CRAN releases of sp, rgdal and rgeos
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 at r-project.org on behalf of Roger.Bivand at 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 at 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 at r-project.org ?? https://stat.ethz.ch/mailman/listinfo/r-sig-geo
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