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
--
Computational Biology
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109
Location: M1-B861
Telephone: 206 667-2793
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