[Bioc-devel] dependency

[Dan Tenenbaum]

CC'ing quantsmooth maintainer.

On Tue, Jun 26, 2012 at 8:19 AM, Vincent Carey
<stvjc at channing.harvard.edu> wrote:
> 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 This package has been archived: it had check WARNINGs since R-2.14.0 (at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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>
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