[Bioc-devel] error message upon installing easyRNASeq
Martin Morgan
mtmorgan at fhcrc.org
Wed Nov 14 15:16:42 CET 2012
On 11/13/2012 02:19 PM, Richard Friedman wrote:
> Dear Bioconductor Developers,
>
> This is my first experience with the development versions of
> Bioconductor and R.
> Some time ago, Nicolas Delhomme recommended that I install
> the development version of easyRNASeq to be able to take advantage
> of some new features. I just got back to the project today and found
> that I had to install the development version of R to run the development
> version of easyRNASeq, I installed R version 2.16.0 (I have a Mac
> OS X, 10.7.5) :
>
> ##################################################################
>
> R Under development (unstable) (2012-11-12 r61105) -- "Unsuffered Consequences"
> Copyright (C) 2012 The R Foundation for Statistical Computing
> ISBN 3-900051-07-0
> Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit)
>
> R is free software and comes with ABSOLUTELY NO WARRANTY.
> You are welcome to redistribute it under certain conditions.
> Type 'license()' or 'licence()' for distribution details.
>
> Natural language support but running in an English locale
>
> R is a collaborative project with many contributors.
> Type 'contributors()' for more information and
> 'citation()' on how to cite R or R packages in publications.
>
> Type 'demo()' for some demos, 'help()' for on-line help, or
> 'help.start()' for an HTML browser interface to help.
> Type 'q()' to quit R.
>
> [R.app GUI 1.53 (6347) x86_64-apple-darwin9.8.0]
>
> [Workspace restored from /Users/friedman/.RData]
> [History restored from /Users/friedman/.Rapp.history]
>
> ##################################################################
>
> Then I installed easyRNASeq and got the following text and error message:
>
> ###################################################################
>
> ==================================================
> downloaded 35.3 Mb
>
> trying URL 'http://www.bioconductor.org/packages/2.12/bioc/bin/macosx/leopard/contrib/2.16/easyRNASeq_1.5.1.tgz'
> Content type 'application/x-gzip' length 638451 bytes (623 Kb)
> opened URL
> ==================================================
> downloaded 623 Kb
>
>
> The downloaded binary packages are in
> /var/folders/9d/pv_lg9dx2s53pqh37v5ln0xs5pvd_d/T//RtmpaV8ra6/downloaded_packages
> Loading required package: parallel
> Loading required package: genomeIntervals
> Loading required package: intervals
> Loading required package: BiocGenerics
>
> Attaching package: ‘BiocGenerics’
>
> The following objects are masked from ‘package:parallel’:
>
> clusterApply, clusterApplyLB, clusterCall, clusterEvalQ, clusterExport, clusterMap, parApply,
> parCapply, parLapply, parLapplyLB, parRapply, parSapply, parSapplyLB
>
> The following object is masked from ‘package:stats’:
>
> xtabs
>
> The following objects are masked from ‘package:base’:
>
> anyDuplicated, cbind, colnames, duplicated, eval, Filter, Find, get, intersect, lapply, Map,
> mapply, mget, order, paste, pmax, pmax.int, pmin, pmin.int, Position, rbind, Reduce, rep.int,
> rownames, sapply, setdiff, table, tapply, union, unique
>
> Loading required package: Biobase
> Welcome to Bioconductor
>
> Vignettes contain introductory material; view with 'browseVignettes()'. To cite Bioconductor,
> see 'citation("Biobase")', and for packages 'citation("pkgname")'.
>
> Loading required package: biomaRt
> Error in dyn.load(file, DLLpath = DLLpath, ...) :
> unable to load shared object '/Library/Frameworks/R.framework/Versions/2.16/Resources/library/RCurl/libs/x86_64/RCurl.so':
> dlopen(/Library/Frameworks/R.framework/Versions/2.16/Resources/library/RCurl/libs/x86_64/RCurl.so, 6): Library not loaded: /Library/Frameworks/R.framework/Versions/2.15/Resources/lib/libR.dylib
> Referenced from: /Library/Frameworks/R.framework/Versions/2.16/Resources/library/RCurl/libs/x86_64/RCurl.so
> Reason: image not found
> In addition: Warning messages:
> 1: replacing previous import ‘coerce’ when loading ‘intervals’
> 2: replacing previous import ‘initialize’ when loading ‘intervals’
> Error: package ‘biomaRt’ could not be loaded
>> sessionInfo()
> R Under development (unstable) (2012-11-12 r61105)
> Platform: x86_64-apple-darwin9.8.0/x86_64 (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] parallel stats graphics grDevices utils datasets methods base
>
> other attached packages:
> [1] Biobase_2.19.0 genomeIntervals_1.15.0 BiocGenerics_0.5.1 intervals_0.13.3
> [5] BiocInstaller_1.9.4
>
> loaded via a namespace (and not attached):
> [1] tools_2.16.0
> Error in dyn.load(file, DLLpath = DLLpath, ...) :
> unable to load shared object '/Library/Frameworks/R.framework/Versions/2.16/Resources/library/RCurl/libs/x86_64/RCurl.so':
> dlopen(/Library/Frameworks/R.framework/Versions/2.16/Resources/library/RCurl/libs/x86_64/RCurl.so, 6): Library not loaded: /Library/Frameworks/R.framework/Versions/2.15/Resources/lib/libR.dylib
> Referenced from: /Library/Frameworks/R.framework/Versions/2.16/Resources/library/RCurl/libs/x86_64/RCurl.so
> Reason: image not found
I think this is at the root of your problem. It implies that RCurl was not
installed correctly. How did you install it, and if not using biocLite, what does
source("http://bioconductor.org/biocLite.R")
biocLite("RCurl")
say (in full)?
Martin
> Error: package or namespace load failed for ‘biomaRt’
> Error in dyn.load(file, DLLpath = DLLpath, ...) :
> unable to load shared object '/Library/Frameworks/R.framework/Versions/2.16/Resources/library/RCurl/libs/x86_64/RCurl.so':
> dlopen(/Library/Frameworks/R.framework/Versions/2.16/Resources/library/RCurl/libs/x86_64/RCurl.so, 6): Library not loaded: /Library/Frameworks/R.framework/Versions/2.15/Resources/lib/libR.dylib
> Referenced from: /Library/Frameworks/R.framework/Versions/2.16/Resources/library/RCurl/libs/x86_64/RCurl.so
> Reason: image not found
> Error: package or namespace load failed for ‘biomaRt’
>>
>
> ###################################################################
>
> It sounds ilke some of these things have to be fixed before i try easyRNAseq,
> I would appreciate any suggestions. Also, I am out of my depth
> working with the development version and am wondering if the most
> advanced version easyRNAseq on the bioconductor page (as distinct from
> the one downloaded from the GUI in the stable release of R)
> should work with the stable release of R, thereby saving me from these difficulties.
> Again, I would appreciate any suggestions.
>
> Thanks and best wishes,
> Rich
> Richard A. Friedman, PhD
> Associate Research Scientist,
> Biomedical Informatics Shared Resource
> Herbert Irving Comprehensive Cancer Center (HICCC)
> Lecturer,
> Department of Biomedical Informatics (DBMI)
> Educational Coordinator,
> Center for Computational Biology and Bioinformatics (C2B2)/
> National Center for Multiscale Analysis of Genomic Networks (MAGNet)
> Room 824
> Irving Cancer Research Center
> Columbia University
> 1130 St. Nicholas Ave
> New York, NY 10032
> (212)851-4765 (voice)
> friedman at cancercenter.columbia.edu
> http://cancercenter.columbia.edu/~friedman/
>
> In memoriam, Ray Bradbury
>
>
> [[alternative HTML version deleted]]
>
>
>
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>
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