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

Tue Apr 21 22:31:33 CEST 2009

Simon,
I just tested the scenario of using standard R-2.x.x.dmg from CRAN is 
installed on a Mac OS X 10.5 machine and download the standard set of 
BioC packages and it worked as you predicted using the default type = 
"mac.binary". My bad. The OS version was a red herring.

Patrick

Simon Urbanek wrote:
> 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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>>
>>
>