[BioC] Error installing impute package

Levi Waldron levi.waldron at hunter.cuny.edu
Fri Jun 13 03:22:47 CEST 2014


I just noticed this problem myself - not with impute itself, but
because WGCNA is not building in CRAN for Mavericks.  I guess CRAN
doesn't have linkable URLs, but here is the error message on the WGCNA
build check for Mavericks:

using R version 3.1.0 Patched (2014-06-11 r65921)
using platform: x86_64-apple-darwin13.1.0 (64-bit)
using session charset: UTF-8
checking for file 'WGCNA/DESCRIPTION' ... OK
this is package 'WGCNA' version '1.34'
checking package namespace information ... OK
checking package dependencies ... ERROR
Package required but not available: 'impute'

Packages suggested but not available for checking:
'GO.db' 'org.Hs.eg.db' 'org.Mm.eg.db' 'AnnotationDbi' 'minet'

See the information on DESCRIPTION files in the chapter 'Creating R
packages' of the 'Writing R Extensions' manual.


On Wed, Apr 10, 2013 at 6:55 PM, Peter Langfelder
<peter.langfelder at gmail.com> wrote:
> 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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>
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-- 
Levi Waldron
Assistant Professor of Biostatistics
City University of New York School of Public Health, Hunter College
2180 3rd Ave Rm 538
New York NY 10035-4003
phone: 212-396-7747
www.waldronlab.org



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