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

[cstrato]

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