[R-sig-Geo] CRAN releases of sp, rgdal and rgeos
Tomislav Hengl
tom@hengl @ending from gm@il@com
Tue Jun 19 16:57:59 CEST 2018
Hi Roger,
I have now managed to reinstall GDAL 2.3 and the latest versions of
rgdal and sf. These are the steps I have followed:
1. First remove existing installation of GDAL using:
sudo apt-get purge --auto-remove gdal-bin
*this also removes QGIS / anything linked with GDAL.
2. Download GDAL source code
(https://trac.osgeo.org/gdal/wiki/DownloadSource) and follow the
instructions to install from source
(https://trac.osgeo.org/gdal/wiki/BuildingOnUnix)
3. Installation from source code takes quite some time (10-15 minutes).
After that I get:
gdalinfo --version
GDAL 2.3.0, released 2018/05/04
4. Install rgdal from R-forge using e.g.:
R CMD INSTALL rgdal_1.3-3.tar.gz
* installing to library ‘/opt/microsoft/ropen/3.4.3/lib64/R/library’
* installing *source* package ‘rgdal’ ...
checking for g++... g++
checking whether the C++ compiler works... yes
checking for C++ compiler default output file name... a.out
checking for suffix of executables...
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C++ compiler... yes
checking whether g++ accepts -g... yes
configure: CC: gcc -std=gnu99
configure: CXX: g++
configure: rgdal: 1.3-3
checking for /usr/bin/svnversion... yes
cat: inst/SVN_VERSION: No such file or directory
configure: svn revision:
checking whether g++ supports C++11 features by default... no
checking whether g++ supports C++11 features with -std=gnu++11... yes
configure: C++11 support available
checking for gdal-config... /usr/local/bin/gdal-config
checking gdal-config usability... yes
configure: GDAL: 2.3.0
checking C++11 support for GDAL >= 2.3.0... yes
checking GDAL version >= 1.11.4... yes
checking gdal: linking with --libs only... yes
checking GDAL: /usr/local/share/gdal/pcs.csv readable... yes
configure: pkg-config proj exists, will use it
configure: PROJ version: 4.9.2
checking proj_api.h presence and usability... yes
checking PROJ version >= 4.8.0... yes
checking projects.h presence and usability... yes
checking PROJ.4: epsg found and readable... yes
checking PROJ.4: conus found and readable... yes
configure: Package CPP flags: -I/usr/local/include
configure: Package LIBS: -L/usr/local/lib -lgdal -lproj
configure: creating ./config.status
For sf I had to manually update DBI and units packages as it requires
newest versions.
So now everything works fine. Thank you!
Tom
On 06/19/2018 10:41 AM, Roger Bivand wrote:
> 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
>>>>
>>>>
>>>>
>>>
>>>
>>>
>>> _______________________________________________
>>> 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]]
>>
>> _______________________________________________
>> R-sig-Geo mailing list
>> R-sig-Geo using r-project.org
>> https://stat.ethz.ch/mailman/listinfo/r-sig-geo
>>
>
More information about the R-sig-Geo
mailing list