[BioC] getAnnMap: package hgu95av2 not available

elva chen [guest] guest at bioconductor.org
Mon Jan 28 07:38:04 CET 2013


Hi, 
I am following the Bioconductor Case studies.  I got:
Error: getAnnMap: package hgu95av2 not available

After appling the code:
 filt_bcrneg = nsFilter(ALL_bcrneg, require.entrez=TRUE, 
     require.GOBP=TRUE, remove.dupEntrez=TRUE,
     var.func=IQR, var.cutoff=varCut, 
     feature.exclude="^AFFX")

Did I miss anything? How can I get the hgu95av2?

thanks,
elva

 -- output of sessionInfo(): 

> varCut=0.5
> filt_bcrneg = nsFilter(ALL_bcrneg, require.entrez=TRUE, 
+     require.GOBP=TRUE, remove.dupEntrez=TRUE,
+     var.func=IQR, var.cutoff=varCut, 
+     feature.exclude="^AFFX")
Error: getAnnMap: package hgu95av2 not available
> help(package="hgu95av2")
starting httpd help server ... done
> help(package="hgu95av2")
> source("http://bioconductor.org/biocLite.R")
> biocLite("hgu95av2.db")
BioC_mirror: http://bioconductor.org
Using Bioconductor version 2.11 (BiocInstaller 1.8.3), R version 2.15.
Installing package(s) 'hgu95av2.db'
also installing the dependency ‘org.Hs.eg.db’

trying URL 'http://bioconductor.org/packages/2.11/data/annotation/bin/windows/contrib/2.15/org.Hs.eg.db_2.8.0.zip'
Content type 'application/zip' length 47453600 bytes (45.3 Mb)
opened URL
downloaded 45.3 Mb

trying URL 'http://bioconductor.org/packages/2.11/data/annotation/bin/windows/contrib/2.15/hgu95av2.db_2.8.0.zip'
Content type 'application/zip' length 552365 bytes (539 Kb)
opened URL
downloaded 539 Kb

package ‘org.Hs.eg.db’ successfully unpacked and MD5 sums checked
Warning: unable to move temporary installation ‘C:\Users\yahuac\Documents\R\win-library\2.15\file1a387065468\org.Hs.eg.db’ to ‘C:\Users\yahuac\Documents\R\win-library\2.15\org.Hs.eg.db’
package ‘hgu95av2.db’ successfully unpacked and MD5 sums checked

The downloaded binary packages are in
        C:\Users\yahuac\AppData\Local\Temp\RtmpK8N0Jl\downloaded_packages
Warning message:
installed directory not writable, cannot update packages 'foreign', 'lattice',
  'MASS', 'Matrix', 'nlme', 'rpart', 'survival' 
> filt_bcrneg = nsFilter(ALL_bcrneg, require.entrez=TRUE, 
+     require.GOBP=TRUE, remove.dupEntrez=TRUE,
+     var.func=IQR, var.cutoff=varCut, 
+     feature.exclude="^AFFX")
Error: getAnnMap: package hgu95av2 not available


--
Sent via the guest posting facility at bioconductor.org.



More information about the Bioconductor mailing list