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Arturo
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10
@arturo-5836
Last seen 9.7 years ago
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.
> >
> > _______________________________________________
> > Bioconductor mailing list
> > Bioconductor at ...
> > https://stat.ethz.ch/mailman/listinfo/bioconductor
> > Search the archives:
http://news.gmane.org/gmane.science.biology.informatics.conductor
>
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