[Rd] R Package Installation Ignores libPaths Setting

2016-02-17 Thread Dario Strbenac
Good day, If the library path is changed with .libPaths, the command install.packages("/nb/dario/Biostrings_2.39.9.tar.gz", repos=NULL) fails with ** testing if installed package can be loaded Error : package ‘S4Vectors’ required by ‘Biostrings’ could not be found However, running

[Bioc-devel] specify the color in plotMutationSpectrum() of SomaticSignatures library

2016-02-17 Thread sun
Hi All, How can I specify the color that I would like to use in plotMutationSpectrum()? eg. plotMutationSpectrum(sca_motifs, "study", normalize = TRUE), I would like to only use "red" color here, how should I do? Thanks, Rebecca [[alternative HTML version deleted]]

[Bioc-devel] GenVisR Release

2016-02-17 Thread Zach Skidmore
GenVisR is now available for use on the devel branch. GenVisR Is designed to produce highly customizable graphical representations of genomic sequence data, focused primarily on cohort-level visuals. Visuals fall into three broad categories, "small variants" (snvs/indels), sturcutral

Re: [R-pkg-devel] Namespace error

2016-02-17 Thread peter dalgaard
On 17 Feb 2016, at 10:25 , Gábor Csárdi wrote: > On Wed, Feb 17, 2016 at 1:04 AM, Duncan Murdoch > wrote: >> On 16/02/2016 12:14 PM, Glenn Schultz wrote: >>> >>> All >>> >>> I am not sure why I am getting this error and I cannot find anything

Re: [R-pkg-devel] Namespace error

2016-02-17 Thread Gábor Csárdi
On Wed, Feb 17, 2016 at 1:04 AM, Duncan Murdoch wrote: > On 16/02/2016 12:14 PM, Glenn Schultz wrote: >> >> All >> >> I am not sure why I am getting this error and I cannot find anything on >> the net other than try to restart R. I am >> using Roxygen2 and it clearly