[R-SIG-Mac] installation of affy under Mac OS X 10.5.6 (Leopard)

Tue Apr 21 21:46:30 CEST 2009

Patrick,

On Apr 21, 2009, at 14:53 , Patrick Aboyoun wrote:

> Massimo,
> I'll break down these issues in two and go through them in turn:
>
> 1) stale binaries for R 2.8 at bioconductor.org
> You had found that the Mac OS X binary packages at bioconductor.org  
> that used fortran, like preprocessCore, had a bad gfortran link in  
> them. I updated those packages last week and they are now properly  
> redirected to the gfortran library that is provided with the pre- 
> built version of R 2.8. To fix this issue, please download the  
> troublesome libraries again for a fix.
>
> 2) Determining which binary packages are appropriate for your Mac
> I think you were downloading the Mac OS X 10.4 binary packages from  
> bioconductor.org rather than the Mac OS X 10.5 binary packages  
> because your pkgType == "mac.binary" instead of  
> "mac.binary.leopard". You and either perform a global setting of the  
> pkgType to "mac.binary.leopard" using options("pkgType" =  
> "mac.binary.leopard") or specify type = "mac.binary.leopard" when  
> using the biocLite / install.packages functions.
>

Do NOT do that manually! You can only use Tiger binaries in Tiger  
build of R even if you are running Leopard system, so the default  
setting is there for a reason (at least in CRAN binaries). The OS  
version is entirely irrelevant in this matter.

> I have also modified the underpinnings of biocLite to produce a  
> warning message when you specify type = "mac.binary" when you are  
> running on Mac OS X 10.5 machine with some suggestions on what you  
> can do to avoid this type of problem in the future.
>
>

That will be very bad for the reason above ... Are you sure you mean  
that? Or am I missing something - are you talking about the running OS  
or the R build OS?

Cheers,
Simon

>
>
> Simon Urbanek wrote:
>> Massimo,
>>
>> On Apr 21, 2009, at 9:10 AM, Massimo Pinto wrote:
>>
>>> Greetings all
>>> last week I attempted to install the genefilter package using
>>> BiocLite(genefilter) from the R prompt. Despite having a Mac OS X  
>>> 10.5.6.
>>> (Tiger), for some reason which I don't understand in full, BioC  
>>> 2.3 believes
>>> I am running on Mac OS X 10.4 (Leopard)
>>>
>>>> sessionInfo()
>>> R version 2.8.1 (2008-12-22)
>>> i386-apple-darwin8.11.1
>>>
>>
>> This shows you what kind of R you are running (i.e. where was the R  
>> compiled), not what your OS is. You are running the Tiger release  
>> of R, which is ok since it is designed for Mac OS X 10.4 (Tiger)  
>> and later which includes your 10.5.
>>
>>
>>> therefore, when I run biocLite, general Mac binaries are installed  
>>> and this results in execution errors.
>>>
>>
>> The "therefore" is wrong here ;).
>>
>>
>>> Much thanks to the help found on this list, I have downloaded the  
>>> tarball for OSX 10.5 binaries and installed manually. It worked  
>>> just fine.
>>>
>>> Today I have encountered a similar problem with the package affy.  
>>> Accordingly, I have downloaded the OS X 10.5 binaries and  
>>> installed manually:
>>>
>>>> install.packages("/Users/massimopinto/Desktop/affy_1.20.2.tgz",  
>>>> repos=NULL, dependencies=TRUE)
>>>
>>> however, when I load the library:
>>>
>>>> library(affy)
>>> Loading required package: Biobase
>>> Loading required package: tools
>>>
>>> Welcome to Bioconductor
>>>
>>> Vignettes contain introductory material. To view, type
>>> 'openVignette()'. To cite Bioconductor, see
>>> 'citation("Biobase")' and for packages 'citation(pkgname)'.
>>>
>>> Error in dyn.load(file, DLLpath = DLLpath, ...) :
>>> unable to load shared library
>>> '/Library/Frameworks/R.framework/Resources/library/preprocessCore/ 
>>> libs/i386/preprocessCore.so':
>>> dlopen(/Library/Frameworks/R.framework/Resources/library/ 
>>> preprocessCore/libs/i386/preprocessCore.so,
>>> 6): Library not loaded: /usr/local/lib/libgfortran.2.dylib
>>> Referenced from:
>>> /Library/Frameworks/R.framework/Resources/library/preprocessCore/ 
>>> libs/i386/preprocessCore.so
>>> Reason: image not found
>>> Error: package/namespace load failed for 'affy'
>>>
>>
>> The problem above doesn't come from affy, but from the  
>> preprocessCore package (see the error). The binary for  
>> preprocessCore you use is not quite correct. It uses local Fortran  
>> libraries on the machine that built it where it should be using the  
>> Fortran library inside R. If this is a binary from the BioC  
>> repository, please notify the maintainers, otherwise re-install the  
>> binary of preprocessCore from BioC. Note the the correct mailing  
>> list for such questions is BioC.
>>
>> A work-around (that fixes the symptom, not the problem) is to  
>> install the full R (you seem to have only the mini version  
>> installed) which includes a local Fortran compiler - or you can  
>> install the Fortran manually from
>> http://cran.r-project.org/bin/macosx/tools/
>>
>> Cheers,
>> Simon
>>
>>
>>
>>
>>> ===the package does not get loaded as a library cannot be found.  
>>> Similarly,
>>> I run into problems if I install as follows:
>>>
>>>> install.packages("affy", repos="
>>> http://www.bioconductor.org/packages/2.3/bioc/bin/macosx/leopard/contrib/2.8/ 
>>> ",
>>> contriburl="
>>> http://www.bioconductor.org/packages/2.3/bioc/bin/macosx/leopard/contrib/2.8/ 
>>> ",
>>> dependencies=TRUE)
>>> trying URL '
>>> http://www.bioconductor.org/packages/2.3/bioc/bin/macosx/leopard/contrib/2.8//affy_1.20.2.tgz
>>> '
>>> Content type 'application/x-gzip' length 1452708 bytes (1.4 Mb)
>>> [...]
>>>
>>> Could it be that the binaries at
>>> http://www.bioconductor.org/packages/2.3/bioc/bin/macosx/leopard/contrib/2.8/are
>>> in fact compiled for Tiger?
>>>
>>> Massimo
>>> -- 
>>>
>>> Massimo Pinto
>>> Post Doctoral Research Fellow
>>> Enrico Fermi Centre and Italian Public Health Research Institute  
>>> (ISS), Rome
>>> http://claimid.com/massimopinto
>>>
>>>    [[alternative HTML version deleted]]
>>>
>>> _______________________________________________
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>>>
>>>
>>
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>
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