Rgdal on osx 10.8 (homebrew)

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I suggest posting on R-SIG-Mac for possibly more rapid and accurate 
feedback. The rgdal developers have no access to OSX at all, let alone 
10.8. It appears in addition that your compile train may be running the 
configure tests with clang rather than gcc, and that the GDAL shared 
objects are not being found where gdal-config says they are located. 
Please report back on this thread when you solve the problem.

Roger

Hi All,

i'm having trouble trying to build Rgdal from source on mac osx 10.8.x

i have R and gfortran installed using Homebrew.

when i try to build rgdal i got this log :

epi:~ epi$ R CMD INSTALL rgdal_0.7-22.tar.gz
* installing to library
???/usr/local/Cellar/r/2.15.2/R.framework/Versions/2.15/Resources/library???
* installing *source* package ???rgdal??? ...
** package ???rgdal??? successfully unpacked and MD5 sums checked
configure: gdal-config: gdal-config
checking gdal-config usability... yes
configure: GDAL: 1.9.2
checking GDAL version > 1.5.4... yes
checking for gcc... cc
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
checking for suffix of executables...
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether cc accepts -g... yes
checking for cc option to accept ISO C89... none needed
checking how to run the C preprocessor... cc -E
checking for grep that handles long lines and -e... /usr/bin/grep
checking for egrep... /usr/bin/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 gdal.h usability... yes
checking gdal.h presence... yes
checking for gdal.h... yes
checking gdal: linking with --libs only... no
checking gdal: linking with --libs and --dep-libs... no
clang: warning: treating 'c' input as 'c++' when in C++ mode, this
behavior is deprecated
gdal_test.c:5:1: error: C++ requires a type specifier for all declarations
main() {
^~~~
1 error generated.
clang: warning: treating 'c' input as 'c++' when in C++ mode, this
behavior is deprecated
gdal_test.c:5:1: error: C++ requires a type specifier for all declarations
main() {
^~~~
1 error generated.
configure: Install failure: compilation and/or linkage problems.
configure: error: GDALAllRegister not found in libgdal.
ERROR: configuration failed for package ???rgdal???
* removing
???/usr/local/Cellar/r/2.15.2/R.framework/Versions/2.15/Resources/library/rgd
al???
epi:~ epi$

have you any clue about it ?

I tried to untar the rgdal.tar.gz
and rerun the R CMD install command ,

i attached a link to the logs :

http://epi.whoi.edu/esr/errors.txt
http://epi.whoi.edu/esr/configure.ac
http://epi.whoi.edu/config.log

?> sessionInfo()
R version 2.15.2 (2012-10-26)
Platform: x86_64-apple-darwin12.2.0 (64-bit)

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

attached base packages:
[1] stats graphics grDevices utils datasets methods base
?>

###

epi:~ epi$ gfortran -v
Using built-in specs.
COLLECT_GCC=gfortran
COLLECT_LTO_WRAPPER=/usr/local/Cellar/gfortran/4.7.2/gfortran/libexec/gcc/x
86_64-apple-darwin12.2.0/4.7.2/lto-wrapper
Target: x86_64-apple-darwin12.2.0
Configured with: ../configure --enable-languages=fortran
--prefix=/usr/local/Cellar/gfortran/4.7.2/gfortran
--datarootdir=/usr/local/Cellar/gfortran/4.7.2/share
--bindir=/usr/local/Cellar/gfortran/4.7.2/bin --with-system-zlib
--with-gmp=/usr/local/opt/gmp --with-mpfr=/usr/local/opt/mpfr
--with-mpc=/usr/local/opt/libmpc --enable-checking=release
--disable-stage1-checking --disable-build-poststage1-with-cxx
--disable-libstdcxx-pc --disable-nls
Thread model: posix
gcc version 4.7.2 (GCC)
epi:~ epi$

Thanks!!!

Massimo.
??????? [[alternative HTML version deleted]]

_______________________________________________
R-sig-Geo mailing list
R-sig-Geo at r-project.org
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Roger Bivand
Department of Economics, NHH Norwegian School of Economics,
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
Thanks Roger!

the compiler was the problem :)

using the terminal instead of R.app (GUI)
i was able to install rgdal correctly exptoring CC & CXX  using gcc & g++  
(the default on OSX 10.8.x , Xcode 4.5.x are :  clang & clang++)

so what i had to do :

wget http://cran.cs.wwu.edu/src/contrib/rgdal_0.7-22.tar.gz

export CC=/usr/bin/gcc
export CXX=/usr/bin/g++ 

R CMD INSTALL rgdal_0.7-22.tar.gz

--Massimo.

Il giorno 26/nov/2012, alle ore 02:40, Roger Bivand <Roger.Bivand at nhh.no> ha scritto:
I suggest posting on R-SIG-Mac for possibly more rapid and accurate feedback. The rgdal developers have no access to OSX at all, let alone 10.8. It appears in addition that your compile train may be running the configure tests with clang rather than gcc, and that the GDAL shared objects are not being found where gdal-config says they are located. Please report back on this thread when you solve the problem.

Roger

On Mon, 26 Nov 2012, rpi wrote:

Hi All,
i'm having trouble trying to build Rgdal from source on mac osx 10.8.x
i have R and gfortran installed using Homebrew.
when i try to build rgdal i got this log :
epi:~ epi$ R CMD INSTALL rgdal_0.7-22.tar.gz
* installing to library
???/usr/local/Cellar/r/2.15.2/R.framework/Versions/2.15/Resources/library???
* installing *source* package ???rgdal??? ...
** package ???rgdal??? successfully unpacked and MD5 sums checked
configure: gdal-config: gdal-config
checking gdal-config usability... yes
configure: GDAL: 1.9.2
checking GDAL version > 1.5.4... yes
checking for gcc... cc
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
checking for suffix of executables...
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether cc accepts -g... yes
checking for cc option to accept ISO C89... none needed
checking how to run the C preprocessor... cc -E
checking for grep that handles long lines and -e... /usr/bin/grep
checking for egrep... /usr/bin/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 gdal.h usability... yes
checking gdal.h presence... yes
checking for gdal.h... yes
checking gdal: linking with --libs only... no
checking gdal: linking with --libs and --dep-libs... no
clang: warning: treating 'c' input as 'c++' when in C++ mode, this
behavior is deprecated
gdal_test.c:5:1: error: C++ requires a type specifier for all declarations
main() {
^~~~
1 error generated.
clang: warning: treating 'c' input as 'c++' when in C++ mode, this
behavior is deprecated
gdal_test.c:5:1: error: C++ requires a type specifier for all declarations
main() {
^~~~
1 error generated.
configure: Install failure: compilation and/or linkage problems.
configure: error: GDALAllRegister not found in libgdal.
ERROR: configuration failed for package ???rgdal???
* removing
???/usr/local/Cellar/r/2.15.2/R.framework/Versions/2.15/Resources/library/rgd
al???
epi:~ epi$
have you any clue about it ?
I tried to untar the rgdal.tar.gz
and rerun the R CMD install command ,
i attached a link to the logs :
http://epi.whoi.edu/esr/errors.txt
http://epi.whoi.edu/esr/configure.ac
http://epi.whoi.edu/config.log
 > sessionInfo()
R version 2.15.2 (2012-10-26)
Platform: x86_64-apple-darwin12.2.0 (64-bit)
locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
attached base packages:
[1] stats graphics grDevices utils datasets methods base
 >
###
epi:~ epi$ gfortran -v
Using built-in specs.
COLLECT_GCC=gfortran
COLLECT_LTO_WRAPPER=/usr/local/Cellar/gfortran/4.7.2/gfortran/libexec/gcc/x
86_64-apple-darwin12.2.0/4.7.2/lto-wrapper
Target: x86_64-apple-darwin12.2.0
Configured with: ../configure --enable-languages=fortran
--prefix=/usr/local/Cellar/gfortran/4.7.2/gfortran
--datarootdir=/usr/local/Cellar/gfortran/4.7.2/share
--bindir=/usr/local/Cellar/gfortran/4.7.2/bin --with-system-zlib
--with-gmp=/usr/local/opt/gmp --with-mpfr=/usr/local/opt/mpfr
--with-mpc=/usr/local/opt/libmpc --enable-checking=release
--disable-stage1-checking --disable-build-poststage1-with-cxx
--disable-libstdcxx-pc --disable-nls
Thread model: posix
gcc version 4.7.2 (GCC)
epi:~ epi$
Thanks!!!
Massimo.
        [[alternative HTML version deleted]]
_______________________________________________
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, NHH Norwegian School of Economics,
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