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-boun...@r-project.org on behalf of roger.biv...@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.biv...@nhh.no
http://orcid.org/0000-0003-2392-6140
https://scholar.google.no/citations?user=AWeghB0AAAAJ&hl=en
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