[Bioc-devel] dependency

[Vincent Carey]

This list probably doesn't get to the quantsmooth maintainer, carboning.

What do you mean by "plot chromosomes"?  See Gviz, geneplotter among others.

On Tue, Jun 26, 2012 at 11:11 AM, Stefano Berri <S.Berri at leeds.ac.uk> wrote:
> Hi.
>
> I wanted to install bioconductor package quantsmooth (see below)
>
> It looks that quantsmooth relies on lodplot which is not available
>
> ****
> Warning: dependency Œlodplot¹ is not available
> ****
>
> lodplot is on CRAN, but at that page (
> http://cran.r-project.org/web/packages/lodplot/index.html) it says
>
> ****
> Package Œlodplot¹ was removed from the CRAN repository.
>
> Formerly available versions can be obtained from the archive
> <http://cran.r-project.org/src/contrib/Archive/lodplot> .
>
> This package has been archived: it had check WARNINGs since R-2.14.0 (at
> least) and was not fixed for more than half a year even after reminders
> ****
>
> Now, what shall I do? I could install lodplot using the latest linked
> archive, but I wanted to write code that depended on quantsmooth and in this
> way everything will break. What will happen to quantsmooth?
>
> I could fix the warnings in the code (it looks there is no NAMESPACE and the
> package is relatively small) but I guess I won't be able to update CRAN,
> right? I can try to contact the author, but if he is not fixing the package
> it might be hard to reach or not interested anymore...
>
> Alternatively, is there an up to date package to plot chromosomes?
>
> Thanks
>
> Stefano
>
>
>
>> source("http://bioconductor.org/biocLite.R")
> BiocInstaller version 1.4.3, ?biocLite for help
>> biocLite("quantsmooth")
> BiocInstaller version 1.4.7, ?biocLite for help
> 'BiocInstaller' updated to version 1.4.7
> BioC_mirror: http://bioconductor.org
> Using R version 2.15, BiocInstaller version 1.4.7.
> Warning: unable to access index for repository
> http://brainarray.mbni.med.umich.edu/bioc/bin/macosx/leopard/contrib/2.15
> Installing package(s) 'quantsmooth'
> Warning: unable to access index for repository
> http://brainarray.mbni.med.umich.edu/bioc/bin/macosx/leopard/contrib/2.15
> Warning: dependency Œlodplot¹ is not available
> also installing the dependencies ŒSparseM¹, Œquantreg¹
>
> trying URL
> 'http://cran.fhcrc.org/bin/macosx/leopard/contrib/2.15/SparseM_0.96.tgz'
> Content type 'application/x-gzip' length 1203076 bytes (1.1 Mb)
> opened URL
> ==================================================
> downloaded 1.1 Mb
>
> trying URL
> 'http://cran.fhcrc.org/bin/macosx/leopard/contrib/2.15/quantreg_4.79.tgz'
> Content type 'application/x-gzip' length 2898654 bytes (2.8 Mb)
> opened URL
> ==================================================
> downloaded 2.8 Mb
>
> trying URL
> 'http://www.bioconductor.org/packages/2.10/bioc/bin/macosx/leopard/contrib/2
> .15/quantsmooth_1.22.0.tgz'
> Content type 'application/x-gzip' length 236545 bytes (231 Kb)
> opened URL
> ==================================================
> downloaded 231 Kb
>
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