[Bioc-devel] Biobase from BioC 2.7 doesn't load in Mac OSX 10.6

Hervé Pagès hpages at fhcrc.org
Tue Oct 19 19:30:04 CEST 2010


Hi,

I'm looking at those binaries and indeed something looks wrong:

PELHAM:bbs-2.7-bioc biocbuild$ otool -L Biobase/libs/*/Biobase.so | grep 
libR.dylib
	/Library/Frameworks/R.framework/Versions/2.11/Resources/lib/libR.dylib 
(compatibility version 2.11.0, current version 2.11.1)
	/Library/Frameworks/R.framework/Versions/2.11/Resources/lib/libR.dylib 
(compatibility version 2.11.0, current version 2.11.1)
	/Library/Frameworks/R.framework/Versions/2.11/Resources/lib/libR.dylib 
(compatibility version 2.11.0, current version 2.11.1)

We have R 2.11 and 2.12 (and 2.13 since yesterday) installed on our
build machine pelham and it seems that somehow the BioC 2.7 builds
(using R 2.12) got the wrong version of libR.dylib.

We are looking into this and will update those binaries ASAP (it
might take another build cycle for this i.e. it might not happen
before tomorrow).

Thanks for your patience,
H.


On 10/19/2010 04:41 AM, Sean Davis wrote:
> On Tue, Oct 19, 2010 at 7:17 AM, Vincent Carey
> <stvjc at channing.harvard.edu>wrote:
>
>> confirmed on my macosx 10.6.4 mac -- will start checking.
>>
>> On Tue, Oct 19, 2010 at 2:31 AM, Robert Castelo<robert.castelo at upf.edu>
>> wrote:
>>> hi,
>>>
>>> i've just tried a new fresh installation of R 2.12 in my Mac OSX 10.6
>> laptop
>>> and found the following problem:
>>>
>>> source("http://www.bioconductor.org/biocLite.R")
>>> biocLite()
>>>
>>> [... installs everything apparently without problems ...]
>>>
>>>
>>> library(Biobase)
>>> Error in dyn.load(file, DLLpath = DLLpath, ...) :
>>>   unable to load shared object
>>>
>> '/Library/Frameworks/R.framework/Versions/2.12/Resources/library/Biobase/libs/x86_64/Biobase.so':
>>>
>>>
>> dlopen(/Library/Frameworks/R.framework/Versions/2.12/Resources/library/Biobase/libs/x86_64/Biobase.so,
>>> 6): Library not loaded:
>>> /Library/Frameworks/R.framework/Versions/2.11/Resources/lib/libR.dylib
>>
>
> I guess it is obvious, but the line above doesn't look right.
>
>
>>>   Referenced from:
>>>
>> /Library/Frameworks/R.framework/Versions/2.12/Resources/library/Biobase/libs/x86_64/Biobase.so
>>>   Reason: image not found
>>> Error: package/namespace load failed for 'Biobase'
>>>
>>> sessionInfo()
>>> R version 2.12.0 (2010-10-15)
>>> Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit)
>>>
>>> locale:
>>> [1] en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8
>>>
>>> attached base packages:
>>> [1] stats     graphics  grDevices utils     datasets  methods   base
>>>
>>> cheers,
>>> robert.
>>>
>>> _______________________________________________
>>> Bioc-devel at stat.math.ethz.ch mailing list
>>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>>>
>>
>> _______________________________________________
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>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>>
>
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>
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-- 
Hervé Pagès

Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N, M2-B876
P.O. Box 19024
Seattle, WA 98109-1024

E-mail: hpages at fhcrc.org
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