[Bioc-devel] check error in SeqVarTools

2019-04-29 Thread Stephanie Gogarten
Hi, I see that SeqVarTools has an error in check on malbec2, after passing checks for a week with no changes to the code. This is a result of a unit test which generates random numbers; once in a while a particular set of random numbers ends up generating a missing value in a calculation which cau

Re: [Bioc-devel] RankProd package update

2019-04-29 Thread Turaga, Nitesh
Hi, You are not listed on the package as a maintainer, even though the DESCRIPTION page shows it. Fangxin Hong http://jimmy.harvard.edu>> is listed as maintainer. I will change the maintainer to you at the email your provided. I will send your a new BiocCredentials app account details privately

[Bioc-devel] ensembl 96 gtfs and fasta twobits have been added to AnnotationHub

2019-04-29 Thread Shepherd, Lori
We apologize for the delay: The ensembl 96 gtf (converted to GRanges on the fly) and fasta (twobit files) been added to AnnotationHub and are currently available in Bioc 3.9 > library(AnnotationHub) > hub = AnnotationHub() snapshotDate(): 2019-04-29 > length(query(hub, c("ensembl", "gtf", "relea

Re: [Bioc-devel] Error: invalid graphics state in creating vignettes

2019-04-29 Thread Jianhong Ou, Ph.D.
Hi Sunyoung, Sorry for the change of motifStack which makes you struggling. Please have a try following codes for plotting: pushViewport(viewport(y =unit(.5, "npc") - unit(2, "lines"), height = unit(1, "npc") - unit(3, "lines"))) pushViewport(viewport(y=.875, height=.25)) plotMotifLogo(pcm2

Re: [Bioc-devel] When to use generics?

2019-04-29 Thread Michael Lawrence via Bioc-devel
On Mon, Apr 29, 2019 at 6:55 AM Pages Gallego, M. < m.pagesgall...@umcutrecht.nl> wrote: > Dear all, > > I am currently developing a package and I am a bit confused in when one > should define a generic. Let me propose an example: > Suppose I have defined 3 classes: one for proteomics data, one fo

[Bioc-devel] When to use generics?

2019-04-29 Thread Pages Gallego, M.
Dear all, I am currently developing a package and I am a bit confused in when one should define a generic. Let me propose an example: Suppose I have defined 3 classes: one for proteomics data, one for metabolomics data and one for transcriptomics data. I have a function “foo(x)” that will do th

[Bioc-devel] RankProd package update

2019-04-29 Thread Francesco Del Carratore
Dear Bioconductor team, I am the maintainer of the RankProd package and I have just realized that the citation reported in the website is incorrect. I am trying to activate my Bioconductor Git Credentials in order to make this change, but it tells me that my email (francescod...@gmail.com) is not a