Dan-

Thank you for that insight. I downloaded the development version and kept around my stable 3.0 version as well. I was then able to successfully download the development version of DESeq. Although, I am nervous about encountering the “Unsuffered Consequences” promised in the title.

Thanks!

Kristina

R Under development (unstable) (2014-01-16 r64804) -- "Unsuffered Consequences"
Copyright (C) 2014 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin10.8.0 (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 1.62 (6623) x86_64-apple-darwin10.8.0]

[History restored from /Users/fontanez/.Rapp.history]

> source("http://bioconductor.org/biocLite.R")
trying URL 'http://www.bioconductor.org/packages/2.14/bioc/bin/macosx/contrib/3.1/BiocInstaller_1.13.3.tgz'
Content type 'application/x-gzip' length 49888 bytes (48 Kb)
opened URL
==================================================
downloaded 48 Kb


The downloaded binary packages are in
/var/folders/90/zq2q8_fs0355_g769gsx46bc0000gn/T//Rtmp56LETx/downloaded_packages
Bioconductor version 2.14 (BiocInstaller 1.13.3), ?biocLite for help
> biocLite("DESeq2")
BioC_mirror: http://bioconductor.org
Using Bioconductor version 2.14 (BiocInstaller 1.13.3), R version 3.1.0.
Installing package(s) 'DESeq2'
also installing the dependencies ‘DBI’, ‘RSQLite’, ‘xtable’, ‘XML’, ‘XVector’, ‘AnnotationDbi’, ‘annotate’, ‘Biobase’, ‘GenomicRanges’, ‘IRanges’, ‘Rcpp’, ‘RcppArmadillo’, ‘BiocGenerics’, ‘locfit’, ‘genefilter’, ‘geneplotter’, ‘RColorBrewer’
…..
> library(DESeq2)
Loading required package: GenomicRanges
Loading required package: BiocGenerics
Loading required package: parallel

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, append, as.data.frame, as.vector, cbind, colnames,
    do.call, duplicated, eval, evalq, Filter, Find, get, intersect,
    is.unsorted, lapply, Map, mapply, match, mget, order, paste, pmax,
    pmax.int, pmin, pmin.int, Position, rank, rbind, Reduce, rep.int,
    rownames, sapply, setdiff, sort, table, tapply, union, unique,
    unlist

Loading required package: IRanges
Loading required package: XVector
Loading required package: Rcpp
Loading required package: RcppArmadillo


On Jan 17, 2014, at 4:47 PM, Dan Tenenbaum <dtenenba@fhcrc.org<mailto:dtenenba@fhcrc.org>> wrote:

No. If you want to run the devel version of a package, you need to install the version of R that Bioc-devel is meant to run on, in this case R-devel a/k/a 3.1. You can have multiple versions of R on your machine, if you want.
For example, you could rename your current version so it's no longer used:
cd /Library/Frameworks
mv R.framework R.framework.release

Then download R-devel. Then when you are done using R-devel:

cd /Library/Frameworks
mv R.framework R.framework.devel
mv R.framework.release R.framework

Others have other preferred ways. I have bash aliases to help make this easier.

Dan






------------------------------------------------------------------
Kristina Fontanez, Postdoctoral Fellow
fontanez@mit.edu<mailto:fontanez@mit.edu>
Massachusetts Institute of Technology
Department of Civil and Environmental Engineering
48-120E
15 Vassar Street
Cambridge, MA 02139


	[[alternative HTML version deleted]]

