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

Edzer Pebesma edzer.pebesma at uni-muenster.de
Wed Jan 13 10:56:17 CET 2016 

To find out, send us the lines that were printed in your console before
the errors occured, those following
* installing *source* package ‘rgdal’ ...



On 13/01/16 10:48, Subhash Karemore wrote:
> Hi,
> 
> 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
> 
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> 

-- 
Edzer Pebesma
Institute for Geoinformatics  (ifgi),  University of Münster
Heisenbergstraße 2, 48149 Münster, Germany; +49 251 83 33081
Journal of Statistical Software:   http://www.jstatsoft.org/
Computers & Geosciences:   http://elsevier.com/locate/cageo/
Spatial Statistics Society http://www.spatialstatistics.info

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