[R-sig-Geo] Regarding installation of R package rgdal

Wed Jan 13 10:57:24 CET 2016

On Wed, 13 Jan 2016, Subhash Karemore wrote:

> Hi,
>

This is a repeat of a mail to me, to which I replied. The guy works for 
Teradata and can afford to solve this using their technicians. The output 
of configure is not included; my conclusion based on guesswork (which I 
sent directly earlier) is that the SLES servers do not have c++11-capable 
g++ versions, while OpenSUSE does.

Corporate subscribers must learn to respect the work put in by the 
community, not just free-ride. This guy is also in a big hurry, and 
doesn't read messages sent.

Roger

> I am trying to install R package 'rgdal' on SUSE Linux Enterprise 
> Server. However it is failing with compilation error.
>
> Errors:
> ----------
> I/usr/lib64/R/include -DNDEBUG -I/usr/local/include -I/usr/local/include -I"/usr/lib64/R/library/sp/include"      -c OGR_write.cpp -o OGR_write.o
> /bin/sh: I/usr/lib64/R/include: No such file or directory
> make: [OGR_write.o] Error 127 (ignored)
> I/usr/lib64/R/include -DNDEBUG -I/usr/local/include -I/usr/local/include -I"/usr/lib64/R/library/sp/include"      -c gdal-bindings.cpp -o gdal-bindings.o
> /bin/sh: I/usr/lib64/R/include: No such file or directory
> make: [gdal-bindings.o] Error 127 (ignored)
> gcc -std=gnu99 -I/usr/lib64/R/include -DNDEBUG -I/usr/local/include -I/usr/local/include -I"/usr/lib64/R/library/sp/include"   -fpic  -fmessage-length=0 -O2 -Wall -D_FORTIFY_SOURCE=2 -fstack-protector -funwind-tables -fasynchronous-unwind-tables  -c init.c -o init.o
> gcc -std=gnu99 -I/usr/lib64/R/include -DNDEBUG -I/usr/local/include -I/usr/local/include -I"/usr/lib64/R/library/sp/include"   -fpic  -fmessage-length=0 -O2 -Wall -D_FORTIFY_SOURCE=2 -fstack-protector -funwind-tables -fasynchronous-unwind-tables  -c local_stubs.c -o local_stubs.o
> I/usr/lib64/R/include -DNDEBUG -I/usr/local/include -I/usr/local/include -I"/usr/lib64/R/library/sp/include"      -c ogr_geom.cpp -o ogr_geom.o
> /bin/sh: I/usr/lib64/R/include: No such file or directory
> make: [ogr_geom.o] Error 127 (ignored)
> gcc -std=gnu99 -I/usr/lib64/R/include -DNDEBUG -I/usr/local/include -I/usr/local/include -I"/usr/lib64/R/library/sp/include"   -fpic  -fmessage-length=0 -O2 -Wall -D_FORTIFY_SOURCE=2 -fstack-protector -funwind-tables -fasynchronous-unwind-tables  -c ogr_polygons.c -o ogr_polygons.o
> I/usr/lib64/R/include -DNDEBUG -I/usr/local/include -I/usr/local/include -I"/usr/lib64/R/library/sp/include"      -c ogr_proj.cpp -o ogr_proj.o
> /bin/sh: I/usr/lib64/R/include: No such file or directory
> make: [ogr_proj.o] Error 127 (ignored)
> I/usr/lib64/R/include -DNDEBUG -I/usr/local/include -I/usr/local/include -I"/usr/lib64/R/library/sp/include"      -c ogrdrivers.cpp -o ogrdrivers.o
> /bin/sh: I/usr/lib64/R/include: No such file or directory
> make: [ogrdrivers.o] Error 127 (ignored)
> I/usr/lib64/R/include -DNDEBUG -I/usr/local/include -I/usr/local/include -I"/usr/lib64/R/library/sp/include"      -c ogrsource.cpp -o ogrsource.o
> /bin/sh: I/usr/lib64/R/include: No such file or directory
> make: [ogrsource.o] Error 127 (ignored)
> I/usr/lib64/R/include -DNDEBUG -I/usr/local/include -I/usr/local/include -I"/usr/lib64/R/library/sp/include"      -c projectit.cpp -o projectit.o
> /bin/sh: I/usr/lib64/R/include: No such file or directory
> make: [projectit.o] Error 127 (ignored)
> -shared -L/usr/lib64/R/lib -L/usr/local/lib64 -o rgdal.so OGR_write.o gdal-bindings.o init.o local_stubs.o ogr_geom.o ogr_polygons.o ogr_proj.o ogrdrivers.o ogrsource.o projectit.o -L/usr/local/lib -lgdal -lproj -L/usr/lib64/R/lib -lR
> /bin/sh: line 2: -shared: command not found
> make: *** [rgdal.so] Error 127
> ERROR: compilation failed for package 'rgdal'
> * removing '/usr/lib64/R/library/rgdal'
>
> The downloaded source packages are in
>        '/tmp/Rtmpd0WifB/downloaded_packages'
> Updating HTML index of packages in '.Library'
> Making 'packages.html' ... done
> Warning message:
> In install.packages("rgdal", repos = "http://cran.r-project.org") :
>  installation of package 'rgdal' had non-zero exit status
>
> However it got installed successfully on openSUSE. Here is the output:
> ---------------------------------------------------------------------------------------
> g++ -std=c++11 -I/usr/lib64/R/include -DNDEBUG -I/usr/include/gdal -I/usr/local/include -I"/usr/lib64/R/library/sp/include"   -fpic  -fmessage-length=0 -grecord-gcc-switches -O2 -Wall -D_FORTIFY_SOURCE=2 -fstack-protector -funwind-tables -fasynchronous-unwind-tables -g -c OGR_write.cpp -o OGR_write.o
> g++ -std=c++11 -I/usr/lib64/R/include -DNDEBUG -I/usr/include/gdal -I/usr/local/include -I"/usr/lib64/R/library/sp/include"   -fpic  -fmessage-length=0 -grecord-gcc-switches -O2 -Wall -D_FORTIFY_SOURCE=2 -fstack-protector -funwind-tables -fasynchronous-unwind-tables -g -c gdal-bindings.cpp -o gdal-bindings.o
> gcc -std=gnu99 -I/usr/lib64/R/include -DNDEBUG -I/usr/include/gdal -I/usr/local/include -I"/usr/lib64/R/library/sp/include"   -fpic  -fmessage-length=0 -grecord-gcc-switches -O2 -Wall -D_FORTIFY_SOURCE=2 -fstack-protector -funwind-tables -fasynchronous-unwind-tables -g  -c init.c -o init.o
> gcc -std=gnu99 -I/usr/lib64/R/include -DNDEBUG -I/usr/include/gdal -I/usr/local/include -I"/usr/lib64/R/library/sp/include"   -fpic  -fmessage-length=0 -grecord-gcc-switches -O2 -Wall -D_FORTIFY_SOURCE=2 -fstack-protector -funwind-tables -fasynchronous-unwind-tables -g  -c local_stubs.c -o local_stubs.o
> g++ -std=c++11 -I/usr/lib64/R/include -DNDEBUG -I/usr/include/gdal -I/usr/local/include -I"/usr/lib64/R/library/sp/include"   -fpic  -fmessage-length=0 -grecord-gcc-switches -O2 -Wall -D_FORTIFY_SOURCE=2 -fstack-protector -funwind-tables -fasynchronous-unwind-tables -g -c ogr_geom.cpp -o ogr_geom.o
> gcc -std=gnu99 -I/usr/lib64/R/include -DNDEBUG -I/usr/include/gdal -I/usr/local/include -I"/usr/lib64/R/library/sp/include"   -fpic  -fmessage-length=0 -grecord-gcc-switches -O2 -Wall -D_FORTIFY_SOURCE=2 -fstack-protector -funwind-tables -fasynchronous-unwind-tables -g  -c ogr_polygons.c -o ogr_polygons.o
> g++ -std=c++11 -I/usr/lib64/R/include -DNDEBUG -I/usr/include/gdal -I/usr/local/include -I"/usr/lib64/R/library/sp/include"   -fpic  -fmessage-length=0 -grecord-gcc-switches -O2 -Wall -D_FORTIFY_SOURCE=2 -fstack-protector -funwind-tables -fasynchronous-unwind-tables -g -c ogr_proj.cpp -o ogr_proj.o
> g++ -std=c++11 -I/usr/lib64/R/include -DNDEBUG -I/usr/include/gdal -I/usr/local/include -I"/usr/lib64/R/library/sp/include"   -fpic  -fmessage-length=0 -grecord-gcc-switches -O2 -Wall -D_FORTIFY_SOURCE=2 -fstack-protector -funwind-tables -fasynchronous-unwind-tables -g -c ogrdrivers.cpp -o ogrdrivers.o
> g++ -std=c++11 -I/usr/lib64/R/include -DNDEBUG -I/usr/include/gdal -I/usr/local/include -I"/usr/lib64/R/library/sp/include"   -fpic  -fmessage-length=0 -grecord-gcc-switches -O2 -Wall -D_FORTIFY_SOURCE=2 -fstack-protector -funwind-tables -fasynchronous-unwind-tables -g -c ogrsource.cpp -o ogrsource.o
> g++ -std=c++11 -I/usr/lib64/R/include -DNDEBUG -I/usr/include/gdal -I/usr/local/include -I"/usr/lib64/R/library/sp/include"   -fpic  -fmessage-length=0 -grecord-gcc-switches -O2 -Wall -D_FORTIFY_SOURCE=2 -fstack-protector -funwind-tables -fasynchronous-unwind-tables -g -c projectit.cpp -o projectit.o
> g++ -std=c++11 -shared -L/usr/lib64/R/lib -L/usr/local/lib64 -o rgdal.so OGR_write.o gdal-bindings.o init.o local_stubs.o ogr_geom.o ogr_polygons.o ogr_proj.o ogrdrivers.o ogrsource.o projectit.o -L/usr/lib64 -lgdal -lproj -L/usr/lib64/R/lib -lR
> installing to /usr/lib64/R/library/rgdal/libs
> ** R
> ** data
> ** inst
> ** preparing package for lazy loading
> ** help
> *** installing help indices
> ** building package indices
> ** installing vignettes
> ** testing if installed package can be loaded
> * DONE (rgdal)
>
> The command I used for installing the package is 
> "install.package('rgdal', repos='http://cran.r-project.org')". I don't 
> know why R package installation is failing on SLES. Even other R 
> packages are getting installed successfully on SLES. It seems that it is 
> not picking gcc compiler on SLES. Could you please let me know, why 
> installation of R package 'rgdal' is failing on SLES? Do I need set 
> anything?
>
> Thanks
> Subhash
>
> _______________________________________________
> R-sig-Geo mailing list
> R-sig-Geo at 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; fax +47 55 95 91 00
e-mail: Roger.Bivand at nhh.no
http://orcid.org/0000-0003-2392-6140
https://scholar.google.no/citations?user=AWeghB0AAAAJ&hl=en
http://depsy.org/person/434412