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) :

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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]

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Then I installed easyRNASeq and got the following text and error message:

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==================================================
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
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’
> 

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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@cancercenter.columbia.edu
http://cancercenter.columbia.edu/~friedman/

In memoriam, Ray Bradbury


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