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conda-forge / r-rgdal-feedstock

A conda-smithy repository for r-rgdal.
BSD 3-Clause "New" or "Revised" License
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r-rgdal, PROJ6 and "+init=epsg" syntax #31

Closed JamesSample closed 5 years ago

JamesSample commented 5 years ago

I am trying to setup r-rgdal within a JupyterLab environment using a Docker container based on Ubuntu 18.04 and derived from the Jupyter Data Science Notebook Docker stack.

The following minimal Dockerfile reproduces my issue, although my "real" Dockerfile is a bit more complicated.

ARG BASE_CONTAINER=jupyter/datascience-notebook:2ce7c06a61a1
FROM $BASE_CONTAINER

# Use strict channel priority for conda
RUN conda config --set channel_priority strict

# Install conda-forge packages
RUN conda install -c conda-forge --quiet --yes \
    'gdal' \
    'proj4' \
    'r-rgdal' && \
    conda clean --all -f -y && \
    fix-permissions $CONDA_DIR && \
    fix-permissions /home/$NB_USER

USER $NB_UID

This builds without errors and I can start JupyterLab using 

 docker run -ti --rm -p 8888:8888 -v ${PWD}:/home/jovyan/work my_image start.sh jupyter lab

If I then create an R notebook and run library(rgdal), I see the following, which looks OK

Loading required package: sp
rgdal: version: 1.4-4, (SVN revision 833)
 Geospatial Data Abstraction Library extensions to R successfully loaded
 Loaded GDAL runtime: GDAL 3.0.1, released 2019/06/28
 Path to GDAL shared files: 
 GDAL binary built with GEOS: TRUE 
 Loaded PROJ.4 runtime: Rel. 6.1.1, July 1st, 2019, [PJ_VERSION: 611]
 Path to PROJ.4 shared files: (autodetected)
 Linking to sp version: 1.3-1

However, if I try CRS("+init=epsg:3035") I get the following error

Error in CRS("+init=epsg:3035"): no arguments in initialization list

The same code works fine using rgdal installed locally via R-Studio. I've also asked on the r-sig-geo mailing list and it appears that this should work with recent versions of rgdal and PROJ version 6 (see the discussion here for further details).

I realise there are various issues for both Python and R relating to API changes in PROJ6, but I think CRS("+init=epsg:3035") should still work (?).

Does anyone have any suggestions, please? I'm currently unsure whether:

  1. This is a "local" problem with my installation
  2. I need to switch to a different syntax for PROJ6 (if so, what?), or
  3. This is a build issue with r-rgdal/proj/gdal on conda-forge?

Thanks in advance for any suggestions! :-)


Environment (conda list):

``` $ conda list # packages in environment at /opt/conda: # # Name Version Build Channel _libgcc_mutex 0.1 main defaults _r-mutex 1.0.1 anacondar_1 conda-forge alembic 1.0.11 py_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 beautifulsoup4 4.8.0 py37_0 conda-forge binutils_impl_linux-64 2.31.1 h6176602_1 defaults binutils_linux-64 2.31.1 h6176602_8 defaults blas 2.11 openblas conda-forge bleach 3.1.0 py_0 conda-forge blinker 1.4 py_1 conda-forge bokeh 1.3.4 py37_0 conda-forge boost-cpp 1.70.0 h8e57a91_2 conda-forge bwidget 1.9.11 0 conda-forge bzip2 1.0.8 h516909a_0 conda-forge ca-certificates 2019.9.11 hecc5488_0 conda-forge cairo 1.16.0 hfb77d84_1002 conda-forge certifi 2019.9.11 py37_0 conda-forge certipy 0.1.3 py_0 conda-forge cffi 1.12.3 py37h8022711_0 conda-forge cfitsio 3.470 hb60a0a2_2 conda-forge chardet 3.0.4 py37_1003 conda-forge click 7.0 py_0 conda-forge cloudpickle 1.2.1 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 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 decorator 4.4.0 py_0 conda-forge defusedxml 0.5.0 py_1 conda-forge dill 0.3.0 py37_0 conda-forge distributed 2.2.0 py_1 conda-forge entrypoints 0.3 py37_1000 conda-forge expat 2.2.5 he1b5a44_1003 conda-forge fastcache 1.1.0 py37h516909a_0 conda-forge fontconfig 2.13.1 h86ecdb6_1001 conda-forge freetype 2.10.0 he983fc9_1 conda-forge freexl 1.0.5 h14c3975_1002 conda-forge fribidi 1.0.5 h516909a_1002 conda-forge fsspec 0.4.1 py_0 conda-forge gcc_impl_linux-64 7.3.0 habb00fd_1 conda-forge gcc_linux-64 7.3.0 h553295d_8 conda-forge gdal 3.0.1 py37hbb6b9fb_8 conda-forge geos 3.7.2 he1b5a44_1 conda-forge geotiff 1.5.1 hcd53e25_3 conda-forge gettext 0.19.8.1 hc5be6a0_1002 conda-forge gfortran_impl_linux-64 7.3.0 hdf63c60_1 defaults gfortran_linux-64 7.3.0 h553295d_8 defaults giflib 5.1.7 h516909a_1 conda-forge glib 2.58.3 h6f030ca_1002 conda-forge gmp 6.1.2 hf484d3e_1000 conda-forge gmpy2 2.1.0b1 py37h04dde30_0 conda-forge graphite2 1.3.13 hf484d3e_1000 conda-forge gsl 2.5 h294904e_0 conda-forge gxx_impl_linux-64 7.3.0 hdf63c60_1 conda-forge gxx_linux-64 7.3.0 h553295d_8 conda-forge h5py 2.9.0 nompi_py37h513d04c_1104 conda-forge harfbuzz 2.4.0 h9f30f68_2 conda-forge hdf4 4.2.13 h9a582f1_1002 conda-forge hdf5 1.10.5 nompi_h3c11f04_1100 conda-forge heapdict 1.0.0 py37_1000 conda-forge icu 64.2 he1b5a44_0 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 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 h58c409b_1005 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 3.20.4 hd3bb157_0 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 defaults libgdal 3.0.1 hf47eb90_8 conda-forge libgfortran-ng 7.3.0 hdf63c60_0 defaults libiconv 1.15 h516909a_1005 conda-forge libkml 1.3.0 h4fcabce_1010 conda-forge liblapack 3.8.0 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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 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 ```


Details about conda and system ( conda info ):

``` $ conda info active environment : None user config file : /home/jovyan/.condarc populated config files : /opt/conda/.condarc /home/jovyan/.condarc conda version : 4.7.10 conda-build version : not installed python version : 3.7.3.final.0 virtual packages : base environment : /opt/conda (writable) channel URLs : https://conda.anaconda.org/conda-forge/linux-64 https://conda.anaconda.org/conda-forge/noarch https://repo.anaconda.com/pkgs/main/linux-64 https://repo.anaconda.com/pkgs/main/noarch https://repo.anaconda.com/pkgs/r/linux-64 https://repo.anaconda.com/pkgs/r/noarch package cache : /opt/conda/pkgs /home/jovyan/.conda/pkgs envs directories : /opt/conda/envs /home/jovyan/.conda/envs platform : linux-64 user-agent : conda/4.7.10 requests/2.22.0 CPython/3.7.3 Linux/4.9.93-linuxkit-aufs ubuntu/18.04.2 glibc/2.27 UID:GID : 1000:100 netrc file : None offline mode : False ```
ocefpaf commented 5 years ago

I don't think this is related to the proj version. It seems to be related to the environment variable for the $PROJ_LIB environment variable. Here is what I get if I installed this in an env and activate:

> library(rgdal)
Loading required package: sp
rgdal: version: 1.4-4, (SVN revision 833)
 Geospatial Data Abstraction Library extensions to R successfully loaded
 Loaded GDAL runtime: GDAL 3.0.1, released 2019/06/28
 Path to GDAL shared files: 
 GDAL binary built with GEOS: TRUE 
 Loaded PROJ.4 runtime: Rel. 6.1.1, July 1st, 2019, [PJ_VERSION: 611]
 Path to PROJ.4 shared files: ~/miniconda3/envs/TEST/share/proj
 Linking to sp version: 1.3-1 
> CRS("+init=epsg:3035")
CRS arguments:
 +init=epsg:3035 +proj=laea +lat_0=52 +lon_0=10 +x_0=4321000
+y_0=3210000 +ellps=GRS80 +units=m +no_defs

Note that I have the right path Path to PROJ.4 shared files: ~/miniconda3/envs/TEST/share/proj instead of (autodetected).

Are you installing things in the base environment? Can you try to activate it before calling jupyterlab? (conda activate base or source activate base).

I'm closing this b/c it is not really a problem with the package but conda's use with a Docker image. We can still discuss things here but ultimately it is a conda "expected" behavior to have things installed in an env and activate that env.

JamesSample commented 5 years ago

Thanks for such a fast and helpful response!

You're absolutely right - this is a path/environment variable problem. When I saw Path to PROJ.4 shared files: (autodetected) I assumed everything was OK, but explicitly setting the path to the proj folder has solved the problem :-)

I am installing everything within my base environment, since this Dockerfile will only ever be used with a single env deployed via JupyterHub. The environment is configured in the Jupyter "base notebook" Dockerfile here and to get things working I had to fix the PROJ_LIB environment variable in my Dockerfile, as follows:

ENV PROJ_LIB $CONDA_DIR/share/proj

Thanks once again for your help on this! I was heading in completely the wrong direction thinking this was something to do with PROJ6/PROJ4 "emulation mode".

ocefpaf commented 5 years ago

I actually had this issue somewhere else and I did not post my solutions here b/c they were all bad. I'm copying your solution now :smile: win-win

Thanks!