[R-sig-Geo] CRAN releases of sp, rgdal and rgeos

Roger Bivand Roger@Biv@nd @ending from nhh@no
Tue Jun 19 10:41:00 CEST 2018 

On Tue, 19 Jun 2018, Tomislav Hengl wrote:

> Two weeks ago I installed new GDAL 2.3.* from source, then tried
> installing rgdal and got the error about GDAL requires C++11. Then I had
> to remove everything and reinstall GDAL 2.2. Would love to be able to
> start using the newest GDAL inside R as it seems that many things have
> been improved
> (https://trac.osgeo.org/gdal/query?group=status&milestone=2.3.0).
> Installing GDAL from source takes >20mins so next time I would like to
> be sure that I will not have to remove GDAL.
>
> Can somebody point to a step-by-step guide to install GDAL 2.3.* and
> rgdal on ubuntu (now that all packages have been updated)?

Tom:

There is too little information here: which g++ compiler version, was R 
installed from source or not, GDAL was installed from source, but was PROJ 
installed from source (and/or GEOS), ... and no verbatim error message.

Please try development rgdal_1.3-3 from R-forge, which has some logic 
fixes in configure:

install.packages("rgdal", repos="http://R-Forge.R-project.org")

Did you check whether sf installed with GDAL 2.3.0 and PROJ 5.1.0?

It looks as though CRAN devel debian is using GDAL 2.3.0 (the test saved 
output is 2.2.4):

https://www.r-project.org/nosvn/R.check/r-devel-linux-x86_64-debian-gcc/rgdal-00check.html

Hope this helps,

Roger

>
> Much appreciated!
>
> My session info:
>
> > library(rgdal)
> Loading required package: sp
> rgdal: version: 1.2-20, (SVN revision 725)
>  Geospatial Data Abstraction Library extensions to R successfully loaded
>  Loaded GDAL runtime: GDAL 2.2.2, released 2017/09/15
>  Path to GDAL shared files: /usr/share/gdal/2.2
>  GDAL binary built with GEOS: TRUE
>  Loaded PROJ.4 runtime: Rel. 4.9.2, 08 September 2015, [PJ_VERSION: 492]
>  Path to PROJ.4 shared files: (autodetected)
>  Linking to sp version: 1.2-7
> > sessionInfo()
> R version 3.5.0 (2018-04-23)
> Platform: x86_64-pc-linux-gnu (64-bit)
> Running under: Ubuntu 16.04.4 LTS
>
> Matrix products: default
> BLAS: /opt/microsoft/ropen/3.5.0/lib64/R/lib/libRblas.so
> LAPACK: /opt/microsoft/ropen/3.5.0/lib64/R/lib/libRlapack.so
>
>
>
> On 19.06.2018 08:47, Roger Bivand wrote:
>> On Mon, 18 Jun 2018, MacQueen, Don wrote:
>>
>>> Success!
>>>
>>> This morning I upgraded a Mac to OS 10.13.5 (the so-called High
>>> Sierra version), then
>>>
>>> - Installed R 3.5.0 from CRAN (installed ever 3.3.x)
>>> - Installed sp 1.3-1, rgdal 1.3-2, rgeos 0.3-28, also sf 0.6-3, from the
>>>   CRAN binaries that are now available
>>> - Ran my personal test suite, which exercises the kinds of tasks I
>>>   perform with those packages
>>>
>>> All tests succeeded.
>>
>> Thanks for reporting - especially on your own test suite. We do what
>> we can to cover typical use cases, but independent testing in
>> production settings is reassuring for everybody. We're expecting more
>> PROJ-based changes later this year and next year, so it is great to
>> have external test sets to be able to check where any changes in
>> output are coming from.
>>
>> This is an encouragement to other users whose production depends on R
>> packages using GDAL, PROJ and/or GEOS to follow this example and keep
>> a script handy to test your use cases, and a history of output files
>> with which to compare (diff). We don't worry about changes in the EPSG
>> versions, but by next year they may be properly anchored too (changes
>> in PROJ may include reference system definitions with timestamps).
>>
>>>
>>> I forgot to control the order of installation, so I don't know if I
>>> installed sp first, as advised. But I expect that with the binary
>>> versions it doesn't matter.
>>
>> Right, the binary builds use the sp version on the build platform.
>>
>> Best wishes,
>>
>> Roger
>>
>>>
>>> (I don't think it matters for the above, but I also installed the
>>> clang and gfortran version provided on CRAN's Mac "tools" page, and
>>> successfully compiled some source packages that require fortran, and
>>> others that require C).
>>>
>>> Thank again for all your work
>>> -Don
>>>
>>> --
>>> Don MacQueen
>>> Lawrence Livermore National Laboratory
>>> 7000 East Ave., L-627
>>> Livermore, CA 94550
>>> 925-423-1062
>>> Lab cell 925-724-7509
>>>
>>>
>>>
>>> On 6/8/18, 11:15 AM, "R-sig-Geo on behalf of Roger Bivand"
>>> <r-sig-geo-bounces using r-project.org on behalf of Roger.Bivand using nhh.no>
>>> wrote:
>>>
>>>    There are new releases of sp, rgdal and rgeos on CRAN. Please
>>> install sp
>>>    first, then the other two, which link to the installed sp. They all
>>>    address so-called rchk issues, which have not so far been a
>>> problem, but
>>>    might have become more fragile as R's internal memory management
>>> is made
>>>    even more efficient. This involves compiled code using memory
>>> allocated by
>>>    R to be freed by R's garbage collector, which has to know if an
>>> object is
>>>    still being used. Tomas Kalibera, the author of rchk, helped
>>> resolve and
>>>    explain the issues encountered - what was good coding practice
>>> fifteen
>>>    years ago isn't always still good practice.
>>>
>>>    In addition, the earliest versions of GDAL and PROJ with which
>>> rgdal will
>>>    work have been updated, and set to PROJ 4.8.0 and GDAL 1.11.4. The
>>> current
>>>    released versions of PROJ and GDAL are to be prefered, as bugs
>>> have been
>>>    fixed and new features and drivers introduced. A check has been put
>>>    in place to trap attempts to install rgdal without a C++11-capable
>>>    compiler when the GDAL version is >=2.3.0 - which requires C++11.
>>> rgeos is
>>>    ready for the forthcoming version of GEOS.
>>>
>>>    The CRAN team has also been very supportive of our efforts to bring
>>>    compiled code in these packages into rchk compliance.
>>>
>>>    Please get in touch if you see any loose ends in these releases.
>>>
>>>    Roger
>>>
>>>    --
>>>    Roger Bivand
>>>    Department of Economics, Norwegian School of Economics,
>>>    Helleveien 30, N-5045 Bergen, Norway.
>>>    voice: +47 55 95 93 55; e-mail: Roger.Bivand using nhh.no
>>>    http://orcid.org/0000-0003-2392-6140
>>> https://scholar.google.no/citations?user=AWeghB0AAAAJ&hl=en
>>>
>>>    _______________________________________________
>>>    R-sig-Geo mailing list
>>>    R-sig-Geo using r-project.org
>>>    https://stat.ethz.ch/mailman/listinfo/r-sig-geo
>>>
>>>
>>>
>>
>>
>>
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-- 
Roger Bivand
Department of Economics, Norwegian School of Economics,
Helleveien 30, N-5045 Bergen, Norway.
voice: +47 55 95 93 55; e-mail: Roger.Bivand using nhh.no
http://orcid.org/0000-0003-2392-6140
https://scholar.google.no/citations?user=AWeghB0AAAAJ&hl=en

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