lpiol/multiverse

multiverse's Issues

R[write to console]: Error in gzfile(file, "rb") : cannot open the connection

I have a similar problem, could you please help me with this? I don't face this problem while I'm using Multiplex network, only appears with heterogeneous one:

[1] "Reading arguments..."
[1] "Input network with 3 Layers"
[1] "Input network with 3 Layers"
[1] "Input network with 1 Layers"
Generating bipartite matrix...
Expanding bipartite matrix to fit the multiplex network...
Computing adjacency matrix of the first input network...
Computing adjacency matrix of the second input network...
Computing inter-subnetworks transitions...
RWR done
R[write to console]: Error in gzfile(file, "rb") : cannot open the connection

R[write to console]: In addition:
R[write to console]: Warning message:

R[write to console]: In gzfile(file, "rb") :
R[write to console]:

R[write to console]: cannot open compressed file './ResultsRWR/MatrixSimilarityMultiplexHettest_MH.rds', probable reason 'No such file or directory'

Traceback (most recent call last):
File "MultiVERSE_MH.py", line 119, in
main()
File "MultiVERSE_MH.py", line 85, in main
r_DistancematrixPPI = r_readRDS('./ResultsRWR/MatrixSimilarityMultiplexHet'+graph_name +'.rds')
File "/home/samira/miniconda3/envs/MP/lib/python3.7/site-packages/rpy2/robjects/functions.py", line 199, in call
.call(*args, **kwargs))
File "/home/samira/miniconda3/envs/MP/lib/python3.7/site-packages/rpy2/robjects/functions.py", line 125, in call
res = super(Function, self).call(*new_args, **new_kwargs)
File "/home/samira/miniconda3/envs/MP/lib/python3.7/site-packages/rpy2/rinterface_lib/conversion.py", line 45, in _
cdata = function(*args, **kwargs)
File "/home/samira/miniconda3/envs/MP/lib/python3.7/site-packages/rpy2/rinterface.py", line 680, in call
raise embedded.RRuntimeError(_rinterface._geterrmessage())
rpy2.rinterface_lib.embedded.RRuntimeError: Error in gzfile(file, "rb") : cannot open the connection

MultiVERSE_M.py: ./ResultsRWR/ directory does not exist

$ python3 MultiVERSE_M.py -k 0

[1] "Saving file ../ResultsRWR/MatrixSimilarityMultiplexCKM-Physicians-Innovation_multiplex.edges.rds"
Error in gzfile(file, mode) : impossible d'ouvrir la connexion
Calls: saveRDS -> gzfile
De plus : Warning message:
In gzfile(file, mode) :
  impossible d'ouvrir le fichier compressé '../ResultsRWR/MatrixSimilarityMultiplexCKM-Physicians-Innovation_multiplex.edges.rds', cause probable : 'Aucun fichier ou dossier de ce type'
Exécution arrêtée
sh: 1: module: not found
R[write to console]: Error in gzfile(file, "rb") : impossible d'ouvrir la connexion

R[write to console]: De plus : 
R[write to console]: Warning message:

R[write to console]: In gzfile(file, "rb") :
R[write to console]: 
 
R[write to console]:  impossible d'ouvrir le fichier compressé './ResultsRWR/MatrixSimilarityMultiplexCKM-Physicians-Innovation_multiplex.edges.rds', cause probable : 'Aucun fichier ou dossier de ce type'

Traceback (most recent call last):
  File "MultiVERSE_M.py", line 97, in <module>
    main()
  File "MultiVERSE_M.py", line 63, in main
    r_DistancematrixPPI = r_readRDS('./ResultsRWR/MatrixSimilarityMultiplex'+graph_name +'.rds') 
  File "/usr/lib/python3/dist-packages/rpy2/robjects/functions.py", line 198, in __call__
    .__call__(*args, **kwargs))
  File "/usr/lib/python3/dist-packages/rpy2/robjects/functions.py", line 125, in __call__
    res = super(Function, self).__call__(*new_args, **new_kwargs)
  File "/usr/lib/python3/dist-packages/rpy2/rinterface_lib/conversion.py", line 44, in _
    cdata = function(*args, **kwargs)
  File "/usr/lib/python3/dist-packages/rpy2/rinterface.py", line 624, in __call__
    raise embedded.RRuntimeError(_rinterface._geterrmessage())
rpy2.rinterface_lib.embedded.RRuntimeError: Error in gzfile(file, "rb") : impossible d'ouvrir la connexion

It is due to the lack of creation of ./ResultsRWR/ directory.
Once the directory is created, the bug does not appear anymore

MultiVERSE_MH.py: syntax error: closing bracket missing

-              '-o', '../ResultsRWR/MatrixSimilarityMultiplexHet'+graph_name, '-c', str(cpu_number))
+              '-o', '../ResultsRWR/MatrixSimilarityMultiplexHet'+graph_name, '-c', str(cpu_number)])

With this modifiication the program runs... it is still runnning

MultiVERSE_M.py: numba error

With numba 0.45.1 installed, i get the following error... With numba 0.51 no error. Yoi should update the version requirement.

$ python3 MultiVERSE_M.py -k 0

[1] "Saving file ../ResultsRWR/MatrixSimilarityMultiplexCKM-Physicians-Innovation_multiplex.edges.rds"
sh: 1: module: not found
/home/laurent/py3m/lib/python3.6/site-packages/numba/ir_utils.py:1959: NumbaPendingDeprecationWarning: 
Encountered the use of a type that is scheduled for deprecation: type 'reflected list' found for argument 'neighborhood' of function 'train'.

For more information visit http://numba.pydata.org/numba-doc/latest/reference/deprecation.html#deprecation-of-reflection-for-list-and-set-types

File "functions.py", line 53:
@njit(parallel=True)
def train(neighborhood, nodes, list_neighbours, NUM_STEPS, NUM_SAMPLED, LEARNING_RATE, CLOSEST_NODES, CHUNK_SIZE, NB_CHUNK, embeddings, reverse_data_DistancematrixPPI):
^

  warnings.warn(NumbaPendingDeprecationWarning(msg, loc=loc))
Traceback (most recent call last):
  File "MultiVERSE_M.py", line 97, in <module>
    main()
  File "MultiVERSE_M.py", line 89, in main
    CLOSEST_NODES, CHUNK_SIZE, NB_CHUNK, embeddings, reverse_data_DistancematrixPPI)
  File "/home/laurent/py3m/lib/python3.6/site-packages/numba/dispatcher.py", line 395, in _compile_for_args
    raise e
  File "/home/laurent/py3m/lib/python3.6/site-packages/numba/dispatcher.py", line 352, in _compile_for_args
    return self.compile(tuple(argtypes))
  File "/home/laurent/py3m/lib/python3.6/site-packages/numba/compiler_lock.py", line 32, in _acquire_compile_lock
    return func(*args, **kwargs)
  File "/home/laurent/py3m/lib/python3.6/site-packages/numba/dispatcher.py", line 693, in compile
    cres = self._compiler.compile(args, return_type)
  File "/home/laurent/py3m/lib/python3.6/site-packages/numba/dispatcher.py", line 76, in compile
    status, retval = self._compile_cached(args, return_type)
  File "/home/laurent/py3m/lib/python3.6/site-packages/numba/dispatcher.py", line 90, in _compile_cached
    retval = self._compile_core(args, return_type)
  File "/home/laurent/py3m/lib/python3.6/site-packages/numba/dispatcher.py", line 108, in _compile_core
    pipeline_class=self.pipeline_class)
  File "/home/laurent/py3m/lib/python3.6/site-packages/numba/compiler.py", line 972, in compile_extra
    return pipeline.compile_extra(func)
  File "/home/laurent/py3m/lib/python3.6/site-packages/numba/compiler.py", line 390, in compile_extra
    return self._compile_bytecode()
  File "/home/laurent/py3m/lib/python3.6/site-packages/numba/compiler.py", line 903, in _compile_bytecode
    return self._compile_core()
  File "/home/laurent/py3m/lib/python3.6/site-packages/numba/compiler.py", line 890, in _compile_core
    res = pm.run(self.status)
  File "/home/laurent/py3m/lib/python3.6/site-packages/numba/compiler_lock.py", line 32, in _acquire_compile_lock
    return func(*args, **kwargs)
  File "/home/laurent/py3m/lib/python3.6/site-packages/numba/compiler.py", line 266, in run
    raise patched_exception
  File "/home/laurent/py3m/lib/python3.6/site-packages/numba/compiler.py", line 257, in run
    stage()
  File "/home/laurent/py3m/lib/python3.6/site-packages/numba/compiler.py", line 764, in stage_nopython_backend
    self._backend(lowerfn, objectmode=False)
  File "/home/laurent/py3m/lib/python3.6/site-packages/numba/compiler.py", line 703, in _backend
    lowered = lowerfn()
  File "/home/laurent/py3m/lib/python3.6/site-packages/numba/compiler.py", line 690, in backend_nopython_mode
    self.metadata)
  File "/home/laurent/py3m/lib/python3.6/site-packages/numba/compiler.py", line 1145, in native_lowering_stage
    lower.create_cpython_wrapper(flags.release_gil)
  File "/home/laurent/py3m/lib/python3.6/site-packages/numba/lowering.py", line 271, in create_cpython_wrapper
    release_gil=release_gil)
  File "/home/laurent/py3m/lib/python3.6/site-packages/numba/targets/cpu.py", line 157, in create_cpython_wrapper
    builder.build()
  File "/home/laurent/py3m/lib/python3.6/site-packages/numba/callwrapper.py", line 122, in build
    self.build_wrapper(api, builder, closure, args, kws)
  File "/home/laurent/py3m/lib/python3.6/site-packages/numba/callwrapper.py", line 155, in build_wrapper
    val = cleanup_manager.add_arg(builder.load(obj), ty)
  File "/home/laurent/py3m/lib/python3.6/site-packages/numba/callwrapper.py", line 32, in add_arg
    native = self.api.to_native_value(ty, obj)
  File "/home/laurent/py3m/lib/python3.6/site-packages/numba/pythonapi.py", line 1425, in to_native_value
    return impl(typ, obj, c)
  File "/home/laurent/py3m/lib/python3.6/site-packages/numba/targets/boxing.py", line 733, in unbox_list
    _python_list_to_native(typ, obj, c, size, listptr, errorptr)
  File "/home/laurent/py3m/lib/python3.6/site-packages/numba/targets/boxing.py", line 663, in _python_list_to_native
    ok, list = listobj.ListInstance.allocate_ex(c.context, c.builder, typ, size)
  File "/home/laurent/py3m/lib/python3.6/site-packages/numba/targets/listobj.py", line 268, in allocate_ex
    self.zfill(self.size.type(0), nitems)
  File "/home/laurent/py3m/lib/python3.6/site-packages/numba/targets/listobj.py", line 222, in zfill
    cgutils.memset(builder, base, size, ir.IntType(8)(0))
  File "/home/laurent/py3m/lib/python3.6/site-packages/numba/cgutils.py", line 866, in memset
    builder.call(fn, [ptr, value, size, int32_t(0), bool_t(0)])
  File "/home/laurent/py3m/lib/python3.6/site-packages/llvmlite/ir/builder.py", line 851, in call
    cconv=cconv, tail=tail, fastmath=fastmath)
  File "/home/laurent/py3m/lib/python3.6/site-packages/llvmlite/ir/instructions.py", line 84, in __init__
    raise TypeError(msg)
TypeError: Failed in nopython mode pipeline (step: nopython mode backend)
Type of #4 arg mismatch: i1 != i32

deop people

people who are deop can not join the world it said "YOU DO NOT HAVE PERMISSION TO ENTER" does anyone have a way to fix this

MultiVERSE_M.py: remove superfluous import

functions.py: l.11: Remove autojit from imports : new numba versions have removed it

- from numba import jit, njit, prange, autojit
+ from numba import jit, njit, prange

Error no such file or directory

I have been running the example code in terminal but I am getting this error:
cannot open compressed file './ResultsRWR/MatrixSimilarityMultiplexCKM-Physicians-Innovation_multiplex.edges.rds', probable reason 'No such file or directory'