[R-sig-Geo] spgrass6 build error on Mac OS X

[Roger Bivand]

On Tue, 22 Jan 2008, Thomas.Adams at noaa.gov wrote:

> List,
>
> I am attempting to build spgrass6 on MacOS X 10.5.1 (Leopard) on a 2.33. 
> GHz Intel Core Duo MacBook Pro. Using the Mac OS X Cocoa GUI, I am 
> trying to install spgrass6 from source. I have gdal installed fine; when 
> I run gdal-config at a term window prompt, I get:
>
> Macintosh-2:bin teaiii$ gdal-config
> Usage: gdal-config [OPTIONS]
> Options:
> 	[--prefix[=DIR]]
> 	[--libs]
> 	[--dep-libs]
> 	[--cflags]
> 	[--version]
> 	[--ogr-enabled]
> 	[--formats]
>
> I have "Install dependencies" checked, so rgdal is downloaded and 
> attempts to build first. (No MacOS X binaries are available). So, I get:


I do not have any useful experience with any OSX systems (there are so 
many and they change so fast), so this is guesswork. Please verify that 
GDAL actually works, since gdal-config is a shell script. Does gdalinfo 
--version work? Does GRASS 6 build and work against GDAL?

Do other R source packages install correctly, that is, is the correct 
build train being chosen? Can you for example install maptools from 
source? Or a source package including c++ code? Is gcc 4.0.1 the version 
you should be using? Should it be looking for the PPC libraries given that 
you are building on i386? Is this a symptom that you are trying to 
build a univeral binary package without the correct tool train? Please try 
to avoid using the GUI for installation if possible, you may have better 
control without it. Does:

R_ARCH=/i386 R CMD INSTALL foo_1.0.tar.gz

in the OSX FAQ mean anything?

If this doesn't help, please try asking on the R-sig-mac list, hopefully 
reporting back here when the issue is resolved.

Roger

>
> /Library/Frameworks/R.framework/Resources/library
> * Installing *source* package 'rgdal' ...
> gdal-config: gdal-config
> checking for gcc... gcc -arch i386 -isysroot /Developer/SDKs/MacOSX10.4u.sdk -mmacosx-version-min=10.4 -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 i386 -isysroot /Developer/SDKs/MacOSX10.4u.sdk -mmacosx-version-min=10.4 -std=gnu99 accepts -g... yes
> checking for gcc -arch i386 -isysroot /Developer/SDKs/MacOSX10.4u.sdk -mmacosx-version-min=10.4 -std=gnu99 option to accept ANSI C... none needed
> checking how to run the C preprocessor... gcc -arch i386 -isysroot /Developer/SDKs/MacOSX10.4u.sdk -mmacosx-version-min=10.4 -std=gnu99 -E
> checking for egrep... 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_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/usr/local/include
> Package LIBS: -L/usr/local/lib -lgdal
> configure: creating ./config.status
> config.status: creating src/Makevars
> ** libs
> ** arch - i386
> g++ -arch i386 -isysroot /Developer/SDKs/MacOSX10.4u.sdk -mmacosx-version-min=10.4 -no-cpp-precomp -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -I/usr/local/include -msse3    -fPIC  -g -O2 -march=nocona -c OGR_write.cpp -o OGR_write.o
> g++ -arch i386 -isysroot /Developer/SDKs/MacOSX10.4u.sdk -mmacosx-version-min=10.4 -no-cpp-precomp -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -I/usr/local/include -msse3    -fPIC  -g -O2 -march=nocona -c gdal-bindings.cpp -o gdal-bindings.o
> g++ -arch i386 -isysroot /Developer/SDKs/MacOSX10.4u.sdk -mmacosx-version-min=10.4 -no-cpp-precomp -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -I/usr/local/include -msse3    -fPIC  -g -O2 -march=nocona -c ogr_geom.cpp -o ogr_geom.o
> g++ -arch i386 -isysroot /Developer/SDKs/MacOSX10.4u.sdk -mmacosx-version-min=10.4 -no-cpp-precomp -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -I/usr/local/include -msse3    -fPIC  -g -O2 -march=nocona -c ogr_proj.cpp -o ogr_proj.o
> g++ -arch i386 -isysroot /Developer/SDKs/MacOSX10.4u.sdk -mmacosx-version-min=10.4 -no-cpp-precomp -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -I/usr/local/include -msse3    -fPIC  -g -O2 -march=nocona -c ogrdrivers.cpp -o ogrdrivers.o
> g++ -arch i386 -isysroot /Developer/SDKs/MacOSX10.4u.sdk -mmacosx-version-min=10.4 -no-cpp-precomp -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -I/usr/local/include -msse3    -fPIC  -g -O2 -march=nocona -c ogrsource.cpp -o ogrsource.o
> g++ -arch i386 -isysroot /Developer/SDKs/MacOSX10.4u.sdk -mmacosx-version-min=10.4 -no-cpp-precomp -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -I/usr/local/include -msse3    -fPIC  -g -O2 -march=nocona -c projectit.cpp -o projectit.o
> g++ -arch i386 -isysroot /Developer/SDKs/MacOSX10.4u.sdk -mmacosx-version-min=10.4 -dynamiclib -Wl,-headerpad_max_install_names -Wl,-macosx_version_min -Wl,10.4 -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/usr/local/lib -lgdal -lproj  -F/Library/Frameworks/R.framework/.. -framework R
> ** Removing '/Library/Frameworks/R.framework/Resources/library/rgdal'
> /usr/bin/libtool: for architecture ppc7400 object: /usr/lib/gcc/i686-apple-darwin8/4.0.1/libstdc++.dylib malformed object (unknown load command 7)
> /usr/bin/libtool: for architecture: (null) file: -lstdc++ is not an object file (not allowed in a library)
> /usr/bin/libtool: for architecture i386 object: /usr/lib/gcc/i686-apple-darwin8/4.0.1/libstdc++.dylib malformed object (unknown load command 8)
> /usr/bin/libtool: for architecture ppc7400 object: /usr/lib/gcc/i686-apple-darwin8/4.0.1/../../../libSystem.dylib malformed object (unknown load command 7)
> /usr/bin/libtool: for architecture: (null) file: -lSystem is not an object file (not allowed in a library)
> /usr/bin/libtool: for architecture ppc64 object: /usr/lib/gcc/i686-apple-darwin8/4.0.1/../../../libSystem.dylib malformed object (unknown load command 7)
> make: *** [rgdal.so] Error 1
> chmod: /Library/Frameworks/R.framework/Resources/library/rgdal/libs/i386/*: No such file or directory
> ERROR: compilation failed for package 'rgdal'
>
> The downloaded packages are in
> 	/private/var/folders/nB/nBmBWJwdFiCTlNzaoS98rk+++TI/-Tmp-/RtmpYsVNHr/downloaded_packages
> /Library/Frameworks/R.framework/Resources/library
> * Installing *source* package 'spgrass6' ...
> ** R
> ** inst
> ** preparing package for lazy loading
> Loading required package: sp
> Loading required package: maptools
> Loading required package: foreign
> Error: package 'rgdal' required by 'spgrass6' could not be found
> Execution halted
> ERROR: lazy loading failed for package 'spgrass6'
> ** Removing '/Library/Frameworks/R.framework/Resources/library/spgrass6'
>
> I'm not sure what to do next. Any suggestions?
>
> Regards,
> Tom
>
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-- 
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