[R-sig-Geo] rgdal, PROJ6 and "+init=epsg" syntax on Jupyter/conda

Thu Sep 12 12:29:59 CEST 2019

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.pebesma using 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]]
>>>>
>>>> _______________________________________________
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>>>> R-sig-Geo using 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 using r-project.org
>>> https://stat.ethz.ch/mailman/listinfo/r-sig-geo
>>>
>>
>> 	[[alternative HTML version deleted]]
>>
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>>
> 
> 
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-- 
Edzer Pebesma
Institute for Geoinformatics
Heisenbergstrasse 2, 48151 Muenster, Germany
Phone: +49 251 8333081

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