bbalasub1
commented
7 years ago Lester,
Unfortunately, I only have access to linux machines now and this was only tested on linux machines extensively. Others have had mixed luck with other OS.
It would be great to fix this problem for OSX. Any chance you might have some time to help?
On Sun, Jul 16, 2017 at 3:57 PM, Lester Mackey notifications@github.com wrote:
I'm encountering the same issue that @PeterJacob https://github.com/peterjacob described in #13 https://github.com/bbalasub1/glmnet_python/issues/13 . I'm running OS X version 10.11.6 (15G1217), and I've tried installing glmnet python via "pip install glmnet_py" and via the source installation instructions. In both cases the installation succeeds, and I'm able to "import glmnet_py" and "import glmnet_python," but when I run "glmnet(x = X.values.astype('float64'), y = y.values, family = 'cox')" in Python 3.6, I get the error
`-----------------------------------------------------------
OSError Traceback (most recent call last) in () 1 from glmnet_python import glmnet ----> 2 glmnet(x = X.values.astype('float64'), y = y.values)
/Users/lmackey/anaconda/envs/python3/lib/python3.6/site- packages/glmnet_python/glmnet.py in glmnet(x, y, family, **options) 448 fit = elnet(x, is_sparse, irs, pcs, y, weights, offset, gtype, parm, 449 lempty, nvars, jd, vp, cl, ne, nx, nlam, flmin, ulam, --> 450 thresh, isd, intr, maxit, family) 451 elif (family == 'binomial') or (family == 'multinomial'): 452 # call lognet
/Users/lmackey/anaconda/envs/python3/lib/python3.6/site- packages/glmnet_python/elnet.py in elnet(x, is_sparse, irs, pcs, y, weights, offset, gtype, parm, lempty, nvars, jd, vp, cl, ne, nx, nlam, flmin, ulam, thresh, isd, intr, maxit, family) 15 16 # load shared fortran library ---> 17 glmlib = loadGlmLib() 18 19 # pre-process data
/Users/lmackey/anaconda/envs/python3/lib/python3.6/site- packages/glmnet_python/loadGlmLib.py in loadGlmLib() 22 def loadGlmLib(): 23 if os.name == 'posix': ---> 24 glmlib = ctypes.cdll.LoadLibrary(glmnet_so) 25 return(glmlib) 26 elif os.name == 'nt':
/Users/lmackey/anaconda/envs/python3/lib/python3.6/ctypes/init.py in LoadLibrary(self, name) 424 425 def LoadLibrary(self, name): --> 426 return self._dlltype(name) 427 428 cdll = LibraryLoader(CDLL)
/Users/lmackey/anaconda/envs/python3/lib/python3.6/ctypes/init.py in init(self, name, mode, handle, use_errno, use_last_error) 346 347 if handle is None: --> 348 self._handle = _dlopen(self._name, mode) 349 else: 350 self._handle = handle
OSError: dlopen(/Users/lmackey/anaconda/envs/python3/lib/ python3.6/site-packages/glmnet_python/GLMnet.so, 6): no suitable image found. Did find: /Users/lmackey/anaconda/envs/python3/lib/python3.6/site- packages/glmnet_python/GLMnet.so: unknown file type, first eight bytes: 0x7F 0x45 0x4C 0x46 0x02 0x01 0x01 0x00 `
I've tried the libgfortran.3.dylib fix that @PeterJacob https://github.com/peterjacob suggested, but my traceback is unchanged. @PeterJacob https://github.com/peterjacob suggested that he may have had an incorrect GLMnet.so file; is a corrected GLMnet.so available for Mac OS X?
Thanks!
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lmackey
PeterJacob
mzhao94
marnixkoops
jcusick13
jadianes
I'm encountering the same issue that @PeterJacob described in #13 . I'm running OS X version 10.11.6 (15G1217), and I've tried installing glmnet python via "pip install glmnet_py" and via the source installation instructions. In both cases the installation succeeds, and I'm able to "import glmnet_py" and "import glmnet_python," but when I run "glmnet(x = X.values.astype('float64'), y = y.values, family = 'cox')" in Python 3.6, I get the error
`--------------------------------------------------------------------------- OSError Traceback (most recent call last) in () 1 from glmnet_python import glmnet ----> 2 glmnet(x = X.values.astype('float64'), y = y.values)
/Users/lmackey/anaconda/envs/python3/lib/python3.6/site-packages/glmnet_python/glmnet.py in glmnet(x, y, family, **options) 448 fit = elnet(x, is_sparse, irs, pcs, y, weights, offset, gtype, parm, 449 lempty, nvars, jd, vp, cl, ne, nx, nlam, flmin, ulam, --> 450 thresh, isd, intr, maxit, family) 451 elif (family == 'binomial') or (family == 'multinomial'): 452 # call lognet
/Users/lmackey/anaconda/envs/python3/lib/python3.6/site-packages/glmnet_python/elnet.py in elnet(x, is_sparse, irs, pcs, y, weights, offset, gtype, parm, lempty, nvars, jd, vp, cl, ne, nx, nlam, flmin, ulam, thresh, isd, intr, maxit, family) 15 16 # load shared fortran library ---> 17 glmlib = loadGlmLib() 18 19 # pre-process data
/Users/lmackey/anaconda/envs/python3/lib/python3.6/site-packages/glmnet_python/loadGlmLib.py in loadGlmLib() 22 def loadGlmLib(): 23 if os.name == 'posix': ---> 24 glmlib = ctypes.cdll.LoadLibrary(glmnet_so) 25 return(glmlib) 26 elif os.name == 'nt':
/Users/lmackey/anaconda/envs/python3/lib/python3.6/ctypes/init.py in LoadLibrary(self, name) 424 425 def LoadLibrary(self, name): --> 426 return self._dlltype(name) 427 428 cdll = LibraryLoader(CDLL)
/Users/lmackey/anaconda/envs/python3/lib/python3.6/ctypes/init.py in init(self, name, mode, handle, use_errno, use_last_error) 346 347 if handle is None: --> 348 self._handle = _dlopen(self._name, mode) 349 else: 350 self._handle = handle
OSError: dlopen(/Users/lmackey/anaconda/envs/python3/lib/python3.6/site-packages/glmnet_python/GLMnet.so, 6): no suitable image found. Did find: /Users/lmackey/anaconda/envs/python3/lib/python3.6/site-packages/glmnet_python/GLMnet.so: unknown file type, first eight bytes: 0x7F 0x45 0x4C 0x46 0x02 0x01 0x01 0x00 `
I've tried the libgfortran.3.dylib fix that @PeterJacob suggested, but my traceback is unchanged. @PeterJacob suggested that he may have had an incorrect GLMnet.so file; is a corrected GLMnet.so available for Mac OS X?
Thanks!