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

[Vincent Carey 525-2265]

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
> _._._._._._._._._._._._._._._._
>
> _______________________________________________
> Bioc-devel at stat.math.ethz.ch mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>

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