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

cstrato wrote:

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/") 

First, you don't want to state the version. By giving the repository 
you will automatically get the correct version.

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 

The above should have given you a big hint: What you gave as the 
repository ended up with 'bin/macosx/universal/contrib/2.6' added on 
the end. So two things are happening.

First, the repository you are giving is wrong -- install.packages() 
will add the specific directory to get the package, so remove the 
src/contrib/ from the end.

Second, you evidently want a source package, but you are not telling 
install.packages(), so it is trying to get the universal binary. Hint: 
type="source".

Best,

Jim

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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