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

Tue Jul 3 19:25:25 CEST 2007

On Jul 2, 2007, at 9:57 PM, Weiwei Shi wrote:

> Hi, there:
>
> I am re-compiling Package supclust for some small modification for my
> own purpose. After running "R CMD check", I got the following
> messenge:
>
> nicebaby:~/Documents/projects/R_customerized_packages wshi$ R CMD  
> check supclust
> * checking for working latex ...sh: line 1: latex: command not found
>  NO
> * using log directory
> '/Users/wshi/Documents/projects/R_customerized_packages/ 
> supclust.Rcheck'
> * using R version 2.5.0 (2007-04-23)
> * checking for file 'supclust/DESCRIPTION' ... OK
> * this is package 'supclust' version '1.0-5'
> * checking package dependencies ... OK
> * checking if this is a source package ... WARNING
> Subdirectory 'supclust/src' contains object files.
> * checking whether package 'supclust' can be installed ... ERROR
> Installation failed.
> See '/Users/wshi/Documents/projects/R_customerized_packages/ 
> supclust.Rcheck/00install.out'
> for details.
>
> The first one is about latex, I am going to install from office
> tomorrow since my home internet is really slow to download that one;
>
> The second is a warning about the source, and I am not sure how to
> find the detailed warning messege;
>
> The third one is the most serious one; check the detail and I found I
> did not have
> libgfortran.dylib and libgcc_s.10.4.dylib;
> so I installed gfortran 4.2, as shown below:
> nicebaby:~/Documents/projects/R_customerized_packages wshi$  
> gfortran --version
> GNU Fortran (GCC) 4.2.0
> Copyright (C) 2007 Free Software Foundation, Inc.
>
> GNU Fortran comes with NO WARRANTY, to the extent permitted by law.
> You may redistribute copies of GNU Fortran
> under the terms of the GNU General Public License.
> For more information about these matters, see the file named COPYING
>
> But splotlight still does not help me find the two files above;

How did you get gfortran? You should get the version form Simon's  
website or the one from the CRAN binary.

> So my third quesiton actually is, how to solve the problem. (For the
> same slow internet reason, my xcode tool is still at 2.2.0 version.
> But I assume it is not related since 2.4.0 might not include gfortran
> either.

You will need Xcode 2.4.x because of the updates to the C compiler

Kasper

> My mac os/x is 10.4.9
>
> Please help!
>
> Thanks,
>
> Weiwei
>
> On 5/30/07, Simon Urbanek <simon.urbanek at r-project.org> wrote:
>> 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
>>>
>>> ______________________________________________
>>> R-devel at r-project.org mailing list
>>> https://stat.ethz.ch/mailman/listinfo/r-devel
>>>
>>>
>>
>> _______________________________________________
>> R-SIG-Mac mailing list
>> R-SIG-Mac at stat.math.ethz.ch
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>>
>
>
> -- 
> Weiwei Shi, Ph.D
> Research Scientist
> GeneGO, Inc.
>
> "Did you always know?"
> "No, I did not. But I believed..."
> ---Matrix III
>
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