[Bioc-devel] How to install a package from bioC devel?

cstrato cstrato at aon.at
Wed Jan 16 20:55:51 CET 2008

Dear all,

How can a user install a package from BioC devel?

I have tried the following:

1. biocLite:
Running biocinstall version 2.1.8 with R version 2.6.1
Your version of R requires version 2.1 of Bioconductor.
Warning in install.packages(pkgs = pkgs, repos = repos, dependencies = 
dependencies,  :
  argument 'lib' is missing: using '/Users/rabbitus/Library/R/library'
Warning message:
In install.packages(pkgs = pkgs, repos = repos, dependencies = 
dependencies,  :
'http://www.bioconductor.org/packages/2.2/bioc/src/contrib/xps' is not 

2. install.package from BioC devel repository:
Warning in install.packages("xps_0.4.1.tar.gz", repos = 
"http://www.bioconductor.org/packages/2.2/bioc/src/contrib/") :
  argument 'lib' is missing: using '/Users/rabbitus/Library/R/library'
Warning: unable to access index for repository 
Warning message:
package 'xps_0.4.1.tar.gz' is not available

3. download the package and use install.package locally:
 > install.packages("/Volumes/CoreData/CRAN/xps_0.4.1.tar.gz",repos=NULL)
Warning in install.packages("/Volumes/CoreData/CRAN/xps_0.4.1.tar.gz", 
repos = NULL) :
  argument 'lib' is missing: using '/Users/rabbitus/Library/R/library'
Error in gzfile(file, "r") : unable to open connection
In addition: Warning message:
In gzfile(file, "r") :
  cannot open compressed file 'xps_0.4.1.tar.gz/DESCRIPTION'

As you see, none of the methods that I have tried works.
Is the URL of the BioC devel repository correct?
Why does the local installation not work?

The only installation method that works is:
R CMD INSTALL -l ~/Library/R/library xps_0.4.1.tar.gz

 > sessionInfo()
R version 2.6.1 (2007-11-26)


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

loaded via a namespace (and not attached):
[1] rcompgen_0.1-17 tools_2.6.1

Best regards
C.h.i.s.t.i.a.n S.t.r.a.t.o.w.a
V.i.e.n.n.a       A.u.s.t.r.i.a
e.m.a.i.l:    cstrato at aon.at

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