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

[Dan Tenenbaum]

On Thu, Apr 14, 2011 at 4:13 PM, Dan Tenenbaum <dtenenba at fhcrc.org> wrote:
> 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
>

Hello,

All Mac binary packages in the new Bioconductor release are working now.

Please install the packages with

source("http://bioconductor.org/biocLite.R")
biocLite("packagename")

Don't use update.packages().

You should be using the version of R available from CRAN:

http://cran.r-project.org/bin/macosx/

To be extra thorough, you may want to uninstall/reinstall R before
reinstalling Biobase or other packages.

Please let us know if you still run into any issues.

Thanks
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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>