[BioC] Error installing development version of DESeq2
Dan Tenenbaum
dtenenba at fhcrc.org
Fri Jan 17 22:47:10 CET 2014
----- Original Message -----
> From: "Kristina M Fontanez" <fontanez at mit.edu>
> To: bioconductor at r-project.org
> Sent: Friday, January 17, 2014 1:36:48 PM
> Subject: [BioC] Error installing development version of DESeq2
>
> 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?
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
> My R session is
> pasted below.
>
> Kristina
>
> R version 3.0.2 (2013-09-25) -- "Frisbee Sailing"
> Copyright (C) 2013 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 (6558) x86_64-apple-darwin10.8.0]
>
> [History restored from /Users/fontanez/.Rapp.history]
>
> > 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 at mit.edu<mailto:fontanez at mit.edu>
> Massachusetts Institute of Technology
> Department of Civil and Environmental Engineering
> 48-120E
> 15 Vassar Street
> Cambridge, MA 02139
>
>
>
>
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>
>
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