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libpoppler.so.76: cannot open shared object file: No such file or directory
See original GitHub issueWhen 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 listbelow:
# 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
Issue Analytics
- State:
- Created 5 years ago
- Comments:13 (4 by maintainers)
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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.