[BioC] Biobase 2.8 with R 2.13.0 fails on my Mac

[Dan Tenenbaum]

Thank you for the report, Vince and Janet.

We have identified the problem and it will be fixed in tomorrow's
builds (around noon Seattle time).

Dan


On Thu, Apr 14, 2011 at 4:08 PM, Vincent Carey
<stvjc at channing.harvard.edu> wrote:
> I reproduced this error with a fresh install of the R for MacOSX
> binary.  I do not know the specific solution for the binary
> installation of Biobase at this time.  However, I do routinely install
> and update Xcode tools for mac osx.  And biocLite("Biobase",
> type="source") created a properly loadable installation.  I would
> recommend installation of Xcode tools to allow you greater versatility
> in such situations.
>
> On Thu, Apr 14, 2011 at 6:29 PM, Janet Young <jayoung at fhcrc.org> wrote:
>> Hi,
>>
>> Thanks for the new version - I'm looking forward to using it.  I've installed it fine on the
>> linux machine I use, but not on Mac - I'm not sure if it's a problem with R, or with
>> Biobase, or with my setup (do I need to to try harder to get rid of R-2.12?).  I think
>> I've given all the relevant information below.
>>
>> all the best,
>>
>> Janet
>>
>>
>>
>>
>>> source("http://www.bioconductor.org/biocLite.R")
>> BioC_mirror = http://bioconductor.org
>> Change using chooseBioCmirror().
>>> biocLite("Biobase")
>> Using R version 2.13.0, biocinstall version 2.8.3.
>> Installing Bioconductor version 2.8 packages:
>> [1] "Biobase"
>> Please wait...
>>
>> trying URL
>> 'http://bioconductor.org/packages/2.8/bioc/bin/macosx/leopard/contrib/2.13/Biobase_2.12.0.tgz'
>> Content type 'application/x-gzip' length 2427717 bytes (2.3 Mb)
>> opened URL
>> ==================================================
>> downloaded 2.3 Mb
>>
>>
>> The downloaded packages are in
>>        /var/folders/z5/z5O6DCxcG60UeeZiA7+v1E+++Tc/-Tmp-//RtmpP6YQAN/downloaded_packages
>>> library(Biobase)
>> Error in dyn.load(file, DLLpath = DLLpath, ...) :
>>  unable to load shared object
>> '/Library/Frameworks/R.framework/Versions/2.13/Resources/library/Biobase/libs/i386/Biobase.so':
>>
>> dlopen(/Library/Frameworks/R.framework/Versions/2.13/Resources/library/Biobase/libs/i386/Biobase.
>> so, 6): Library not loaded: /Library/Frameworks/R.framework/Versions/2.12/Resources/lib/libR.dylib
>>  Referenced from:
>> /Library/Frameworks/R.framework/Versions/2.13/Resources/library/Biobase/libs/i386/Biobase.so
>>  Reason: image not found
>> Error: package/namespace load failed for 'Biobase'
>>
>>
>>
>>> sessionInfo()
>> R version 2.13.0 (2011-04-13)
>> Platform: i386-apple-darwin9.8.0/i386 (32-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
>>
>> loaded via a namespace (and not attached):
>> [1] tools_2.13.0
>>
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>
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