Re: [Bioc-devel] vectorize default dist2 function in genefilter

2013-03-13 Thread James F. Reid
Hi Wolfgang, On 12/03/13 21:11, Wolfgang Huber wrote: Dear James Thank you. What would the saved time be (e.g. compared to the overall runtime of arrayQualityMetrics)? I would be surprised if the saving was worth the added complexity, but am always happy to be surprised. I believe so but

Re: [Bioc-devel] vectorize default dist2 function in genefilter

2013-03-13 Thread James F. Reid
Hi Wolfgang, On 12/03/13 21:11, Wolfgang Huber wrote: Dear James Thank you. What would the saved time be (e.g. compared to the overall runtime of arrayQualityMetrics)? I would be surprised if the saving was worth the added complexity, but am always happy to be surprised. I believe so but

[Bioc-devel] Recent issue with plot method dispatch

2013-03-13 Thread Joern Toedling
Hello, I have encountered a strange issue with the plotting function in my package girafe that I need some help with. I haven't changed anything in the plot methods or the NAMESPACE of the package recently, and it worked before, yet I observe the following error now. When calling the plot

Re: [Bioc-devel] Recent issue with plot method dispatch

2013-03-13 Thread Dan Tenenbaum
On Wed, Mar 13, 2013 at 4:02 AM, Joern Toedling j.toedl...@imb-mainz.de wrote: Hello, I have encountered a strange issue with the plotting function in my package girafe that I need some help with. I haven't changed anything in the plot methods or the NAMESPACE of the package recently, and it

Re: [Bioc-devel] Recent issue with plot method dispatch

2013-03-13 Thread Nikolas Pontikos
Have a look at showMethods(), see if your method shows up in the registry. See Access to the Registry section of this presentation for more information: http://www.r-project.org/conferences/useR-2004/Keynotes/Leisch.pdf On 13 March 2013 16:59, Dan Tenenbaum dtene...@fhcrc.org wrote: On Wed,

Re: [Bioc-devel] Recent issue with plot method dispatch

2013-03-13 Thread Martin Morgan
On 03/13/2013 04:02 AM, Joern Toedling wrote: Hello, I have encountered a strange issue with the plotting function in my package girafe that I need some help with. I haven't changed anything in the plot methods or the NAMESPACE of the package recently, and it worked before, yet I observe the

[Bioc-devel] Custom CRAN repository in biocLite.R not working

2013-03-13 Thread Cristobal Fresno Rodríguez
Greetings!! I am trying to use a local CRAN and Bioconductor repository for academic purposes. In this context, in biocLite.R script at bioconductor.org suggests to use: options(repos = http://localCRANsite;) options(BioC_mirror = http://localBioconductorSite;)

Re: [Bioc-devel] Custom CRAN repository in biocLite.R not working

2013-03-13 Thread Dan Tenenbaum
On Wed, Mar 13, 2013 at 1:37 PM, Cristobal Fresno Rodríguez cristobalfre...@gmail.com wrote: Dear Dan The solution you suggested did the trick. In addition I also tried options(repos = c(CRAN=http://mycranmirror;)) which successfully did the trick in changing biocinstallRepos() output. I