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[Bioc-devel] dependency

3 messages · Stefano Berri, Vincent Carey, Dan Tenenbaum

Original
Stefano Berri
# 
Hi. 

I wanted to install bioconductor package quantsmooth (see below)

It looks that quantsmooth relies on lodplot which is not available

****
Warning: dependency ?lodplot? is not available
****

lodplot is on CRAN, but at that page (
http://cran.r-project.org/web/packages/lodplot/index.html) it says

****
Package ?lodplot? 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This package has been archived: it had check WARNINGs since R-2.14.0 (at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
BiocInstaller version 1.4.3, ?biocLite for help
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 ?lodplot? is not available
also installing the dependencies ?SparseM?, ?quantreg?

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
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:
Dan Tenenbaum
# 
CC'ing quantsmooth maintainer.

On Tue, Jun 26, 2012 at 8:19 AM, Vincent Carey
<stvjc at channing.harvard.edu> wrote: