[Bioc-devel] How to install a package from bioC devel?
Dear Vincent Thank you, but this is not what I want. I would like to install the package from BioC devel in R-2.6.1. In: https://stat.ethz.ch/pipermail/bioc-devel/2008-January/001454.html Seth mentioned that it is possible to use install.packages for this purpose, but I get the error mentioned. Did I make a mistake or is the URL wrong? Best regards Christian
Vincent Carey 525-2265 wrote:
biocLite will install the devel version of the package if invoked from R devel (2.7.0 at this time) --- Vince Carey, PhD Assoc. Prof Med (Biostatistics) Harvard Medical School Channing Laboratory - ph 6175252265 fa 6177311541 181 Longwood Ave Boston MA 02115 USA stvjc at channing.harvard.edu On Wed, 16 Jan 2008, cstrato wrote:
Dear all, How can a user install a package from BioC devel? I have tried the following: 1. biocLite:
>
biocLite("http://www.bioconductor.org/packages/2.2/bioc/src/contrib/xps",
type="source")
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, :
package
'http://www.bioconductor.org/packages/2.2/bioc/src/contrib/xps' is not
available
2. install.package from BioC devel repository:
>
install.packages("xps_0.4.1.tar.gz",repos="http://www.bioconductor.org/packages/2.2/bioc/src/contrib/")
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
http://www.bioconductor.org/packages/2.2/bioc/src/contrib/bin/macosx/universal/contrib/2.6
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) i386-apple-darwin8.10.1 locale: C 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 Christian _._._._._._._._._._._._._._._._ 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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