[R] DESeq package install error

Martin Morgan
Tue, 06 Mar 2012 10:34:27 -0000

On 03/06/2012 02:20 AM, nathalie wrote:
> HI, I would like to update my DESeq package version on R-2-14 using
> bioclite() and get this message, could somebody help please?
>
>
>  > biocLite("DESeq")
> BioC_mirror: 'http://www.bioconductor.org'
> Using R version 2.14, BiocInstaller version 1.2.1.
> Installing package(s) 'DESeq'
> Installing package(s) into ?/nfs/team82/nac/R-modules?
> (as ?lib? is unspecified)
> trying URL
>
'http://www.bioconductor.org/packages/2.9/bioc/src/contrib/DESeq_1.6.1.tar.gz'
>
> Content type 'application/x-gzip' length 1853430 bytes (1.8 Mb)
> opened URL
> =================================================> downloaded 1.8 Mb
>
> * installing *source* package ?DESeq? ...
> ** libs
> cc -std=gnu99 -I/software/R-2.14.1/lib64/R/include -I/usr/local/include
> -fpic -O2 -c pval.c -o pval.o
> cc -std=gnu99 -shared -L/usr/local/lib64 -o DESeq.so pval.o
> -L/software/R-2.14.1/lib64/R/lib -lR
> installing to /nfs/team82/nac/R-modules/DESeq/libs
> ** R
> ** inst
> ** preparing package for lazy loading
> Error in library(pkg, character.only = TRUE, logical.return = TRUE,
> lib.loc = lib.loc) :
> package ?locfit? does not have a NAMESPACE and should be re-installed
> ERROR: lazy loading failed for package ?DESeq?
> * removing ?/nfs/team82/nac/R-modules/DESeq?

Hi Natalie -- please continue to ask questions about Bioconductor
packages on the Bioconductor mailing list. Have you tried to update
locfit, or more generally all of your currently installed packages?

   source("http://bioconductor.org/biocLite.R")
   biocLite('locfit")
   biocLite(character())

?

Martin

>
>
>


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