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
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)
fried...@cancercenter.columbia.edu
http://cancercenter.columbia.edu/~friedman/
In memoriam, Ray Bradbury
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