[BioC] Error installing impute package
Peter Langfelder
peter.langfelder at gmail.com
Sat Jun 14 02:35:38 CEST 2014
Hi all,
Simon already installed impute on the Mavericks machine, per my
request. I just submitted a new version of WGCNA to CRAN and it should
be up in a day or two, hopefully including the Mavericks binary.
To the best of my knowledge Bioconductor packages are not necessarily
all installed on all CRAN machines, sometimes one has to ask for it
specifically.
Best,
Peter
On Fri, Jun 13, 2014 at 5:02 PM, Dan Tenenbaum <dtenenba at fhcrc.org> wrote:
> Hi Levi,
>
> ----- Original Message -----
>> From: "Levi Waldron" <levi.waldron at hunter.cuny.edu>
>> To: "Peter Langfelder" <peter.langfelder at gmail.com>
>> Cc: "Dan Tenenbaum" <dtenenba at fhcrc.org>, "Stephanie M. Gogarten" <sdmorris at u.washington.edu>,
>> bioconductor at r-project.org
>> Sent: Thursday, June 12, 2014 6:22:47 PM
>> Subject: Re: [BioC] Error installing impute package
>>
>> 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.
>>
>>
>
> The url is
>
> http://www.r-project.org/nosvn/R.check/r-release-osx-x86_64-mavericks/WGCNA-00check.html
>
> I have written to Simon Urbanek who is running the Mavericks CRAN builds and asked him about this. impute is available on all platforms so I don't think the problem is on the BioC end. That build report also says that other BioC packages in WGCNA's Suggests field are not available, but they all should be.
>
> Will let you know what I find out.
>
> Thanks,
> Dan
>
>
>> 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'
>> >>>>
>> >>>> _______________________________________________
>> >>>> Bioconductor mailing list
>> >>>> Bioconductor at r-project.org
>> >>>> https://stat.ethz.ch/mailman/listinfo/bioconductor
>> >>>> Search the archives:
>> >>>> http://news.gmane.org/gmane.science.biology.informatics.conductor
>> >>>>
>> >>>
>> >>> _______________________________________________
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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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