Mike-

I tried downloading the development version of DESeq2 following your directions but it didn’t work. It seems I have 2 problems, 1) I am not using the development version of R (3.1) and therefore this prevents me from using the development version of Bioconductor (2.14). Is that right? I don’t particularly want to use an unstable version of R. Can I get the development version of Bioconductor without having to use the development version of R? My R session is pasted below.

Kristina

R version 3.0.2 (2013-09-25) -- "Frisbee Sailing"
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[R.app GUI 1.62 (6558) x86_64-apple-darwin10.8.0]

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> source("http://bioconductor.org/biocLite.R")
Bioconductor version 2.13 (BiocInstaller 1.12.0), ?biocLite for help
> biocLite()
BioC_mirror: http://bioconductor.org
Using Bioconductor version 2.13 (BiocInstaller 1.12.0), R version 3.0.2.
> useDevel()
Error: 'devel' version requires a more recent R
> install.packages("DESeq2_1.3.28.tgz",repos=NULL)
> 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,
    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
Error in dyn.load(file, DLLpath = DLLpath, ...) :
  unable to load shared object '/Library/Frameworks/R.framework/Versions/3.0/Resources/library/DESeq2/libs/DESeq2.so':
  dlopen(/Library/Frameworks/R.framework/Versions/3.0/Resources/library/DESeq2/libs/DESeq2.so, 6): Library not loaded: /Library/Frameworks/R.framework/Versions/3.1/Resources/lib/libRlapack.dylib
  Referenced from: /Library/Frameworks/R.framework/Versions/3.0/Resources/library/DESeq2/libs/DESeq2.so
  Reason: image not found
In addition: Warning message:
package ‘DESeq2’ was built under R version 3.1.0
Error: package or namespace load failed for ‘DESeq2’
> traceback()
2: stop(gettextf("package or namespace load failed for %s", sQuote(package)),
       call. = FALSE, domain = NA)
1: library(DESeq2)
> sessionInfo()
R version 3.0.2 (2013-09-25)
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] parallel  stats     graphics  grDevices utils     datasets  methods
[8] base

other attached packages:
[1] RcppArmadillo_0.4.000 Rcpp_0.10.6           GenomicRanges_1.14.4
[4] XVector_0.2.0         IRanges_1.20.6        BiocGenerics_0.8.0
[7] BiocInstaller_1.12.0

loaded via a namespace (and not attached):
 [1] annotate_1.40.0      AnnotationDbi_1.24.0 Biobase_2.22.0
 [4] DBI_0.2-7            genefilter_1.44.0    geneplotter_1.40.0
 [7] grid_3.0.2           lattice_0.20-24      locfit_1.5-9.1
[10] RColorBrewer_1.0-5   RSQLite_0.11.4       splines_3.0.2
[13] stats4_3.0.2         survival_2.37-4      tools_3.0.2
[16] XML_3.95-0.2         xtable_1.7-1

------------------------------------------------------------------
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




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