[BioC] Unable to install package

[Arturo]

Thank you very much Dan.

I installed version 3.0.0 alpha and tried again:

> source("http://bioconductor.org/biocLite.R")
> biocLite("CAGEr")
BioC_mirror: http://bioconductor.org
Using Bioconductor version 2.12 (BiocInstaller 1.9.8), R version 3.0.0.
Installing package(s) 'CAGEr'

   package ‘CAGEr’ is available as a source package but not as a binary

Warning message:
package ‘CAGEr’ is not available (for R version 3.0.0 alpha) 

Then I tried installing it from the source as follows:

install.packages("/path/CAGEr_0.99.1.tar", repos = NULL, type="source")
ERROR: dependencies ‘BSgenome’, ‘BSgenome.Mmusculus.UCSC.mm9’, ‘Rsamtools’, 
‘GenomicRanges’,‘IRanges’, ‘beanplot’, ‘rtracklayer’, ‘som’, ‘VGAM’ are not
available for package ‘CAGEr’ 
*removing‘/Library/Frameworks/R.framework/Versions/3.0/Resources
/library/CAGEr’
Warning message:
In install.packages("/path/CAGEr_0.99.1.tar",  :
  installation of package ‘/path/CAGEr_0.99.1.tar’ had non-zero exit status

I tried installing those dependencies using the normal:
>source("http://bioconductor.org/biocLite.R")
>biocLite("IRanges")

It however gives me the same error, that -package ‘IRanges’ is available as a
source package but not as a binary-.
So I am assuming I have to install all dependencies from the source. Is there 
a way to automatize this? so that R searches for the dependencies by itself 
instead of doing one by one manually? 

Thank you very much for your help.


Dan Tenenbaum <dtenenba at ...> writes:

> 
> On Tue, Mar 19, 2013 at 7:35 AM, Arturo Mora [guest]
> <guest at ...> wrote:
> >
> > Hello,
> >
> > I am currently trying to install package "CAGEr" with the described commands 
but I got the following 
errors:
> >
> >> source("http://bioconductor.org/biocLite.R")
> >> biocLite("CAGEr")
> > BioC_mirror: http://bioconductor.org
> > Using Bioconductor version 2.11 (BiocInstaller 1.8.3), R version 2.15.
> > Installing package(s) 'CAGEr'
> > Warning message:
> > package ‘CAGEr’ is not available (for R version 2.15.3)
> >
> > I also tried doing:
> > install.packages("CAGEr", repos = "http://bioconductor.org/biocLite.R")
> > Warning: unable to access index for repository 
http://bioconductor.org/biocLite.R/bin/macosx/leopard/contrib/2.15
> > Warning message:
> > package ‘CAGEr’ is not available (for R version 2.15.3)
> >
> > Your help will be greatly appreciated.
> > Regards,
> > Arturo
> >
> >  -- output of sessionInfo():
> >
> >> sessionInfo()
> > R version 2.15.3 (2013-03-01)
> > Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit)
> >
> > locale:
> > [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
> >
> > attached base packages:
> > [1] stats     graphics  grDevices utils     datasets  methods   base
> >
> > other attached packages:
> > [1] BiocInstaller_1.8.3
> >
> > loaded via a namespace (and not attached):
> > [1] tools_2.15.3
> >
> >
> 
> This package was added to Bioconductor 2.12 and you are using
> Bioconductor 2.11. You can wait for 2.12 to be released in a few
> weeks, or install it as the devel version:
> 
> http://bioconductor.org/developers/useDevel/
> 
> Dan
> 
> > --
> > Sent via the guest posting facility at bioconductor.org.
> >
> > _______________________________________________
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