[BioC] Error installing development version of DESeq2
Steve Lianoglou
lianoglou.steve at gene.com
Fri Jan 17 23:05:04 CET 2014
Hi,
Perhaps a more user-friendly way to run w/ both versions is to simply
install the R-devel *.pkg available from http://r.research.att.com
specifically:
http://r.research.att.com/snowleopard/R-devel/R-devel-snowleopard-signed.pkg
Make sure you pay close attention to the installer and follow the
instructions provided in the splash window so that the installation
doesn't blow out your current (release) install (this will involve
running some command from the terminal that has to do w/ the install
receipts, or something).
Then, to switch between R and R-devel, you "simply" use the RSwitch
app available from the same site:
http://r.research.att.com/RSwitch-1.2.dmg
Which is an app front end w/ simply does some swapping of symlinks so
that the right links point to the right version of R that you want to
run.
Note that I believe this approach isn't amenable to running both
versions of R *at the same time.*
-steve
On Fri, Jan 17, 2014 at 1:47 PM, Dan Tenenbaum <dtenenba at fhcrc.org> wrote:
>
>
> ----- 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
>>
>>
>>
>>
>> [[alternative HTML version deleted]]
>>
>>
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>
> _______________________________________________
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--
Steve Lianoglou
Computational Biologist
Genentech
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