[Bioc-devel] Error in DESeq Installation

Obenchain, Valerie Valerie.Obenchain at roswellpark.org
Tue Oct 25 16:11:14 CEST 2016


I'm not having problems installing DESeq with Bioconductor 3.4 and R
3.3.1. Please try installing the package in a fresh R session, show the
commands you ran and the output of sessionInfo(). Here's mine:

> sessionInfo()
R version 3.3.1 (2016-06-21)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Fedora 24 (Workstation Edition)

 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C             
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8   
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                
 [9] LC_ADDRESS=C               LC_TELEPHONE=C           

attached base packages:
[1] parallel  stats4    stats     graphics  grDevices utils     datasets
[8] methods   base    

other attached packages:
[1] BiocInstaller_1.24.0 reactome.db_1.58.0   AnnotationDbi_1.36.0
[4] IRanges_2.8.0        S4Vectors_0.12.0     Biobase_2.34.0     
[7] BiocGenerics_0.20.0

loaded via a namespace (and not attached):
[1] tools_3.3.1   DBI_0.5-1     RSQLite_1.0.0

As for the 'upgrade' error, Bioconductor 3.4 (release) is the most
recent version that can be run with R 3.3.1 so it can't upgrade. If you
want to use Bioconductor 3.5 (devel) you need to install a newer version
of R. See this page for details:



On 10/24/2016 01:37 AM, Yogesh Gupta wrote:
> Dear All,
> I am getting error in DESeq installation in R.
> package ‘DESeq’ is not available (for R version 3.3.1)
>> source("http://www.Bioconductor.org/biocLite.R
> <http://www.bioconductor.org/biocLite.R>")
> Bioconductor version 3.4 (BiocInstaller 1.24.0), ?biocLite for help
>> biocLite("BiocUpgrade")
> Error: Bioconductor version 3.4 cannot be upgraded with R version 3.3.1
> Can you suggest me I How I can resolve it.
> Thanks
> Yogesh
> *Yogesh Gupta*
> *Postdoctoral Researcher*
> *Department of Biological Science*
> *Seoul National University*
> *Seoul, South Korea*
> web) http://biosci.snu.ac.kr/jiyounglee
> *Cell No. +82-10-6453-0716*
> 	[[alternative HTML version deleted]]
> _______________________________________________
> Bioc-devel at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel

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