[R-sig-Geo] Trouble installing rgdal

Roger Bivand Roger@B|v@nd @end|ng |rom nhh@no
Fri Jul 3 11:45:34 CEST 2020 

On Thu, 2 Jul 2020, Thomas Adams wrote:

> Roger,
>
> Thank you so much; after downloading the *.tar.gz file, the that did the
> trick, using:
>
> sudo R CMD INSTALL --configure-args=--with-proj_api="proj_api.h"
> rgdal_1.5-13.tar.gz

Since you have GDAL: 3.0.0 and PROJ version: 6.1.0, you can drop 
--configure-args=--with-proj_api="proj_api.h", which is only needed if 
GDAL < 3 and PROJ >= 6. I'm uncertain how stable a system will be if GDAL 
>= 3 && PROJ >= 6 with this configure argument, as it is only a 
work-around for systems with GDAL < 3 and PROJ >= 6, and onnly tested in 
that setting.

Thanks for reporting back!

Roger

>
> Best regards!
> Tom
>
>
> On Thu, Jul 2, 2020 at 3:15 PM Roger Bivand <Roger.Bivand using nhh.no> wrote:
>
>> On Thu, 2 Jul 2020, Thomas Adams wrote:
>>
>>> Hi Bennet!
>>>
>>> Thank you for your help, but I get the same error...
>>
>> Tom,
>>
>> Once rgdal revision 1029 completes building (check first) on:
>>
>> https://r-forge.r-project.org/R/?group_id=884
>>
>> please re-try. The missing function is not in the GDAL 3.0.0 headers, but
>> is in the 3.0.1 headers. I've modified the check so as not to try for just
>>> = 3 to >= 3.0.1.
>>
>> Roger
>>
>>>
>>> Tom
>>>
>>> On Thu, Jul 2, 2020 at 2:01 PM Bennet Fauber <bennet using umich.edu> wrote:
>>>
>>>> You might try this
>>>>
>>>> install.packages("rgdal", "/sw/arcts/centos7/Rgeospatial/062020",
>>>> repos="http://R-Forge.R-project.org")
>>>>
>>>> as there have been recent patches to rgdal that might help that have
>>>> been incorporated there.
>>>>
>>>>
>>>> On Thu, Jul 2, 2020 at 1:47 PM Thomas Adams <tea3rd using gmail.com> wrote:
>>>>>
>>>>> Hi all,
>>>>>
>>>>> I have searched the internet and have spent a few days trying to get to
>>>> the
>>>>> problem when I try to install rgdal into my Ubuntu 18.04 system. I have
>>>>> done this many times previously, but cannot seem to track down what I
>> am
>>>>> doing wrong now. I have tried a forced install from sources with and
>>>>> without dependencies. Below is what I get. Any help is appreciated.
>>>>>
>>>>> Tom
>>>>>
>>>>>> install.packages("rgdal")
>>>>> Installing package into
>> ‘/home/teaiii/R/x86_64-pc-linux-gnu-library/4.0’
>>>>> (as ‘lib’ is unspecified)
>>>>> trying URL 'https://cran.case.edu/src/contrib/rgdal_1.5-12.tar.gz'
>>>>> Content type 'application/x-gzip' length 2302403 bytes (2.2 MB)
>>>>> ==================================================
>>>>> downloaded 2.2 MB
>>>>>
>>>>> * installing *source* package ‘rgdal’ ...
>>>>> ** package ‘rgdal’ successfully unpacked and MD5 sums checked
>>>>> ** using staged installation
>>>>> configure: R_HOME: /usr/local/lib/R
>>>>> configure: CC: gcc
>>>>> configure: CXX: g++ -std=gnu++11
>>>>> configure: CXX11 is: g++, CXX11STD is: -std=gnu++11
>>>>> configure: CXX is: g++ -std=gnu++11
>>>>> configure: C++11 support available
>>>>> configure: rgdal: 1.5-12
>>>>> checking for /usr/bin/svnversion... yes
>>>>> configure: svn revision: 1018
>>>>> checking for gdal-config... /usr/local/bin/gdal-config
>>>>> checking gdal-config usability... yes
>>>>> configure: GDAL: 3.0.0
>>>>> checking GDAL version >= 1.11.4... yes
>>>>> checking GDAL version <= 2.5 or >= 3.0... yes
>>>>> checking GDAL: linking with --libs only... yes
>>>>> checking GDAL: gdal-config data directory readable... yes
>>>>> checking GDAL: /usr/local/share/gdal/stateplane.csv readable... yes
>>>>> configure: pkg-config proj exists, will use it
>>>>> configure: PROJ version: 6.1.0
>>>>> configure: PROJ CPP flags: -DPROJ_H_API -I/usr/local/include
>>>>> configure: PROJ LIBS: -L/usr/local/lib -lproj
>>>>> checking PROJ header API:... yes
>>>>> 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++ -std=gnu++11 accepts -g... yes
>>>>> checking how to run the C++ preprocessor... g++ -std=gnu++11 -E
>>>>> checking for grep that handles long lines and -e... /bin/grep
>>>>> checking for egrep... /bin/grep -E
>>>>> checking for ANSI C header files... yes
>>>>> checking for sys/types.h... yes
>>>>> checking for sys/stat.h... yes
>>>>> checking for stdlib.h... yes
>>>>> checking for string.h... yes
>>>>> checking for memory.h... yes
>>>>> checking for strings.h... yes
>>>>> checking for inttypes.h... yes
>>>>> checking for stdint.h... yes
>>>>> checking for unistd.h... yes
>>>>> checking proj.h usability... yes
>>>>> checking proj.h presence... yes
>>>>> checking for proj.h... yes
>>>>> checking for proj_context_create in -lproj... yes
>>>>> checking Using GDAL < 3 with PROJ >= 6... no
>>>>> checking PROJ version >= 4.8.0... yes
>>>>> checking PROJ: proj.db found and readable... yes
>>>>> configure: Package CPP flags:  -I/usr/local/include
>> -I/usr/local/include
>>>>> -DPROJ_H_API
>>>>> configure: Package LIBS:  -L/usr/local/lib -lgdal -L/usr/local/lib
>> -lproj
>>>>> configure: creating ./config.status
>>>>> config.status: creating src/Makevars
>>>>> ** libs
>>>>> g++ -std=gnu++11 -I"/usr/local/lib/R/include" -DNDEBUG
>>>> -I/usr/local/include
>>>>> -I/usr/local/include -DPROJ_H_API
>>>>> -I'/home/teaiii/R/x86_64-pc-linux-gnu-library/4.0/sp/include'
>>>>> -I/usr/local/include   -fpic  -g -O2  -c OGR_write.cpp -o OGR_write.o
>>>>> g++ -std=gnu++11 -I"/usr/local/lib/R/include" -DNDEBUG
>>>> -I/usr/local/include
>>>>> -I/usr/local/include -DPROJ_H_API
>>>>> -I'/home/teaiii/R/x86_64-pc-linux-gnu-library/4.0/sp/include'
>>>>> -I/usr/local/include   -fpic  -g -O2  -c gdal-bindings.cpp -o
>>>>> gdal-bindings.o
>>>>> gcc -I"/usr/local/lib/R/include" -DNDEBUG -I/usr/local/include
>>>>> -I/usr/local/include -DPROJ_H_API
>>>>> -I'/home/teaiii/R/x86_64-pc-linux-gnu-library/4.0/sp/include'
>>>>> -I/usr/local/include   -fpic  -g -O2  -c init.c -o init.o
>>>>> gcc -I"/usr/local/lib/R/include" -DNDEBUG -I/usr/local/include
>>>>> -I/usr/local/include -DPROJ_H_API
>>>>> -I'/home/teaiii/R/x86_64-pc-linux-gnu-library/4.0/sp/include'
>>>>> -I/usr/local/include   -fpic  -g -O2  -c inverser.c -o inverser.o
>>>>> gcc -I"/usr/local/lib/R/include" -DNDEBUG -I/usr/local/include
>>>>> -I/usr/local/include -DPROJ_H_API
>>>>> -I'/home/teaiii/R/x86_64-pc-linux-gnu-library/4.0/sp/include'
>>>>> -I/usr/local/include   -fpic  -g -O2  -c local_stubs.c -o local_stubs.o
>>>>> g++ -std=gnu++11 -I"/usr/local/lib/R/include" -DNDEBUG
>>>> -I/usr/local/include
>>>>> -I/usr/local/include -DPROJ_H_API
>>>>> -I'/home/teaiii/R/x86_64-pc-linux-gnu-library/4.0/sp/include'
>>>>> -I/usr/local/include   -fpic  -g -O2  -c ogr_geom.cpp -o ogr_geom.o
>>>>> gcc -I"/usr/local/lib/R/include" -DNDEBUG -I/usr/local/include
>>>>> -I/usr/local/include -DPROJ_H_API
>>>>> -I'/home/teaiii/R/x86_64-pc-linux-gnu-library/4.0/sp/include'
>>>>> -I/usr/local/include   -fpic  -g -O2  -c ogr_polygons.c -o
>> ogr_polygons.o
>>>>> g++ -std=gnu++11 -I"/usr/local/lib/R/include" -DNDEBUG
>>>> -I/usr/local/include
>>>>> -I/usr/local/include -DPROJ_H_API
>>>>> -I'/home/teaiii/R/x86_64-pc-linux-gnu-library/4.0/sp/include'
>>>>> -I/usr/local/include   -fpic  -g -O2  -c ogr_proj.cpp -o ogr_proj.o
>>>>> ogr_proj.cpp: In function ‘SEXPREC* R_GDAL_OSR_PROJ()’:
>>>>> ogr_proj.cpp:163:9: error: ‘OSRGetPROJVersion’ was not declared in this
>>>>> scope
>>>>>          OSRGetPROJVersion(&pnMajor, &pnMinor, &pnPatch);
>>>>>          ^~~~~~~~~~~~~~~~~
>>>>> ogr_proj.cpp:163:9: note: suggested alternative: ‘OSRProjVersion’
>>>>>          OSRGetPROJVersion(&pnMajor, &pnMinor, &pnPatch);
>>>>>          ^~~~~~~~~~~~~~~~~
>>>>>          OSRProjVersion
>>>>> /usr/local/lib/R/etc/Makeconf:176: recipe for target 'ogr_proj.o'
>> failed
>>>>> make: *** [ogr_proj.o] Error 1
>>>>> ERROR: compilation failed for package ‘rgdal’
>>>>> * removing ‘/home/teaiii/R/x86_64-pc-linux-gnu-library/4.0/rgdal’
>>>>>
>>>>> The downloaded source packages are in
>>>>> ‘/tmp/RtmpNkdFOf/downloaded_packages’
>>>>> Warning message:
>>>>> In install.packages("rgdal") :
>>>>>   installation of package ‘rgdal’ had non-zero exit status
>>>>>
>>>>>
>>>>> --
>>>>> Thomas E Adams, III
>>>>> 1724 Sage Lane
>>>>> Blacksburg, VA 24060
>>>>> tea3rd using gmail.com (personal)
>>>>> tea using terrapredictions.org (work)
>>>>>
>>>>> 1 (513) 739-9512 (cell)
>>>>>
>>>>>         [[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
>>>>
>>>
>>>
>>>
>>
>> --
>> 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
>> https://orcid.org/0000-0003-2392-6140
>> https://scholar.google.no/citations?user=AWeghB0AAAAJ&hl=en
>
>
>
>

-- 
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
https://orcid.org/0000-0003-2392-6140
https://scholar.google.no/citations?user=AWeghB0AAAAJ&hl=en

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