MohamadHarastani
commented
1 year ago Closed MohamadHarastani closed 9 months ago
MohamadHarastani
commented
1 year ago MohamadHarastani
commented
1 year ago Okay after installing scipion-em-reliontomo it passed! The documentation says that the plugin Dynamo should be installed, but it should also say that the latest version of reliontomo plugin should be installed too.
Cheers Mohamad
MohamadHarastani
commented
1 year ago I got an error in the TestFromPresegToPicking in step Graphs. The test keeps going for an hour without telling me that there is an error. I stopped it manually. Here is a copy of the error:
00001: /bin/sh: 15: eval: dirname: not found
00002: /bin/sh: 16: eval: dirname: not found
00003: /shared/miniconda3/envs/pySeg-v2.0.5/lib/python3.7/site-packages/sklearn/linear_model/least_angle.py:35: DeprecationWarning: `np.float` is a deprecated alias for the builtin `float`. To silence this warning, use `float` by itself. Doing this will not modify any behavior and is safe. If you specifically wanted the numpy scalar type, use `np.float64` here.
00004: Deprecated in NumPy 1.20; for more details and guidance: https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations
00005: eps=np.finfo(np.float).eps,
00006: /shared/miniconda3/envs/pySeg-v2.0.5/lib/python3.7/site-packages/sklearn/linear_model/least_angle.py:597: DeprecationWarning: `np.float` is a deprecated alias for the builtin `float`. To silence this warning, use `float` by itself. Doing this will not modify any behavior and is safe. If you specifically wanted the numpy scalar type, use `np.float64` here.
00007: Deprecated in NumPy 1.20; for more details and guidance: https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations
00008: eps=np.finfo(np.float).eps, copy_X=True, fit_path=True,
00009: /shared/miniconda3/envs/pySeg-v2.0.5/lib/python3.7/site-packages/sklearn/linear_model/least_angle.py:836: DeprecationWarning: `np.float` is a deprecated alias for the builtin `float`. To silence this warning, use `float` by itself. Doing this will not modify any behavior and is safe. If you specifically wanted the numpy scalar type, use `np.float64` here.
00010: Deprecated in NumPy 1.20; for more details and guidance: https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations
00011: eps=np.finfo(np.float).eps, copy_X=True, fit_path=True,
00012: /shared/miniconda3/envs/pySeg-v2.0.5/lib/python3.7/site-packages/sklearn/linear_model/least_angle.py:862: DeprecationWarning: `np.float` is a deprecated alias for the builtin `float`. To silence this warning, use `float` by itself. Doing this will not modify any behavior and is safe. If you specifically wanted the numpy scalar type, use `np.float64` here.
00013: Deprecated in NumPy 1.20; for more details and guidance: https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations
00014: eps=np.finfo(np.float).eps, positive=False):
00015: /shared/miniconda3/envs/pySeg-v2.0.5/lib/python3.7/site-packages/sklearn/linear_model/least_angle.py:1097: DeprecationWarning: `np.float` is a deprecated alias for the builtin `float`. To silence this warning, use `float` by itself. Doing this will not modify any behavior and is safe. If you specifically wanted the numpy scalar type, use `np.float64` here.
00016: Deprecated in NumPy 1.20; for more details and guidance: https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations
00017: max_n_alphas=1000, n_jobs=None, eps=np.finfo(np.float).eps,
00018: /shared/miniconda3/envs/pySeg-v2.0.5/lib/python3.7/site-packages/sklearn/linear_model/least_angle.py:1344: DeprecationWarning: `np.float` is a deprecated alias for the builtin `float`. To silence this warning, use `float` by itself. Doing this will not modify any behavior and is safe. If you specifically wanted the numpy scalar type, use `np.float64` here.
00019: Deprecated in NumPy 1.20; for more details and guidance: https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations
00020: max_n_alphas=1000, n_jobs=None, eps=np.finfo(np.float).eps,
00021: /shared/miniconda3/envs/pySeg-v2.0.5/lib/python3.7/site-packages/sklearn/linear_model/least_angle.py:1480: DeprecationWarning: `np.float` is a deprecated alias for the builtin `float`. To silence this warning, use `float` by itself. Doing this will not modify any behavior and is safe. If you specifically wanted the numpy scalar type, use `np.float64` here.
00022: Deprecated in NumPy 1.20; for more details and guidance: https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations
00023: eps=np.finfo(np.float).eps, copy_X=True, positive=False):
00024: /shared/miniconda3/envs/pySeg-v2.0.5/lib/python3.7/site-packages/sklearn/linear_model/randomized_l1.py:152: DeprecationWarning: `np.float` is a deprecated alias for the builtin `float`. To silence this warning, use `float` by itself. Doing this will not modify any behavior and is safe. If you specifically wanted the numpy scalar type, use `np.float64` here.
00025: Deprecated in NumPy 1.20; for more details and guidance: https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations
00026: precompute=False, eps=np.finfo(np.float).eps,
00027: /shared/miniconda3/envs/pySeg-v2.0.5/lib/python3.7/site-packages/sklearn/linear_model/randomized_l1.py:320: DeprecationWarning: `np.float` is a deprecated alias for the builtin `float`. To silence this warning, use `float` by itself. Doing this will not modify any behavior and is safe. If you specifically wanted the numpy scalar type, use `np.float64` here.
00028: Deprecated in NumPy 1.20; for more details and guidance: https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations
00029: eps=np.finfo(np.float).eps, random_state=None,
00030: /shared/miniconda3/envs/pySeg-v2.0.5/lib/python3.7/site-packages/sklearn/linear_model/randomized_l1.py:580: DeprecationWarning: `np.float` is a deprecated alias for the builtin `float`. To silence this warning, use `float` by itself. Doing this will not modify any behavior and is safe. If you specifically wanted the numpy scalar type, use `np.float64` here.
00031: Deprecated in NumPy 1.20; for more details and guidance: https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations
00032: eps=4 * np.finfo(np.float).eps, n_jobs=None,
00033: /shared/miniconda3/envs/pySeg-v2.0.5/lib/python3.7/site-packages/sklearn/decomposition/online_lda.py:31: DeprecationWarning: `np.float` is a deprecated alias for the builtin `float`. To silence this warning, use `float` by itself. Doing this will not modify any behavior and is safe. If you specifically wanted the numpy scalar type, use `np.float64` here.
00034: Deprecated in NumPy 1.20; for more details and guidance: https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations
00035: EPS = np.finfo(np.float).eps
00036: /shared/scipion3/software/em/pySeg-v2.0.5/pyseg_system-2.0.5/code/tutorials/synth_sumb/tracing/mb_graph_mp.py:169: DeprecationWarning: `np.int` is a deprecated alias for the builtin `int`. To silence this warning, use `int` by itself. Doing this will not modify any behavior and is safe. When replacing `np.int`, you may wish to use e.g. `np.int64` or `np.int32` to specify the precision. If you wish to review your current use, check the release note link for additional information.
00037: Deprecated in NumPy 1.20; for more details and guidance: https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations
00038: maskh = np.ones(shape=segh.shape, dtype=np.int)
00039: /shared/scipion3/software/em/pySeg-v2.0.5/pyseg_system-2.0.5/code/tutorials/synth_sumb/tracing/mb_graph_mp.py:171: DeprecationWarning: `np.int` is a deprecated alias for the builtin `int`. To silence this warning, use `int` by itself. Doing this will not modify any behavior and is safe. When replacing `np.int`, you may wish to use e.g. `np.int64` or `np.int32` to specify the precision. If you wish to review your current use, check the release note link for additional information.
00040: Deprecated in NumPy 1.20; for more details and guidance: https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations
00041: mask = np.asarray(tomod > (max_len + mb_dst_off + 2 * DILATE_NITER * res), dtype=np.int)
00042: /shared/scipion3/software/em/pySeg-v2.0.5/pyseg_system-2.0.5/code/tutorials/synth_sumb/tracing/mb_graph_mp.py:174: DeprecationWarning: `np.float` is a deprecated alias for the builtin `float`. To silence this warning, use `float` by itself. Doing this will not modify any behavior and is safe. If you specifically wanted the numpy scalar type, use `np.float64` here.
00043: Deprecated in NumPy 1.20; for more details and guidance: https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations
00044: mask = np.asarray(maskh > 0, dtype=np.float)
00045: /shared/scipion3/software/em/pySeg-v2.0.5/pyseg_system-2.0.5/code/tutorials/synth_sumb/tracing/mb_graph_mp.py:185: DeprecationWarning: `np.bool` is a deprecated alias for the builtin `bool`. To silence this warning, use `bool` by itself. Doing this will not modify any behavior and is safe. If you specifically wanted the numpy scalar type, use `np.bool_` here.
00046: Deprecated in NumPy 1.20; for more details and guidance: https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations
00047: mask_den = np.asarray(tomod <= mb_dst_off, dtype=np.bool)
00048: Process Process-2:
00049: Traceback (most recent call last):
00050: File "/shared/scipion3/software/em/pySeg-v2.0.5/pyseg_system-2.0.5/code/pyseg/disperse_io/handler.py", line 360, in mse
00051: subprocess.call(mse_cmd, stdout=file_log, stderr=file_log)
00052: File "/shared/miniconda3/envs/pySeg-v2.0.5/lib/python3.7/subprocess.py", line 339, in call
00053: with Popen(*popenargs, **kwargs) as p:
00054: File "/shared/miniconda3/envs/pySeg-v2.0.5/lib/python3.7/subprocess.py", line 800, in __init__
00055: restore_signals, start_new_session)
00056: File "/shared/miniconda3/envs/pySeg-v2.0.5/lib/python3.7/subprocess.py", line 1551, in _execute_child
00057: raise child_exception_type(errno_num, err_msg, err_filename)
00058: FileNotFoundError: [Errno 2] No such file or directory: 'mse': 'mse'
00059:
00060: During handling of the above exception, another exception occurred:
00061:
00062: Traceback (most recent call last):
00063: File "/shared/miniconda3/envs/pySeg-v2.0.5/lib/python3.7/multiprocessing/process.py", line 297, in _bootstrap
00064: self.run()
00065: File "/shared/miniconda3/envs/pySeg-v2.0.5/lib/python3.7/multiprocessing/process.py", line 99, in run
00066: self._target(*self._args, **self._kwargs)
00067: File "/shared/scipion3/software/em/pySeg-v2.0.5/pyseg_system-2.0.5/code/tutorials/synth_sumb/tracing/mb_graph_mp.py", line 216, in pr_worker
00068: disperse.mse(no_cut=False, inv=False)
00069: File "/shared/scipion3/software/em/pySeg-v2.0.5/pyseg_system-2.0.5/code/pyseg/disperse_io/handler.py", line 367, in mse
00070: raise pexceptions.PySegInputError(expr='mse DisPerSe', msg=error_msg)
00071: pyseg.pexceptions.pexceptions.PySegInputError
00072: /shared/miniconda3/envs/pySeg-v2.0.5/lib/python3.7/multiprocessing/process.py:313: ResourceWarning: unclosed file <_io.TextIOWrapper name='Runs/000293_ProtPySegGraphs/extra/disperse_pr_1/disperse.log' mode='a' encoding='UTF-8'>
00073: traceback.print_exc()
00074: /shared/scipion3/software/em/pySeg-v2.0.5/pyseg_system-2.0.5/code/tutorials/synth_sumb/tracing/mb_graph_mp.py:169: DeprecationWarning: `np.int` is a deprecated alias for the builtin `int`. To silence this warning, use `int` by itself. Doing this will not modify any behavior and is safe. When replacing `np.int`, you may wish to use e.g. `np.int64` or `np.int32` to specify the precision. If you wish to review your current use, check the release note link for additional information.
00075: Deprecated in NumPy 1.20; for more details and guidance: https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations
00076: maskh = np.ones(shape=segh.shape, dtype=np.int)
00077: /shared/scipion3/software/em/pySeg-v2.0.5/pyseg_system-2.0.5/code/tutorials/synth_sumb/tracing/mb_graph_mp.py:171: DeprecationWarning: `np.int` is a deprecated alias for the builtin `int`. To silence this warning, use `int` by itself. Doing this will not modify any behavior and is safe. When replacing `np.int`, you may wish to use e.g. `np.int64` or `np.int32` to specify the precision. If you wish to review your current use, check the release note link for additional information.
00078: Deprecated in NumPy 1.20; for more details and guidance: https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations
00079: mask = np.asarray(tomod > (max_len + mb_dst_off + 2 * DILATE_NITER * res), dtype=np.int)
00080: /shared/scipion3/software/em/pySeg-v2.0.5/pyseg_system-2.0.5/code/tutorials/synth_sumb/tracing/mb_graph_mp.py:174: DeprecationWarning: `np.float` is a deprecated alias for the builtin `float`. To silence this warning, use `float` by itself. Doing this will not modify any behavior and is safe. If you specifically wanted the numpy scalar type, use `np.float64` here.
00081: Deprecated in NumPy 1.20; for more details and guidance: https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations
00082: mask = np.asarray(maskh > 0, dtype=np.float)
00083: /shared/scipion3/software/em/pySeg-v2.0.5/pyseg_system-2.0.5/code/tutorials/synth_sumb/tracing/mb_graph_mp.py:185: DeprecationWarning: `np.bool` is a deprecated alias for the builtin `bool`. To silence this warning, use `bool` by itself. Doing this will not modify any behavior and is safe. If you specifically wanted the numpy scalar type, use `np.bool_` here.
00084: Deprecated in NumPy 1.20; for more details and guidance: https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations
00085: mask_den = np.asarray(tomod <= mb_dst_off, dtype=np.bool)
00086: Process Process-3:
00087: Traceback (most recent call last):
00088: File "/shared/scipion3/software/em/pySeg-v2.0.5/pyseg_system-2.0.5/code/pyseg/disperse_io/handler.py", line 360, in mse
00089: subprocess.call(mse_cmd, stdout=file_log, stderr=file_log)
00090: File "/shared/miniconda3/envs/pySeg-v2.0.5/lib/python3.7/subprocess.py", line 339, in call
00091: with Popen(*popenargs, **kwargs) as p:
00092: File "/shared/miniconda3/envs/pySeg-v2.0.5/lib/python3.7/subprocess.py", line 800, in __init__
00093: restore_signals, start_new_session)
00094: File "/shared/miniconda3/envs/pySeg-v2.0.5/lib/python3.7/subprocess.py", line 1551, in _execute_child
00095: raise child_exception_type(errno_num, err_msg, err_filename)
00096: FileNotFoundError: [Errno 2] No such file or directory: 'mse': 'mse'
00097:
00098: During handling of the above exception, another exception occurred:
00099:
00100: Traceback (most recent call last):
00101: File "/shared/miniconda3/envs/pySeg-v2.0.5/lib/python3.7/multiprocessing/process.py", line 297, in _bootstrap
00102: self.run()
00103: File "/shared/miniconda3/envs/pySeg-v2.0.5/lib/python3.7/multiprocessing/process.py", line 99, in run
00104: self._target(*self._args, **self._kwargs)
00105: File "/shared/scipion3/software/em/pySeg-v2.0.5/pyseg_system-2.0.5/code/tutorials/synth_sumb/tracing/mb_graph_mp.py", line 216, in pr_worker
00106: disperse.mse(no_cut=False, inv=False)
00107: File "/shared/scipion3/software/em/pySeg-v2.0.5/pyseg_system-2.0.5/code/pyseg/disperse_io/handler.py", line 367, in mse
00108: raise pexceptions.PySegInputError(expr='mse DisPerSe', msg=error_msg)
00109: pyseg.pexceptions.pexceptions.PySegInputError
00110: /shared/miniconda3/envs/pySeg-v2.0.5/lib/python3.7/multiprocessing/process.py:313: ResourceWarning: unclosed file <_io.TextIOWrapper name='Runs/000293_ProtPySegGraphs/extra/disperse_pr_2/disperse.log' mode='a' encoding='UTF-8'>
00111: traceback.print_exc()
00112: /shared/scipion3/software/em/pySeg-v2.0.5/pyseg_system-2.0.5/code/tutorials/synth_sumb/tracing/mb_graph_mp.py:169: DeprecationWarning: `np.int` is a deprecated alias for the builtin `int`. To silence this warning, use `int` by itself. Doing this will not modify any behavior and is safe. When replacing `np.int`, you may wish to use e.g. `np.int64` or `np.int32` to specify the precision. If you wish to review your current use, check the release note link for additional information.
00113: Deprecated in NumPy 1.20; for more details and guidance: https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations
00114: maskh = np.ones(shape=segh.shape, dtype=np.int)
00115: /shared/scipion3/software/em/pySeg-v2.0.5/pyseg_system-2.0.5/code/tutorials/synth_sumb/tracing/mb_graph_mp.py:171: DeprecationWarning: `np.int` is a deprecated alias for the builtin `int`. To silence this warning, use `int` by itself. Doing this will not modify any behavior and is safe. When replacing `np.int`, you may wish to use e.g. `np.int64` or `np.int32` to specify the precision. If you wish to review your current use, check the release note link for additional information.
00116: Deprecated in NumPy 1.20; for more details and guidance: https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations
00117: mask = np.asarray(tomod > (max_len + mb_dst_off + 2 * DILATE_NITER * res), dtype=np.int)
00118: /shared/scipion3/software/em/pySeg-v2.0.5/pyseg_system-2.0.5/code/tutorials/synth_sumb/tracing/mb_graph_mp.py:174: DeprecationWarning: `np.float` is a deprecated alias for the builtin `float`. To silence this warning, use `float` by itself. Doing this will not modify any behavior and is safe. If you specifically wanted the numpy scalar type, use `np.float64` here.
00119: Deprecated in NumPy 1.20; for more details and guidance: https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations
00120: mask = np.asarray(maskh > 0, dtype=np.float)
00121: /shared/scipion3/software/em/pySeg-v2.0.5/pyseg_system-2.0.5/code/tutorials/synth_sumb/tracing/mb_graph_mp.py:185: DeprecationWarning: `np.bool` is a deprecated alias for the builtin `bool`. To silence this warning, use `bool` by itself. Doing this will not modify any behavior and is safe. If you specifically wanted the numpy scalar type, use `np.bool_` here.
00122: Deprecated in NumPy 1.20; for more details and guidance: https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations
00123: mask_den = np.asarray(tomod <= mb_dst_off, dtype=np.bool)
00124: Process Process-1:
00125: Traceback (most recent call last):
00126: File "/shared/scipion3/software/em/pySeg-v2.0.5/pyseg_system-2.0.5/code/pyseg/disperse_io/handler.py", line 360, in mse
00127: subprocess.call(mse_cmd, stdout=file_log, stderr=file_log)
00128: File "/shared/miniconda3/envs/pySeg-v2.0.5/lib/python3.7/subprocess.py", line 339, in call
00129: with Popen(*popenargs, **kwargs) as p:
00130: File "/shared/miniconda3/envs/pySeg-v2.0.5/lib/python3.7/subprocess.py", line 800, in __init__
00131: restore_signals, start_new_session)
00132: File "/shared/miniconda3/envs/pySeg-v2.0.5/lib/python3.7/subprocess.py", line 1551, in _execute_child
00133: raise child_exception_type(errno_num, err_msg, err_filename)
00134: FileNotFoundError: [Errno 2] No such file or directory: 'mse': 'mse'
00135:
00136: During handling of the above exception, another exception occurred:
00137:
00138: Traceback (most recent call last):
00139: File "/shared/miniconda3/envs/pySeg-v2.0.5/lib/python3.7/multiprocessing/process.py", line 297, in _bootstrap
00140: self.run()
00141: File "/shared/miniconda3/envs/pySeg-v2.0.5/lib/python3.7/multiprocessing/process.py", line 99, in run
00142: self._target(*self._args, **self._kwargs)
00143: File "/shared/scipion3/software/em/pySeg-v2.0.5/pyseg_system-2.0.5/code/tutorials/synth_sumb/tracing/mb_graph_mp.py", line 216, in pr_worker
00144: disperse.mse(no_cut=False, inv=False)
00145: File "/shared/scipion3/software/em/pySeg-v2.0.5/pyseg_system-2.0.5/code/pyseg/disperse_io/handler.py", line 367, in mse
00146: raise pexceptions.PySegInputError(expr='mse DisPerSe', msg=error_msg)
00147: pyseg.pexceptions.pexceptions.PySegInputError
00148: /shared/miniconda3/envs/pySeg-v2.0.5/lib/python3.7/multiprocessing/process.py:313: ResourceWarning: unclosed file <_io.TextIOWrapper name='Runs/000293_ProtPySegGraphs/extra/disperse_pr_0/disperse.log' mode='a' encoding='UTF-8'>
00149: traceback.print_exc()
00150: Traceback (most recent call last):
00151: File "/shared/scipion3/software/em/pySeg-v2.0.5/pyseg_system-2.0.5/code/tutorials/synth_sumb/tracing/mb_graph_mp.py", line 329, in <module>
00152: hold_out_pkl = q_pkls.get()
00153: File "/shared/miniconda3/envs/pySeg-v2.0.5/lib/python3.7/multiprocessing/queues.py", line 94, in get
00154: res = self._recv_bytes()
00155: File "/shared/miniconda3/envs/pySeg-v2.0.5/lib/python3.7/multiprocessing/connection.py", line 216, in recv_bytes
00156: buf = self._recv_bytes(maxlength)
00157: File "/shared/miniconda3/envs/pySeg-v2.0.5/lib/python3.7/multiprocessing/connection.py", line 407, in _recv_bytes
00158: buf = self._recv(4)
00159: File "/shared/miniconda3/envs/pySeg-v2.0.5/lib/python3.7/multiprocessing/connection.py", line 379, in _recv
00160: chunk = read(handle, remaining)
00161: KeyboardInterrupt
00162: Traceback (most recent call last):
00163: File "/shared/miniconda3/envs/scipion3/lib/python3.8/site-packages/pyworkflow/apps/pw_protocol_run.py", line 41, in <module>
00164: runProtocolMain(projPath, dbPath, protId)
00165: File "/shared/miniconda3/envs/scipion3/lib/python3.8/site-packages/pyworkflow/protocol/protocol.py", line 2371, in runProtocolMain
00166: protocol.run()
00167: File "/shared/miniconda3/envs/scipion3/lib/python3.8/site-packages/pyworkflow/protocol/protocol.py", line 1521, in run
00168: Step.run(self)
00169: File "/shared/miniconda3/envs/scipion3/lib/python3.8/site-packages/pyworkflow/protocol/protocol.py", line 202, in run
00170: self._run()
00171: File "/shared/miniconda3/envs/scipion3/lib/python3.8/site-packages/pyworkflow/protocol/protocol.py", line 1458, in _run
00172: self._runSteps(startIndex)
00173: File "/shared/miniconda3/envs/scipion3/lib/python3.8/site-packages/pyworkflow/protocol/protocol.py", line 1300, in _runSteps
00174: self._stepsExecutor.runSteps(self._steps,
00175: File "/shared/miniconda3/envs/scipion3/lib/python3.8/site-packages/pyworkflow/protocol/executor.py", line 113, in runSteps
00176: step.run()
00177: File "/shared/miniconda3/envs/scipion3/lib/python3.8/site-packages/pyworkflow/protocol/protocol.py", line 202, in run
00178: self._run()
00179: File "/shared/miniconda3/envs/scipion3/lib/python3.8/site-packages/pyworkflow/protocol/protocol.py", line 253, in _run
00180: resultFiles = self._runFunc()
00181: File "/shared/miniconda3/envs/scipion3/lib/python3.8/site-packages/pyworkflow/protocol/protocol.py", line 249, in _runFunc
00182: return self._func(*self._args)
00183: File "/shared/scipion3/plugins/scipion-em-pyseg/pyseg/protocols/protocol_graphs.py", line 128, in pysegGraphs
00184: Plugin.runPySeg(self, PYTHON, self._getGraphsCommand(starFile))
00185: File "/shared/scipion3/plugins/scipion-em-pyseg/pyseg/__init__.py", line 170, in runPySeg
00186: protocol.runJob(fullProgram, args, env=cls.getEnviron(), cwd=cwd)
00187: File "/shared/miniconda3/envs/scipion3/lib/python3.8/site-packages/pyworkflow/protocol/protocol.py", line 1480, in runJob
00188: self._stepsExecutor.runJob(self._log, program, arguments, **kwargs)
00189: File "/shared/miniconda3/envs/scipion3/lib/python3.8/site-packages/pyworkflow/protocol/executor.py", line 65, in runJob
00190: process.runJob(log, programName, params,
00191: File "/shared/miniconda3/envs/scipion3/lib/python3.8/site-packages/pyworkflow/utils/process.py", line 55, in runJob
00192: return runCommand(command, env, cwd)
00193: File "/shared/miniconda3/envs/scipion3/lib/python3.8/site-packages/pyworkflow/utils/process.py", line 70, in runCommand
00194: check_call(command, shell=True, stdout=sys.stdout, stderr=sys.stderr,
00195: File "/shared/miniconda3/envs/scipion3/lib/python3.8/subprocess.py", line 359, in check_call
00196: retcode = call(*popenargs, **kwargs)
00197: File "/shared/miniconda3/envs/scipion3/lib/python3.8/subprocess.py", line 342, in call
00198: return p.wait(timeout=timeout)
00199: File "/shared/miniconda3/envs/scipion3/lib/python3.8/subprocess.py", line 1083, in wait
00200: return self._wait(timeout=timeout)
00201: File "/shared/miniconda3/envs/scipion3/lib/python3.8/subprocess.py", line 1806, in _wait
00202: (pid, sts) = self._try_wait(0)
00203: File "/shared/miniconda3/envs/scipion3/lib/python3.8/subprocess.py", line 1764, in _try_wait
00204: (pid, sts) = os.waitpid(self.pid, wait_flags)
00205: KeyboardInterrupt
JorMaister
commented
1 year ago Hi, @MohamadHarastani,
This is a problematic issue that happens when the DisPerSe program called by the graphs protocol didn't compile correctly. If the gcc/g++ were pointing to a version higher than 7, the compilation doesn't complain, but the graphs dies someway the process remains (need to be checked). The best approach we considered to offer is to inform the user if we detect it during the plugin installation. But if you weren't pointing to compatible versions of the compilers, the last version of the plugin should have info you about that. Can you confirm that?
Many thanks!
MohamadHarastani
commented
1 year ago Hi @JorMaister Thanks for the followup. I will check that asap and return to you. Cheers Mohamad
MohamadHarastani
commented
1 year ago It is true that I had gcc/g++ version 7 when I installed the plugin. I did that by relinking it manually. After the installation, I returned back to version 8. Before switching to version 7 the installation of the plugin fails. If there is something that I can test from my side, let me know. Cheers
JorMaister
commented
9 months ago Passing now. Current version admits the compiler gcc/g++ from 5 to 12, both included.