libpoppler.so.76: cannot open shared object file: No such file or directory

[eamonustc]

When I install gmt-python on Ubuntu 18.04, I got the following error. I have checked conda list. I used gdal from conda-forge

Are you willing to help implement and maintain this feature? Yes/No
Yes

Full code that generated the error

import gmt

Full error message

/home/eamon/anaconda2/envs/gmt-python/lib/python3.6/importlib/_bootstrap.py:219: RuntimeWarning: numpy.dtype size changed, may indicate binary incompatibility. Expected 96, got 88
  return f(*args, **kwds)
Traceback (most recent call last):
  File "/home/eamon/anaconda2/envs/gmt-python/lib/python3.6/site-packages/gmt/clib/loading.py", line 42, in load_libgmt
    libgmt = ctypes.CDLL(libpath)
  File "/home/eamon/anaconda2/envs/gmt-python/lib/python3.6/ctypes/__init__.py", line 348, in __init__
    self._handle = _dlopen(self._name, mode)
OSError: libpoppler.so.76: 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 "/home/eamon/anaconda2/envs/gmt-python/lib/python3.6/site-packages/gmt/__init__.py", line 25, in <module>
    _begin()
  File "/home/eamon/anaconda2/envs/gmt-python/lib/python3.6/site-packages/gmt/session_management.py", line 17, in begin
    with Session() as lib:
  File "/home/eamon/anaconda2/envs/gmt-python/lib/python3.6/site-packages/gmt/clib/session.py", line 172, in __enter__
    self.create("gmt-python-session")
  File "/home/eamon/anaconda2/envs/gmt-python/lib/python3.6/site-packages/gmt/clib/session.py", line 313, in create
    restype=ctp.c_void_p,
  File "/home/eamon/anaconda2/envs/gmt-python/lib/python3.6/site-packages/gmt/clib/session.py", line 263, in get_libgmt_func
    self._libgmt = load_libgmt()
  File "/home/eamon/anaconda2/envs/gmt-python/lib/python3.6/site-packages/gmt/clib/loading.py", line 51, in load_libgmt
    raise GMTCLibNotFoundError(msg)
gmt.exceptions.GMTCLibNotFoundError: Error loading the GMT shared library '/home/eamon/anaconda2/envs/gmt-python/lib/libgmt.so':
libpoppler.so.76: cannot open shared object file: No such file or directory

System information

• Operating system: Ubuntu 18.04
• Python installation (Anaconda, system, ETS): Anaconda
• Version of GMT: 6.0.0a14
• Version of Python: 3.6
• Version of this package: Latest
• If using conda, paste the output of conda list below:

# packages in environment at /home/eamon/anaconda2/envs/gmt-python:
#
# Name                    Version                   Build  Channel
blas                      1.1                    openblas    conda-forge
bokeh                     0.13.0                   py36_0    conda-forge
boost-cpp                 1.67.0               h3a22d5f_0    conda-forge
bottleneck                1.2.1            py36h7eb728f_1    conda-forge
bzip2                     1.0.6                h470a237_2    conda-forge
ca-certificates           2018.4.16                     0    conda-forge
cairo                     1.14.12              he56eebe_3    conda-forge
certifi                   2018.4.16                py36_0    conda-forge
click                     6.7                        py_1    conda-forge
cloudpickle               0.5.3                      py_0    conda-forge
curl                      7.61.0               h84994c4_0  
cytoolz                   0.9.0.1          py36h470a237_0    conda-forge
dask                      0.18.2                     py_0    conda-forge
dask-core                 0.18.2                     py_0    conda-forge
dcw-gmt                   1.1.4                         0    conda-forge
distributed               1.22.0                   py36_0    conda-forge
expat                     2.2.5                hfc679d8_1    conda-forge
fftw                      3.3.8                h470a237_0    conda-forge
fontconfig                2.13.0               h0c61d53_4    conda-forge
freetype                  2.8.1                hfa320df_1    conda-forge
freexl                    1.0.5                hf837533_1    conda-forge
gdal                      2.2.4            py36hb00a9d7_1    conda-forge
geos                      3.6.2                hfc679d8_2    conda-forge
gettext                   0.19.8.1                      0    conda-forge
ghostscript               9.22                 hfc679d8_1    conda-forge
giflib                    5.1.4                h470a237_0    conda-forge
glib                      2.55.0               h464dc38_2    conda-forge
gmt                       6.0.0a14        blas_openblas_201  [blas_openblas]  conda-forge/label/dev
gmt-python                0+unknown                 <pip>
gshhg-gmt                 2.3.7                         0    conda-forge
h5netcdf                  0.6.1                      py_0    conda-forge
h5py                      2.8.0            py36h470a237_0    conda-forge
hdf4                      4.2.13                        0    conda-forge
hdf5                      1.10.1                        2    conda-forge
heapdict                  1.0.0                    py36_0    conda-forge
icu                       58.2                 hfc679d8_0    conda-forge
jinja2                    2.10                       py_1    conda-forge
jpeg                      9c                   h470a237_0    conda-forge
json-c                    0.13.1               h470a237_0    conda-forge
kealib                    1.4.8                hfc679d8_0    conda-forge
krb5                      1.16.1               hbb41f41_0    conda-forge
libcurl                   7.61.0               h1ad7b7a_0  
libdap4                   3.19.1                        0    conda-forge
libedit                   3.1.20170329         haf1bffa_1    conda-forge
libffi                    3.2.1                         3    conda-forge
libgcc-ng                 7.2.0                hdf63c60_3  
libgdal                   2.2.4                hc8d23f9_1  
libgfortran               3.0.0                         1  
libiconv                  1.15                 h470a237_1    conda-forge
libkml                    1.3.0                hccc92b1_8    conda-forge
libnetcdf                 4.4.1.1                      10    conda-forge
libpng                    1.6.35               ha92aebf_0    conda-forge
libpq                     10.4                 h1ad7b7a_0  
libspatialite             4.3.0a              hdfcc80b_21    conda-forge
libssh2                   1.8.0                h5b517e9_2    conda-forge
libstdcxx-ng              7.2.0                hdf63c60_3  
libtiff                   4.0.9                he6b73bb_1    conda-forge
libuuid                   1.0.3                         1    conda-forge
libxcb                    1.13                 h470a237_2    conda-forge
libxml2                   2.9.8                h422b904_2    conda-forge
locket                    0.2.0                      py_2    conda-forge
markupsafe                1.0                      py36_0    conda-forge
msgpack-python            0.5.6            py36h2d50403_2    conda-forge
ncurses                   6.1                  hfc679d8_1    conda-forge
netcdf4                   1.3.1                    py36_1    conda-forge
numpy                     1.15.0          py36_blas_openblashd3ea46f_200  [blas_openblas]  conda-forge
openblas                  0.2.20                        8    conda-forge
openjpeg                  2.3.0                h0e734dc_3    conda-forge
openssl                   1.0.2o               h470a237_1    conda-forge
packaging                 17.1                       py_0    conda-forge
pandas                    0.23.3           py36hf8a1672_1    conda-forge
partd                     0.3.8                      py_1    conda-forge
pcre                      8.42                 h439df22_0  
pip                       18.0                     py36_1    conda-forge
pixman                    0.34.0                        2    conda-forge
poppler                   0.67.0               hb55ee21_1    conda-forge
poppler-data              0.4.9                         0    conda-forge
proj4                     4.9.3                         5    conda-forge
psutil                    5.4.6                    py36_0    conda-forge
pthread-stubs             0.4                  h470a237_1    conda-forge
pyparsing                 2.2.0                      py_1    conda-forge
python                    3.6.6                h5001a0f_0    conda-forge
python-dateutil           2.7.3                      py_0    conda-forge
pytz                      2018.5                     py_0    conda-forge
pyyaml                    3.12                     py36_1    conda-forge
readline                  7.0                  haf1bffa_1    conda-forge
scipy                     1.1.0           py36_blas_openblash7943236_201  [blas_openblas]  conda-forge
setuptools                40.0.0                   py36_1    conda-forge
six                       1.11.0                   py36_1    conda-forge
sortedcontainers          2.0.4                      py_1    conda-forge
sqlite                    3.24.0               h2f33b56_0    conda-forge
tblib                     1.3.2                      py_1    conda-forge
tk                        8.6.8                         0    conda-forge
toolz                     0.9.0                      py_0    conda-forge
tornado                   5.1              py36h14c3975_1    conda-forge
util-linux                2.21                          0  
wheel                     0.31.1                   py36_1    conda-forge
xarray                    0.10.8                   py36_0    conda-forge
xerces-c                  3.2.1                h5d6a6da_2    conda-forge
xorg-kbproto              1.0.7                h470a237_2    conda-forge
xorg-libice               1.0.9                h470a237_4    conda-forge
xorg-libsm                1.2.2                h470a237_5    conda-forge
xorg-libx11               1.6.5                h470a237_2    conda-forge
xorg-libxau               1.0.8                h470a237_6    conda-forge
xorg-libxdmcp             1.1.2                h470a237_7    conda-forge
xorg-libxext              1.3.3                h470a237_4    conda-forge
xorg-libxrender           0.9.10               h470a237_2    conda-forge
xorg-renderproto          0.11.1               h470a237_2    conda-forge
xorg-xextproto            7.3.0                h470a237_2    conda-forge
xorg-xproto               7.0.31               h470a237_7    conda-forge
xz                        5.2.4                h470a237_0    conda-forge
yaml                      0.1.7                         0    conda-forge
zict                      0.1.3                      py_0    conda-forge
zlib                      1.2.11               h470a237_3    conda-forge

[welcome]

👋 Thanks for opening your first issue here! Please make sure you filled out the template with as much detail as possible. You might also want to take a look at our contributing guidelines and code of conduct.

[eamonustc]

I also tried to use old version of poppler (0.65.0) and kealib (1.4.7), but still got errors:

>>> import gmt
/home/eamon/anaconda2/envs/gmt-python/lib/python3.6/importlib/_bootstrap.py:219: RuntimeWarning: numpy.dtype size changed, may indicate binary incompatibility. Expected 96, got 88
  return f(*args, **kwds)
Traceback (most recent call last):
  File "/home/eamon/anaconda2/envs/gmt-python/lib/python3.6/site-packages/gmt/clib/loading.py", line 42, in load_libgmt
    libgmt = ctypes.CDLL(libpath)
  File "/home/eamon/anaconda2/envs/gmt-python/lib/python3.6/ctypes/__init__.py", line 348, in __init__
    self._handle = _dlopen(self._name, mode)
OSError: /home/eamon/anaconda2/envs/gmt-python/lib/./libgdal.so.20: undefined symbol: _ZN11xercesc_3_211InputSource11setEncodingEPKDs

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "/home/eamon/anaconda2/envs/gmt-python/lib/python3.6/site-packages/gmt/__init__.py", line 25, in <module>
    _begin()
  File "/home/eamon/anaconda2/envs/gmt-python/lib/python3.6/site-packages/gmt/session_management.py", line 17, in begin
    with Session() as lib:
  File "/home/eamon/anaconda2/envs/gmt-python/lib/python3.6/site-packages/gmt/clib/session.py", line 172, in __enter__
    self.create("gmt-python-session")
  File "/home/eamon/anaconda2/envs/gmt-python/lib/python3.6/site-packages/gmt/clib/session.py", line 313, in create
    restype=ctp.c_void_p,
  File "/home/eamon/anaconda2/envs/gmt-python/lib/python3.6/site-packages/gmt/clib/session.py", line 263, in get_libgmt_func
    self._libgmt = load_libgmt()
  File "/home/eamon/anaconda2/envs/gmt-python/lib/python3.6/site-packages/gmt/clib/loading.py", line 51, in load_libgmt
    raise GMTCLibNotFoundError(msg)
gmt.exceptions.GMTCLibNotFoundError: Error loading the GMT shared library '/home/eamon/anaconda2/envs/gmt-python/lib/libgmt.so':
/home/eamon/anaconda2/envs/gmt-python/lib/./libgdal.so.20: undefined symbol: _ZN11xercesc_3_211InputSource11setEncodingEPKDs

[philcummins]

Hi,
I get the same problem with Mac OS High Sierra. I think in your case both the versions of poppler you installed, 0.67.0 and 0.65.0 are too old, as GDAL seems to want 0.76.0, isn't that right?
In my case, conda seems to have installed a version that's too new, I have 0.78.0 whereas GDAL (n my case libgdal.20.dylib) seems to be looking for 0.76.0.
No one has nay suggestions for a workaround?

• phil

[eamonustc]

Hi Phil,
In Ubuntu, poppler 0.65.0 correspond to libpoppler.so.76.

find ~ -name libpoppler.so.76

/home/eamon/anaconda2/envs/gmt-python/lib/libpoppler.so.76
/home/eamon/anaconda2/pkgs/poppler-0.65.0-h581218d_1/lib/libpoppler.so.76
/home/eamon/anaconda2/pkgs/poppler-0.65.0-ha54bb34_0/lib/libpoppler.so.76

[leouieda]

Hi all, this is still related to some of the headaches from #221 and conda/conda#7656. The problem happens because conda insists on mixing packages from conda-forge and defaults. One way to getting rid of this problem is to remove the "defaults" channel and add conda-forge/label/dev instead:

conda config --remove channels defaults
conda config --append channels conda-forge/label/dev`

If you have problems installing a package that is only in "defaults" you can enable it by using the -c defaults command line option on conda install.

[leouieda]

If you do get GMT properly installed, you'll still run into #224 but at least that's an error that we can actually fix.

[eamonustc]

Hi, after

conda remove --name gmt-python --all
conda config --remove channels defaults
conda config --append channels conda-forge/label/dev

conda create --name gmt-python python=3.6 pip
source activate gmt-python
conda install gmt -c conda-forge/label/dev
conda install numpy pandas xarray
pip install https://github.com/GenericMappingTools/gmt-python/archive/master.zip
conda install pytest pytest-mpl ipython

I still got errors

>>> import gmt
/home/eamon/anaconda2/envs/gmt-python/lib/python3.6/importlib/_bootstrap.py:219: RuntimeWarning: numpy.dtype size changed, may indicate binary incompatibility. Expected 96, got 88
  return f(*args, **kwds)
/home/eamon/anaconda2/envs/gmt-python/lib/python3.6/importlib/_bootstrap.py:219: RuntimeWarning: numpy.dtype size changed, may indicate binary incompatibility. Expected 96, got 88
  return f(*args, **kwds)
Segmentation fault (core dumped)

[philcummins]

Hi Leonardo, Thanks! As you suggested I tried replacing the command: conda config --add channels conda-forge in the install instructions with: conda config --remove channels defaults conda config --append channels conda-forge/label/dev Everything seemed to install fine, but I get the errors indicated below when I try to import gmt. Oddly, the whole thing worked fine (and still does) on my Macbook Pro, which is also running High Sierra and on which I installed gmt-python using the same instructions only last week. But it would be really useful to get it running on my iMac desktop as well... Cheers, - Phil python Python 3.6.6 | packaged by conda-forge | (default, Jul 26 2018, 09:55:02) [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 gmt

/Users/philcummins/anaconda3/envs/gmt-python/lib/python3.6/importlib/_bootstrap.py:219: RuntimeWarning: numpy.dtype size changed, may indicate binary incompatibility. Expected 96, got 88 return f(*args, **kwds) /Users/philcummins/anaconda3/envs/gmt-python/lib/python3.6/importlib/_bootstrap.py:219: RuntimeWarning: numpy.dtype size changed, may indicate binary incompatibility. Expected 96, got 88 return f(*args, **kwds) Traceback (most recent call last): File "<stdin>", line 1, in <module> File "/Users/philcummins/anaconda3/envs/gmt-python/lib/python3.6/site-packages/gmt/__init__.py", line 25, in <module> _begin() File "/Users/philcummins/anaconda3/envs/gmt-python/lib/python3.6/site-packages/gmt/session_management.py", line 17, in begin with Session() as lib: File "/Users/philcummins/anaconda3/envs/gmt-python/lib/python3.6/site-packages/gmt/clib/session.py", line 172, in __enter__ self.create("gmt-python-session") File "/Users/philcummins/anaconda3/envs/gmt-python/lib/python3.6/site-packages/gmt/clib/session.py", line 313, in create restype=ctp.c_void_p, File "/Users/philcummins/anaconda3/envs/gmt-python/lib/python3.6/site-packages/gmt/clib/session.py", line 263, in get_libgmt_func self._libgmt = load_libgmt() File "/Users/philcummins/anaconda3/envs/gmt-python/lib/python3.6/site-packages/gmt/clib/loading.py", line 43, in load_libgmt check_libgmt(libgmt) File "/Users/philcummins/anaconda3/envs/gmt-python/lib/python3.6/site-packages/gmt/clib/loading.py", line 146, in check_libgmt raise GMTCLibError(msg) gmt.exceptions.GMTCLibError: Error loading libgmt. Couldn't access function GMT_Get_Enum.

…

________________________________ From: Leonardo Uieda <notifications@github.com> Sent: Thursday, August 16, 2018 2:06:46 PM To: GenericMappingTools/gmt-python Cc: Phil Cummins; Comment Subject: Re: [GenericMappingTools/gmt-python] libpoppler.so.76: cannot open shared object file: No such file or directory (#223) If you do get GMT properly installed, you'll still run into #224<#224> but at least that's an error that we can actually fix. — You are receiving this because you commented. Reply to this email directly, view it on GitHub<#223 (comment)>, or mute the thread<https://github.com/notifications/unsubscribe-auth/ABZkc42oCKTly91cLbSxfy0kLbEPOo8uks5uRO_WgaJpZM4Vu7yS>.

[leouieda]

Alright, since #224 and conda-forge/gmt-feedstock#53 got merged/fixed things should be back to normal operations. Please update/recreate your environments and installations of GMT/Python. Let me know if anything is still breaking.

[philcummins]

Hi Leonardo, Thanks so much! It does work now. When I use "import gmt", it produces some warnings: $ python Python 3.6.6 | packaged by conda-forge | (default, Jul 26 2018, 09:55:02) [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 gmt

/Users/philcummins/anaconda3/envs/gmt-python/lib/python3.6/importlib/_bootstrap.py:219: RuntimeWarning: numpy.dtype size changed, may indicate binary incompatibility. Expected 96, got 88 return f(*args, **kwds) /Users/philcummins/anaconda3/envs/gmt-python/lib/python3.6/importlib/_bootstrap.py:219: RuntimeWarning: numpy.dtype size changed, may indicate binary incompatibility. Expected 96, got 88 return f(*args, **kwds) Also, I find I have to install docutils and sphinx in order to get the tests to run. But once I do that, gmt.test() works fine and I can make maps. Thanks again, - Phil

…

________________________________ From: Leonardo Uieda <notifications@github.com> Sent: Saturday, August 18, 2018 7:34:11 AM To: GenericMappingTools/gmt-python Cc: Phil Cummins; Comment Subject: Re: [GenericMappingTools/gmt-python] libpoppler.so.76: cannot open shared object file: No such file or directory (#223) Alright, since #224<#224> and conda-forge/gmt-feedstock#53<conda-forge/gmt-feedstock#53> got merged/fixed things should be back to normal operations. Please update/recreate your environments and installations of GMT/Python. Let me know if anything is still breaking. — You are receiving this because you commented. Reply to this email directly, view it on GitHub<#223 (comment)>, or mute the thread<https://github.com/notifications/unsubscribe-auth/ABZkc9vrEUhjBfx1WFRqVt4-BcY0Z-4Mks5uRzbTgaJpZM4Vu7yS>.

[eamonustc]

Finally, I also installed it successfully! Thank you all so much!

>>> gmt.test()
Loaded libgmt:
  binary dir: /home/eamon/anaconda2/envs/gmt-python/bin
  cores: 16
  grid layout: rows
  image layout: 
  library path: /home/eamon/anaconda2/envs/gmt-python/lib/libgmt.so
  padding: 2
  plugin dir: /home/eamon/anaconda2/envs/gmt-python/lib/gmt/plugins
  share dir: /home/eamon/anaconda2/envs/gmt-python/share/gmt
  version: 6.0.0
============================================================ test session starts ============================================================
platform linux -- Python 3.6.6, pytest-3.7.1, py-1.5.4, pluggy-0.7.1 -- /home/eamon/anaconda2/envs/gmt-python/bin/python3
cachedir: .pytest_cache
Matplotlib: 2.2.3
Freetype: 2.9.1
rootdir: /home/eamon/anaconda2/envs/gmt-python/bin, inifile:
plugins: mpl-0.9
collected 144 items                                                                                                                         

gmt/base_plotting.py::gmt.base_plotting.BasePlotting._preprocess <- ../lib/python3.6/site-packages/gmt/base_plotting.py PASSED        [  0%]
gmt/figure.py::gmt.figure.Figure <- ../lib/python3.6/site-packages/gmt/figure.py PASSED                                               [  1%]
gmt/clib/conversion.py::gmt.clib.conversion._as_array <- ../lib/python3.6/site-packages/gmt/clib/conversion.py PASSED                 [  2%]
gmt/clib/conversion.py::gmt.clib.conversion.as_c_contiguous <- ../lib/python3.6/site-packages/gmt/clib/conversion.py PASSED           [  2%]
gmt/clib/conversion.py::gmt.clib.conversion.dataarray_to_matrix <- ../lib/python3.6/site-packages/gmt/clib/conversion.py PASSED       [  3%]
gmt/clib/conversion.py::gmt.clib.conversion.kwargs_to_ctypes_array <- ../lib/python3.6/site-packages/gmt/clib/conversion.py PASSED    [  4%]
gmt/clib/conversion.py::gmt.clib.conversion.vectors_to_arrays <- ../lib/python3.6/site-packages/gmt/clib/conversion.py PASSED         [  4%]
gmt/clib/session.py::gmt.clib.session.Session <- ../lib/python3.6/site-packages/gmt/clib/session.py PASSED                            [  5%]
gmt/clib/session.py::gmt.clib.session.Session._check_dtype_and_dim <- ../lib/python3.6/site-packages/gmt/clib/session.py PASSED       [  6%]
gmt/clib/session.py::gmt.clib.session.Session.extract_region <- ../lib/python3.6/site-packages/gmt/clib/session.py PASSED             [  6%]
gmt/clib/session.py::gmt.clib.session.Session.get_libgmt_func <- ../lib/python3.6/site-packages/gmt/clib/session.py PASSED            [  7%]
gmt/clib/session.py::gmt.clib.session.Session.open_virtual_file <- ../lib/python3.6/site-packages/gmt/clib/session.py PASSED          [  8%]
gmt/clib/session.py::gmt.clib.session.Session.virtualfile_from_grid <- ../lib/python3.6/site-packages/gmt/clib/session.py PASSED      [  9%]
gmt/clib/session.py::gmt.clib.session.Session.virtualfile_from_matrix <- ../lib/python3.6/site-packages/gmt/clib/session.py PASSED    [  9%]
gmt/clib/session.py::gmt.clib.session.Session.virtualfile_from_vectors <- ../lib/python3.6/site-packages/gmt/clib/session.py PASSED   [ 10%]
gmt/datasets/earth_relief.py::gmt.datasets.earth_relief._is_valid_resolution <- ../lib/python3.6/site-packages/gmt/datasets/earth_relief.py PASSED [ 11%]
gmt/datasets/earth_relief.py::gmt.datasets.earth_relief._shape_from_resolution <- ../lib/python3.6/site-packages/gmt/datasets/earth_relief.py PASSED [ 11%]
gmt/helpers/decorators.py::gmt.helpers.decorators.fmt_docstring <- ../lib/python3.6/site-packages/gmt/helpers/decorators.py PASSED    [ 12%]
gmt/helpers/decorators.py::gmt.helpers.decorators.kwargs_to_strings <- ../lib/python3.6/site-packages/gmt/helpers/decorators.py PASSED [ 13%]
gmt/helpers/decorators.py::gmt.helpers.decorators.use_alias <- ../lib/python3.6/site-packages/gmt/helpers/decorators.py PASSED        [ 13%]
gmt/helpers/tempfile.py::gmt.helpers.tempfile.GMTTempFile <- ../lib/python3.6/site-packages/gmt/helpers/tempfile.py PASSED            [ 14%]
gmt/helpers/utils.py::gmt.helpers.utils.build_arg_string <- ../lib/python3.6/site-packages/gmt/helpers/utils.py PASSED                [ 15%]
gmt/helpers/utils.py::gmt.helpers.utils.data_kind <- ../lib/python3.6/site-packages/gmt/helpers/utils.py PASSED                       [ 15%]
gmt/helpers/utils.py::gmt.helpers.utils.dummy_context <- ../lib/python3.6/site-packages/gmt/helpers/utils.py PASSED                   [ 16%]
gmt/helpers/utils.py::gmt.helpers.utils.is_nonstr_iter <- ../lib/python3.6/site-packages/gmt/helpers/utils.py PASSED                  [ 17%]
gmt/tests/test_basemap.py::test_basemap_required_args <- ../lib/python3.6/site-packages/gmt/tests/test_basemap.py PASSED              [ 18%]
gmt/tests/test_basemap.py::test_basemap_d <- ../lib/python3.6/site-packages/gmt/tests/test_basemap.py PASSED                          [ 18%]
gmt/tests/test_basemap.py::test_basemap_d_raises <- ../lib/python3.6/site-packages/gmt/tests/test_basemap.py PASSED                   [ 19%]
gmt/tests/test_basemap.py::test_basemap <- ../lib/python3.6/site-packages/gmt/tests/test_basemap.py PASSED                            [ 20%]
gmt/tests/test_basemap.py::test_basemap_list_region <- ../lib/python3.6/site-packages/gmt/tests/test_basemap.py PASSED                [ 20%]
gmt/tests/test_basemap.py::test_basemap_loglog <- ../lib/python3.6/site-packages/gmt/tests/test_basemap.py PASSED                     [ 21%]
gmt/tests/test_basemap.py::test_basemap_power_axis <- ../lib/python3.6/site-packages/gmt/tests/test_basemap.py PASSED                 [ 22%]
gmt/tests/test_basemap.py::test_basemap_polar <- ../lib/python3.6/site-packages/gmt/tests/test_basemap.py PASSED                      [ 22%]
gmt/tests/test_basemap.py::test_basemap_winkel_tripel <- ../lib/python3.6/site-packages/gmt/tests/test_basemap.py PASSED              [ 23%]
gmt/tests/test_basemap.py::test_basemap_aliases <- ../lib/python3.6/site-packages/gmt/tests/test_basemap.py PASSED                    [ 24%]
gmt/tests/test_clib.py::test_load_libgmt <- ../lib/python3.6/site-packages/gmt/tests/test_clib.py PASSED                              [ 25%]
gmt/tests/test_clib.py::test_load_libgmt_fail <- ../lib/python3.6/site-packages/gmt/tests/test_clib.py PASSED                         [ 25%]
gmt/tests/test_clib.py::test_get_clib_path <- ../lib/python3.6/site-packages/gmt/tests/test_clib.py PASSED                            [ 26%]
gmt/tests/test_clib.py::test_check_libgmt <- ../lib/python3.6/site-packages/gmt/tests/test_clib.py PASSED                             [ 27%]
gmt/tests/test_clib.py::test_clib_extension <- ../lib/python3.6/site-packages/gmt/tests/test_clib.py PASSED                           [ 27%]
gmt/tests/test_clib.py::test_getitem <- ../lib/python3.6/site-packages/gmt/tests/test_clib.py PASSED                                  [ 28%]
gmt/tests/test_clib.py::test_create_destroy_session <- ../lib/python3.6/site-packages/gmt/tests/test_clib.py PASSED                   [ 29%]
gmt/tests/test_clib.py::test_create_session_fails <- ../lib/python3.6/site-packages/gmt/tests/test_clib.py PASSED                     [ 29%]
gmt/tests/test_clib.py::test_destroy_session_fails <- ../lib/python3.6/site-packages/gmt/tests/test_clib.py PASSED                    [ 30%]
gmt/tests/test_clib.py::test_call_module <- ../lib/python3.6/site-packages/gmt/tests/test_clib.py PASSED                              [ 31%]
gmt/tests/test_clib.py::test_call_module_invalid_arguments <- ../lib/python3.6/site-packages/gmt/tests/test_clib.py PASSED            [ 31%]
gmt/tests/test_clib.py::test_call_module_invalid_name <- ../lib/python3.6/site-packages/gmt/tests/test_clib.py PASSED                 [ 32%]
gmt/tests/test_clib.py::test_call_module_error_message <- ../lib/python3.6/site-packages/gmt/tests/test_clib.py PASSED                [ 33%]
gmt/tests/test_clib.py::test_method_no_session <- ../lib/python3.6/site-packages/gmt/tests/test_clib.py PASSED                        [ 34%]
gmt/tests/test_clib.py::test_parse_constant_single <- ../lib/python3.6/site-packages/gmt/tests/test_clib.py PASSED                    [ 34%]
gmt/tests/test_clib.py::test_parse_constant_composite <- ../lib/python3.6/site-packages/gmt/tests/test_clib.py PASSED                 [ 35%]
gmt/tests/test_clib.py::test_parse_constant_fails <- ../lib/python3.6/site-packages/gmt/tests/test_clib.py PASSED                     [ 36%]
gmt/tests/test_clib.py::test_create_data_dataset <- ../lib/python3.6/site-packages/gmt/tests/test_clib.py PASSED                      [ 36%]
gmt/tests/test_clib.py::test_create_data_grid_dim <- ../lib/python3.6/site-packages/gmt/tests/test_clib.py PASSED                     [ 37%]
gmt/tests/test_clib.py::test_create_data_grid_range <- ../lib/python3.6/site-packages/gmt/tests/test_clib.py PASSED                   [ 38%]
gmt/tests/test_clib.py::test_create_data_fails <- ../lib/python3.6/site-packages/gmt/tests/test_clib.py PASSED                        [ 38%]
gmt/tests/test_clib.py::test_put_vector <- ../lib/python3.6/site-packages/gmt/tests/test_clib.py PASSED                               [ 39%]
gmt/tests/test_clib.py::test_put_vector_invalid_dtype <- ../lib/python3.6/site-packages/gmt/tests/test_clib.py PASSED                 [ 40%]
gmt/tests/test_clib.py::test_put_vector_wrong_column <- ../lib/python3.6/site-packages/gmt/tests/test_clib.py PASSED                  [ 40%]
gmt/tests/test_clib.py::test_put_vector_2d_fails <- ../lib/python3.6/site-packages/gmt/tests/test_clib.py PASSED                      [ 41%]
gmt/tests/test_clib.py::test_put_matrix <- ../lib/python3.6/site-packages/gmt/tests/test_clib.py PASSED                               [ 42%]
gmt/tests/test_clib.py::test_put_matrix_fails <- ../lib/python3.6/site-packages/gmt/tests/test_clib.py PASSED                         [ 43%]
gmt/tests/test_clib.py::test_put_matrix_grid <- ../lib/python3.6/site-packages/gmt/tests/test_clib.py PASSED                          [ 43%]
gmt/tests/test_clib.py::test_virtual_file <- ../lib/python3.6/site-packages/gmt/tests/test_clib.py PASSED                             [ 44%]
gmt/tests/test_clib.py::test_virtual_file_fails <- ../lib/python3.6/site-packages/gmt/tests/test_clib.py PASSED                       [ 45%]
gmt/tests/test_clib.py::test_virtual_file_bad_direction <- ../lib/python3.6/site-packages/gmt/tests/test_clib.py PASSED               [ 45%]
gmt/tests/test_clib.py::test_virtualfile_from_vectors <- ../lib/python3.6/site-packages/gmt/tests/test_clib.py PASSED                 [ 46%]
gmt/tests/test_clib.py::test_virtualfile_from_vectors_transpose <- ../lib/python3.6/site-packages/gmt/tests/test_clib.py PASSED       [ 47%]
gmt/tests/test_clib.py::test_virtualfile_from_vectors_diff_size <- ../lib/python3.6/site-packages/gmt/tests/test_clib.py PASSED       [ 47%]
gmt/tests/test_clib.py::test_virtualfile_from_matrix <- ../lib/python3.6/site-packages/gmt/tests/test_clib.py PASSED                  [ 48%]
gmt/tests/test_clib.py::test_virtualfile_from_matrix_slice <- ../lib/python3.6/site-packages/gmt/tests/test_clib.py PASSED            [ 49%]
gmt/tests/test_clib.py::test_virtualfile_from_vectors_pandas <- ../lib/python3.6/site-packages/gmt/tests/test_clib.py PASSED          [ 50%]
gmt/tests/test_clib.py::test_virtualfile_from_vectors_arraylike <- ../lib/python3.6/site-packages/gmt/tests/test_clib.py PASSED       [ 50%]
gmt/tests/test_clib.py::test_extract_region_fails <- ../lib/python3.6/site-packages/gmt/tests/test_clib.py PASSED                     [ 51%]
gmt/tests/test_clib.py::test_extract_region_two_figures <- ../lib/python3.6/site-packages/gmt/tests/test_clib.py PASSED               [ 52%]
gmt/tests/test_clib.py::test_write_data_fails <- ../lib/python3.6/site-packages/gmt/tests/test_clib.py PASSED                         [ 52%]
gmt/tests/test_clib.py::test_dataarray_to_matrix_dims_fails <- ../lib/python3.6/site-packages/gmt/tests/test_clib.py PASSED           [ 53%]
gmt/tests/test_clib.py::test_dataarray_to_matrix_inc_fails <- ../lib/python3.6/site-packages/gmt/tests/test_clib.py PASSED            [ 54%]
gmt/tests/test_clib.py::test_get_default <- ../lib/python3.6/site-packages/gmt/tests/test_clib.py PASSED                              [ 54%]
gmt/tests/test_clib.py::test_get_default_fails <- ../lib/python3.6/site-packages/gmt/tests/test_clib.py PASSED                        [ 55%]
gmt/tests/test_clib.py::test_info_dict <- ../lib/python3.6/site-packages/gmt/tests/test_clib.py PASSED                                [ 56%]
gmt/tests/test_clib.py::test_fails_for_wrong_version <- ../lib/python3.6/site-packages/gmt/tests/test_clib.py PASSED                  [ 56%]
gmt/tests/test_coast.py::test_coast <- ../lib/python3.6/site-packages/gmt/tests/test_coast.py PASSED                                  [ 57%]
gmt/tests/test_coast.py::test_coast_iceland <- ../lib/python3.6/site-packages/gmt/tests/test_coast.py PASSED                          [ 58%]
gmt/tests/test_coast.py::test_coast_aliases <- ../lib/python3.6/site-packages/gmt/tests/test_coast.py PASSED                          [ 59%]
gmt/tests/test_coast.py::test_coast_world_mercator <- ../lib/python3.6/site-packages/gmt/tests/test_coast.py PASSED                   [ 59%]
gmt/tests/test_contour.py::test_contour_fail_no_data <- ../lib/python3.6/site-packages/gmt/tests/test_contour.py PASSED               [ 60%]
gmt/tests/test_contour.py::test_contour_vec <- ../lib/python3.6/site-packages/gmt/tests/test_contour.py PASSED                        [ 61%]
gmt/tests/test_contour.py::test_contour_matrix <- ../lib/python3.6/site-packages/gmt/tests/test_contour.py PASSED                     [ 61%]
gmt/tests/test_contour.py::test_contour_from_file <- ../lib/python3.6/site-packages/gmt/tests/test_contour.py PASSED                  [ 62%]
gmt/tests/test_datasets.py::test_japan_quakes <- ../lib/python3.6/site-packages/gmt/tests/test_datasets.py PASSED                     [ 63%]
gmt/tests/test_datasets.py::test_usgs_quakes <- ../lib/python3.6/site-packages/gmt/tests/test_datasets.py PASSED                      [ 63%]
gmt/tests/test_datasets.py::test_earth_relief_fails <- ../lib/python3.6/site-packages/gmt/tests/test_datasets.py PASSED               [ 64%]
gmt/tests/test_datasets.py::test_earth_relief_60 <- ../lib/python3.6/site-packages/gmt/tests/test_datasets.py PASSED                  [ 65%]
gmt/tests/test_datasets.py::test_earth_relief_30 <- ../lib/python3.6/site-packages/gmt/tests/test_datasets.py PASSED                  [ 65%]
gmt/tests/test_figure.py::test_figure_region <- ../lib/python3.6/site-packages/gmt/tests/test_figure.py PASSED                        [ 66%]
gmt/tests/test_figure.py::test_figure_region_multiple <- ../lib/python3.6/site-packages/gmt/tests/test_figure.py PASSED               [ 67%]
gmt/tests/test_figure.py::test_figure_region_country_codes <- ../lib/python3.6/site-packages/gmt/tests/test_figure.py PASSED          [ 68%]
gmt/tests/test_figure.py::test_figure_savefig_exists <- ../lib/python3.6/site-packages/gmt/tests/test_figure.py PASSED                [ 68%]
gmt/tests/test_figure.py::test_figure_savefig_transparent <- ../lib/python3.6/site-packages/gmt/tests/test_figure.py PASSED           [ 69%]
gmt/tests/test_figure.py::test_figure_savefig <- ../lib/python3.6/site-packages/gmt/tests/test_figure.py PASSED                       [ 70%]
gmt/tests/test_figure.py::test_figure_show <- ../lib/python3.6/site-packages/gmt/tests/test_figure.py PASSED                          [ 70%]
gmt/tests/test_grdimage.py::test_grdimage <- ../lib/python3.6/site-packages/gmt/tests/test_grdimage.py PASSED                         [ 71%]
gmt/tests/test_grdimage.py::test_grdimage_slice <- ../lib/python3.6/site-packages/gmt/tests/test_grdimage.py PASSED                   [ 72%]
gmt/tests/test_grdimage.py::test_grdimage_file <- ../lib/python3.6/site-packages/gmt/tests/test_grdimage.py PASSED                    [ 72%]
gmt/tests/test_grdimage.py::test_grdimage_fails <- ../lib/python3.6/site-packages/gmt/tests/test_grdimage.py PASSED                   [ 73%]
gmt/tests/test_helpers.py::test_unique_name <- ../lib/python3.6/site-packages/gmt/tests/test_helpers.py PASSED                        [ 74%]
gmt/tests/test_helpers.py::test_kwargs_to_strings_fails <- ../lib/python3.6/site-packages/gmt/tests/test_helpers.py PASSED            [ 75%]
gmt/tests/test_helpers.py::test_kwargs_to_strings_no_bools <- ../lib/python3.6/site-packages/gmt/tests/test_helpers.py PASSED         [ 75%]
gmt/tests/test_helpers.py::test_gmttempfile <- ../lib/python3.6/site-packages/gmt/tests/test_helpers.py PASSED                        [ 76%]
gmt/tests/test_helpers.py::test_gmttempfile_unique <- ../lib/python3.6/site-packages/gmt/tests/test_helpers.py PASSED                 [ 77%]
gmt/tests/test_helpers.py::test_gmttempfile_prefix_suffix <- ../lib/python3.6/site-packages/gmt/tests/test_helpers.py PASSED          [ 77%]
gmt/tests/test_helpers.py::test_gmttempfile_read <- ../lib/python3.6/site-packages/gmt/tests/test_helpers.py PASSED                   [ 78%]
gmt/tests/test_info.py::test_info <- ../lib/python3.6/site-packages/gmt/tests/test_info.py PASSED                                     [ 79%]
gmt/tests/test_info.py::test_info_c <- ../lib/python3.6/site-packages/gmt/tests/test_info.py PASSED                                   [ 79%]
gmt/tests/test_info.py::test_info_i <- ../lib/python3.6/site-packages/gmt/tests/test_info.py PASSED                                   [ 80%]
gmt/tests/test_info.py::test_info_c_i <- ../lib/python3.6/site-packages/gmt/tests/test_info.py PASSED                                 [ 81%]
gmt/tests/test_info.py::test_info_t <- ../lib/python3.6/site-packages/gmt/tests/test_info.py PASSED                                   [ 81%]
gmt/tests/test_info.py::test_info_fails <- ../lib/python3.6/site-packages/gmt/tests/test_info.py PASSED                               [ 82%]
gmt/tests/test_info.py::test_grdinfo <- ../lib/python3.6/site-packages/gmt/tests/test_info.py PASSED                                  [ 83%]
gmt/tests/test_info.py::test_grdinfo_file <- ../lib/python3.6/site-packages/gmt/tests/test_info.py PASSED                             [ 84%]
gmt/tests/test_info.py::test_grdinfo_fails <- ../lib/python3.6/site-packages/gmt/tests/test_info.py PASSED                            [ 84%]
gmt/tests/test_logo.py::test_logo <- ../lib/python3.6/site-packages/gmt/tests/test_logo.py PASSED                                     [ 85%]
gmt/tests/test_logo.py::test_logo_on_a_map <- ../lib/python3.6/site-packages/gmt/tests/test_logo.py PASSED                            [ 86%]
gmt/tests/test_logo.py::test_logo_fails <- ../lib/python3.6/site-packages/gmt/tests/test_logo.py PASSED                               [ 86%]
gmt/tests/test_plot.py::test_plot_red_circles <- ../lib/python3.6/site-packages/gmt/tests/test_plot.py PASSED                         [ 87%]
gmt/tests/test_plot.py::test_plot_fail_no_data <- ../lib/python3.6/site-packages/gmt/tests/test_plot.py PASSED                        [ 88%]
gmt/tests/test_plot.py::test_plot_fail_size_color <- ../lib/python3.6/site-packages/gmt/tests/test_plot.py PASSED                     [ 88%]
gmt/tests/test_plot.py::test_plot_projection <- ../lib/python3.6/site-packages/gmt/tests/test_plot.py PASSED                          [ 89%]
gmt/tests/test_plot.py::test_plot_colors <- ../lib/python3.6/site-packages/gmt/tests/test_plot.py PASSED                              [ 90%]
gmt/tests/test_plot.py::test_plot_sizes <- ../lib/python3.6/site-packages/gmt/tests/test_plot.py PASSED                               [ 90%]
gmt/tests/test_plot.py::test_plot_colors_sizes <- ../lib/python3.6/site-packages/gmt/tests/test_plot.py PASSED                        [ 91%]
gmt/tests/test_plot.py::test_plot_colors_sizes_proj <- ../lib/python3.6/site-packages/gmt/tests/test_plot.py PASSED                   [ 92%]
gmt/tests/test_plot.py::test_plot_matrix <- ../lib/python3.6/site-packages/gmt/tests/test_plot.py PASSED                              [ 93%]
gmt/tests/test_plot.py::test_plot_matrix_color <- ../lib/python3.6/site-packages/gmt/tests/test_plot.py PASSED                        [ 93%]
gmt/tests/test_plot.py::test_plot_from_file <- ../lib/python3.6/site-packages/gmt/tests/test_plot.py PASSED                           [ 94%]
gmt/tests/test_plot.py::test_plot_vectors <- ../lib/python3.6/site-packages/gmt/tests/test_plot.py PASSED                             [ 95%]
gmt/tests/test_psconvert.py::test_psconvert <- ../lib/python3.6/site-packages/gmt/tests/test_psconvert.py PASSED                      [ 95%]
gmt/tests/test_psconvert.py::test_psconvert_twice <- ../lib/python3.6/site-packages/gmt/tests/test_psconvert.py PASSED                [ 96%]
gmt/tests/test_psconvert.py::test_psconvert_int_options <- ../lib/python3.6/site-packages/gmt/tests/test_psconvert.py PASSED          [ 97%]
gmt/tests/test_psconvert.py::test_psconvert_aliases <- ../lib/python3.6/site-packages/gmt/tests/test_psconvert.py PASSED              [ 97%]
gmt/tests/test_session_management.py::test_begin_end <- ../lib/python3.6/site-packages/gmt/tests/test_session_management.py PASSED    [ 98%]
gmt/tests/test_which.py::test_which <- ../lib/python3.6/site-packages/gmt/tests/test_which.py PASSED                                  [ 99%]
gmt/tests/test_which.py::test_which_fails <- ../lib/python3.6/site-packages/gmt/tests/test_which.py PASSED                            [100%]

======================================================== 144 passed in 40.92 seconds ========================================================

[leouieda]

@eamonustc @philcummins Great to know!

I've been having those warnings about numpy but it seems fine.

[shaunwbell]

ahh the seemingly ubiquitous RuntimeWarning: numpy.dtype size changed, may indicate binary incompatibility - pandas is throwing it for me too as are a number of other conda installed packages
for my other programs. I've found this stackoverflow conversation to be what most other issues point to:

https://stackoverflow.com/questions/40845304/runtimewarning-numpy-dtype-size-changed-may-indicate-binary-incompatibility

@leouieda - I've successfully been able to get an install on my system (#202) - 🎉

Only odd things where that I had to install docutils, sphinx, and ghostscript all independently after seeing failures or warnings when the libraries were called but they hadn't been installed by the package instructions.