jorisvandenbossche
commented
5 years ago (note, this is not in a clean env. But still, you would expect that conda should be able to handle such update of an env)
Closed jorisvandenbossche closed 5 years ago
jorisvandenbossche
commented
5 years ago (note, this is not in a clean env. But still, you would expect that conda should be able to handle such update of an env)
ocefpaf
commented
5 years ago :unamused:
Try conda install cfitsio=3.430 to fix the env, but send me the conda list so I can debug why you are getting a version of gdal that has unpinned cfitsio. (I may have left some out there.)
jorisvandenbossche
commented
5 years ago Conda list:
(geo) joris@joris-XPS-13-9380:~$ conda list
# packages in environment at /home/joris/miniconda3/envs/geo:
#
# Name Version Build Channel
_libgcc_mutex 0.1 main
affine 2.2.2 py_0 conda-forge
altair 3.1.0 py37_0 conda-forge
asn1crypto 0.24.0 py37_1003 conda-forge
attrs 19.1.0 py_0 conda-forge
backcall 0.1.0 py_0 conda-forge
bleach 3.1.0 py_0 conda-forge
boost-cpp 1.70.0 ha2d47e9_1 conda-forge
branca 0.3.1 py_0 conda-forge
bzip2 1.0.8 h516909a_0 conda-forge
ca-certificates 2019.6.16 hecc5488_0 conda-forge
cairo 1.16.0 h18b612c_1001 conda-forge
cartopy 0.17.0 py37h0aa2c8f_1004 conda-forge
certifi 2019.6.16 py37_1 conda-forge
cffi 1.12.3 py37h8022711_0 conda-forge
cfitsio 3.470 hb60a0a2_1 conda-forge
chardet 3.0.4 py37_1003 conda-forge
click 7.0 py_0 conda-forge
click-plugins 1.1.1 py_0 conda-forge
cligj 0.5.0 py_0 conda-forge
contextily 1.0rc2 py_0 conda-forge
cryptography 2.7 py37h72c5cf5_0 conda-forge
curl 7.65.3 hf8cf82a_0 conda-forge
cycler 0.10.0 py_1 conda-forge
dbus 1.13.6 he372182_0 conda-forge
decorator 4.4.0 py_0 conda-forge
defusedxml 0.5.0 py_1 conda-forge
descartes 1.1.0 py_3 conda-forge
entrypoints 0.3 py37_1000 conda-forge
expat 2.2.5 he1b5a44_1003 conda-forge
fiona 1.8.6 py37hf242f0b_3 conda-forge
folium 0.9.1 py_0 conda-forge
fontconfig 2.13.1 he4413a7_1000 conda-forge
freetype 2.10.0 he983fc9_0 conda-forge
freexl 1.0.5 h14c3975_1002 conda-forge
gdal 2.4.1 py37h5f563d9_5 conda-forge
geographiclib 1.49 py_0 conda-forge
geopandas 0.5.0 py_2 conda-forge
geoplot 0.2.4 py_0 conda-forge
geopy 1.20.0 py_0 conda-forge
geos 3.7.1 hf484d3e_1000 conda-forge
geotiff 1.4.3 h1105359_1000 conda-forge
gettext 0.19.8.1 hc5be6a0_1002 conda-forge
giflib 5.1.7 h516909a_1 conda-forge
glib 2.58.3 h6f030ca_1002 conda-forge
gst-plugins-base 1.14.5 h0935bb2_0 conda-forge
gstreamer 1.14.5 h36ae1b5_0 conda-forge
hdf4 4.2.13 h9a582f1_1002 conda-forge
hdf5 1.10.5 nompi_h3c11f04_1100 conda-forge
icu 58.2 hf484d3e_1000 conda-forge
idna 2.8 py37_1000 conda-forge
ipykernel 5.1.1 py37h5ca1d4c_0 conda-forge
ipyleaflet 0.10.5 py37_0 conda-forge
ipython 7.7.0 py37h5ca1d4c_0 conda-forge
ipython_genutils 0.2.0 py_1 conda-forge
ipywidgets 7.5.1 py_0 conda-forge
jedi 0.14.1 py37_0 conda-forge
jinja2 2.10.1 py_0 conda-forge
joblib 0.13.2 py_0 conda-forge
jpeg 9c h14c3975_1001 conda-forge
json-c 0.13.1 h14c3975_1001 conda-forge
jsonschema 3.0.2 py37_0 conda-forge
jupyter_client 5.3.1 py_0 conda-forge
jupyter_core 4.4.0 py_0 conda-forge
kealib 1.4.10 h58c409b_1005 conda-forge
kiwisolver 1.1.0 py37hc9558a2_0 conda-forge
krb5 1.16.3 h05b26f9_1001 conda-forge
libblas 3.8.0 11_openblas conda-forge
libcblas 3.8.0 11_openblas conda-forge
libcurl 7.65.3 hda55be3_0 conda-forge
libdap4 3.19.1 hd48c02d_1000 conda-forge
libedit 3.1.20170329 hf8c457e_1001 conda-forge
libffi 3.2.1 he1b5a44_1006 conda-forge
libgcc-ng 9.1.0 hdf63c60_0
libgdal 2.4.1 h677e3de_5 conda-forge
libgfortran-ng 7.3.0 hdf63c60_0
libiconv 1.15 h516909a_1005 conda-forge
libkml 1.3.0 h4fcabce_1010 conda-forge
liblapack 3.8.0 11_openblas conda-forge
libnetcdf 4.6.2 h056eaf5_1002 conda-forge
libopenblas 0.3.6 h6e990d7_6 conda-forge
libpng 1.6.37 hed695b0_0 conda-forge
libpq 11.4 h4e4e079_0 conda-forge
libsodium 1.0.17 h516909a_0 conda-forge
libspatialindex 1.9.0 he1b5a44_1 conda-forge
libspatialite 4.3.0a hb5ec416_1026 conda-forge
libssh2 1.8.2 h22169c7_2 conda-forge
libstdcxx-ng 9.1.0 hdf63c60_0
libtiff 4.0.10 h57b8799_1003 conda-forge
libuuid 2.32.1 h14c3975_1000 conda-forge
libxcb 1.13 h14c3975_1002 conda-forge
libxml2 2.9.9 h13577e0_2 conda-forge
lz4-c 1.8.3 he1b5a44_1001 conda-forge
mapclassify 2.0.1 py_0 conda-forge
markupsafe 1.1.1 py37h14c3975_0 conda-forge
matplotlib 3.1.1 py37_0 conda-forge
matplotlib-base 3.1.1 py37hfd891ef_0 conda-forge
mercantile 1.1.1 py_0 conda-forge
mistune 0.8.4 py37h14c3975_1000 conda-forge
munch 2.3.2 py_0 conda-forge
nbconvert 5.5.0 py_0 conda-forge
nbformat 4.4.0 py_1 conda-forge
ncurses 6.1 hf484d3e_1002 conda-forge
notebook 5.7.8 py37_1 conda-forge
numpy 1.17.0 py37h95a1406_0 conda-forge
olefile 0.46 py_0 conda-forge
openjpeg 2.3.1 h58a6597_0 conda-forge
openssl 1.1.1c h516909a_0 conda-forge
owslib 0.18.0 py_0 conda-forge
pandas 0.25.0 py37hb3f55d8_0 conda-forge
pandoc 2.7.3 0 conda-forge
pandocfilters 1.4.2 py_1 conda-forge
parso 0.5.1 py_0 conda-forge
patsy 0.5.1 py_0 conda-forge
pcre 8.41 hf484d3e_1003 conda-forge
pexpect 4.7.0 py37_0 conda-forge
pickleshare 0.7.5 py37_1000 conda-forge
pillow 6.1.0 py37he7afcd5_0 conda-forge
pip 19.2.1 py37_0 conda-forge
pixman 0.38.0 h516909a_1003 conda-forge
poppler 0.67.0 ha967d66_7 conda-forge
poppler-data 0.4.9 1 conda-forge
postgresql 11.4 hbeee2d4_0 conda-forge
proj4 5.2.0 he1b5a44_1004 conda-forge
prometheus_client 0.7.1 py_0 conda-forge
prompt_toolkit 2.0.9 py_0 conda-forge
pthread-stubs 0.4 h14c3975_1001 conda-forge
ptyprocess 0.6.0 py_1001 conda-forge
pycparser 2.19 py37_1 conda-forge
pyepsg 0.4.0 py_0 conda-forge
pygments 2.4.2 py_0 conda-forge
pykdtree 1.3.1 py37h3010b51_1002 conda-forge
pyopenssl 19.0.0 py37_0 conda-forge
pyparsing 2.4.2 py_0 conda-forge
pyproj 1.9.6 py37h516909a_1002 conda-forge
pyqt 5.9.2 py37hcca6a23_1 conda-forge
pyrsistent 0.15.4 py37h516909a_0 conda-forge
pyshp 2.1.0 py_0 conda-forge
pysocks 1.7.0 py37_0 conda-forge
python 3.7.3 h5b0a415_0 conda-forge
python-dateutil 2.8.0 py_0 conda-forge
pytz 2019.2 py_0 conda-forge
pyzmq 18.0.2 py37h1768529_2 conda-forge
qt 5.9.7 h52cfd70_2 conda-forge
rasterio 1.0.24 py37hdff7cfa_0 conda-forge
rasterstats 0.13.1 py_0 conda-forge
readline 7.0 hf8c457e_1001 conda-forge
requests 2.22.0 py37_1 conda-forge
rtree 0.8.3 py37h666c49c_1002 conda-forge
scipy 1.3.0 py37h921218d_1 conda-forge
seaborn 0.9.0 py_1 conda-forge
send2trash 1.5.0 py_0 conda-forge
setuptools 41.0.1 py37_0 conda-forge
shapely 1.6.4 py37h06cd6f9_1005 conda-forge
simplejson 3.16.0 py37h14c3975_1002 conda-forge
sip 4.19.8 py37hf484d3e_1000 conda-forge
six 1.12.0 py37_1000 conda-forge
snuggs 1.4.6 py_0 conda-forge
sqlite 3.28.0 h8b20d00_0 conda-forge
statsmodels 0.10.1 py37hc1659b7_0 conda-forge
terminado 0.8.2 py37_0 conda-forge
testpath 0.4.2 py_1001 conda-forge
tk 8.6.9 hed695b0_1002 conda-forge
toolz 0.10.0 py_0 conda-forge
tornado 6.0.3 py37h516909a_0 conda-forge
traitlets 4.3.2 py37_1000 conda-forge
traittypes 0.2.1 py_1 conda-forge
tzcode 2019a h516909a_1002 conda-forge
urllib3 1.25.3 py37_0 conda-forge
vincent 0.4.4 py_1 conda-forge
wcwidth 0.1.7 py_1 conda-forge
webencodings 0.5.1 py_1 conda-forge
wheel 0.33.4 py37_0 conda-forge
widgetsnbextension 3.5.1 py37_0 conda-forge
xarray 0.12.3 py_0 conda-forge
xerces-c 3.2.2 hea5cb30_1003 conda-forge
xorg-kbproto 1.0.7 h14c3975_1002 conda-forge
xorg-libice 1.0.10 h516909a_0 conda-forge
xorg-libsm 1.2.3 h84519dc_1000 conda-forge
xorg-libx11 1.6.8 h516909a_0 conda-forge
xorg-libxau 1.0.9 h14c3975_0 conda-forge
xorg-libxdmcp 1.1.3 h516909a_0 conda-forge
xorg-libxext 1.3.4 h516909a_0 conda-forge
xorg-libxrender 0.9.10 h516909a_1002 conda-forge
xorg-renderproto 0.11.1 h14c3975_1002 conda-forge
xorg-xextproto 7.3.0 h14c3975_1002 conda-forge
xorg-xproto 7.0.31 h14c3975_1007 conda-forge
xz 5.2.4 h14c3975_1001 conda-forge
zeromq 4.3.2 he1b5a44_2 conda-forge
zlib 1.2.11 h516909a_1005 conda-forge
zstd 1.4.0 h3b9ef0a_0 conda-forgeAh, I see. That is an old env with gdal 2.4.1 build number 5, which is now in broken. conda does not know that can keeps trying to optimize things. Only new envs will avoid a broken package.
In theory, it would be nice for conda to clean up packages or always move to the latest build number, but I don't think that feature would work b/c build numbers in conda are not really a latest version of the packages. They are just a "variant" build.
ocefpaf
commented
5 years ago PS: the only way to debug this is to do a search, conda search gdal | grep "2.4.1", and check what are the "valid" build number available in the channel.
jorisvandenbossche
commented
5 years ago The conda install cfitsio=3.430 did the trick in any case
And thanks for the explanation
and check what are the "valid" build number available in the channel.
Eg I now see only build numbers 8, 9 and 10. Does that mean that all others are removed manually to avoid broken packages?
And in my conda list, I see I have build number 5. But so what to do in such a case? If you see that you have a build number installed that is not in that list, you should update your package?
But how to do that? Because conda update gdal does not do anything? Specify the exact build number?
ocefpaf
commented
5 years ago Eg I now see only build numbers 8, 9 and 10. Does that mean that all others are removed manually to avoid broken packages?
Yep. cfitsio was not pinned and when a new version was release everything that was built with it got broken. The best way to fix this is to rebuild everything with a pinned cfitsio, that is why we have the new build numbers. Another way to fix this is to "hot-fix" pre-existing packages with a new metadata and change the pin. I don't really like the latter b/c it breaks reproducibility, the package changed under you without a build number update.
And in my conda list, I see I have build number 5. But so what to do in such a case? If you see that you have a build number installed that is not in that list, you should update your package? But how to do that? Because conda update gdal does not do anything? Specify the exact build number?
conda has no elegant way to do that and conda update may not work. Only a new env will be correct. In my workflow I remove and re-create envs constantly, so I don't really suffer from that. However, people who have stable envs and rely on them, are affected by this. I guess that it would be nice to request a feature in conda were the command conda update would prune packages that are no longer in the index from the local env.
darribas
commented
5 years ago It's not exactly the same, but I'm trying to update the gds_env and keep running into issues. First I had to pin poppler<0.67, which seem to do that trick, but also to then trigger this one:
In [1]: import geopandas
---------------------------------------------------------------------------
ImportError Traceback (most recent call last)
<ipython-input-1-fc7d1d298f0c> in <module>
----> 1 import geopandas
/opt/conda/lib/python3.7/site-packages/geopandas/__init__.py in <module>
3 from geopandas.geodataframe import points_from_xy
4
----> 5 from geopandas.io.file import read_file
6 from geopandas.io.sql import read_postgis
7 from geopandas.tools import sjoin
/opt/conda/lib/python3.7/site-packages/geopandas/io/file.py in <module>
2 from distutils.version import LooseVersion
3
----> 4 import fiona
5 import numpy as np
6
/opt/conda/lib/python3.7/site-packages/fiona/__init__.py in <module>
81 os.environ["PATH"] = os.environ["PATH"] + ";" + libdir
82
---> 83 from fiona.collection import BytesCollection, Collection
84 from fiona.drvsupport import supported_drivers
85 from fiona.env import ensure_env_with_credentials, Env
/opt/conda/lib/python3.7/site-packages/fiona/collection.py in <module>
7
8 from fiona import compat, vfs
----> 9 from fiona.ogrext import Iterator, ItemsIterator, KeysIterator
10 from fiona.ogrext import Session, WritingSession
11 from fiona.ogrext import buffer_to_virtual_file, remove_virtual_file, GEOMETRY_TYPES
ImportError: libkea.so.1.4.7: cannot open shared object file: No such file or directory
In [2]:This is the full conda list that is giving me that error:
jovyan@0fca380488f2:~$ conda list
# packages in environment at /opt/conda:
#
# Name Version Build Channel
_libgcc_mutex 0.1 main defaults
affine 2.2.2 py_0 conda-forge
alembic 1.0.11 py_0 conda-forge
altair 3.1.0 py37_0 conda-forge
appdirs 1.4.3 py_1 conda-forge
arrow-cpp 0.14.1 py37h6b969ab_0 conda-forge
asn1crypto 0.24.0 py37_1003 conda-forge
async_generator 1.10 py_0 conda-forge
attrs 19.1.0 py_0 conda-forge
backcall 0.1.0 py_0 conda-forge
bambi 0.1.5 pypi_0 pypi
binutils_impl_linux-64 2.31.1 h6176602_1 defaults
binutils_linux-64 2.31.1 h6176602_7 defaults
black 19.3b0 py_0 conda-forge
bleach 3.1.0 py_0 conda-forge
blinker 1.4 py_1 conda-forge
blosc 1.17.0 he1b5a44_0 conda-forge
bokeh 1.3.1 py37_0 conda-forge
boost-cpp 1.70.0 ha2d47e9_1 conda-forge
branca 0.3.1 py_0 conda-forge
brotli 1.0.7 he1b5a44_1000 conda-forge
bzip2 1.0.8 h516909a_0 conda-forge
c-ares 1.15.0 h516909a_1001 conda-forge
ca-certificates 2019.6.16 hecc5488_0 conda-forge
cairo 1.14.12 h8948797_3 defaults
certifi 2019.6.16 py37_1 conda-forge
certipy 0.1.3 py_0 conda-forge
cffi 1.12.3 py37h8022711_0 conda-forge
chardet 3.0.4 py37_1003 conda-forge
click 7.0 py_0 conda-forge
click-plugins 1.1.1 py_0 conda-forge
cligj 0.5.0 py_0 conda-forge
cloudpickle 1.2.1 py_0 conda-forge
colorama 0.4.1 pypi_0 pypi
colorcet 2.0.1 py_0 conda-forge
conda 4.7.10 py37_0 conda-forge
conda-package-handling 1.4.0 py37_0 conda-forge
configurable-http-proxy 4.1.0 node11_1 conda-forge
contextily 1.0rc2 py_0 conda-forge
cryptography 2.7 py37h72c5cf5_0 conda-forge
curl 7.65.3 hf8cf82a_0 conda-forge
cycler 0.10.0 py_1 conda-forge
cython 0.29.13 py37he1b5a44_0 conda-forge
cytoolz 0.10.0 py37h516909a_0 conda-forge
dask 2.2.0 py_0 conda-forge
dask-core 2.2.0 py_0 conda-forge
dask-glm 0.1.0 0 conda-forge
dask-ml 1.0.0 py_0 conda-forge
datashader 0.7.0 py_0 conda-forge
datashape 0.5.4 py_1 conda-forge
dbus 1.13.6 h746ee38_0 defaults
decorator 4.4.0 py_0 conda-forge
defusedxml 0.5.0 py_1 conda-forge
descartes 1.1.0 py_3 conda-forge
distributed 2.2.0 py_1 conda-forge
double-conversion 3.1.5 he1b5a44_1 conda-forge
entrypoints 0.3 py37_1000 conda-forge
expat 2.2.6 he6710b0_0 defaults
feather-format 0.4.0 py_1003 conda-forge
fiona 1.8.4 py37hc38cc03_0 defaults
folium 0.10.0 py_0 conda-forge
fontconfig 2.13.0 h9420a91_0 defaults
freetype 2.10.0 he983fc9_0 conda-forge
freexl 1.0.5 h14c3975_1002 conda-forge
fsspec 0.4.0 py_0 conda-forge
gcc_impl_linux-64 7.3.0 habb00fd_1 conda-forge
gcc_linux-64 7.3.0 h553295d_7 conda-forge
gdal 2.3.3 py37hbb2a789_0 defaults
geographiclib 1.49 py_0 conda-forge
geopandas 0.5.1 py_0 conda-forge
geopy 1.20.0 py_0 conda-forge
geos 3.7.1 hf484d3e_1000 conda-forge
gettext 0.19.8.1 hc5be6a0_1002 conda-forge
gflags 2.2.2 he1b5a44_1001 conda-forge
giflib 5.1.9 h516909a_0 conda-forge
gitdb2 2.0.5 pypi_0 pypi
gitpython 2.1.13 pypi_0 pypi
glib 2.56.2 had28632_1001 conda-forge
glog 0.4.0 he1b5a44_1 conda-forge
grpc-cpp 1.22.0 h18db393_0 conda-forge
gst-plugins-base 1.14.0 hbbd80ab_1 defaults
gstreamer 1.14.0 hb453b48_1 defaults
gxx_impl_linux-64 7.3.0 hdf63c60_1 conda-forge
gxx_linux-64 7.3.0 h553295d_7 conda-forge
h5py 2.9.0 nompi_py37hcafd542_1103 conda-forge
hdbscan 0.8.22 py37hd352d35_1 conda-forge
hdf4 4.2.13 h9a582f1_1002 conda-forge
hdf5 1.10.4 nompi_h3c11f04_1106 conda-forge
heapdict 1.0.0 py37_1000 conda-forge
icu 58.2 hf484d3e_1000 conda-forge
idna 2.8 py37_1000 conda-forge
imageio 2.5.0 py37_0 conda-forge
ipykernel 5.1.1 py37h5ca1d4c_0 conda-forge
ipyleaflet 0.11.1 py37_1 conda-forge
ipyparallel 6.2.4 py37_0 conda-forge
ipython 7.7.0 py37h5ca1d4c_0 conda-forge
ipython_genutils 0.2.0 py_1 conda-forge
ipywidgets 7.5.1 py_0 conda-forge
jedi 0.14.1 py37_0 conda-forge
jinja2 2.10.1 py_0 conda-forge
joblib 0.13.2 py_0 conda-forge
jpeg 9c h14c3975_1001 conda-forge
json-c 0.13.1 h14c3975_1001 conda-forge
json5 0.8.5 py_0 conda-forge
jsonschema 3.0.2 py37_0 conda-forge
jupyter_client 5.3.1 py_0 conda-forge
jupyter_core 4.4.0 py_0 conda-forge
jupyterhub 1.0.0 py37_0 conda-forge
jupyterlab 1.0.4 py37_0 conda-forge
jupyterlab_server 1.0.0 py_1 conda-forge
kealib 1.4.10 h1978553_1003 conda-forge
kiwisolver 1.1.0 py37hc9558a2_0 conda-forge
krb5 1.16.3 h05b26f9_1001 conda-forge
libarchive 3.3.3 hb44662c_1005 conda-forge
libblas 3.8.0 11_openblas conda-forge
libcblas 3.8.0 11_openblas conda-forge
libcurl 7.65.3 hda55be3_0 conda-forge
libdap4 3.19.1 h6ec2957_0 defaults
libedit 3.1.20170329 hf8c457e_1001 conda-forge
libevent 2.1.10 h72c5cf5_0 conda-forge
libffi 3.2.1 he1b5a44_1006 conda-forge
libgcc-ng 9.1.0 hdf63c60_0 defaults
libgdal 2.3.3 h2e7e64b_0 defaults
libgfortran-ng 7.3.0 hdf63c60_0 defaults
libgpuarray 0.7.6 h14c3975_1003 conda-forge
libiconv 1.15 h516909a_1005 conda-forge
libkml 1.3.0 h4fcabce_1010 conda-forge
liblapack 3.8.0 11_openblas conda-forge
libnetcdf 4.6.2 hbdf4f91_1001 conda-forge
libopenblas 0.3.6 h6e990d7_6 conda-forge
libpng 1.6.37 hed695b0_0 conda-forge
libpq 11.4 hd9ab2ff_3 conda-forge
libprotobuf 3.8.0 h8b12597_0 conda-forge
libsodium 1.0.17 h516909a_0 conda-forge
libspatialindex 1.9.0 he1b5a44_1 conda-forge
libspatialite 4.3.0a hb5ec416_1026 conda-forge
libssh2 1.8.2 h22169c7_2 conda-forge
libstdcxx-ng 9.1.0 hdf63c60_0 defaults
libtiff 4.0.10 h57b8799_1003 conda-forge
libuuid 1.0.3 h1bed415_2 defaults
libxcb 1.13 h14c3975_1002 conda-forge
libxml2 2.9.9 h13577e0_2 conda-forge
llvmlite 0.29.0 py37hfd453ef_1 conda-forge
locket 0.2.0 py_2 conda-forge
lz4-c 1.8.3 he1b5a44_1001 conda-forge
lzo 2.10 h14c3975_1000 conda-forge
mako 1.0.14 py_0 conda-forge
markupsafe 1.1.1 py37h14c3975_0 conda-forge
matplotlib 3.1.1 py37_0 conda-forge
matplotlib-base 3.1.1 py37hfd891ef_0 conda-forge
mercantile 1.1.1 py_0 conda-forge
mistune 0.8.4 py37h14c3975_1000 conda-forge
mock 3.0.5 py37_0 conda-forge
mplleaflet 0.0.5 py_2 conda-forge
msgpack-python 0.6.1 py37h6bb024c_0 conda-forge
multipledispatch 0.6.0 py_0 conda-forge
munch 2.3.2 py_0 conda-forge
nbconvert 5.5.0 py_0 conda-forge
nbdime 1.0.7 pypi_0 pypi
nbformat 4.4.0 py_1 conda-forge
ncurses 6.1 hf484d3e_1002 conda-forge
networkx 2.3 py_0 conda-forge
nodejs 11.14.0 he1b5a44_1 conda-forge
notebook 6.0.0 py37_0 conda-forge
numba 0.45.1 py37hb3f55d8_0 conda-forge
numexpr 2.6.9 py37h637b7d7_1000 conda-forge
numpy 1.17.0 py37h95a1406_0 conda-forge
oauthlib 3.0.1 py_0 conda-forge
olefile 0.46 py_0 conda-forge
openjpeg 2.3.1 h58a6597_0 conda-forge
openssl 1.1.1c h516909a_0 conda-forge
osmnet 0.1.5 py_2 conda-forge
osmnx 0.10 py_1 conda-forge
packaging 19.0 py_0 conda-forge
palettable 3.2.0 py_0 conda-forge
pamela 1.0.0 py_0 conda-forge
pandana 0.4.1 py37hb3f55d8_0 conda-forge
pandas 0.25.0 py37hb3f55d8_0 conda-forge
pandoc 2.7.3 0 conda-forge
pandocfilters 1.4.2 py_1 conda-forge
param 1.9.1 py_0 conda-forge
parquet-cpp 1.5.1 2 conda-forge
parso 0.5.1 py_0 conda-forge
partd 1.0.0 py_0 conda-forge
patsy 0.5.1 py_0 conda-forge
pcre 8.43 he6710b0_0 defaults
pexpect 4.7.0 py37_0 conda-forge
pickleshare 0.7.5 py37_1000 conda-forge
pillow 6.1.0 py37he7afcd5_0 conda-forge
pip 19.2.1 py37_0 conda-forge
pixman 0.38.0 h516909a_1003 conda-forge
polyline 1.4.0 pypi_0 pypi
poppler 0.65.0 h581218d_1 defaults
poppler-data 0.4.9 1 conda-forge
proj4 5.2.0 he1b5a44_1004 conda-forge
prometheus_client 0.7.1 py_0 conda-forge
prompt_toolkit 2.0.9 py_0 conda-forge
psutil 5.6.3 py37h516909a_0 conda-forge
pthread-stubs 0.4 h14c3975_1001 conda-forge
ptyprocess 0.6.0 py_1001 conda-forge
pyarrow 0.14.1 py37h8b68381_0 conda-forge
pycosat 0.6.3 py37h14c3975_1001 conda-forge
pycparser 2.19 py37_1 conda-forge
pyct 0.4.6 py_0 conda-forge
pyct-core 0.4.6 py_0 conda-forge
pycurl 7.43.0.2 py37h16ce93b_1 conda-forge
pygments 2.4.2 py_0 conda-forge
pygpu 0.7.6 py37h3010b51_1000 conda-forge
pyjwt 1.7.1 py_0 conda-forge
pymc3 3.7 py_0 conda-forge
pyopenssl 19.0.0 py37_0 conda-forge
pyparsing 2.4.2 py_0 conda-forge
pyproj 1.9.6 py37h516909a_1002 conda-forge
pyqt 5.9.2 py37hcca6a23_2 conda-forge
pyrsistent 0.15.4 py37h516909a_0 conda-forge
pysal 2.1.0 pypi_0 pypi
pysocks 1.7.0 py37_0 conda-forge
pystan 2.19.0.0 pypi_0 pypi
pytables 3.5.2 py37ha1aa75f_0 conda-forge
python 3.7.3 h33d41f4_1 conda-forge
python-dateutil 2.8.0 py_0 conda-forge
python-editor 1.0.4 py_0 conda-forge
python-libarchive-c 2.8 py37_1004 conda-forge
pytz 2019.2 py_0 conda-forge
pywavelets 1.0.3 py37hd352d35_1 conda-forge
pyyaml 5.1.2 py37h516909a_0 conda-forge
pyzmq 18.0.2 py37h1768529_2 conda-forge
qgrid 1.1.1 py37_1001 conda-forge
qt 5.9.7 h5867ecd_1 defaults
rasterio 1.0.21 py37hc38cc03_0 defaults
rasterstats 0.13.1 py_1 conda-forge
re2 2019.08.01 he1b5a44_0 conda-forge
readline 8.0 hf8c457e_0 conda-forge
requests 2.22.0 py37_1 conda-forge
rtree 0.8.3 py37h666c49c_1002 conda-forge
ruamel_yaml 0.15.71 py37h14c3975_1000 conda-forge
scikit-image 0.15.0 py37hb3f55d8_2 conda-forge
scikit-learn 0.21.3 py37hcdab131_0 conda-forge
scipy 1.3.0 py37h921218d_1 conda-forge
seaborn 0.9.0 py_1 conda-forge
send2trash 1.5.0 py_0 conda-forge
setuptools 41.0.1 py37_0 conda-forge
shapely 1.6.4 py37h06cd6f9_1005 conda-forge
simplejson 3.16.0 py37h14c3975_1002 conda-forge
sip 4.19.8 py37hf484d3e_1000 conda-forge
six 1.12.0 py37_1000 conda-forge
smmap2 2.0.5 pypi_0 pypi
snappy 1.1.7 he1b5a44_1002 conda-forge
snuggs 1.4.6 py_0 conda-forge
sortedcontainers 2.1.0 py_0 conda-forge
sqlalchemy 1.3.6 py37h516909a_0 conda-forge
sqlite 3.29.0 hcee41ef_0 conda-forge
statsmodels 0.10.1 py37hc1659b7_0 conda-forge
tblib 1.4.0 py_0 conda-forge
terminado 0.8.2 py37_0 conda-forge
testpath 0.4.2 py_1001 conda-forge
theano 1.0.4 py37hf484d3e_1000 conda-forge
thrift-cpp 0.12.0 hf3afdfd_1004 conda-forge
tini 0.18.0 h14c3975_1001 conda-forge
tk 8.6.9 hed695b0_1002 conda-forge
toml 0.10.0 py_0 conda-forge
toolz 0.10.0 py_0 conda-forge
tornado 6.0.3 py37h516909a_0 conda-forge
tqdm 4.32.2 py_0 conda-forge
traitlets 4.3.2 py37_1000 conda-forge
traittypes 0.2.1 py_1 conda-forge
tzlocal 2.0.0 pypi_0 pypi
urbanaccess 0.2.0 py_0 conda-forge
uriparser 0.9.3 he1b5a44_1 conda-forge
urllib3 1.25.3 py37_0 conda-forge
vincent 0.4.4 py_1 conda-forge
wcwidth 0.1.7 py_1 conda-forge
webencodings 0.5.1 py_1 conda-forge
wheel 0.33.4 py37_0 conda-forge
widgetsnbextension 3.5.1 py37_0 conda-forge
xarray 0.12.3 py_0 conda-forge
xerces-c 3.2.2 hea5cb30_1003 conda-forge
xlrd 1.2.0 py_0 conda-forge
xlsxwriter 1.1.8 py_0 conda-forge
xorg-libxau 1.0.9 h14c3975_0 conda-forge
xorg-libxdmcp 1.1.3 h516909a_0 conda-forge
xz 5.2.4 h14c3975_1001 conda-forge
yaml 0.1.7 h14c3975_1001 conda-forge
zeromq 4.3.2 he1b5a44_2 conda-forge
zict 1.0.0 py_0 conda-forge
zlib 1.2.11 h516909a_1005 conda-forge
zstd 1.4.0 h3b9ef0a_0 conda-forge
jovyan@0fca380488f2:~$This is on a clean environment, albeit with a bunch of libraries so dependencies might be complex. Any ideas on how to get around this please? Thank you very much in advance!
Ps. Let me know if I should post this somewhere else if it's too different from the original issue.
jorisvandenbossche
commented
5 years ago You have a mixture of conda-forge and defaults (fiona, rasterio and gdal are coming from defaults, but not all their dependencies are, so that is a clear no go).
But, I am not sure how you got there. The above output is after pinning poppler right? Can you show the output of the original error you got without pinning poppler?
If I try to create an environment with the list of packages in https://github.com/darribas/gds_env/blob/master/gds_py/Dockerfile locally, that goes fine. Maybe there is some interaction with the packages already installed in the base images (although it should only be things like notebook, jupyterhub and jupyterlab, and they are also using conda-forge, https://github.com/jupyter/docker-stacks/blob/master/base-notebook/Dockerfile)
darribas
commented
5 years ago If I don't pin poppler, this is the set up that loads:
# packages in environment at /opt/conda:
#
# Name Version Build Channel
_libgcc_mutex 0.1 main defaults
affine 2.2.2 py_0 conda-forge
alembic 1.0.11 py_0 conda-forge
altair 3.1.0 py37_0 conda-forge
appdirs 1.4.3 py_1 conda-forge
arrow-cpp 0.14.1 py37h6b969ab_0 conda-forge
asn1crypto 0.24.0 py37_1003 conda-forge
async_generator 1.10 py_0 conda-forge
attrs 19.1.0 py_0 conda-forge
backcall 0.1.0 py_0 conda-forge
bambi 0.1.5 pypi_0 pypi
binutils_impl_linux-64 2.31.1 h6176602_1 defaults
binutils_linux-64 2.31.1 h6176602_7 defaults
black 19.3b0 py_0 conda-forge
bleach 3.1.0 py_0 conda-forge
blinker 1.4 py_1 conda-forge
blosc 1.17.0 he1b5a44_0 conda-forge
bokeh 1.3.1 py37_0 conda-forge
boost-cpp 1.70.0 ha2d47e9_1 conda-forge
branca 0.3.1 py_0 conda-forge
brotli 1.0.7 he1b5a44_1000 conda-forge
bzip2 1.0.8 h516909a_0 conda-forge
c-ares 1.15.0 h516909a_1001 conda-forge
ca-certificates 2019.6.16 hecc5488_0 conda-forge
cairo 1.14.12 h8948797_3 defaults
certifi 2019.6.16 py37_1 conda-forge
certipy 0.1.3 py_0 conda-forge
cffi 1.12.3 py37h8022711_0 conda-forge
chardet 3.0.4 py37_1003 conda-forge
click 7.0 py_0 conda-forge
click-plugins 1.1.1 py_0 conda-forge
cligj 0.5.0 py_0 conda-forge
cloudpickle 1.2.1 py_0 conda-forge
colorama 0.4.1 pypi_0 pypi
colorcet 2.0.1 py_0 conda-forge
conda 4.7.10 py37_0 conda-forge
conda-package-handling 1.3.11 py37_0 conda-forge
configurable-http-proxy 4.1.0 node11_1 conda-forge
contextily 1.0rc2 py_0 conda-forge
cryptography 2.7 py37h72c5cf5_0 conda-forge
curl 7.65.3 hf8cf82a_0 conda-forge
cycler 0.10.0 py_1 conda-forge
cython 0.29.13 py37he1b5a44_0 conda-forge
cytoolz 0.10.0 py37h516909a_0 conda-forge
dask 2.2.0 py_0 conda-forge
dask-core 2.2.0 py_0 conda-forge
dask-glm 0.1.0 0 conda-forge
dask-ml 1.0.0 py_0 conda-forge
datashader 0.7.0 py_0 conda-forge
datashape 0.5.4 py_1 conda-forge
dbus 1.13.6 h746ee38_0 defaults
decorator 4.4.0 py_0 conda-forge
defusedxml 0.5.0 py_1 conda-forge
descartes 1.1.0 py_3 conda-forge
distributed 2.2.0 py_1 conda-forge
double-conversion 3.1.5 he1b5a44_1 conda-forge
entrypoints 0.3 py37_1000 conda-forge
expat 2.2.6 he6710b0_0 defaults
feather-format 0.4.0 py_1003 conda-forge
fiona 1.8.4 py37hc38cc03_0 defaults
folium 0.10.0 py_0 conda-forge
fontconfig 2.13.0 h9420a91_0 defaults
freetype 2.10.0 he983fc9_0 conda-forge
freexl 1.0.5 h14c3975_1002 conda-forge
fsspec 0.4.0 py_0 conda-forge
gcc_impl_linux-64 7.3.0 habb00fd_1 conda-forge
gcc_linux-64 7.3.0 h553295d_7 conda-forge
gdal 2.3.3 py37hbb2a789_0 defaults
geographiclib 1.49 py_0 conda-forge
geopandas 0.5.1 py_0 conda-forge
geopy 1.20.0 py_0 conda-forge
geos 3.7.1 hf484d3e_1000 conda-forge
gettext 0.19.8.1 hc5be6a0_1002 conda-forge
gflags 2.2.2 he1b5a44_1001 conda-forge
giflib 5.1.9 h516909a_0 conda-forge
gitdb2 2.0.5 pypi_0 pypi
gitpython 2.1.13 pypi_0 pypi
glib 2.56.2 had28632_1001 conda-forge
glog 0.4.0 he1b5a44_1 conda-forge
grpc-cpp 1.22.0 h18db393_0 conda-forge
gst-plugins-base 1.14.0 hbbd80ab_1 defaults
gstreamer 1.14.0 hb453b48_1 defaults
gxx_impl_linux-64 7.3.0 hdf63c60_1 conda-forge
gxx_linux-64 7.3.0 h553295d_7 conda-forge
h5py 2.9.0 nompi_py37hcafd542_1103 conda-forge
hdbscan 0.8.22 py37hd352d35_1 conda-forge
hdf4 4.2.13 h9a582f1_1002 conda-forge
hdf5 1.10.4 nompi_h3c11f04_1106 conda-forge
heapdict 1.0.0 py37_1000 conda-forge
icu 58.2 hf484d3e_1000 conda-forge
idna 2.8 py37_1000 conda-forge
imageio 2.5.0 py37_0 conda-forge
ipykernel 5.1.1 py37h5ca1d4c_0 conda-forge
ipyleaflet 0.11.1 py37_1 conda-forge
ipyparallel 6.2.4 py37_0 conda-forge
ipython 7.7.0 py37h5ca1d4c_0 conda-forge
ipython_genutils 0.2.0 py_1 conda-forge
ipywidgets 7.5.1 py_0 conda-forge
jedi 0.14.1 py37_0 conda-forge
jinja2 2.10.1 py_0 conda-forge
joblib 0.13.2 py_0 conda-forge
jpeg 9c h14c3975_1001 conda-forge
json-c 0.13.1 h14c3975_1001 conda-forge
json5 0.8.5 py_0 conda-forge
jsonschema 3.0.2 py37_0 conda-forge
jupyter_client 5.3.1 py_0 conda-forge
jupyter_core 4.4.0 py_0 conda-forge
jupyterhub 1.0.0 py37_0 conda-forge
jupyterlab 1.0.4 py37_0 conda-forge
jupyterlab_server 1.0.0 py_1 conda-forge
kealib 1.4.10 h1978553_1003 conda-forge
kiwisolver 1.1.0 py37hc9558a2_0 conda-forge
krb5 1.16.3 h05b26f9_1001 conda-forge
libarchive 3.3.3 hb44662c_1005 conda-forge
libblas 3.8.0 11_openblas conda-forge
libcblas 3.8.0 11_openblas conda-forge
libcurl 7.65.3 hda55be3_0 conda-forge
libdap4 3.19.1 h6ec2957_0 defaults
libedit 3.1.20170329 hf8c457e_1001 conda-forge
libevent 2.1.10 h72c5cf5_0 conda-forge
libffi 3.2.1 he1b5a44_1006 conda-forge
libgcc-ng 9.1.0 hdf63c60_0 defaults
libgdal 2.3.3 h2e7e64b_0 defaults
libgfortran-ng 7.3.0 hdf63c60_0 defaults
libgpuarray 0.7.6 h14c3975_1003 conda-forge
libiconv 1.15 h516909a_1005 conda-forge
libkml 1.3.0 h4fcabce_1010 conda-forge
liblapack 3.8.0 11_openblas conda-forge
libnetcdf 4.6.2 hbdf4f91_1001 conda-forge
libopenblas 0.3.6 h6e990d7_6 conda-forge
libpng 1.6.37 hed695b0_0 conda-forge
libpq 11.4 hd9ab2ff_3 conda-forge
libprotobuf 3.8.0 h8b12597_0 conda-forge
libsodium 1.0.17 h516909a_0 conda-forge
libspatialindex 1.9.0 he1b5a44_1 conda-forge
libspatialite 4.3.0a hb5ec416_1026 conda-forge
libssh2 1.8.2 h22169c7_2 conda-forge
libstdcxx-ng 9.1.0 hdf63c60_0 defaults
libtiff 4.0.10 h57b8799_1003 conda-forge
libuuid 1.0.3 h1bed415_2 defaults
libxcb 1.13 h14c3975_1002 conda-forge
libxml2 2.9.9 h13577e0_2 conda-forge
llvmlite 0.29.0 py37hfd453ef_1 conda-forge
locket 0.2.0 py_2 conda-forge
lz4-c 1.8.3 he1b5a44_1001 conda-forge
lzo 2.10 h14c3975_1000 conda-forge
mako 1.0.14 py_0 conda-forge
markupsafe 1.1.1 py37h14c3975_0 conda-forge
matplotlib 3.1.1 py37_0 conda-forge
matplotlib-base 3.1.1 py37hfd891ef_0 conda-forge
mercantile 1.1.1 py_0 conda-forge
mistune 0.8.4 py37h14c3975_1000 conda-forge
mock 3.0.5 py37_0 conda-forge
mplleaflet 0.0.5 py_2 conda-forge
msgpack-python 0.6.1 py37h6bb024c_0 conda-forge
multipledispatch 0.6.0 py_0 conda-forge
munch 2.3.2 py_0 conda-forge
nbconvert 5.5.0 py_0 conda-forge
nbdime 1.0.7 pypi_0 pypi
nbformat 4.4.0 py_1 conda-forge
ncurses 6.1 hf484d3e_1002 conda-forge
networkx 2.3 py_0 conda-forge
nodejs 11.14.0 he1b5a44_1 conda-forge
notebook 6.0.0 py37_0 conda-forge
numba 0.45.1 py37hb3f55d8_0 conda-forge
numexpr 2.6.9 py37h637b7d7_1000 conda-forge
numpy 1.17.0 py37h95a1406_0 conda-forge
oauthlib 3.0.1 py_0 conda-forge
olefile 0.46 py_0 conda-forge
openjpeg 2.3.1 h58a6597_0 conda-forge
openssl 1.1.1c h516909a_0 conda-forge
osmnet 0.1.5 py_2 conda-forge
osmnx 0.10 py_1 conda-forge
packaging 19.0 py_0 conda-forge
palettable 3.2.0 py_0 conda-forge
pamela 1.0.0 py_0 conda-forge
pandana 0.4.1 py37hb3f55d8_0 conda-forge
pandas 0.25.0 py37hb3f55d8_0 conda-forge
pandoc 2.7.3 0 conda-forge
pandocfilters 1.4.2 py_1 conda-forge
param 1.9.1 py_0 conda-forge
parquet-cpp 1.5.1 2 conda-forge
parso 0.5.1 py_0 conda-forge
partd 1.0.0 py_0 conda-forge
patsy 0.5.1 py_0 conda-forge
pcre 8.43 he6710b0_0 defaults
pexpect 4.7.0 py37_0 conda-forge
pickleshare 0.7.5 py37_1000 conda-forge
pillow 6.1.0 py37he7afcd5_0 conda-forge
pip 19.2.1 py37_0 conda-forge
pixman 0.38.0 h516909a_1003 conda-forge
polyline 1.4.0 pypi_0 pypi
poppler 0.67.0 h2fc8fa2_1002 conda-forge
poppler-data 0.4.9 1 conda-forge
proj4 5.2.0 he1b5a44_1004 conda-forge
prometheus_client 0.7.1 py_0 conda-forge
prompt_toolkit 2.0.9 py_0 conda-forge
psutil 5.6.3 py37h516909a_0 conda-forge
pthread-stubs 0.4 h14c3975_1001 conda-forge
ptyprocess 0.6.0 py_1001 conda-forge
pyarrow 0.14.1 py37h8b68381_0 conda-forge
pycosat 0.6.3 py37h14c3975_1001 conda-forge
pycparser 2.19 py37_1 conda-forge
pyct 0.4.6 py_0 conda-forge
pyct-core 0.4.6 py_0 conda-forge
pycurl 7.43.0.2 py37h16ce93b_1 conda-forge
pygments 2.4.2 py_0 conda-forge
pygpu 0.7.6 py37h3010b51_1000 conda-forge
pyjwt 1.7.1 py_0 conda-forge
pymc3 3.7 py_0 conda-forge
pyopenssl 19.0.0 py37_0 conda-forge
pyparsing 2.4.2 py_0 conda-forge
pyproj 1.9.6 py37h516909a_1002 conda-forge
pyqt 5.9.2 py37hcca6a23_1 conda-forge
pyrsistent 0.15.4 py37h516909a_0 conda-forge
pysal 2.1.0 pypi_0 pypi
pysocks 1.7.0 py37_0 conda-forge
pystan 2.19.0.0 pypi_0 pypi
pytables 3.5.2 py37ha1aa75f_0 conda-forge
python 3.7.3 h33d41f4_1 conda-forge
python-dateutil 2.8.0 py_0 conda-forge
python-editor 1.0.4 py_0 conda-forge
python-libarchive-c 2.8 py37_1004 conda-forge
pytz 2019.2 py_0 conda-forge
pywavelets 1.0.3 py37hd352d35_1 conda-forge
pyyaml 5.1.2 py37h516909a_0 conda-forge
pyzmq 18.0.2 py37h1768529_2 conda-forge
qgrid 1.1.1 py37_1001 conda-forge
qt 5.9.7 h5867ecd_1 defaults
rasterio 1.0.21 py37hc38cc03_0 defaults
rasterstats 0.13.1 py_1 conda-forge
re2 2019.08.01 he1b5a44_0 conda-forge
readline 8.0 hf8c457e_0 conda-forge
requests 2.22.0 py37_1 conda-forge
rtree 0.8.3 py37h666c49c_1002 conda-forge
ruamel_yaml 0.15.71 py37h14c3975_1000 conda-forge
scikit-image 0.15.0 py37hb3f55d8_2 conda-forge
scikit-learn 0.21.3 py37hcdab131_0 conda-forge
scipy 1.3.0 py37h921218d_1 conda-forge
seaborn 0.9.0 py_1 conda-forge
send2trash 1.5.0 py_0 conda-forge
setuptools 41.0.1 py37_0 conda-forge
shapely 1.6.4 py37h06cd6f9_1005 conda-forge
simplejson 3.16.0 py37h14c3975_1002 conda-forge
sip 4.19.8 py37hf484d3e_1000 conda-forge
six 1.12.0 py37_1000 conda-forge
smmap2 2.0.5 pypi_0 pypi
snappy 1.1.7 he1b5a44_1002 conda-forge
snuggs 1.4.6 py_0 conda-forge
sortedcontainers 2.1.0 py_0 conda-forge
sqlalchemy 1.3.6 py37h516909a_0 conda-forge
sqlite 3.29.0 hcee41ef_0 conda-forge
statsmodels 0.10.1 py37hc1659b7_0 conda-forge
tblib 1.4.0 py_0 conda-forge
terminado 0.8.2 py37_0 conda-forge
testpath 0.4.2 py_1001 conda-forge
theano 1.0.4 py37hf484d3e_1000 conda-forge
thrift-cpp 0.12.0 hf3afdfd_1004 conda-forge
tini 0.18.0 h14c3975_1001 conda-forge
tk 8.6.9 hed695b0_1002 conda-forge
toml 0.10.0 py_0 conda-forge
toolz 0.10.0 py_0 conda-forge
tornado 6.0.3 py37h516909a_0 conda-forge
tqdm 4.32.2 py_0 conda-forge
traitlets 4.3.2 py37_1000 conda-forge
traittypes 0.2.1 py_1 conda-forge
tzlocal 2.0.0 pypi_0 pypi
urbanaccess 0.2.0 py_0 conda-forge
uriparser 0.9.3 he1b5a44_1 conda-forge
urllib3 1.25.3 py37_0 conda-forge
vincent 0.4.4 py_1 conda-forge
wcwidth 0.1.7 py_1 conda-forge
webencodings 0.5.1 py_1 conda-forge
wheel 0.33.4 py37_0 conda-forge
widgetsnbextension 3.5.1 py37_0 conda-forge
xarray 0.12.3 py_0 conda-forge
xerces-c 3.2.2 hea5cb30_1003 conda-forge
xlrd 1.2.0 py_0 conda-forge
xlsxwriter 1.1.8 py_0 conda-forge
xorg-libxau 1.0.9 h14c3975_0 conda-forge
xorg-libxdmcp 1.1.3 h516909a_0 conda-forge
xz 5.2.4 h14c3975_1001 conda-forge
yaml 0.1.7 h14c3975_1001 conda-forge
zeromq 4.3.2 he1b5a44_2 conda-forge
zict 1.0.0 py_0 conda-forge
zlib 1.2.11 h516909a_1005 conda-forge
zstd 1.4.0 h3b9ef0a_0 conda-forgeand the error I get when importing fiona:
import fiona
---------------------------------------------------------------------------
ImportError Traceback (most recent call last)
<ipython-input-1-4c762272c079> in <module>
----> 1 import fiona
/opt/conda/lib/python3.7/site-packages/fiona/__init__.py in <module>
81 os.environ["PATH"] = os.environ["PATH"] + ";" + libdir
82
---> 83 from fiona.collection import BytesCollection, Collection
84 from fiona.drvsupport import supported_drivers
85 from fiona.env import ensure_env_with_credentials, Env
/opt/conda/lib/python3.7/site-packages/fiona/collection.py in <module>
7
8 from fiona import compat, vfs
----> 9 from fiona.ogrext import Iterator, ItemsIterator, KeysIterator
10 from fiona.ogrext import Session, WritingSession
11 from fiona.ogrext import buffer_to_virtual_file, remove_virtual_file, GEOMETRY_TYPES
ImportError: libpoppler.so.76: cannot open shared object file: No such file or directoryIt still brings things like rasterio from defaults...
jorisvandenbossche
commented
5 years ago maybe qt is one of the problems (some other package might force it to come from defaults, wild guess here)
In the install command, I think you should be able to do something like
'conda-forge::rasterio' \to indicate that a certain package should come from conda-forge.
darribas
commented
5 years ago surprisingly, putting defaults first now seems to do the trick. Would you have any suggestion against this?
ocefpaf
commented
5 years ago @darribas note that without strict there is no guarantee that one channel or the other will work.
darribas
commented
5 years ago mmm... did not know about strict. How could I use it to enforce an all-conda-forge setup?
jorisvandenbossche
commented
5 years ago you can add a call to conda config --system --set channel_priority strict before installing the packages in the dockerfile
ocefpaf
commented
5 years ago mmm... did not know about
strict. How could I use it to enforce an all-conda-forgesetup?
We should make that more prominent in our docs, but see https://conda-forge.org/docs/user/tipsandtricks.html#how-to-fix-it
PS: I'm testing it at this moment with your docker image. I can send a PR as soon as the testing is done.
darribas
commented
5 years ago In the meantime, I've caught a couple of missing packages too: deprecated and mkl-service, both on conda, if you want to add them...
ocefpaf
commented
5 years ago In the meantime, I've caught a couple of missing packages too:
deprecatedandmkl-service, both on conda, if you want to add them...
Let's move this to the PR. It is no longer a fiona feedstock issue.
In an env with geospatial packages, I did an update of contextily. This updated a lot as side effect (among others: cfitsio):
but that broke the fiona install:
and I don't directly find a way to repair the environment (
conda update fionaorconda update gdal cfitsioonly suggest to update geopandas, which will not help)