[R-SIG-Mac] [Rd] R 2.5.0 MAC OS X version

[Simon Urbanek]

On May 30, 2007, at 10:44 AM, Recai Yucel wrote:

> Right. I thought the problems might be obvious enough for MAC  
> users, probably not!

How can "the problems" be obvious when most Mac users don't have  
any? ;) If it was that obvious, why would you ask? The answer would  
be on the list already...


> I was mistaken with the GNU Fortran version, it is 4.0 as seen below.

Not really, run gfortran --version to find out.


> A  specific example where I had problems is given below:
>
> When I try to install a package called lmm (which was installed  
> with no problem with the previous versions of R), I get the  
> following messages, specifically on the make, chmod, etc.
>

Just out of curiosity, why don't you just install it from CRAN in  
binary form as suggested? Just type in R: install.packages("lmm")  
That works without problems and saves you all the hassle...

If you really insist on re-compiling the package yourself (you didn't  
even tell us what you are really doing), make sure you have all the  
necessary tools (Xcode 2.4.1 and GNU Fortran from the R distribution  
- see also http://r.research.att.com/tools/ ). From the output it  
appears as if your Fortran installation is broken.

Cheers,
Simon


> *************************************
> trying URL 'http://cran.us.r-project.org/src/contrib/lmm_0.3-4.tar.gz'
> Content type 'application/x-tar' length 31471 bytes
> opened URL
> ==================================================
> downloaded 30Kb
>
> WARNING: ignoring environment value of R_HOME
> tar: Read 4096 bytes from -
> * Installing *source* package 'lmm' ...
> ** libs
> ** arch - i386
> gfortran-4.0 -arch i386  -isysroot /Developer/SDKs/MacOSX10.4u.sdk
> -fPIC  -g -O2 -march=nocona -c lmm.f -o lmm.o
> gcc-4.0 -arch i386 -isysroot /Developer/SDKs/MacOSX10.4u.sdk - 
> dynamiclib
> -Wl,-macosx_version_min -Wl,10.3 -undefined dynamic_lookup
> -single_module -multiply_defined suppress -L/usr/local/lib -o lmm.so
> lmm.o  -L/usr/local/lib/gcc/i686-apple-darwin8/4.2.0 -lgfortran
> -lgcc_s.10.4 -F/Library/Frameworks/R.framework/.. -framework R
> /usr/bin/libtool: for architecture cputype (16777223) cpusubtype (3)
> object: /usr/local/lib/libgfortran.dylib malformed object (unknown  
> load
> command 4)
> /usr/bin/libtool: for architecture cputype (16777223) cpusubtype (3)
> object: /usr/local/lib/libgcc_s.10.4.dylib malformed object (unknown
> load command 4)
> ** arch - ppc
> gfortran-4.0 -arch ppc  -isysroot /Developer/SDKs/MacOSX10.4u.sdk
> -fPIC  -g -O2 -c lmm.f -o lmm.o
> make: *** [lmm.so] Error 1
> chmod:
> /Library/Frameworks/R.framework/Versions/2.5/Resources/library/lmm/ 
> libs/i386/*:
> No such file or directory
> gcc-4.0 -arch ppc -isysroot /Developer/SDKs/MacOSX10.4u.sdk -std=gnu99
> -dynamiclib -Wl,-macosx_version_min -Wl,10.3 -undefined dynamic_lookup
> -single_module -multiply_defined suppress -L/usr/local/lib -o lmm.so
> lmm.o  -L/usr/local/lib/gcc/powerpc-apple-darwin8/4.2.0 -lgfortran
> -lgcc_s.10.4 -lSystemStubs -F/Library/Frameworks/R.framework/..
> -framework R
>
> The downloaded packages are in
>    /private/tmp/Rtmpe4c9Of/downloaded_packages
> ** Removing
> '/Library/Frameworks/R.framework/Versions/2.5/Resources/library/lmm'
> ** Restoring previous
> '/Library/Frameworks/R.framework/Versions/2.5/Resources/library/lmm'
> /usr/bin/libtool: for architecture cputype (16777223) cpusubtype (3)
> object: /usr/local/lib/libgfortran.dylib malformed object (unknown  
> load
> command 4)
> /usr/bin/libtool: for architecture cputype (16777223) cpusubtype (3)
> object: /usr/local/lib/libgcc_s.10.4.dylib malformed object (unknown
> load command 4)
> make: *** [lmm.so] Error 1
> chmod:
> /Library/Frameworks/R.framework/Versions/2.5/Resources/library/lmm/ 
> libs/ppc/*:
> No such file or directory
> ERROR: compilation failed for package 'lmm'
> *************************************
>
>
>
> Prof Brian Ripley wrote:
>> And beyond that good advice, the mailing list for MacOS issues is
>> R-sig-mac.
>>
>> Are you really using 'GNU Fortran 4.2.0' (which was released well
>> after R 2.5.0), or some pre-release of it?  Such details do matter.
>>
>>
>> On Wed, 30 May 2007, Roy Mendelssohn wrote:
>>
>>> Hi Recal:
>>>
>>> To save you from some possible flames, it would probably help if you
>>> describe what the problems are, with specific examples and some of
>>> the relevant error messages. It would be difficult to for someone to
>>> know if they are seeing similar problems without knowing what the
>>> problems are.
>>>
>>> I believe such information is in the posting guides, which do  
>>> contain
>>> good information on how to frame a question to the mail list that
>>> will elicit useful responses.
>>>
>>> -Roy
>>>
>>>
>>>
>>>
>>> On May 30, 2007, at 7:08 AM, Recai Yucel wrote:
>>>
>>>> Please accept my apologies if this was addressed before, I could  
>>>> not
>>>> find any solution so I am posting my question here.
>>>>
>>>> I am having a lot of difficulties with installing and developing R
>>>> packages with the latest version of R 2.5.0. I am using a MacBook
>>>> Pro. I
>>>> never had these problems with the previous versions of R. I  
>>>> think part
>>>> of the problem is caused by the GNU Fortran 4.2.0 or my lack of
>>>> knowledge...
>>>>
>>>> If anybody else had similar problems and found the solution, please
>>>> let
>>>> me know.
>>>>
>>>> Best.
>>>>
>>>> -- 
>>>> Recai Yucel, Ph.D.
>>>> Assistant Professor of Biostatistics
>>>> Biostatistics and Epidemiology
>>>> UMASS-Amherst
>>
>
> -- 
> Recai Yucel, Ph.D.
> Assistant Professor of Biostatistics
> Biostatistics and Epidemiology
> UMASS-Amherst
>
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