pygmt: libpoppler.so.71: cannot open shared object file: No such file or directory

>>> import gmt
Traceback (most recent call last):
  File "/users1j/cliu/soft/anaconda2/envs/gmt-python/lib/python3.6/site-packages/gmt/clib/utils.py", line 159, in load_libgmt
    libgmt = ctypes.CDLL('.'.join([libname, clib_extension()]))
  File "/users1j/cliu/soft/anaconda2/envs/gmt-python/lib/python3.6/ctypes/__init__.py", line 348, in __init__
    self._handle = _dlopen(self._name, mode)
OSError: libpoppler.so.71: cannot open shared object file: No such file or directory

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "/users1j/cliu/soft/anaconda2/envs/gmt-python/lib/python3.6/site-packages/gmt/__init__.py", line 27, in <module>
    _begin()
  File "/users1j/cliu/soft/anaconda2/envs/gmt-python/lib/python3.6/site-packages/gmt/session_management.py", line 17, in begin
    with LibGMT() as lib:
  File "/users1j/cliu/soft/anaconda2/envs/gmt-python/lib/python3.6/site-packages/gmt/clib/core.py", line 103, in __init__
    self._bind_clib_functions(libname)
  File "/users1j/cliu/soft/anaconda2/envs/gmt-python/lib/python3.6/site-packages/gmt/clib/core.py", line 136, in _bind_clib_functions
    self._libgmt = load_libgmt(libname)
  File "/users1j/cliu/soft/anaconda2/envs/gmt-python/lib/python3.6/site-packages/gmt/clib/utils.py", line 168, in load_libgmt
    raise GMTCLibNotFoundError(msg)
gmt.exceptions.GMTCLibNotFoundError: Couldn't find the GMT shared library 'libgmt'. Have you tried setting the LD_LIBRARY_PATH environment variable?
Original error message:

    libpoppler.so.71: cannot open shared object file: No such file or directory

About this issue

Original URL
State: closed
Created 7 years ago
Comments: 19 (9 by maintainers)

Commits related to this issue

Instruct users to enable conda-forge channel Not having conda-forge in the conda config can cause problems with conflicting versions of gdal and other dependencies. This can be fixed by calling `cond... — committed to GenericMappingTools/pygmt by leouieda 6 years ago
Instruct users to enable conda-forge channel (#137) Not having conda-forge in the conda config can cause problems with conflicting versions of gdal and other dependencies. This can be fixed by call... — committed to GenericMappingTools/pygmt by leouieda 6 years ago

Most upvoted comments

This is the line of syntax seemed to have fixed by issue.

source activate [env-name]
conda config --add channels conda-forge
conda install gdal

After which run the

conda list

command to make sure packages are coming from conda-forge

+14

adamnicholasprice on Mar 1, 2018

@adamnicholasprice thanks! I think I see a problem. Your gdal isn’t coming from conda-forge for some reason but poppler is. That might be causing the linking issue. Could you try the following please?

Delete the gmt-python environment:

conda env remove --name gmt-python

Create (or edit) a .condarc file in your home directory to include this (it will make conda-forge a priority):

channels:
  - conda-forge
  - defaults

Repeat the install process. If things don’t work, check conda list to see if gdal is coming from the conda-forge channel and report back.

More information about these issues on the conda-forge documentation: https://conda-forge.org/docs/conda-forge_gotchas.html

leouieda on Feb 27, 2018

I know this is closed but…I had a lot of problem recently with these issues. gmt would switch down to 5.4 when trying to work the conda-forge feedstock, having errors like @rpath/libpoppler.76.dylib Referenced from: /anaconda3/envs/gmt-python/lib/libgdal.20.dylib.

I checked my conda list and gdal was from the conda feedstock. But libgdal wasnt. So…

conda install -c conda-forge libgdal

This worked.

Great program - Only thing with the install instructions I would say may help is to link/integrate the install instructions to the feedstock instructions a little more. Just a bit of friendly feedback - feel free to ignore if Im being an idiot! I got a little confused - thanks 😃

hammytheham on Oct 22, 2018

@DennisScuba I’ve had the same issue as yours and ended up building a new conda env.

AloshkaD on Jun 12, 2018

@adamnicholasprice thanks for reporting the issue.

Did you follow the instructions in http://www.gmtpython.xyz/install.html for installing in a conda environment? If so, could you please post the output of conda list?

leouieda on Feb 26, 2018