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

[Patrick Aboyoun]

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.

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.


Cheers,
Patrick



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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