[BioC] Error installing impute package

[Peter Langfelder]

Thanks Dan and Stephanie,

both solutions have worked.

Best,

Peter


On Wed, Apr 10, 2013 at 3:29 PM, Dan Tenenbaum <dtenenba at fhcrc.org> wrote:
> On Wed, Apr 10, 2013 at 3:08 PM, Stephanie M. Gogarten
> <sdmorris at u.washington.edu> wrote:
>> Is the error occurring just in the R GUI, or in any R session?  I'm having a
>> similar problem with DNAcopy when I try to load in the R GUI, but it works
>> fine in the terminal or in Emacs.
>>
>
> I have the same results; I get the error in the GUI but not in the
> command line. So I have two workarounds:
>
> 1) Use the command line version of R for the time being; and
> 2) Start the GUI R like this:
>
> Open Terminal.app (in /Applications/Utilities)
>
> then paste the following:
> export DYLD_FALLBACK_LIBRARY_PATH=/Library/Frameworks/R.framework/Resources/lib
> open /Applications/R.app
>
> Then loading the impute package should work. I need to get back to you
> with a better solution.
>
> Dan
>
>
>
>> This is what I get with the GUI:
>>> library(DNAcopy)
>>
>> Error in dyn.load(file, DLLpath = DLLpath, ...) :
>>   unable to load shared object
>> '/Library/Frameworks/R.framework/Versions/3.0/Resources/library/DNAcopy/libs/DNAcopy.so':
>>
>> dlopen(/Library/Frameworks/R.framework/Versions/3.0/Resources/library/DNAcopy/libs/DNAcopy.so,
>> 6): Library not loaded: /usr/local/lib/libgfortran.2.dylib
>>   Referenced from:
>> /Library/Frameworks/R.framework/Versions/3.0/Resources/library/DNAcopy/libs/DNAcopy.so
>>   Reason: image not found
>> Error: package or namespace load failed for ‘DNAcopy’
>>> sessionInfo()
>> R version 3.0.0 (2013-04-03)
>> Platform: x86_64-apple-darwin10.8.0 (64-bit)
>>
>> locale:
>> [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
>>
>> attached base packages:
>> [1] stats     graphics  grDevices utils     datasets  methods   base
>>
>> other attached packages:
>> [1] BiocInstaller_1.10.0
>>
>> loaded via a namespace (and not attached):
>> [1] tools_3.0.0
>>
>> Stephanie
>>
>>
>> On 4/10/13 2:41 PM, Peter Langfelder wrote:
>>>
>>> Hello,
>>>
>>> a user of my (CRAN) package WGCNA which depends on impute has a
>>> problem installing impute on his Mac OSX 10.8.3 under R 3.0.0. The
>>> problem seems to be loading the compiled libary impute.so. Can anyone
>>> please suggest a solution? Below is a transcript of his session.
>>>
>>> Thanks,
>>>
>>> Peter
>>>
>>>> biocLite("impute", lib = .libPaths())
>>>
>>> BioC_mirror: http://bioconductor.org
>>> Using Bioconductor version 2.12 (BiocInstaller 1.10.0), R version 3.0.0.
>>> Installing package(s) 'impute'
>>> trying URL
>>> 'http://bioconductor.org/packages/2.12/bioc/bin/macosx/contrib/3.0/impute_1.34.0.tgz'
>>> Content type 'application/x-gzip' length 652872 bytes (637 Kb)
>>> opened URL
>>> ==================================================
>>> downloaded 637 Kb
>>>
>>>
>>> The downloaded binary packages are in
>>>
>>> /var/folders/x_/wps51c0n0tx33tx406_xt9n80000gn/T//Rtmpd8CN5X/downloaded_packages
>>>>
>>>> library(impute)
>>>
>>> Error in dyn.load(file, DLLpath = DLLpath, ...) :
>>>    unable to load shared object
>>>
>>> '/Library/Frameworks/R.framework/Versions/3.0/Resources/library/impute/libs/impute.so':
>>>
>>> dlopen(/Library/Frameworks/R.framework/Versions/3.0/Resources/library/impute/libs/impute.so,
>>> 6): Library not loaded: /usr/local/lib/libgfortran.2.dylib
>>>    Referenced from:
>>>
>>> /Library/Frameworks/R.framework/Versions/3.0/Resources/library/impute/libs/impute.so
>>>    Reason: image not found
>>> Error: package or namespace load failed for ‘impute’
>>>
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>>
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