[R-SIG-Mac] mac OS X 10.5.7 rgdal installation problems
Steve Lianoglou
mailinglist.honeypot at gmail.com
Thu Jul 2 21:02:06 CEST 2009
Hi,
On Jul 2, 2009, at 2:43 PM, stephen sefick wrote:
> Where is the config.log?
Isn't it in the directory you're trying to compile from?
But also, here's another idea: I notice /sw/* and /opt/* in your
include library paths, so I wonder if maybe there is an other gcc
getting in your way which can't compile to different architecture
targets, ie: the "-arch i386" stuff you see in the "checking for gcc"
line here.
If you type "which gcc", which one pops up? Is it the one in /usr/bin,
or is there another installed via MacPorts of fink?
Just curious,
-steve
>
> On Thu, Jul 2, 2009 at 11:33 AM, Jan de Leeuw<deleeuw at stat.ucla.edu>
> wrote:
>> As the error message says: see config.log more more details,
>> search for "cannot create". It's usually a linking problem,
>> or a problem with include files, not a compiler problem per se.
>>
>> On Jul 2, 2009, at 08:47 , stephen sefick wrote:
>>
>>> sudo R CMD install --configure-args='--with-proj-include=/sw/bin/
>>> proj'
>>> rgdal_0.6-9.tar.gz
>>> * Installing to library
>>> ‘/Library/Frameworks/R.framework/Resources/library’
>>> * Installing *source* package ‘rgdal’ ...
>>> gdal-config: gdal-config
>>> checking for gcc... gcc -arch i386 -std=gnu99
>>> checking for C compiler default output file name... configure:
>>> error:
>>> C compiler cannot create executables
>>> See `config.log' for more details.
>>> ERROR: configuration failed for package ‘rgdal’
>>> * Removing ‘/Library/Frameworks/R.framework/Resources/library/rgdal’
>>>
>>> there is a C compiler problem? I have XCode 3.1.2.
>>>
>>> Stephen Sefick
>>>
>>> On Thu, Jul 2, 2009 at 10:05 AM, stephen sefick<ssefick at gmail.com>
>>> wrote:
>>>>
>>>> platform i386-apple-darwin8.11.1
>>>> arch i386
>>>> os darwin8.11.1
>>>> system i386, darwin8.11.1
>>>> status
>>>> major 2
>>>> minor 9.1
>>>> year 2009
>>>> month 06
>>>> day 26
>>>> svn rev 48839
>>>> language R
>>>> version.string R version 2.9.1 (2009-06-26)
>>>>
>>>> gdal-config, proj, and ogr are in my path. I type them at the
>>>> shell
>>>> prompt and they work. They were installed using fink so they are
>>>> in
>>>> the /sw/bin directory. The installation did not work without
>>>> configuration flags and gave me the same error message that is at
>>>> the
>>>> end of the transcript, so I decided to tell R CMD install where
>>>> proj
>>>> was. Below is the transcript of my session:
>>>>
>>>> sudo R CMD install --configure-args='--with-proj=/sw/bin/proj'
>>>> rgdal_0.6-9.tar.gz
>>>> Password:
>>>> * Installing to library
>>>> ‘/Library/Frameworks/R.framework/Resources/library’
>>>> * Installing *source* package ‘rgdal’ ...
>>>> gdal-config: gdal-config
>>>> checking for gcc... gcc -arch i386 -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 -std=gnu99 accepts -g... yes
>>>> checking for gcc -arch i386 -std=gnu99 option to accept ANSI C...
>>>> none
>>>> needed
>>>> checking how to run the C preprocessor... gcc -arch i386 -
>>>> 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... no
>>>> checking proj_api.h presence... no
>>>> checking for proj_api.h... no
>>>> Error: proj_api.h not found.
>>>> If the PROJ.4 library is installed in a non-standard location,
>>>> use --configure-args='--with-proj-include=/opt/local/include'
>>>> for example, replacing /opt/local/* with appropriate values
>>>> for your installation. If PROJ.4 is not installed, install it.
>>>> ERROR: configuration failed for package ‘rgdal’
>>>> * Removing ‘/Library/Frameworks/R.framework/Resources/library/
>>>> rgdal’
>>>>
>>>> any help would be greatly appreciated.
>>>
>>> --
>>> Stephen Sefick
>>>
>>> Let's not spend our time and resources thinking about things that
>>> are
>>> so little or so large that all they really do for us is puff us up
>>> and
>>> make us feel like gods. We are mammals, and have not exhausted the
>>> annoying little problems of being mammals.
>>>
>>> -K.
>>> Mullis
>>>
>>> _______________________________________________
>>> R-SIG-Mac mailing list
>>> R-SIG-Mac at stat.math.ethz.ch
>>> https://stat.ethz.ch/mailman/listinfo/r-sig-mac
>>
>> ===
>> Jan de Leeuw; Distinguished Professor and Chair, UCLA Department of
>> Statistics;
>> Director: UCLA Center for Environmental Statistics (CES);
>> Editor: Journal of Multivariate Analysis, Journal of Statistical
>> Software;
>> US mail: 8125 Math Sciences Bldg, Box 951554, Los Angeles, CA
>> 90095-1554
>> phone (310)-825-9550; fax (310)-206-5658; email: deleeuw at stat.ucla.edu
>> .mac: jdeleeuw ++++++ aim: deleeuwjan ++++++ skype: j_deleeuw
>> homepages: http://gifi.stat.ucla.edu ++++++ http://
>> www.cuddyvalley.org
>>
>> -------------------------------------------------------------------------------------------------
>> No matter where you go, there you are. --- Buckaroo Banzai
>> http://gifi.stat.ucla.edu/sounds/nomatter.au
>>
>> -------------------------------------------------------------------------------------------------
>>
>>
>>
>>
>>
>>
>
>
>
> --
> Stephen Sefick
>
> Let's not spend our time and resources thinking about things that are
> so little or so large that all they really do for us is puff us up and
> make us feel like gods. We are mammals, and have not exhausted the
> annoying little problems of being mammals.
>
> -K. Mullis
>
> _______________________________________________
> R-SIG-Mac mailing list
> R-SIG-Mac at stat.math.ethz.ch
> https://stat.ethz.ch/mailman/listinfo/r-sig-mac
--
Steve Lianoglou
Graduate Student: Physiology, Biophysics and Systems Biology
Weill Medical College of Cornell University
Contact Info: http://cbio.mskcc.org/~lianos/contact
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