[BioC] ggbio and R-2.14.0

[Martin Morgan]

On 01/16/2012 07:26 AM, Weiner, Michael wrote:
> I am trying to install ggbio on a server running 2.14.0 and I am running into issues when it attempts to install some of the dependencies for the ggbio package. Basically it revolves around the NAMESPACE issue for various packages that are dependencies for ggbio, as in the following:
>
>
>
> ** preparing package for lazy loading
>
> Error in library(pkg, character.only = TRUE, logical.return = TRUE, lib.loc = lib.loc) :
>
>    package âbitopsâ does not have a NAMESPACE and should be re-installed
>
> ERROR: lazy loading failed for package ârtracklayerâ
>
> * removing â/usr/lib64/R/library/rtracklayerâ
>
> ERROR: dependency ârtracklayerâ is not available for package âGenomicFeaturesâ
>
> * removing â/usr/lib64/R/library/GenomicFeaturesâ
>
> ERROR: dependency ârtracklayerâ is not available for package âRsamtoolsâ
>
> * removing â/usr/lib64/R/library/Rsamtoolsâ
>
> ERROR: dependencies âGenomicFeaturesâ, âRsamtoolsâ are not available for package âggbioâ
>
> * removing â/usr/lib64/R/library/ggbioâ
>
>
>
> Not being an R expert, just a systems administrator trying to upgrade and install this package for a researcher, I was wondering if there was an ETA on when ggbio might be updated OR if there are any other ways around this issue?  Should I upgrade to 2.14.1 ??

Hi Michael

Some of your packages are out of date, and some additional dependencies 
need to be installed. You should

   source("http://bioconductor.org/biocLite.R")
   biocLite(character()) ## to update old packages
   biocLite('ggbio")     ## to install new pkg and dependencies

It looks like perhaps other packages have not been installed correctly; 
I'd guess at biocLite('GenomicFeatures') as another step to iterate if 
ggbio continues to fail to install.

Martin

>
>
> Thank you all in advance
>
> Michael Weiner
>
> Lead Analyst/UNIX Systems Administrator
>
> Lerner Research Institute Computing Services
>
> Lerner Research Institute
>
> Cleveland Clinic
>
>
> ===================================
>
>   Please consider the environment before printing this e-mail
>
> Cleveland Clinic is ranked one of the top hospitals
> in America by U.S.News&  World Report (2010).
> Visit us online at http://www.clevelandclinic.org for
> a complete listing of our services, staff and
> locations.
>
>
> Confidentiality Note:  This message is intended for use\...{{dropped:16}}
>
>
>
>
> _______________________________________________
> Bioconductor mailing list
> Bioconductor at r-project.org
> https://stat.ethz.ch/mailman/listinfo/bioconductor
> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor


-- 
Computational Biology
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109

Location: M1-B861
Telephone: 206 667-2793