Après avoir reproduit le problème sur une autre session.
Il s'avère que c'est juste le fait de upgrade pip qui fait bugger.
J'ai utiliser la commande: 'pip install --upgrade pip --user'
quand je rappel pip pour installer un package:
$pip install biopython --user
Traceback (most recent call last):
File "/usr/bin/pip", line 10, in <module>
sys.exit(main())
TypeError: 'module' object is not callable
En appelant sur .local/bin, pip ne marche pas, le message d'erreur en fin.
Si c'est long à réparer, est-ce possible de simplement réinitialiser les sessions aye@core.cluster.france-bioinformatique.fr et gbohl@core.cluster.france-bioinformatique.fr ?
Comme j'ai télécharger les fichiers en local.
Ensuite, comment upgrade pip correctement ? Afin d'installer les packages:
-numpy
-biopython
-psutil
-ray
et d'autres à l'avenir
Le message d'erreur tronqué lorsque je lance pip depuis ~/.local/bin (j’ai surtout enlever les nombreux message copying/creating indiqué par [...]):
[gbohl@clust-slurm-client ~]$ .local/bin/pip install biopython --user
DEPRECATION: Python 2.7 will reach the end of its life on January 1st, 2020. Please upgrade your Python as Python 2.7 won't be maintained after that date. A future version of pip will drop support for Python 2.7. More details about Python 2 support in pip, can be found at https://pip.pypa.io/en/latest/development/release-process/#python-2-support
Collecting biopython
Using cached https://files.pythonhosted.org/packages/33/55/becf2b99556588d22b542f3412990bfc79b674e198d9bc58f7bbc333439e/biopython-1.75.tar.gz
Requirement already satisfied: numpy in ./.local/lib/python2.7/site-packages (from biopython) (1.16.5)
Building wheels for collected packages: biopython
Building wheel for biopython (setup.py) ... error
ERROR: Command errored out with exit status 1:
command: /bin/python -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-install-7l6oDq/biopython/setup.py'"'"'; __file__='"'"'/tmp/pip-install-7l6oDq/biopython/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-3i8Ud2 --python-tag cp27
cwd: /tmp/pip-install-7l6oDq/biopython/
Complete output (721 lines):
==================================================================
WARNING: Biopython will drop support for Python 2.7 in early 2020.
==================================================================
running bdist_wheel
running build
running build_py
creating build
creating build/lib.linux-x86_64-2.7
creating build/lib.linux-x86_64-2.7/Bio
copying Bio/File.py -> build/lib.linux-x86_64-2.7/Bio
copying Bio/Index.py -> build/lib.linux-x86_64-2.7/Bio
[…]
copying Bio/KDTree/Neighbor.h -> build/lib.linux-x86_64-2.7/Bio/KDTree
running build_ext
building 'Bio.Align._aligners' extension
creating build/temp.linux-x86_64-2.7
creating build/temp.linux-x86_64-2.7/Bio
creating build/temp.linux-x86_64-2.7/Bio/Align
gcc -pthread -fno-strict-aliasing -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -D_GNU_SOURCE -fPIC -fwrapv -DNDEBUG -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -D_GNU_SOURCE -fPIC -fwrapv -fPIC -I/usr/include/python2.7 -c Bio/Align/_aligners.c -o build/temp.linux-x86_64-2.7/Bio/Align/_aligners.o
Bio/Align/_aligners.c:11:20: fatal error: Python.h: No such file or directory
#include "Python.h"
^
compilation terminated.
error: command 'gcc' failed with exit status 1
----------------------------------------
ERROR: Failed building wheel for biopython
Running setup.py clean for biopython
Failed to build biopython
Installing collected packages: biopython
Running setup.py install for biopython ... error
ERROR: Command errored out with exit status 1:
command: /bin/python -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-install-7l6oDq/biopython/setup.py'"'"'; __file__='"'"'/tmp/pip-install-7l6oDq/biopython/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-record-ss_I2f/install-record.txt --single-version-externally-managed --compile --user --prefix=
cwd: /tmp/pip-install-7l6oDq/biopython/
Complete output (721 lines):
==================================================================
WARNING: Biopython will drop support for Python 2.7 in early 2020.
==================================================================
running install
running build
running build_py
creating build
creating build/lib.linux-x86_64-2.7
creating build/lib.linux-x86_64-2.7/Bio
copying Bio/File.py -> build/lib.linux-x86_64-2.7/Bio
[…]
copying Bio/motifs/applications/__init__.py -> build/lib.linux-x86_64-2.7/Bio/motifs/applications
copying Bio/motifs/applications/_xxmotif.py -> build/lib.linux-x86_64-2.7/Bio/motifs/applications
creating build/lib.linux-x86_64-2.7/Bio/motifs/jaspar
copying Bio/motifs/jaspar/__init__.py -> build/lib.linux-x86_64-2.7/Bio/motifs/jaspar
running egg_info
writing requirements to biopython.egg-info/requires.txt
writing biopython.egg-info/PKG-INFO
writing top-level names to biopython.egg-info/top_level.txt
writing dependency_links to biopython.egg-info/dependency_links.txt
reading manifest file 'biopython.egg-info/SOURCES.txt'
reading manifest template 'MANIFEST.in'
warning: no previously-included files found matching 'Tests/Gck/DGVC_GCK.zip'
warning: no previously-included files matching '*.pyc' found anywhere in distribution
warning: no previously-included files matching '*.pyo' found anywhere in distribution
warning: no previously-included files matching '*.py{}' found anywhere in distribution
warning: no previously-included files matching '*.py-e' found anywhere in distribution
warning: no previously-included files found matching 'Bio/Align/substitution_matrices/data/README.txt'
writing manifest file 'biopython.egg-info/SOURCES.txt'
copying Bio/cpairwise2module.c -> build/lib.linux-x86_64-2.7/Bio
copying Bio/trie.c -> build/lib.linux-x86_64-2.7/Bio
copying Bio/trie.h -> build/lib.linux-x86_64-2.7/Bio
copying Bio/triemodule.c -> build/lib.linux-x86_64-2.7/Bio
copying Bio/Align/_aligners.c -> build/lib.linux-x86_64-2.7/Bio/Align
creating build/lib.linux-x86_64-2.7/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/Docsum_3_0.dtd -> build/lib.linux-x86_64-2.7/Bio/Entrez/DTDs
[…]
copying Bio/KDTree/Neighbor.h -> build/lib.linux-x86_64-2.7/Bio/KDTree
running build_ext
building 'Bio.Align._aligners' extension
creating build/temp.linux-x86_64-2.7
creating build/temp.linux-x86_64-2.7/Bio
creating build/temp.linux-x86_64-2.7/Bio/Align
gcc -pthread -fno-strict-aliasing -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -D_GNU_SOURCE -fPIC -fwrapv -DNDEBUG -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -D_GNU_SOURCE -fPIC -fwrapv -fPIC -I/usr/include/python2.7 -c Bio/Align/_aligners.c -o build/temp.linux-x86_64-2.7/Bio/Align/_aligners.o
Bio/Align/_aligners.c:11:20: fatal error: Python.h: No such file or directory
#include "Python.h"
^
compilation terminated.
error: command 'gcc' failed with exit status 1
----------------------------------------
ERROR: Command errored out with exit status 1: /bin/python -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-install-7l6oDq/biopython/setup.py'"'"'; __file__='"'"'/tmp/pip-install-7l6oDq/biopython/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-record-ss_I2f/install-record.txt --single-version-externally-managed --compile --user --prefix= Check the logs for full command output.
[gbohl@clust-slurm-client ~]$