[R-sig-Geo] Building rgdal 0.6-7 on Mac
Corey Sparks
corey.sparks at UTSA.EDU
Mon Apr 20 21:10:53 CEST 2009
Roger,
Here's the strange thing: it works! I assumed that the error on
install was fatal and nothing was built, but the bloody thing functions!
The 0.6-5 version I had before was built under 2.8.1, and following
your suggestion, I tried to install 0.6-5 in R 2.9.0 and it gave the
same error, but it seems to work alright, I can read in datafiles so
far.
If I try to install 0.6-7 over 0.6-5 it won't replace the previous
version because of the error apparently, hence the
ERROR: lazy loading failed for package ‘rgdal’
* Removing ‘/Library/Frameworks/R.framework/Resources/library/rgdal’
* Restoring previous ‘/Library/Frameworks/R.framework/Resources/
library/rgdal’
But there is a functional version there. If I go in and by brute
force remove the version that is there (say 0.6-5) and run the install
script for 0.6-7, it installs despite the error.
Thanks for you quick reply
Corey Sparks
Assistant Professor
Department of Demography and Organization Studies
College of Public Policy
One UTSA Circle
San Antonio, TX 78239
corey.sparks 'at' utsa.edu
On Apr 20, 2009, at 1:59 PM, Roger Bivand wrote:
> On Mon, 20 Apr 2009, Corey Sparks wrote:
>
>> Dear list,
>> I've just built my new version of R 2.9.0 and installed my packages.
>>
>>> sessionInfo()
>> R version 2.9.0 Patched (2009-04-20 r48365)
>> i386-apple-darwin9.6.0
>>
>> locale:
>> C
>>
>> attached base packages:
>> [1] stats graphics grDevices datasets utils methods base
>>
>>
>> I use rgdal for reading and writing raster data but when I try to
>> install version 0.6-7 (I already have 0.6-5 installed) from source,
>> I get an error.
>
> Was 0.6-5 built with R 2.8.1? If you feel like taking risks, please
> try to see whether installing rgdal_0.6-5 under R 2.9.0 provokes the
> same problem. Have you tried asking on R-sig-mac - the changes from
> 0.6-5 to 0.6-7 were very small (a "[" subsetting operation with an
> omitted drop=FALSE)?
>
> See for example:
>
> http://rgdal.cvs.sourceforge.net/viewvc/rgdal/rgdal/R/sp_gdal.R?r1=1.30&r2=1.31
>
> Nothing there should trigger problems, so I'd look to see whether
> there is something platform and/or R release related.
>
> On Linux i386 and x86_64, and Windows i386, everything looks OK.
>
> Roger
>
>> I have installed all of the external dependencies (GDAL, PROJ4,
>> etc) and think I am specifying the installation command correctly.
>> I have rgdal_0.6-7.tar.gz in my home directory, here is my command
>>
>> R --arch=x86_64 CMD INSTALL rgdal_0.6-7.tar.gz --configure-args='--
>> with-gdal-config=/Library/Frameworks/GDAL.framework/Versions/1.6/
>> Programs/gdal-config --with-proj-lib=/Library/Frameworks/
>> PROJ.framework/Versions/4.6/unix/lib --with-proj-include=/Library/
>> Frameworks/PROJ.framework/Versions/4.6/Headers' rgdal_0.6-7.tar.gz
>>
>> Here is what happens: Please forgive the voluminous output.
>>
>> * Installing to library '/Library/Frameworks/R.framework/Resources/
>> library'
>> * Installing *source* package 'rgdal' ...
>> gdal-config: /Library/Frameworks/GDAL.framework/Versions/1.6/
>> Programs/gdal-config
>> checking for gcc... gcc -arch x86_64 -std=gnu99
>> checking for C compiler default output file name... a.out
>> checking whether the C compiler works... yes
>> checking whether we are cross compiling... no
>> checking for suffix of executables...
>> checking for suffix of object files... o
>> checking whether we are using the GNU C compiler... yes
>> checking whether gcc -arch x86_64 -std=gnu99 accepts -g... yes
>> checking for gcc -arch x86_64 -std=gnu99 option to accept ANSI C...
>> none needed
>> checking how to run the C preprocessor... gcc -arch x86_64 -
>> std=gnu99 -E
>> checking for egrep... grep -E
>> checking for ANSI C header files... rm: conftest.dSYM: is a directory
>> rm: conftest.dSYM: is a directory
>> 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_api.h usability... yes
>> checking proj_api.h presence... yes
>> checking for proj_api.h... yes
>> checking for pj_init_plus in -lproj... yes
>> Package CPP flags: -I/Library/Frameworks/PROJ.framework/Versions/
>> 4.6/Headers -I/Library/Frameworks/GDAL.framework/Versions/1.6/Headers
>> Package LIBS: -L/Library/Frameworks/PROJ.framework/Versions/4.6/
>> unix/lib -L/Library/Frameworks/GDAL.framework/Versions/1.6/unix/lib
>> -lgdal
>> configure: creating ./config.status
>> config.status: creating src/Makevars
>> ** libs
>> ** arch - x86_64
>> g++ -arch x86_64 -I/Library/Frameworks/R.framework/Resources/
>> include -I/Library/Frameworks/R.framework/Resources/include/x86_64 -
>> I/Library/Frameworks/PROJ.framework/Versions/4.6/Headers -I/Library/
>> Frameworks/GDAL.framework/Versions/1.6/Headers -I/usr/local/
>> include -fPIC -g -O2 -c OGR_write.cpp -o OGR_write.o
>> g++ -arch x86_64 -I/Library/Frameworks/R.framework/Resources/
>> include -I/Library/Frameworks/R.framework/Resources/include/x86_64 -
>> I/Library/Frameworks/PROJ.framework/Versions/4.6/Headers -I/Library/
>> Frameworks/GDAL.framework/Versions/1.6/Headers -I/usr/local/
>> include -fPIC -g -O2 -c gdal-bindings.cpp -o gdal-bindings.o
>> g++ -arch x86_64 -I/Library/Frameworks/R.framework/Resources/
>> include -I/Library/Frameworks/R.framework/Resources/include/x86_64 -
>> I/Library/Frameworks/PROJ.framework/Versions/4.6/Headers -I/Library/
>> Frameworks/GDAL.framework/Versions/1.6/Headers -I/usr/local/
>> include -fPIC -g -O2 -c ogr_geom.cpp -o ogr_geom.o
>> g++ -arch x86_64 -I/Library/Frameworks/R.framework/Resources/
>> include -I/Library/Frameworks/R.framework/Resources/include/x86_64 -
>> I/Library/Frameworks/PROJ.framework/Versions/4.6/Headers -I/Library/
>> Frameworks/GDAL.framework/Versions/1.6/Headers -I/usr/local/
>> include -fPIC -g -O2 -c ogr_proj.cpp -o ogr_proj.o
>> g++ -arch x86_64 -I/Library/Frameworks/R.framework/Resources/
>> include -I/Library/Frameworks/R.framework/Resources/include/x86_64 -
>> I/Library/Frameworks/PROJ.framework/Versions/4.6/Headers -I/Library/
>> Frameworks/GDAL.framework/Versions/1.6/Headers -I/usr/local/
>> include -fPIC -g -O2 -c ogrdrivers.cpp -o ogrdrivers.o
>> g++ -arch x86_64 -I/Library/Frameworks/R.framework/Resources/
>> include -I/Library/Frameworks/R.framework/Resources/include/x86_64 -
>> I/Library/Frameworks/PROJ.framework/Versions/4.6/Headers -I/Library/
>> Frameworks/GDAL.framework/Versions/1.6/Headers -I/usr/local/
>> include -fPIC -g -O2 -c ogrsource.cpp -o ogrsource.o
>> g++ -arch x86_64 -I/Library/Frameworks/R.framework/Resources/
>> include -I/Library/Frameworks/R.framework/Resources/include/x86_64 -
>> I/Library/Frameworks/PROJ.framework/Versions/4.6/Headers -I/Library/
>> Frameworks/GDAL.framework/Versions/1.6/Headers -I/usr/local/
>> include -fPIC -g -O2 -c projectit.cpp -o projectit.o
>> g++ -arch x86_64 -dynamiclib -Wl,-headerpad_max_install_names -
>> undefined dynamic_lookup -single_module -multiply_defined suppress -
>> L/usr/local/lib -o rgdal.so OGR_write.o gdal-bindings.o ogr_geom.o
>> ogr_proj.o ogrdrivers.o ogrsource.o projectit.o -L/Library/
>> Frameworks/PROJ.framework/Versions/4.6/unix/lib -L/Library/
>> Frameworks/GDAL.framework/Versions/1.6/unix/lib -lgdal -lproj -F/
>> Library/Frameworks/R.framework/.. -framework R -Wl,-framework -
>> Wl,CoreFoundation
>> ** R
>> ** inst
>> ** preparing package for lazy loading
>> ** help
>> *** installing help indices
>>>>> Building/Updating help pages for package 'rgdal'
>> Formats: text html latex example
>> CRS-class text html latex example
>> GDALDataset-class text html latex
>> GDALDriver-class text html latex example
>> GDALMajorObject-class text html latex example
>> GDALRasterBand-class text html latex example
>> GDALReadOnlyDataset-class text html latex example
>> GDALReadOnlyDataset-methods text html latex example
>> GDALTransientDataset-class text html latex example
>> RGB2PCT text html latex example
>> SGDF2PCT text html latex example
>> SpatialGDAL-class text html latex example
>> closeDataset-methods text html latex
>> displayDataset text html latex example
>> make_EPSG text html latex example
>> projInfo text html latex example
>> project text html latex example
>> readGDAL text html latex example
>> readOGR text html latex example
>> showWKT text html latex example
>> spTransform-methods text html latex example
>> writeOGR text html latex example
>> ** building package indices ...
>> * DONE (rgdal)
>>
>> * Installing *source* package 'rgdal' ...
>> mv: rename /Library/Frameworks/R.framework/Resources/library/rgdal
>> to /Library/Frameworks/R.framework/Resources/library/00LOCK/rgdal/
>> rgdal: Directory not empty
>> gdal-config: /Library/Frameworks/GDAL.framework/Versions/1.6/
>> Programs/gdal-config
>> checking for gcc... gcc -arch x86_64 -std=gnu99
>> checking for C compiler default output file name... a.out
>> checking whether the C compiler works... yes
>> checking whether we are cross compiling... no
>> checking for suffix of executables...
>> checking for suffix of object files... o
>> checking whether we are using the GNU C compiler... yes
>> checking whether gcc -arch x86_64 -std=gnu99 accepts -g... yes
>> checking for gcc -arch x86_64 -std=gnu99 option to accept ANSI C...
>> none needed
>> checking how to run the C preprocessor... gcc -arch x86_64 -
>> std=gnu99 -E
>> checking for egrep... grep -E
>> checking for ANSI C header files... rm: conftest.dSYM: is a directory
>> rm: conftest.dSYM: is a directory
>> 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_api.h usability... yes
>> checking proj_api.h presence... yes
>> checking for proj_api.h... yes
>> checking for pj_init_plus in -lproj... yes
>> Package CPP flags: -I/Library/Frameworks/PROJ.framework/Versions/
>> 4.6/Headers -I/Library/Frameworks/GDAL.framework/Versions/1.6/Headers
>> Package LIBS: -L/Library/Frameworks/PROJ.framework/Versions/4.6/
>> unix/lib -L/Library/Frameworks/GDAL.framework/Versions/1.6/unix/lib
>> -lgdal
>> configure: creating ./config.status
>> config.status: creating src/Makevars
>> ** libs
>> ** arch - x86_64
>> make: Nothing to be done for `all'.
>> ** R
>> ** inst
>> ** preparing package for lazy loading
>> Error in nchar(filename) : element 1 is empty;
>> the part of the args list of '.Internal' being evaluated was:
>> (x, type, allowNA)
>> Error : unable to load R code in package 'rgdal'
>> ERROR: lazy loading failed for package 'rgdal'
>> * Removing '/Library/Frameworks/R.framework/Resources/library/rgdal'
>> * Restoring previous '/Library/Frameworks/R.framework/Resources/
>> library/rgdal'
>>
>> Any thoughts would be greatly appreciated. Thanks
>> Corey
>>
>> Corey Sparks
>> Assistant Professor
>> Department of Demography and Organization Studies
>> University of Texas at San Antonio
>> One UTSA Circle
>> San Antonio, TX 78249
>> 210 458 6858
>> corey.sparks 'at' utsa.edu
>>
>> _______________________________________________
>> R-sig-Geo mailing list
>> R-sig-Geo at stat.math.ethz.ch
>> https://stat.ethz.ch/mailman/listinfo/r-sig-geo
>
> --
> Roger Bivand
> Economic Geography Section, Department of Economics, Norwegian
> School of
> Economics and Business Administration, Helleveien 30, N-5045 Bergen,
> Norway. voice: +47 55 95 93 55; fax +47 55 95 95 43
> e-mail: Roger.Bivand at nhh.no
>
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