[BioC] failure to install: aCGH depends on unavailable package

[Ramon Diaz-Uriarte]

Dear Patrick,

Thanks a lot!


Best,

R.


On Friday 25 September 2009 19:10:03 Patrick Aboyoun wrote:
> Ramon,
> I am not sure what happened to the sma package on CRAN. It must have
> been removed from the repository over the past week since our build
> system had fresh installations last week and sma was still available. I
> e-mailed the package author and CRAN maintainer to find out why this
> change happened. I'll e-mail back my findings and what if any actions we
> in BioC will have to take.
> 
> 
> Patrick
> 
> Ramon Diaz-Uriarte wrote:
> > Dear All,
> >
> > I just noticed (failures installing a bunch of BioC packages in new R
> > installations) that aCGH depends on "sma", but sma is no longer
> > available. Thus, the recommended procedure
> >
> > source("http://bioconductor.org/biocLite.R")
> > biocLite("aCGH")
> > will fail. And any package which depends on aCGH (e.g., snapCGH) will
> > fail to install too.
> >
> > I guess this is a bug in sma but, if I understand correctly, it should
> > not be possible for a package to fail the standard installation procedure
> > for the stable release?
> >
> >
> >
> > Best,
> >
> > R.
> >
> > P.D. sma used to be available in CRAN, so it is possible to get an old
> > version from
> > http://cran.r-project.org/src/contrib/Archive/sma/
> > install that, and then install aCGH.
> >
> >
> > ### this is one example; it fails on at least two other different systems
> > too.
> >
> >> version
> >
> >                _
> > platform       x86_64-pc-linux-gnu
> > arch           x86_64
> > os             linux-gnu
> > system         x86_64, linux-gnu
> > status
> > major          2
> > minor          9.2
> > year           2009
> > month          08
> > day            24
> > svn rev        49384
> > language       R
> > version.string R version 2.9.2 (2009-08-24)
> >
> >
> > ------------------------------------------------------------------------
> >
> > _______________________________________________
> > Bioconductor mailing list
> > Bioconductor at stat.math.ethz.ch
> > https://stat.ethz.ch/mailman/listinfo/bioconductor
> > Search the archives:
> > http://news.gmane.org/gmane.science.biology.informatics.conductor
> 

-- 
Ramón Díaz-Uriarte
Biocomputing Programm
Centro Nacional de Investigaciones Oncológicas (CNIO)
(Spanish National Cancer Center)
Melchor Fernández Almagro, 3
28029 Madrid (Spain)
Fax: +-34-91-224-6972
Phone: +-34-91-224-6900

http://ligarto.org/rdiaz




**NOTA DE CONFIDENCIALIDAD** Este correo electrónico, y ...{{dropped:3}}