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Building rgdal 0.6-7 on Mac

4 messages · Roger Bivand, Rich Grenyer, Corey Sparks

Original
Corey Sparks
# 
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.  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
Roger Bivand
#
On Mon, 20 Apr 2009, Corey Sparks wrote:

            

      
      
      
    

        
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

            

      
      
      
    

        

      
      
    

        

  
    

      
      
    

  


  


      

    

    

      
      

        


  

        

      Rich Grenyer
    

    

      
      #
    

  


  

          

      
      
      
    

        
I built 0.6-7 from source this morning on i386-apple-darwin8.11.1  
without problem, linking to the Kyngesbury frameworks; it didn't fail  
with that error.

Rich

  
  


  


      

    

    

      
      

        


  

        

      Corey Sparks
    

    

      
      #
    

  


  

      
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: