Looks like there was quite a lot to learn here. Thank you.I have resorted to
install R 2.9 and the fortan package which was probably my major miss.gra
So far, problems solved.
Cheers
Massimo


On Tue, Apr 21, 2009 at 10:31 PM, Patrick Aboyoun <paboyoun@fhcrc.org>wrote:

> 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]]
>>>>>
>>>>> _______________________________________________
>>>>> R-SIG-Mac mailing list
>>>>> R-SIG-Mac@stat.math.ethz.ch
>>>>> https://stat.ethz.ch/mailman/listinfo/r-sig-mac
>>>>>
>>>>>
>>>>>
>>>> _______________________________________________
>>>> R-SIG-Mac mailing list
>>>> R-SIG-Mac@stat.math.ethz.ch
>>>> https://stat.ethz.ch/mailman/listinfo/r-sig-mac
>>>>
>>>
>>>
>>>
>>
>


-- 
Massimo Pinto
Post Doctoral Research Fellow
Enrico Fermi Centre and Italian Public Health Research Institute (ISS), Rome
http://claimid.com/massimopinto

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