Install Cellprofiler 2.2.0 stable version on CentOS7 cluster


#1

I try to install CellProfiler 2.2.0 stable release version on CentOS7 cluster.

python/2.7.12, Cython, matplotlib/py27/1.5.3, numpy/py27/1.11.2, JDK/jdk.8_x64 and SciPy/py27/0.18.1 are loaded in my environment.

When i run pip install --editable . install failed with this output :

Obtaining file:///nfs/work/hcs_mri/CellProfiler
Complete output from command python setup.py egg_info:
no previously-included directories found matching '*.pyx’
warning: [options] bootstrap class path not set in conjunction with -source 1.6
1 warning
warning: [options] bootstrap class path not set in conjunction with -source 1.6
1 warning
warning: [options] bootstrap class path not set in conjunction with -source 1.6
Note: /tmp/easy_install-RYAp6f/javabridge-1.0.14/java/org/cellprofiler/javabridge/CPythonInvocationHandler.java uses unchecked or unsafe operations.
Note: Recompile with -Xlint:unchecked for details.
1 warning
In file included from /trinity/shared/apps/cv-standard/numpy/py27/1.11.2/lib/python2.7/site-packages/numpy/core/include/numpy/ndarraytypes.h:1777:0,
from /trinity/shared/apps/cv-standard/numpy/py27/1.11.2/lib/python2.7/site-packages/numpy/core/include/numpy/ndarrayobject.h:18,
from /trinity/shared/apps/cv-standard/numpy/py27/1.11.2/lib/python2.7/site-packages/numpy/core/include/numpy/arrayobject.h:4,
from _javabridge.c:242:
/trinity/shared/apps/cv-standard/numpy/py27/1.11.2/lib/python2.7/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:15:2: attention : #warning "Using deprecated NumPy API, disable it by " “#defining NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION” [-Wcpp]
#warning "Using deprecated NumPy API, disable it by "
^~~~~~~
In file included from _javabridge.c:245:0:
mac_javabridge_utils.h:47:1: attention : function declaration isn’t a prototype [-Wstrict-prototypes]
JNIEXPORT void MacStopVM();
^~~~~~~~~
mac_javabridge_utils.h:55:1: attention : function declaration isn’t a prototype [-Wstrict-prototypes]
JNIEXPORT void MacRunLoopInit();
^~~~~~~~~
mac_javabridge_utils.h:63:1: attention : function declaration isn’t a prototype [-Wstrict-prototypes]
JNIEXPORT void MacRunLoopRun();
^~~~~~~~~
mac_javabridge_utils.h:71:1: attention : function declaration isn’t a prototype [-Wstrict-prototypes]
JNIEXPORT void MacRunLoopReset();
^~~~~~~~~
mac_javabridge_utils.h:79:1: attention : function declaration isn’t a prototype [-Wstrict-prototypes]
JNIEXPORT void MacStopRunLoop();
^~~~~~~~~
mac_javabridge_utils.h:88:1: attention : function declaration isn’t a prototype [-Wstrict-prototypes]
JNIEXPORT int MacIsMainThread();
^~~~~~~~~
mac_javabridge_utils.h:103:1: attention : function declaration isn’t a prototype [-Wstrict-prototypes]
void MacRunLoopStop();
^~~~
_javabridge.c: Dans la fonction ‘pyx_pf_11_javabridge_9JB_Object_2__repr’:
_javabridge.c:4303:37: attention : transtypage d’un pointeur vers un entier de taille différente [-Wpointer-to-int-cast]
__pyx_t_1 = __Pyx_PyInt_From_int(((int)__pyx_v_self->o)); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 458; __pyx_clineno = LINE; goto __pyx_L1_error;}
^
_javabridge.c: Dans la fonction ‘__pyx_pf_11_javabridge_9JB_Object_6addr’:
_javabridge.c:4612:37: attention : transtypage d’un pointeur vers un entier de taille différente [-Wpointer-to-int-cast]
__pyx_t_1 = __Pyx_PyInt_From_int(((int)__pyx_v_self->o)); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 476; __pyx_clineno = LINE; goto __pyx_L1_error;}
^
_javabridge.c: Dans la fonction ‘pyx_pf_11_javabridge_8JB_Class_2__repr’:
_javabridge.c:4737:37: attention : transtypage d’un pointeur vers un entier de taille différente [-Wpointer-to-int-cast]
__pyx_t_1 = __Pyx_PyInt_From_int(((int)__pyx_v_self->c)); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 485; __pyx_clineno = LINE; goto __pyx_L1_error;}
^
_javabridge.c: Dans la fonction ‘pyx_pf_11_javabridge_13__JB_MethodID_2__repr’:
_javabridge.c:4883:37: attention : transtypage d’un pointeur vers un entier de taille différente [-Wpointer-to-int-cast]
__pyx_t_1 = __Pyx_PyInt_From_int(((int)__pyx_v_self->id)); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 499; __pyx_clineno = LINE; goto __pyx_L1_error;}
^
_javabridge.c: Dans la fonction ‘pyx_pf_11_javabridge_12__JB_FieldID_2__repr’:
_javabridge.c:5037:37: attention : transtypage d’un pointeur vers un entier de taille différente [-Wpointer-to-int-cast]
__pyx_t_1 = __Pyx_PyInt_From_int(((int)__pyx_v_self->id)); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 513; __pyx_clineno = LINE; goto __pyx_L1_error;}
^
_javabridge.c: Dans la fonction ‘__pyx_pf_11_javabridge_6JB_Env_118get_string’:
_javabridge.c:18985:18: attention : transtypage d’un pointeur vers un entier de taille différente [-Wpointer-to-int-cast]
__pyx_t_1 = ((((int)__pyx_v_s->o) == 0) != 0);
^
_javabridge.c: Dans la fonction ‘__pyx_pf_11_javabridge_6JB_Env_120get_string_utf’:
_javabridge.c:19120:18: attention : transtypage d’un pointeur vers un entier de taille différente [-Wpointer-to-int-cast]
__pyx_t_1 = ((((int)__pyx_v_s->o) == 0) != 0);
^
/usr/bin/ld: ne peut trouver -ljvm
collect2: erreur : ld a retourné 1 code d’état d’exécution
Traceback (most recent call last):
File “”, line 1, in
File “/nfs/work/hcs_mri/CellProfiler/setup.py”, line 53, in
“setup_requires”: packages
File “/trinity/shared/apps/cv-standard/python/2.7.12/lib/python2.7/site-packages/setuptools/dist.py”, line 315, in init
self.fetch_build_eggs(attrs[‘setup_requires’])
File “/trinity/shared/apps/cv-standard/python/2.7.12/lib/python2.7/site-packages/setuptools/dist.py”, line 361, in fetch_build_eggs
replace_conflicting=True,
File “/trinity/shared/apps/cv-standard/python/2.7.12/lib/python2.7/site-packages/pkg_resources/init.py”, line 851, in resolve
dist = best[req.key] = env.best_match(req, ws, installer)
File “/trinity/shared/apps/cv-standard/python/2.7.12/lib/python2.7/site-packages/pkg_resources/init.py”, line 1123, in best_match
return self.obtain(req, installer)
File “/trinity/shared/apps/cv-standard/python/2.7.12/lib/python2.7/site-packages/pkg_resources/init.py”, line 1135, in obtain
return installer(requirement)
File “/trinity/shared/apps/cv-standard/python/2.7.12/lib/python2.7/site-packages/setuptools/dist.py”, line 428, in fetch_build_egg
return cmd.easy_install(req)
File “/trinity/shared/apps/cv-standard/python/2.7.12/lib/python2.7/site-packages/setuptools/command/easy_install.py”, line 664, in easy_install
return self.install_item(spec, dist.location, tmpdir, deps)
File “/trinity/shared/apps/cv-standard/python/2.7.12/lib/python2.7/site-packages/setuptools/command/easy_install.py”, line 694, in install_item
dists = self.install_eggs(spec, download, tmpdir)
File “/trinity/shared/apps/cv-standard/python/2.7.12/lib/python2.7/site-packages/setuptools/command/easy_install.py”, line 875, in install_eggs
return self.build_and_install(setup_script, setup_base)
File “/trinity/shared/apps/cv-standard/python/2.7.12/lib/python2.7/site-packages/setuptools/command/easy_install.py”, line 1114, in build_and_install
self.run_setup(setup_script, setup_base, args)
File “/trinity/shared/apps/cv-standard/python/2.7.12/lib/python2.7/site-packages/setuptools/command/easy_install.py”, line 1102, in run_setup
raise DistutilsError(“Setup script exited with %s” % (v.args[0],))
distutils.errors.DistutilsError: Setup script exited with error: command ‘gcc’ failed with exit status 1

Thanks


#2

Can you share the output of pip freeze?