/bin/sh: ./configure: Permission denied
/bin/sh: ./configure: Permission denied
make: execvp: ./version.sh: Permission denied
make: execvp: ./version.sh: Permission denied
/bin/sh: ./hts_probe_cc.sh: No such file or directory
Makefile:137: htscodecs.mk: No such file or directory
make: *** [Makefile:123: htscodecs.mk] Error 127
pysam: htslib configure options: None
Traceback (most recent call last):
File "/data/duann2/deeplearning/conda/envs/propagate/lib/python3.6/site-packages/pip/_vendor/pep517/_in_process.py", line 257, in
main()
File "/data/duann2/deeplearning/conda/envs/propagate/lib/python3.6/site-packages/pip/_vendor/pep517/_in_process.py", line 240, in main
json_out['return_val'] = hook(hook_input['kwargs'])
File "/data/duann2/deeplearning/conda/envs/propagate/lib/python3.6/site-packages/pip/_vendor/pep517/_in_process.py", line 91, in get_requires_for_build_wheel
return hook(config_settings)
File "/tmp/pip-build-env-7um5tg6p/overlay/lib/python3.6/site-packages/setuptools/build_meta.py", line 163, in get_requires_for_build_wheel
config_settings, requirements=['wheel'])
File "/tmp/pip-build-env-7um5tg6p/overlay/lib/python3.6/site-packages/setuptools/build_meta.py", line 143, in _get_build_requires
self.run_setup()
File "/tmp/pip-build-env-7um5tg6p/overlay/lib/python3.6/site-packages/setuptools/build_meta.py", line 268, in run_setup
self).run_setup(setup_script=setup_script)
File "/tmp/pip-build-env-7um5tg6p/overlay/lib/python3.6/site-packages/setuptools/build_meta.py", line 158, in run_setup
exec(compile(code, file, 'exec'), locals())
File "setup.py", line 383, in
htslib_make_options = run_make_print_config()
File "setup.py", line 79, in run_make_print_config
stdout = subprocess.check_output(["make", "-s", "print-config"])
File "/data/duann2/deeplearning/conda/envs/propagate/lib/python3.6/subprocess.py", line 356, in check_output
kwargs).stdout
File "/data/duann2/deeplearning/conda/envs/propagate/lib/python3.6/subprocess.py", line 438, in run
output=stdout, stderr=stderr)
subprocess.CalledProcessError: Command '['make', '-s', 'print-config']' returned non-zero exit status 2.
ERROR: Command errored out with exit status 1: /data/duann2/deeplearning/conda/envs/propagate/bin/python /data/duann2/deeplearning/conda/envs/propagate/lib/python3.6/site-packages/pip/_vendor/pep517/_in_process.py get_requires_for_build_wheel /tmp/tmpjzu90rut Check the logs for full command output.
Hi,
I got this error at "pip install ." step. Could I have some instructions?
pysam 0.8.3 py36haf49e46_9 bioconda python 3.6.15 hb7a2778_0_cpython conda-forge numba 0.51.2 py36h7c3b610_0 conda-forge numpy 1.19.5 py36hfc0c790_2 conda-forge
The error message:
(propagate) [duann2@biowulf PropagAtE]$ pip install . Processing /gpfs/gsfs12/users/EmiolaLab/duann2/niki_proj/propagate/PropagAtE Requirement already satisfied: numpy>=1.17.0 in /vf/users/duann2/deeplearning/conda/envs/propagate/lib/python3.6/site-packages (from PropagAtE==1.1.0) (1.19.5) Collecting pysam>=0.15 Using cached pysam-0.21.0.tar.gz (4.1 MB) Installing build dependencies ... done Getting requirements to build wheel ... error ERROR: Command errored out with exit status 1: command: /data/duann2/deeplearning/conda/envs/propagate/bin/python /data/duann2/deeplearning/conda/envs/propagate/lib/python3.6/site-packages/pip/_vendor/pep517/_in_process.py get_requires_for_build_wheel /tmp/tmpjzu90rut cwd: /tmp/pip-install-m_bg0m_h/pysam Complete output (38 lines):
pysam: cython is available - using cythonize if necessary
pysam: htslib mode is shared
pysam: HTSLIB_CONFIGURE_OPTIONS=None
pysam: (sysconfig) CC=gcc -pthread -B /data/duann2/deeplearning/conda/envs/propagate/compiler_compat -Wl,--sysroot=/
pysam: (sysconfig) CFLAGS=-Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC
pysam: (sysconfig) LDFLAGS=-L/data/duann2/deeplearning/conda/envs/propagate/lib -Wl,-rpath=/data/duann2/deeplearning/conda/envs/propagate/lib -Wl,--no-as-needed -Wl,--sysroot=/
/bin/sh: ./configure: Permission denied /bin/sh: ./configure: Permission denied make: execvp: ./version.sh: Permission denied make: execvp: ./version.sh: Permission denied /bin/sh: ./hts_probe_cc.sh: No such file or directory Makefile:137: htscodecs.mk: No such file or directory make: *** [Makefile:123: htscodecs.mk] Error 127
pysam: htslib configure options: None
Traceback (most recent call last): File "/data/duann2/deeplearning/conda/envs/propagate/lib/python3.6/site-packages/pip/_vendor/pep517/_in_process.py", line 257, in
main()
File "/data/duann2/deeplearning/conda/envs/propagate/lib/python3.6/site-packages/pip/_vendor/pep517/_in_process.py", line 240, in main
json_out['return_val'] = hook(hook_input['kwargs'])
File "/data/duann2/deeplearning/conda/envs/propagate/lib/python3.6/site-packages/pip/_vendor/pep517/_in_process.py", line 91, in get_requires_for_build_wheel
return hook(config_settings)
File "/tmp/pip-build-env-7um5tg6p/overlay/lib/python3.6/site-packages/setuptools/build_meta.py", line 163, in get_requires_for_build_wheel
config_settings, requirements=['wheel'])
File "/tmp/pip-build-env-7um5tg6p/overlay/lib/python3.6/site-packages/setuptools/build_meta.py", line 143, in _get_build_requires
self.run_setup()
File "/tmp/pip-build-env-7um5tg6p/overlay/lib/python3.6/site-packages/setuptools/build_meta.py", line 268, in run_setup
self).run_setup(setup_script=setup_script)
File "/tmp/pip-build-env-7um5tg6p/overlay/lib/python3.6/site-packages/setuptools/build_meta.py", line 158, in run_setup
exec(compile(code, file, 'exec'), locals())
File "setup.py", line 383, in
htslib_make_options = run_make_print_config()
File "setup.py", line 79, in run_make_print_config
stdout = subprocess.check_output(["make", "-s", "print-config"])
File "/data/duann2/deeplearning/conda/envs/propagate/lib/python3.6/subprocess.py", line 356, in check_output
kwargs).stdout
File "/data/duann2/deeplearning/conda/envs/propagate/lib/python3.6/subprocess.py", line 438, in run
output=stdout, stderr=stderr)
subprocess.CalledProcessError: Command '['make', '-s', 'print-config']' returned non-zero exit status 2.
ERROR: Command errored out with exit status 1: /data/duann2/deeplearning/conda/envs/propagate/bin/python /data/duann2/deeplearning/conda/envs/propagate/lib/python3.6/site-packages/pip/_vendor/pep517/_in_process.py get_requires_for_build_wheel /tmp/tmpjzu90rut Check the logs for full command output.
Thanks!
Ning