[BioC] Error installing impute package

[Dan Tenenbaum]

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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