[BioC] Unable to install package

[Dan Tenenbaum]

On Wed, Mar 20, 2013 at 4:42 AM, Arturo <arturo.mora at kaust.edu.sa> wrote:
> 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?
>


Yes:
biocLite("CAGEr", type="source")
Will install CAGEr and all its dependencies from source.
Dan


> 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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>>
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>
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