Import Error on Mac OS-X with 1.12.0 #47

csadorf · 2017-01-19T20:37:08Z

After installing the latest version I get the following error on importing the package:

  File "/Users/csadorf/miniconda3/envs/numpy/lib/python3.6/site-packages/numpy/core/__init__.py", line 16, in <module>
    from . import multiarray
ImportError: dlopen(/Users/csadorf/miniconda3/envs/numpy/lib/python3.6/site-packages/numpy/core/multiarray.cpython-36m-darwin.so, 2): Library not loaded: @rpath/./libgfortran.3.dylib
  Referenced from: /Users/csadorf/miniconda3/envs/numpy/lib/libopenblasp-r0.2.19.dylib
  Reason: image not found

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "<string>", line 1, in <module>
  File "/Users/csadorf/miniconda3/envs/numpy/lib/python3.6/site-packages/numpy/__init__.py", line 142, in <module>
    from . import add_newdocs
  File "/Users/csadorf/miniconda3/envs/numpy/lib/python3.6/site-packages/numpy/add_newdocs.py", line 13, in <module>
    from numpy.lib import add_newdoc
  File "/Users/csadorf/miniconda3/envs/numpy/lib/python3.6/site-packages/numpy/lib/__init__.py", line 8, in <module>
    from .type_check import *
  File "/Users/csadorf/miniconda3/envs/numpy/lib/python3.6/site-packages/numpy/lib/type_check.py", line 11, in <module>
    import numpy.core.numeric as _nx
  File "/Users/csadorf/miniconda3/envs/numpy/lib/python3.6/site-packages/numpy/core/__init__.py", line 24, in <module>
    raise ImportError(msg)
ImportError:
Importing the multiarray numpy extension module failed.  Most
likely you are trying to import a failed build of numpy.
If you're working with a numpy git repo, try `git clean -xdf` (removes all
files not under version control).  Otherwise reinstall numpy.

(numpy) $ conda info
Using Anaconda API: https://api.anaconda.org
Current conda install:

             platform : osx-64
        conda version : 4.0.11
  conda-build version : not installed
       python version : 3.5.2.final.0
     requests version : 2.11.1
     root environment : /Users/csadorf/miniconda3  (writable)
  default environment : /Users/csadorf/miniconda3/envs/numpy
     envs directories : /Users/csadorf/miniconda3/envs
        package cache : /Users/csadorf/miniconda3/pkgs
         channel URLs : https://repo.continuum.io/pkgs/free/osx-64/
                        https://repo.continuum.io/pkgs/free/noarch/
                        https://repo.continuum.io/pkgs/pro/osx-64/
                        https://repo.continuum.io/pkgs/pro/noarch/
                        https://conda.anaconda.org/conda-forge/osx-64/
                        https://conda.anaconda.org/conda-forge/noarch/
                        https://conda.anaconda.org/glotzer/osx-64/
                        https://conda.anaconda.org/glotzer/noarch/
                        file:///nfs/glotzer/software/conda-private/osx-64/
                        file:///nfs/glotzer/software/conda-private/noarch/
          config file : /Users/csadorf/.condarc
    is foreign system : False

(numpy) $ conda list
# packages in environment at /Users/csadorf/miniconda3/envs/numpy:
#
DEPRECATION: The default format will switch to columns in the future. You can use --format=(legacy|columns) (or define a format=(legacy|columns) in your pip.conf under the [list] section) to disable this warning.
blas                      1.1                    openblas    conda-forge
certifi                   2016.9.26                py36_0    conda-forge
numpy                     1.12.0          py36_blas_openblas_200  [blas_openblas]  conda-forge
openblas                  0.2.19                        0    conda-forge
openssl                   1.0.2j                        0    defaults
pip                       9.0.1                    py36_1    defaults
python                    3.6.0                         1    conda-forge
readline                  6.2                           2    defaults
setuptools                32.3.1                   py36_0    conda-forge
sqlite                    3.13.0                        1    conda-forge
tk                        8.5.19                        1    conda-forge
wheel                     0.29.0                   py36_0    defaults
xz                        5.2.2                         1    defaults
zlib                      1.2.8                         3    conda-forge

The text was updated successfully, but these errors were encountered:

csadorf · 2017-01-19T20:52:24Z

So I think I was able to determine that the issue only occurs when the defaults channel has a higher priority than conda-forge.

So I assume that is not a supported conda configuration?

jakirkham · 2017-01-19T21:15:49Z

Correct, conda-forge needs to be higher priority than defaults for things to work. It is also the configuration used for building and testing here.

jjhelmus · 2017-01-31T15:52:13Z

There does not appear to be a libgfortan package installed in the environment even though openblas declares it as a requirement.

Note that the numpy, openblas and the libgfortran packages in the defaults and conda-forge channels are not interchangeable. All three packages should be installed from the same channel, mixing and matching them can results in errors like this.

laventura · 2017-07-14T07:25:04Z

Hello --

Is the problem above resolved?? I'm kinda stuck. Appreciate any pointers! Thanks!

I installed a new conda environment called tfk-py35 (with py35) on Mac OS X 10.11.6 - and I get the same error that was listed above.

 tfk-py35 ▶ ~ ▶ $ ▶ python
Python 3.5.3 | packaged by conda-forge | (default, May 12 2017, 15:35:12)
[GCC 4.2.1 Compatible Apple LLVM 6.1.0 (clang-602.0.53)] on darwin
Type "help", "copyright", "credits" or "license" for more information.
>>> import scipy
Traceback (most recent call last):
  File "/Users/aa/Developer/miniconda/envs/tfk-py35/lib/python3.5/site-packages/numpy/core/__init__.py", line 16, in <module>
    from . import multiarray
ImportError: dlopen(/Users/aa/Developer/miniconda/envs/tfk-py35/lib/python3.5/site-packages/numpy/core/multiarray.cpython-35m-darwin.so, 2): Library not loaded: @rpath/libgfortran.3.dylib
  Referenced from: /Users/aa/Developer/miniconda/envs/tfk-py35/lib/libopenblasp-r0.2.19.dylib
  Reason: image not found

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "/Users/aa/Developer/miniconda/envs/tfk-py35/lib/python3.5/site-packages/scipy/__init__.py", line 61, in <module>
    from numpy import show_config as show_numpy_config
  File "/Users/aa/Developer/miniconda/envs/tfk-py35/lib/python3.5/site-packages/numpy/__init__.py", line 142, in <module>
    from . import add_newdocs
  File "/Users/aa/Developer/miniconda/envs/tfk-py35/lib/python3.5/site-packages/numpy/add_newdocs.py", line 13, in <module>
    from numpy.lib import add_newdoc
  File "/Users/aa/Developer/miniconda/envs/tfk-py35/lib/python3.5/site-packages/numpy/lib/__init__.py", line 8, in <module>
    from .type_check import *
  File "/Users/aa/Developer/miniconda/envs/tfk-py35/lib/python3.5/site-packages/numpy/lib/type_check.py", line 11, in <module>
    import numpy.core.numeric as _nx
  File "/Users/aa/Developer/miniconda/envs/tfk-py35/lib/python3.5/site-packages/numpy/core/__init__.py", line 26, in <module>
    raise ImportError(msg)
ImportError:
Importing the multiarray numpy extension module failed.  Most
likely you are trying to import a failed build of numpy.
If you're working with a numpy git repo, try `git clean -xdf` (removes all
files not under version control).  Otherwise reinstall numpy.

Original error was: dlopen(/Users/aa/Developer/miniconda/envs/tfk-py35/lib/python3.5/site-packages/numpy/core/multiarray.cpython-35m-darwin.so, 2): Library not loaded: @rpath/libgfortran.3.dylib
  Referenced from: /Users/aa/Developer/miniconda/envs/tfk-py35/lib/libopenblasp-r0.2.19.dylib
  Reason: image not found

Here's the conda info:

 ~ ▶ $ ▶ conda info
Using Anaconda Cloud api site https://api.anaconda.org
Current conda install:

             platform : osx-64
        conda version : 4.0.5
  conda-build version : not installed
       python version : 2.7.11.final.0
     requests version : 2.9.1
     root environment : /Users/aa/Developer/miniconda  (writable)
  default environment : /Users/aa/Developer/miniconda
     envs directories : /Users/aa/Developer/miniconda/envs
        package cache : /Users/aa/Developer/miniconda/pkgs
         channel URLs : https://conda.anaconda.org/conda-forge/osx-64/
                        https://conda.anaconda.org/conda-forge/noarch/
                        https://repo.continuum.io/pkgs/free/osx-64/
                        https://repo.continuum.io/pkgs/free/noarch/
                        https://repo.continuum.io/pkgs/pro/osx-64/
                        https://repo.continuum.io/pkgs/pro/noarch/
          config file : /Users/aa/.condarc
    is foreign system : False

Here are the packages installed in the env tfk-py35 below:

 tfk-py35 ▶ ~ ▶ $ ▶ conda list
# packages in environment at /Users/aa/Developer/miniconda/envs/tfk-py35:
#
DEPRECATION: The default format will switch to columns in the future. You can use --format=(legacy|columns) (or define a format=(legacy|columns) in your pip.conf under the [list] section) to disable this warning.
blas                      1.1                    openblas    conda-forge
ca-certificates           2017.4.17                     0    conda-forge
certifi                   2017.4.17                py35_0    conda-forge
libgfortran               3.0.0                         1    defaults
numpy                     1.13.1          py35_blas_openblas_200  [blas_openblas]  conda-forge
openblas                  0.2.19                        2    conda-forge
openssl                   1.0.2l                        0    conda-forge
pip                       9.0.1                    py35_1    defaults
python                    3.5.3                         3    conda-forge
readline                  6.2                           2    <unknown>
scipy                     0.19.1          np113py35_blas_openblas_200  [blas_openblas]  conda-forge
setuptools                33.1.1                   py35_0    conda-forge
sqlite                    3.13.0                        1    conda-forge
tk                        8.5.19                        1    conda-forge
wheel                     0.29.0                   py35_0    defaults
xz                        5.2.2                         1    defaults
zlib                      1.2.11                        0    conda-forge
 tfk-py35 ▶ ~ ▶ $ ▶

Here's how the env was created:

 ~ ▶ $ ▶ conda create --name tfk-py35 python=3.5 numpy scipy
Using Anaconda Cloud api site https://api.anaconda.org
Fetching package metadata: ......
Solving package specifications: .........

Package plan for installation in environment /Users/aa/Developer/miniconda/envs/tfk-py35:

The following packages will be downloaded:

    package                    |            build
    ---------------------------|-----------------
    scipy-0.19.1               |np113py35_blas_openblas_200        15.1 MB

The following NEW packages will be INSTALLED:

    blas:            1.1-openblas
    ca-certificates: 2017.4.17-0
    certifi:         2017.4.17-py35_0
    libgfortran:     3.0.0-1
    numpy:           1.13.1-py35_blas_openblas_200      [blas_openblas]
    openblas:        0.2.19-2
    openssl:         1.0.2l-0
    pip:             9.0.1-py35_1
    python:          3.5.3-3
    readline:        6.2-2
    scipy:           0.19.1-np113py35_blas_openblas_200 [blas_openblas]
    setuptools:      33.1.1-py35_0
    sqlite:          3.13.0-1
    tk:              8.5.19-1
    wheel:           0.29.0-py35_0
    xz:              5.2.2-1
    zlib:            1.2.11-0

Proceed ([y]/n)? y

Fetching packages ...
scipy-0.19.1-n 100% |#########################################################################################| Time: 0:00:02   6.54 MB/s
Extracting packages ...
[      COMPLETE      ]|############################################################################################################| 100%
Linking packages ...
[      COMPLETE      ]|############################################################################################################| 100%
#
# To activate this environment, use:
# $ source activate tfk-py35
#
# To deactivate this environment, use:
# $ source deactivate
#
 ~ ▶ $ ▶ source activate tfk-py35
discarding /Users/aa/Developer/miniconda/bin from PATH
prepending /Users/aa/Developer/miniconda/envs/tfk-py35/bin to PATH
 tfk-py35 ▶ ~ ▶ $ ▶ python -V
Python 3.5.3
 tfk-py35 ▶ ~ ▶ $ ▶ conda list
# packages in environment at /Users/aa/Developer/miniconda/envs/tfk-py35:
#
DEPRECATION: The default format will switch to columns in the future. You can use --format=(legacy|columns) (or define a format=(legacy|columns) in your pip.conf under the [list] section) to disable this warning.
blas                      1.1                    openblas    conda-forge
ca-certificates           2017.4.17                     0    conda-forge
certifi                   2017.4.17                py35_0    conda-forge
libgfortran               3.0.0                         1    defaults
numpy                     1.13.1          py35_blas_openblas_200  [blas_openblas]  conda-forge
openblas                  0.2.19                        2    conda-forge
openssl                   1.0.2l                        0    conda-forge
pip                       9.0.1                    py35_1    defaults
python                    3.5.3                         3    conda-forge
readline                  6.2                           2    <unknown>
scipy                     0.19.1          np113py35_blas_openblas_200  [blas_openblas]  conda-forge
setuptools                33.1.1                   py35_0    conda-forge
sqlite                    3.13.0                        1    conda-forge
tk                        8.5.19                        1    conda-forge
wheel                     0.29.0                   py35_0    defaults
xz                        5.2.2                         1    defaults
zlib                      1.2.11                        0    conda-forge

csadorf · 2017-07-14T15:16:09Z

When I created this issue having conda-forge prioritized was an immediate solution. But since then, I have tried again to prioritize defaults and haven't had any issues with that lately.

jakirkham · 2017-07-14T15:27:39Z

Again that is not a supported configuration. So while you can use it, it remains unsupported. Issues stemming from the wrong channel ordering will be closed out.

csadorf · 2017-07-14T15:30:47Z

Again that is not a supported configuration. So while you can use it, it remains unsupported. Issues stemming from the wrong channel ordering will be closed out.

That's perfectly fine with me. I just wanted to let @laventura know that this particular problem is currently no issue for me.

laventura · 2017-07-14T16:04:44Z

I have this in ~/.condarc, (which I haven't touched). I'm assuming this is the normal config.

 tfk-py35 ▶ ~ ▶ $ ▶ more ~/.condarc
channels:
  - conda-forge
  - defaults
 tfk-py35 ▶ ~ ▶ $ ▶

SO - as it stands -- what's the solution for this import numpy error that has a problem with @rpath/libgfortran.3.dylib? Any other avenues to try out? Thanks!

jakirkham · 2017-07-14T17:46:18Z

It looks like you got libgfortran from defaults though. Not sure why though. 😕 Could you please try forcing it to install the libgfortran from conda-forge?

laventura · 2017-07-14T18:04:15Z

@jakirkham I tried re-installing libgfortran from conda-forge.

See what happens:

It still says: libgfortran is from defaults
In the miniconda/pkgs directory, there are TWO directories: libgfortran-3.0.0-0 and libgfortran-3.0.0-1. The latter one has a missing libgfortran3.dylib

Current conda list:

 tfk-py35 ▶ ~ ▶ Developer ❯ … ❯ envs ❯ tfk-py35 ❯ lib ▶ $ ▶ conda list
# packages in environment at /Users/aa/Developer/miniconda/envs/tfk-py35:
#
DEPRECATION: The default format will switch to columns in the future. You can use --format=(legacy|columns) (or define a format=(legacy|columns) in your pip.conf under the [list] section) to disable this warning.
blas                      1.1                    openblas    conda-forge
ca-certificates           2017.4.17                     0    conda-forge
certifi                   2017.4.17                py35_0    conda-forge
libgfortran               3.0.0                         1    defaults
numpy                     1.13.1          py35_blas_openblas_200  [blas_openblas]  conda-forge
openblas                  0.2.19                        2    conda-forge
openssl                   1.0.2l                        0    conda-forge
pip                       9.0.1                    py35_1    defaults
python                    3.5.3                         3    conda-forge
readline                  6.2                           2    <unknown>
scipy                     0.19.1          np113py35_blas_openblas_200  [blas_openblas]  conda-forge
setuptools                33.1.1                   py35_0    conda-forge
sqlite                    3.13.0                        1    conda-forge
tk                        8.5.19                        1    conda-forge
wheel                     0.29.0                   py35_0    defaults
xz                        5.2.2                         1    defaults
zlib                      1.2.11                        0    conda-forge

Now re-installing libgfortran:

 tfk-py35 ▶ ~ ▶ Developer ❯ … ❯ envs ❯ tfk-py35 ❯ lib ▶ $ ▶ conda install -c conda-forge -f libgfortran
Using Anaconda Cloud api site https://api.anaconda.org
Fetching package metadata: ........
Solving package specifications: .........

Package plan for installation in environment /Users/aa/Developer/miniconda/envs/tfk-py35:

The following packages will be UPDATED:

    libgfortran: 3.0.0-1 --> 3.0.0-1

Proceed ([y]/n)? y

[      COMPLETE      ]|############################################################################################################| 100%
Extracting packages ...
[      COMPLETE      ]|############################################################################################################| 100%
Unlinking packages ...
[      COMPLETE      ]|############################################################################################################| 100%
Linking packages ...
[      COMPLETE      ]|############################################################################################################| 100%
 tfk-py35 ▶ ~ ▶ Developer ❯ … ❯ envs ❯ tfk-py35 ❯ lib ▶ $ ▶

NEW conda list

 tfk-py35 ▶ ~ ▶ Developer ❯ … ❯ envs ❯ tfk-py35 ❯ lib ▶ $ ▶ conda list
# packages in environment at /Users/aa/Developer/miniconda/envs/tfk-py35:
#
DEPRECATION: The default format will switch to columns in the future. You can use --format=(legacy|columns) (or define a format=(legacy|columns) in your pip.conf under the [list] section) to disable this warning.
blas                      1.1                    openblas    conda-forge
ca-certificates           2017.4.17                     0    conda-forge
certifi                   2017.4.17                py35_0    conda-forge
libgfortran               3.0.0                         1    defaults
numpy                     1.13.1          py35_blas_openblas_200  [blas_openblas]  conda-forge
openblas                  0.2.19                        2    conda-forge
openssl                   1.0.2l                        0    conda-forge
pip                       9.0.1                    py35_1    defaults
python                    3.5.3                         3    conda-forge
readline                  6.2                           2    <unknown>
scipy                     0.19.1          np113py35_blas_openblas_200  [blas_openblas]  conda-forge
setuptools                33.1.1                   py35_0    conda-forge
sqlite                    3.13.0                        1    conda-forge
tk                        8.5.19                        1    conda-forge
wheel                     0.29.0                   py35_0    defaults
xz                        5.2.2                         1    defaults
zlib                      1.2.11                        0    conda-forge
 tfk-py35 ▶ ~ ▶ Developer ❯ … ❯ envs ❯ tfk-py35 ❯ lib ▶ $ ▶

When I go:
** Now navigate to /Users/aa/Developer/miniconda/pkgs where the pkgs are:**

 ~ ▶ Developer ❯ miniconda ❯ pkgs ▶ $ ▶ ls -l *fortran*
-rw-r--r--  1 aa  staff  476327 Jan 13 16:59 libgfortran-3.0.0-0.tar.bz2
-rw-r--r--  1 aa  staff  220995 Jul 13 23:15 libgfortran-3.0.0-1.tar.bz2

libgfortran-3.0.0-0:
total 0
drwxr-xr-x  6 aa  staff  204 Jan 13 17:00 info
drwxr-xr-x  9 aa  staff  306 Jan 13 17:00 lib

libgfortran-3.0.0-1:
total 0
drwxr-xr-x  8 aa  staff  272 Jul 14 10:49 info
drwxr-xr-x  3 aa  staff  102 Jul 14 10:49 lib

Inside libgfortran-3.0.0.-0, here are all the files, which clearly shows libgfortran.3.dylib:

 ~ ▶ Developer ❯ miniconda ❯ pkgs ▶ $ ▶ ls -lR libgfortran-3.0.0-0
total 0
drwxr-xr-x  6 aa  staff  204 Jan 13 17:00 info
drwxr-xr-x  9 aa  staff  306 Jan 13 17:00 lib

libgfortran-3.0.0-0/info:
total 24
-rw-r--r--  1 aa  staff   168 Jul 13  2016 files
-rw-r--r--  1 aa  staff   229 Jul 13  2016 index.json
drwxr-xr-x  3 aa  staff   102 Jan 13 17:00 recipe
-rw-r--r--  1 aa  staff  1498 Jul 13  2016 recipe.json

libgfortran-3.0.0-0/info/recipe:
total 8
-rw-r--r--  1 aa  staff  2148 Jul 13  2016 meta.yaml

libgfortran-3.0.0-0/lib:
total 3128
-rw-r--r--  2 aa  staff   130336 Sep 18  2015 libgcc_s.1.dylib
lrwxr-xr-x  1 aa  staff       16 Jan 13 17:00 libgcc_s_ppc64.1.dylib -> libgcc_s.1.dylib
lrwxr-xr-x  1 aa  staff       16 Jan 13 17:00 libgcc_s_x86_64.1.dylib -> libgcc_s.1.dylib
-rwxr-xr-x  2 aa  staff  1220864 Sep 18  2015 libgfortran.3.dylib
lrwxr-xr-x  1 aa  staff       19 Jan 13 17:00 libgfortran.dylib -> libgfortran.3.dylib
-rwxr-xr-x  2 aa  staff   228048 Sep 18  2015 libquadmath.0.dylib
lrwxr-xr-x  1 aa  staff       19 Jan 13 17:00 libquadmath.dylib -> libquadmath.0.dylib

But inside libgfortran-3.0.0-1, the libgfortran.3.dylib is missing!!

~ ▶ Developer ❯ miniconda ❯ pkgs ▶ $ ▶ ls -lR libgfortran-3.0.0-1
total 0
drwxr-xr-x  8 aa  staff  272 Jul 14 10:49 info
drwxr-xr-x  3 aa  staff  102 Jul 14 10:49 lib

libgfortran-3.0.0-1/info:
total 88
-rw-r--r--  1 aa  staff  12693 Jan 24 17:42 about.json
-rw-r--r--  1 aa  staff     24 Jan 24 17:42 files
-rw-r--r--  1 aa  staff    195 Jan 24 17:42 index.json
-rw-r--r--  1 aa  staff    242 Jan 24 17:42 paths.json
-rw-r--r--  1 aa  staff    342 Jan 24 17:42 platform
-rw-r--r--  1 aa  staff  10240 Jan 24 17:42 recipe.tar

libgfortran-3.0.0-1/lib:
total 2008
-rwxrwxr-x  2 aa  staff  1027349 Jan 24 17:42 libgfortran.2.dylib
 ~ ▶ Developer ❯ miniconda ❯ pkgs ▶ $ ▶

Am I doing something wrong?? Am I missing something small and stupid somewhere?
Appreciate your help! Thanks!

laventura · 2017-07-14T18:22:37Z

@jakirkham Well, I looked into the bz2 archives for libgfortran-3.0.0-1.

Looks like it is missing a whole bunch of files.

See here for comparison:

 tmp ▶ $ ▶ tar tvf libgfortran-3.0.0-0.tar
-rw-r--r--  0 travis staff     168 Jul 13  2016 info/files
-rw-r--r--  0 travis staff     229 Jul 13  2016 info/index.json
-rw-r--r--  0 travis staff    1498 Jul 13  2016 info/recipe.json
-rw-r--r--  0 travis staff    2148 Jul 13  2016 info/recipe/meta.yaml
-rw-r--r--  0 travis staff  130336 Sep 18  2015 lib/libgcc_s.1.dylib
lrwxr-xr-x  0 travis staff       0 Jul 13  2016 lib/libgcc_s_ppc64.1.dylib -> libgcc_s.1.dylib
lrwxr-xr-x  0 travis staff       0 Jul 13  2016 lib/libgcc_s_x86_64.1.dylib -> libgcc_s.1.dylib
-rwxr-xr-x  0 travis staff 1220864 Sep 18  2015 lib/libgfortran.3.dylib
lrwxr-xr-x  0 travis staff       0 Jul 13  2016 lib/libgfortran.dylib -> libgfortran.3.dylib
-rwxr-xr-x  0 travis staff  228048 Sep 18  2015 lib/libquadmath.0.dylib
lrwxr-xr-x  0 travis staff       0 Jul 13  2016 lib/libquadmath.dylib -> libquadmath.0.dylib
 tmp ▶ $ ▶
 tmp ▶ $ ▶ tar tvf libgfortran-3.0.0-1.tar
-rw-r--r--  0 ilan   wheel   12693 Jan 24 17:42 info/about.json
-rw-r--r--  0 ilan   wheel      24 Jan 24 17:42 info/files
-rw-r--r--  0 ilan   wheel     195 Jan 24 17:42 info/index.json
-rw-r--r--  0 ilan   wheel     242 Jan 24 17:42 info/paths.json
-rw-r--r--  0 ilan   wheel     342 Jan 24 17:42 info/platform
-rw-r--r--  0 ilan   wheel   10240 Jan 24 17:42 info/recipe.tar
-rwxrwxr-x  0 ilan   wheel 1027349 Jan 24 17:42 lib/libgfortran.2.dylib
 tmp ▶ $ ▶

What's the best approach to get the latest (and correct) libgfortran files? Thanks!

jakirkham · 2017-07-14T18:35:17Z

There is no libgfortran-3.0.0-1 in conda-forge. That is from defaults. It is bad that the package doesn't seem to have a version that matches the SONAME and has missing file. Not sure why that is the case. 😕 In any event, that would be an issue to raise at anaconda-recipes.

There are a few ways to solve this. First given the channel order that you showed above with conda-forge as the highest priority, running conda update --all or conda update libgfortran should fix it. May also try adding the argument -c conda-forge. If that doesn't work, you could try conda install libgfortran=3.0.0=0 as this version/build number is unique to conda-forge.

laventura · 2017-07-14T19:20:27Z

@jakirkham Ok great! Something worked!

I tried conda update -c conda-forge --all but that did nothing.

So finally conda install libgfortran=3.0.0=0 worked!!
Phew. Spent 10+ hours since last night trying to sort this out. Thanks for your help!! 👍👍

Now I can proceed with installing other packages 😑

jakirkham · 2017-07-14T20:52:38Z

Glad to hear it worked. Sorry to hear it's been so much trouble.

It's a bit strange conda didn't respect channel priority, which version of conda are you using?

Yeah, I know that feeling. Hopefully the rest are not so painful.

hopefully this will fix the build on osx which seems to suffer from the problems described in conda-forge/numpy-feedstock#47

quantshah · 2017-08-03T06:35:45Z

Well, this keeps propping up for me too when I update Keras. Updating everything from the conda-forge channel and elevating the conda-forge channel to the highest priority does not solve it.

conda update -c conda-forge --all
conda config --add channels conda-forge

add_anaconda_token: True
add_pip_as_python_dependency: True
allow_non_channel_urls: True
allow_softlinks: True
always_copy: False
always_softlink: False
always_yes: False
anaconda_upload: None
auto_update_conda: True
changeps1: True
channel_alias: https://conda.anaconda.org
channel_priority: True
channels:
  - conda-forge
  - defaults

I still have this error

ImportError:
Importing the multiarray numpy extension module failed.  Most
likely you are trying to import a failed build of numpy.
If you're working with a numpy git repo, try `git clean -xdf` (removes all
files not under version control).  Otherwise reinstall numpy.

Original error was: dlopen(/Users/shahnawaz/miniconda3/lib/python3.5/site-packages/numpy/core/multiarray.cpython-35m-darwin.so, 2): Library not loaded: @rpath/libgfortran.3.dylib
  Referenced from: /Users/shahnawaz/miniconda3/lib/libopenblasp-r0.2.19.dylib
  Reason: image not found

quantshah · 2017-08-03T07:19:33Z

@jakirkham Thanks for the libgfortran fix. Everything works now ! I was just going nuts for the last few days with this issue. It happened after I updated libgfortran some time back.

jakirkham · 2017-08-03T17:49:43Z

Probably someone should raise a conda issue if channel priority is not being respected.

jakirkham closed this as completed Jan 19, 2017

laventura mentioned this issue Jul 14, 2017

libgfortran-3.0.0-1 tar file missing several files (in conda-forge channel) ContinuumIO/anaconda-recipes#119

Open

megies added a commit to obspy/anaconda-installers that referenced this issue Jul 15, 2017

elevate conda-forge channel to highest priority

4ffca67

hopefully this will fix the build on osx which seems to suffer from the problems described in conda-forge/numpy-feedstock#47

megies mentioned this issue Jul 16, 2017

Problem with osx-64 obspy/anaconda-installers#4

Open

kyleabeauchamp mentioned this issue Dec 12, 2017

openblas requirement conda-forge/pymc-feedstock#1

Closed

andyharless mentioned this issue Feb 24, 2019

import scipy.stats fails (Reason: image not found) scipy/scipy#6412

Closed

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Import Error on Mac OS-X with 1.12.0 #47

Import Error on Mac OS-X with 1.12.0 #47

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Import Error on Mac OS-X with 1.12.0 #47

Import Error on Mac OS-X with 1.12.0 #47

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