After going round in circles most of the day, I finally discovered that the PROJ_LIB environment variable within my Dockerfile did not match my conda environment. When I loaded rgdal I saw
Path to PROJ.4 shared files: (autodetected) in the output and assumed all was OK, but having explicitly set the environment variable I now see Path to PROJ.4 shared files: /opt/conda/share/proj and everything works as expected. On a related note, some of my Python code also has started to give errors similar to those reported by Edzer e.g. init=epsg:/init=IGNF: syntax not supported in non-PROJ4 emulation mode I suspect these issues probably *are *caused by API changes in PROJ6, but my original issue is unrelated and was due to incorrect paths in my conda/Docker environment. Thanks for your help, Edzer! I look forward to working more with R spatial tools in the future :-) James. On Thu, 12 Sep 2019 at 12:30, Edzer Pebesma <edzer.pebe...@uni-muenster.de> wrote: > CRAN, btw, reports similar errors on all debian testing platforms, of > the kind > > > st_crs("+init=epsg:3857")$epsg > proj_create: init=epsg:/init=IGNF: syntax not supported in non-PROJ4 > emulation mode > > see > > https://cran.r-project.org/web/checks/check_results_edzer.pebesma_at_uni-muenster.de.html#sf > > I failed to reproduce these because I can't build the CRAN debian > testing docker image from https://github.com/jeroen/rcheckserver , > reported here: https://github.com/jeroen/rcheckserver/issues/2 > > I would appreciate any help here. > > On 9/12/19 11:08 AM, Edzer Pebesma wrote: > > > > > > On 9/12/19 10:55 AM, James Sample wrote: > >> Thanks Edzer - that's very helpful! > >> > >> Would it be possible for you to link/share your Ubuntu Dockerfile, > please? > >> (I completely understand if you'd rather not, of course). > > > > https://github.com/r-spatial/sf/tree/master/inst/docker/gdal > > > >> > >> Perhaps if I can see how you're setting thing up in Ubuntu I can modify > my > >> Jupyter Dockerfile accordingly, and if I can convince myself that this > is a > >> actually conda-forge/build issue (rather than my own mistake) I can > open an > >> issue on the conda r-rgdal feedstock ( > >> https://github.com/conda-forge/r-rgdal-feedstock). > > > > Great, please also report back here! > > > >> > >> Thanks again for your help! > >> > >> Best wishes, > >> > >> > >> James. > >> > >> > >> > >> On Wed, 11 Sep 2019 at 23:10, Edzer Pebesma < > edzer.pebe...@uni-muenster.de> > >> wrote: > >> > >>> On an ubuntu docker image with gdal 3.0.1 and PROJ 6.2.0, I see: > >>> > >>>> library(rgdal) > >>> Loading required package: sp > >>> rgdal: version: 1.4-6, (SVN revision (unknown)) > >>> 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: FALSE > >>> Loaded PROJ.4 runtime: Rel. 6.2.0, September 1st, 2019, [PJ_VERSION: > 620] > >>> Path to PROJ.4 shared files: (autodetected) > >>> 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 > >>> > >>> but also a warning with sf: > >>> > >>>> library(sf) > >>> Linking to GEOS 3.7.2, GDAL 3.0.1, PROJ 6.2.0 > >>>> st_crs("+init=epsg:3035") > >>> Coordinate Reference System: > >>> No EPSG code > >>> proj4string: "+proj=laea +lat_0=52 +lon_0=10 +x_0=4321000 > +y_0=3210000 > >>> +ellps=GRS80 +units=m +no_defs" > >>> Warning message: > >>> In CPL_crs_from_proj4string(x) : > >>> GDAL Message 1: +init=epsg:XXXX syntax is deprecated. It might return > >>> a CRS with a non-EPSG compliant axis order. > >>> > >>> so it feels like a combination of how PROJ has been installed, and how > >>> it has been compiled into the R packages. > >>> > >>> > >>> On 9/11/19 9:38 PM, James Sample wrote: > >>>> Dear all, > >>>> > >>>> I am trying to setup R and rgdal within a JupyterLab environment > >>> alongside > >>>> my usual Python tools. I realise this is probably an unfamiliar setup > for > >>>> many, but I hope someone might be able to help nevertheless. > >>>> > >>>> I'm using a Docker container based on Ubuntu 18.04 and derived from > the > >>>> Jupyter Data Science Notebook ( > >>>> > >>> > https://github.com/jupyter/docker-stacks/tree/master/datascience-notebook > >>> ). > >>>> I have Python 3.7 and R 3.6 installed, and I'm using "conda" as my > >>> package > >>>> manager. > >>>> > >>>> I have successfully installed GDAL and PROJ, together with various > Python > >>>> and R packages, including 'sp' and 'rgdal'. When I run > >>>> > >>>> require(rgdal) > >>>> > >>>> I see the following > >>>> > >>>> Loading required package: 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 2.4.2, released 2019/06/28 > >>>> Path to GDAL shared files: /opt/conda/share/gdal > >>>> GDAL binary built with GEOS: TRUE > >>>> Loaded PROJ.4 runtime: Rel. 6.1.0, May 15th, 2019, [PJ_VERSION: 610] > >>>> Path to PROJ.4 shared files: (autodetected) > >>>> Linking to sp version: 1.3-1 > >>>> > >>>> > >>>> which seems OK. Most things work as expected, but this > >>>> > >>>> CRS("+init=epsg:3035") > >>>> > >>>> gives an exception > >>>> > >>>> Error in CRS("+init=epsg:3035"): no arguments in initialization > list > >>>> > >>>> The same code works fine in R-Studio, although I note that my R-Studio > >>>> installation has PROJ 4.9.2 (with the same versions of rgdal and sp as > >>>> listed above). Unfortunately I can't downgrade PROJ, since some of my > >>>> Python packages require version 6.1. > >>>> > >>>> I have read that rgdal is compatible with PROJ6 and I haven't been > able > >>> to > >>>> find (m)any similar issues online, so I assume I'm doing something > wrong. > >>>> As a workaround, this runs successfully > >>>> > >>>> showP4(showWKT("+init=epsg:3035")) > >>>> > >>>> But the original syntax is cleaner and I'd rather not refactor all my > old > >>>> code if I can help it. Can anyone point me in the right direction, > >>> please? > >>>> Is the "+init=epsg" syntax supported with PROJ 6, or should I be > using an > >>>> alternative? > >>>> > >>>> Thanks and best wishes, > >>>> > >>>> > >>>> James. > >>>> > >>>> [[alternative HTML version deleted]] > >>>> > >>>> _______________________________________________ > >>>> R-sig-Geo mailing list > >>>> R-sig-Geo@r-project.org > >>>> https://stat.ethz.ch/mailman/listinfo/r-sig-geo > >>>> > >>> > >>> -- > >>> Edzer Pebesma > >>> Institute for Geoinformatics > >>> Heisenbergstrasse 2, 48151 Muenster, Germany > >>> Phone: +49 251 8333081 > >>> _______________________________________________ > >>> R-sig-Geo mailing list > >>> R-sig-Geo@r-project.org > >>> https://stat.ethz.ch/mailman/listinfo/r-sig-geo > >>> > >> > >> [[alternative HTML version deleted]] > >> > >> _______________________________________________ > >> R-sig-Geo mailing list > >> R-sig-Geo@r-project.org > >> https://stat.ethz.ch/mailman/listinfo/r-sig-geo > >> > > > > > > _______________________________________________ > > R-sig-Geo mailing list > > R-sig-Geo@r-project.org > > https://stat.ethz.ch/mailman/listinfo/r-sig-geo > > > > -- > Edzer Pebesma > Institute for Geoinformatics > Heisenbergstrasse 2, 48151 Muenster, Germany > Phone: +49 251 8333081 > _______________________________________________ > R-sig-Geo mailing list > R-sig-Geo@r-project.org > https://stat.ethz.ch/mailman/listinfo/r-sig-geo > [[alternative HTML version deleted]] _______________________________________________ R-sig-Geo mailing list R-sig-Geo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-geo