[BioC] error while loading the genefilter package [R 2.8.1. on Mac OSX 10.5.6]

Wed Apr 15 21:00:09 CEST 2009

Richard,
According to your sessionInfo, you are running i386-apple-darwin8.11.1, 
which is Mac OS X 10.4 (Tiger).

These two issues are related, however, and I just pushed a fix to 
bioconductor.org, that is available through biocLite. There were some 
older builds of Mac OS X binary packages for BioC 2.3 at 
bioconductor.org that didn't have its dynamic links revised to work with 
libraries supplied in the pre-built versions of R for Macs OS X. Due to 
web caching it may take up to 24 hours for the new packages to be 
available using biocLite, so you can try now and if it doesn't work wait 
some hours and try again. Hopefully the cache will clear sooner rather 
than later.

Patrick

Richard Pearson wrote:
> Patrick
>
> I think I've got a similar problem with a collaborator who is also on 
> OS X 10.5.6 and R 2.8.1, but here the problem is with the affy 
> package. For some reason, it appears that biocLite is installing the 
> OS X 10.4 version of the binary (from 
> http://bioconductor.org/packages/2.3/bioc/bin/macosx/universal) rather 
> then the 10.5 version (from 
> http://bioconductor.org/packages/2.3/bioc/bin/macosx/leopard). Could 
> this be a bug in biocLite?
>
> Here is the output from trying to install and load "affy", and the 
> sessionInfo()
>
> > source("http://bioconductor.org/biocLite.R")
> > biocLite("affy")
> Running biocinstall version 2.3.10 with R version 2.8.1
> Your version of R requires version 2.3 of Bioconductor.
> trying URL 
> 'http://bioconductor.org/packages/2.3/bioc/bin/macosx/universal/contrib/2.8/affy_1.20.2.tgz' 
>
> Content type 'application/x-gzip' length 1439037 bytes (1.4 Mb)
> opened URL
> ==================================================
> downloaded 1.4 Mb
>
>
> The downloaded packages are in
>
> /var/folders/B7/B77yjISEE1iKVBJQ80Q+lk+++TI/-Tmp-//Rtmp0yyhTV/downloaded_packages 
>
> > 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'
>
>
>
> >sessionInfo()
>
> R version 2.8.1 (2008-12-22)
> i386-apple-darwin8.11.1
>
> locale:
> en_GB.UTF-8/en_GB.UTF-8/C/C/en_GB.UTF-8/en_GB.UTF-8
>
> attached base packages:
> [1] tools     stats     graphics  grDevices utils     datasets  
> methods   base
> other attached packages:
> [1] Biobase_2.2.2
>
> loaded via a namespace (and not attached):
> [1] affyio_1.10.1
>
> Cheers
>
> Richard
>
>
> Massimo Pinto wrote:
>> Hi Patrick, thank you for your assistance.
>> Here is my SessionInfo()
>>
>>> sessionInfo()
>> R version 2.8.1 (2008-12-22)
>> i386-apple-darwin8.11.1
>>
>> locale:
>> C
>>
>> attached base packages:
>> [1] splines   tools     stats     graphics  grDevices utils
>> [7] datasets  methods   base
>>
>> other attached packages:
>> [1] survival_2.34-1 Biobase_2.2.2
>>
>> loaded via a namespace (and not attached):
>> [1] AnnotationDbi_1.4.3 DBI_0.2-4           RSQLite_0.7-1
>> [4] annotate_1.20.1
>>
>> ====
>>
>> If I install genefilter from BioC, right from the R console, I am 
>> getting
>> the same results as I indicated in my earlier message. Perhaps you 
>> mean that
>> I should download the sources and re-compile? Mmm I used to do these 
>> things
>> in Linux, I need to take some dust off my neurons if I need to get 
>> this done
>> on a Mac.
>>
>> Massimo
>>
>>
>>
>> On Wed, Apr 15, 2009 at 6:27 PM, Patrick Aboyoun <paboyoun at fhcrc.org> 
>> wrote:
>>
>>> Massimo,
>>> The problem is in the version of the genefilter Mac OS X 10.5 (Leopard)
>>> binary package you are using. I just downloaded genefilter version 
>>> 1.22 for
>>> BioC 2.3 from bioconductor.org and don't see the dynamic linking to
>>> libgfortran that is suggested by your error message:
>>>
>>> sandbox$ otool -L genefilter/libs/i386/genefilter.so
>>> genefilter/libs/i386/genefilter.so:
>>>   genefilter.so (compatibility version 0.0.0, current version 0.0.0)
>>>   /Library/Frameworks/R.framework/Versions/2.8/Resources/lib/libR.dylib
>>> (compatibility version 2.8.0, current version 2.8.0)
>>>
>>> /System/Library/Frameworks/CoreFoundation.framework/Versions/A/CoreFoundation 
>>>
>>> (compatibility version 150.0.0, current version 476.15.0)
>>>   /usr/lib/libstdc++.6.dylib (compatibility version 7.0.0, current 
>>> version
>>> 7.4.0)
>>>   /usr/lib/libgcc_s.1.dylib (compatibility version 1.0.0, current 
>>> version
>>> 1.0.0)
>>>   /usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current 
>>> version
>>> 111.1.1)
>>>
>>> Try to reinstall genefilter using biocLite("genefilter") and let me 
>>> know if
>>> the problem persists. Perhaps it is with a different library. 
>>> Include your
>>> sessionInfo() in your response so I can help troubleshoot any 
>>> problems that
>>> arise.
>>>
>>>
>>> Patrick
>>>
>>>
>>>
>>> Massimo Pinto wrote:
>>>
>>>> Greetings BioC list readers,
>>>>
>>>> on a Mac OSX 10.5.6 with R 2.8.1 I have successfully installed a 
>>>> series of
>>>> packages by typing the following code on the R Console.
>>>>
>>>>
>>>>
>>>>>    source("http://bioconductor.org/biocLite.R")
>>>>>    biocLite()
>>>>>
>>>>>
>>>> [...]
>>>>
>>>> however, this is what I am getting when I try to load genefilter, 
>>>> which is
>>>> required by the package Agi4x44PreProcess
>>>>
>>>>
>>>>
>>>>> library(genefilter)
>>>>>
>>>>>
>>>> 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)'.
>>>>
>>>> Loading required package: survival
>>>> Loading required package: splines
>>>> Error in dyn.load(file, DLLpath = DLLpath, ...) :
>>>>  unable to load shared library
>>>>
>>>> '/Library/Frameworks/R.framework/Resources/library/genefilter/libs/i386/genefilter.so': 
>>>>
>>>>
>>>>  dlopen(/Library/Frameworks/R.framework/Resources/library/genefilter/libs/i386/genefilter.so, 
>>>>
>>>> 6): Library not loaded: /usr/local/lib/libgfortran.2.dylib
>>>>  Referenced from:
>>>>
>>>> /Library/Frameworks/R.framework/Resources/library/genefilter/libs/i386/genefilter.so 
>>>>
>>>>  Reason: image not found
>>>> Error: package/namespace load failed for 'genefilter'
>>>>
>>>> There is no /Library/Frameworks/ directory on my disk. Looks like I 
>>>> have
>>>> got
>>>> a messy installation. Does this look familiar to any of you?
>>>> Yours,
>>>> Massimo
>>>>
>>>>
>>>>
>>>
>>
>>
>