x86_64-linux-gnu-gcc: _configtest.c
x86_64-linux-gnu-gcc -pthread _configtest.o -o _configtest
success!
removing: _configtest.c _configtest.o _configtest.o.d _configtest
C compiler: x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC
compile options: '-Inumpy/core/src/common -Inumpy/core/src -Inumpy/core -Inumpy/core/src/npymath -Inumpy/core/src/multiarray -Inumpy/core/src/umath -Inumpy/core/src/npysort -I/usr/include/python3.8 -I/home/jyaron/galaxy/.venv/include/python3.8 -c'
x86_64-linux-gnu-gcc: _configtest.c
_configtest.c:1:5: warning: conflicting types for built-in function ‘exp’; expected ‘double(double)’ [-Wbuiltin-declaration-mismatch]
1 | int exp (void);
| ^~~
_configtest.c:1:1: note: ‘exp’ is declared in header ‘<math.h>’
+++ |+#include <math.h>
1 | int exp (void);
x86_64-linux-gnu-gcc -pthread _configtest.o -o _configtest
/usr/bin/ld: _configtest.o: in function `main':
/tmp/pip-install-ro11f7y5/numpy/_configtest.c:6: undefined reference to `exp'
collect2: error: ld returned 1 exit status
failure.
removing: _configtest.c _configtest.o _configtest.o.d
C compiler: x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC
compile options: '-Inumpy/core/src/common -Inumpy/core/src -Inumpy/core -Inumpy/core/src/npymath -Inumpy/core/src/multiarray -Inumpy/core/src/umath -Inumpy/core/src/npysort -I/usr/include/python3.8 -I/home/jyaron/galaxy/.venv/include/python3.8 -c'
x86_64-linux-gnu-gcc: _configtest.c
_configtest.c:1:5: warning: conflicting types for built-in function ‘exp’; expected ‘double(double)’ [-Wbuiltin-declaration-mismatch]
1 | int exp (void);
| ^~~
_configtest.c:1:1: note: ‘exp’ is declared in header ‘<math.h>’
+++ |+#include <math.h>
1 | int exp (void);
x86_64-linux-gnu-gcc -pthread _configtest.o -lm -o _configtest
success!
removing: _configtest.c _configtest.o _configtest.o.d _configtest
creating build/src.linux-x86_64-3.8/numpy/core
creating build/src.linux-x86_64-3.8/numpy/core/src
creating build/src.linux-x86_64-3.8/numpy/core/src/npymath
conv_template:> build/src.linux-x86_64-3.8/numpy/core/src/npymath/npy_math_internal.h
adding 'build/src.linux-x86_64-3.8/numpy/core/src/npymath' to include_dirs.
conv_template:> build/src.linux-x86_64-3.8/numpy/core/src/npymath/ieee754.c
conv_template:> build/src.linux-x86_64-3.8/numpy/core/src/npymath/npy_math_complex.c
None - nothing done with h_files = ['build/src.linux-x86_64-3.8/numpy/core/src/npymath/npy_math_internal.h']
building library "npysort" sources
creating build/src.linux-x86_64-3.8/numpy/core/src/common
conv_template:> build/src.linux-x86_64-3.8/numpy/core/src/common/npy_sort.h
adding 'build/src.linux-x86_64-3.8/numpy/core/src/common' to include_dirs.
creating build/src.linux-x86_64-3.8/numpy/core/src/npysort
conv_template:> build/src.linux-x86_64-3.8/numpy/core/src/npysort/quicksort.c
conv_template:> build/src.linux-x86_64-3.8/numpy/core/src/npysort/mergesort.c
conv_template:> build/src.linux-x86_64-3.8/numpy/core/src/npysort/heapsort.c
conv_template:> build/src.linux-x86_64-3.8/numpy/core/src/common/npy_partition.h
conv_template:> build/src.linux-x86_64-3.8/numpy/core/src/npysort/selection.c
conv_template:> build/src.linux-x86_64-3.8/numpy/core/src/common/npy_binsearch.h
conv_template:> build/src.linux-x86_64-3.8/numpy/core/src/npysort/binsearch.c
None - nothing done with h_files = ['build/src.linux-x86_64-3.8/numpy/core/src/common/npy_sort.h', 'build/src.linux-x86_64-3.8/numpy/core/src/common/npy_partition.h', 'build/src.linux-x86_64-3.8/numpy/core/src/common/npy_binsearch.h']
building extension "numpy.core._dummy" sources
Generating build/src.linux-x86_64-3.8/numpy/core/include/numpy/config.h
C compiler: x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC
compile options: '-Inumpy/core/src/common -Inumpy/core/src -Inumpy/core -Inumpy/core/src/npymath -Inumpy/core/src/multiarray -Inumpy/core/src/umath -Inumpy/core/src/npysort -I/usr/include/python3.8 -I/home/jyaron/galaxy/.venv/include/python3.8 -c'
x86_64-linux-gnu-gcc: _configtest.c
_configtest.c:1:10: fatal error: Python.h: No such file or directory
1 | #include <Python.h>
| ^~~~~~~~~~
compilation terminated.
failure.
removing: _configtest.c _configtest.o
Traceback (most recent call last):
File "<string>", line 1, in <module>
File "/tmp/pip-install-ro11f7y5/numpy/setup.py", line 419, in <module>
setup_package()
File "/tmp/pip-install-ro11f7y5/numpy/setup.py", line 411, in setup_package
setup(**metadata)
File "/tmp/pip-install-ro11f7y5/numpy/numpy/distutils/core.py", line 171, in setup
return old_setup(**new_attr)
File "/home/jyaron/galaxy/.venv/lib/python3.8/site-packages/setuptools/__init__.py", line 144, in setup
return distutils.core.setup(**attrs)
File "/usr/lib/python3.8/distutils/core.py", line 148, in setup
dist.run_commands()
File "/usr/lib/python3.8/distutils/dist.py", line 966, in run_commands
self.run_command(cmd)
File "/usr/lib/python3.8/distutils/dist.py", line 985, in run_command
cmd_obj.run()
File "/home/jyaron/galaxy/.venv/lib/python3.8/site-packages/wheel/bdist_wheel.py", line 223, in run
self.run_command('build')
File "/usr/lib/python3.8/distutils/cmd.py", line 313, in run_command
self.distribution.run_command(command)
File "/usr/lib/python3.8/distutils/dist.py", line 985, in run_command
cmd_obj.run()
File "/tmp/pip-install-ro11f7y5/numpy/numpy/distutils/command/build.py", line 47, in run
old_build.run(self)
File "/usr/lib/python3.8/distutils/command/build.py", line 135, in run
self.run_command(cmd_name)
File "/usr/lib/python3.8/distutils/cmd.py", line 313, in run_command
self.distribution.run_command(command)
File "/usr/lib/python3.8/distutils/dist.py", line 985, in run_command
cmd_obj.run()
File "/tmp/pip-install-ro11f7y5/numpy/numpy/distutils/command/build_src.py", line 148, in run
self.build_sources()
File "/tmp/pip-install-ro11f7y5/numpy/numpy/distutils/command/build_src.py", line 165, in build_sources
self.build_extension_sources(ext)
File "/tmp/pip-install-ro11f7y5/numpy/numpy/distutils/command/build_src.py", line 322, in build_extension_sources
sources = self.generate_sources(sources, ext)
File "/tmp/pip-install-ro11f7y5/numpy/numpy/distutils/command/build_src.py", line 375, in generate_sources
source = func(extension, build_dir)
File "numpy/core/setup.py", line 423, in generate_config_h
moredefs, ignored = cocache.check_types(config_cmd, ext, build_dir)
File "numpy/core/setup.py", line 47, in check_types
out = check_types(*a, **kw)
File "numpy/core/setup.py", line 279, in check_types
raise SystemError(
SystemError: Cannot compile 'Python.h'. Perhaps you need to install python-dev|python-devel.
----------------------------------------
ERROR: Failed building wheel for numpy
Running setup.py clean for numpy
ERROR: Command errored out with exit status 1:
command: /home/jyaron/galaxy/.venv/bin/python3 -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-install-ro11f7y5/numpy/setup.py'"'"'; __file__='"'"'/tmp/pip-install-ro11f7y5/numpy/setup.py'"'"';f=getattr(tokenize, '"'"'open'"'"', open)(__file__);code=f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' clean --all
cwd: /tmp/pip-install-ro11f7y5/numpy
Complete output (10 lines):
Running from numpy source directory.
`setup.py clean` is not supported, use one of the following instead:
- `git clean -xdf` (cleans all files)
- `git clean -Xdf` (cleans all versioned files, doesn't touch
files that aren't checked into the git repo)
Add `--force` to your command to use it anyway if you must (unsupported).
----------------------------------------
ERROR: Failed cleaning build dir for numpy
Building wheel for pysam (setup.py) ... error
ERROR: Command errored out with exit status 1:
command: /home/jyaron/galaxy/.venv/bin/python3 -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-install-ro11f7y5/pysam/setup.py'"'"'; __file__='"'"'/tmp/pip-install-ro11f7y5/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/pip-wheel-emyzxxpx
cwd: /tmp/pip-install-ro11f7y5/pysam/
Complete output (215 lines):
# pysam: no cython available - using pre-compiled C
# pysam: htslib mode is shared
# pysam: HTSLIB_CONFIGURE_OPTIONS=None
checking for gcc... gcc
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
checking for suffix of executables...
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether gcc accepts -g... yes
checking for gcc option to accept ISO C89... none needed
checking for ranlib... ranlib
checking for grep that handles long lines and -e... /usr/bin/grep
checking for C compiler warning flags... -Wall
checking for special C compiler options needed for large files... no
checking for _FILE_OFFSET_BITS value needed for large files... no
checking for _LARGEFILE_SOURCE value needed for large files... no
checking shared library type for unknown-Linux... plain .so
checking how to run the C preprocessor... gcc -E
checking for egrep... /usr/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... no
checking for libdeflate_deflate_compress in -ldeflate... no
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
make: ./version.sh: Command not found
# pysam: htslib_config LDFLAGS=
# pysam: htslib_config LIBHTS_OBJS=kfunc.o knetfile.o kstring.o bcf_sr_sort.o bgzf.o errmod.o faidx.o hfile.o hfile_net.o hts.o hts_os.o md5.o multipart.o probaln.o realn.o regidx.o sam.o synced_bcf_reader.o vcf_sweep.o tbx.o textutils.o thread_pool.o vcf.o vcfutils.o cram/cram_codecs.o cram/cram_decode.o cram/cram_encode.o cram/cram_external.o cram/cram_index.o cram/cram_io.o cram/cram_samtools.o cram/cram_stats.o cram/files.o cram/mFILE.o cram/open_trace_file.o cram/pooled_alloc.o cram/rANS_static.o cram/sam_header.o cram/string_alloc.o hfile_libcurl.o hfile_gcs.o hfile_s3.o
# pysam: htslib_config LIBS=-llzma -lbz2 -lz -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_64-3.8
creating build/lib.linux-x86_64-3.8/pysam
copying pysam/config.py -> build/lib.linux-x86_64-3.8/pysam
copying pysam/Pileup.py -> build/lib.linux-x86_64-3.8/pysam
copying pysam/samtools.py -> build/lib.linux-x86_64-3.8/pysam
copying pysam/bcftools.py -> build/lib.linux-x86_64-3.8/pysam
copying pysam/__init__.py -> build/lib.linux-x86_64-3.8/pysam
copying pysam/version.py -> build/lib.linux-x86_64-3.8/pysam
copying pysam/utils.py -> build/lib.linux-x86_64-3.8/pysam
creating build/lib.linux-x86_64-3.8/pysam/include
copying pysam/include/__init__.py -> build/lib.linux-x86_64-3.8/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/libcbcftools.pxd -> build/lib.linux-x86_64-3.8/pysam
copying pysam/libcvcf.pxd -> build/lib.linux-x86_64-3.8/pysam
copying pysam/libctabix.pxd -> build/lib.linux-x86_64-3.8/pysam
copying pysam/libctabixproxies.pxd -> build/lib.linux-x86_64-3.8/pysam
copying pysam/libcsamfile.pxd -> build/lib.linux-x86_64-3.8/pysam
copying pysam/libcsamtools.pxd -> build/lib.linux-x86_64-3.8/pysam
copying pysam/libcfaidx.pxd -> build/lib.linux-x86_64-3.8/pysam
copying pysam/libcalignedsegment.pxd -> build/lib.linux-x86_64-3.8/pysam
copying pysam/libcutils.pxd -> build/lib.linux-x86_64-3.8/pysam
copying pysam/libcalignmentfile.pxd -> build/lib.linux-x86_64-3.8/pysam
copying pysam/libchtslib.pxd -> build/lib.linux-x86_64-3.8/pysam
copying pysam/libcbcf.pxd -> build/lib.linux-x86_64-3.8/pysam
copying pysam/csamtools_util.h -> build/lib.linux-x86_64-3.8/pysam
copying pysam/cbcftools_util.h -> build/lib.linux-x86_64-3.8/pysam
copying pysam/htslib_util.h -> build/lib.linux-x86_64-3.8/pysam
copying pysam/pysam_util.h -> build/lib.linux-x86_64-3.8/pysam
copying pysam/pysam_stream.h -> build/lib.linux-x86_64-3.8/pysam
creating build/lib.linux-x86_64-3.8/pysam/include/samtools
copying samtools/sample.h -> build/lib.linux-x86_64-3.8/pysam/include/samtools
copying samtools/bam_lpileup.h -> build/lib.linux-x86_64-3.8/pysam/include/samtools
copying samtools/config.h -> build/lib.linux-x86_64-3.8/pysam/include/samtools
copying samtools/version.h -> build/lib.linux-x86_64-3.8/pysam/include/samtools
copying samtools/bam_endian.h -> build/lib.linux-x86_64-3.8/pysam/include/samtools
copying samtools/sam.h -> build/lib.linux-x86_64-3.8/pysam/include/samtools
copying samtools/stats_isize.h -> build/lib.linux-x86_64-3.8/pysam/include/samtools
copying samtools/bedidx.h -> build/lib.linux-x86_64-3.8/pysam/include/samtools
copying samtools/samtools.pysam.h -> build/lib.linux-x86_64-3.8/pysam/include/samtools
copying samtools/samtools.h -> build/lib.linux-x86_64-3.8/pysam/include/samtools
copying samtools/bam_plbuf.h -> build/lib.linux-x86_64-3.8/pysam/include/samtools
copying samtools/sam_opts.h -> build/lib.linux-x86_64-3.8/pysam/include/samtools
copying samtools/bam.h -> build/lib.linux-x86_64-3.8/pysam/include/samtools
copying samtools/tmp_file.h -> build/lib.linux-x86_64-3.8/pysam/include/samtools
copying samtools/bam2bcf.h -> build/lib.linux-x86_64-3.8/pysam/include/samtools
copying samtools/sam_header.h -> build/lib.linux-x86_64-3.8/pysam/include/samtools
creating build/lib.linux-x86_64-3.8/pysam/include/bcftools
copying bcftools/HMM.h -> build/lib.linux-x86_64-3.8/pysam/include/bcftools
copying bcftools/kmin.h -> build/lib.linux-x86_64-3.8/pysam/include/bcftools
copying bcftools/call.h -> build/lib.linux-x86_64-3.8/pysam/include/bcftools
copying bcftools/vcmp.h -> build/lib.linux-x86_64-3.8/pysam/include/bcftools
copying bcftools/config.h -> build/lib.linux-x86_64-3.8/pysam/include/bcftools
copying bcftools/version.h -> build/lib.linux-x86_64-3.8/pysam/include/bcftools
copying bcftools/rbuf.h -> build/lib.linux-x86_64-3.8/pysam/include/bcftools
copying bcftools/prob1.h -> build/lib.linux-x86_64-3.8/pysam/include/bcftools
copying bcftools/bcftools.h -> build/lib.linux-x86_64-3.8/pysam/include/bcftools
copying bcftools/mw.h -> build/lib.linux-x86_64-3.8/pysam/include/bcftools
copying bcftools/khash_str2str.h -> build/lib.linux-x86_64-3.8/pysam/include/bcftools
copying bcftools/bcftools.pysam.h -> build/lib.linux-x86_64-3.8/pysam/include/bcftools
copying bcftools/filter.h -> build/lib.linux-x86_64-3.8/pysam/include/bcftools