Re: [Bioc-devel] Using LaTeX packages in vignettes

Hi, On 03/30/2017 03:20 AM, Janssen-10, R.R.E. wrote: > Hello all, > > We wrote our vignette in Sweave/LaTeX, and I am running into a problem with > citing to other papers. > I would like to use the APA style of citing which looks like: "Determine the > optimal factorization rank using the NMF

Re: [Bioc-devel] condition tests on vectors with length greater than 1

Hi Martin, My apologies to Tomas Kalibera. I read too fast and missed the part where you gave him credit for the report. As I wrote in my previous email, I have started a significant clean-up of the GOexpress package to improve both the coding standards and the user experience. I haven't reached

Re: [Bioc-devel] condition tests on vectors with length greater than 1

On 03/31/2017 08:21 AM, Kevin RUE wrote: Hi Martin, Thanks a lot for systematically identifying the issue. Looking at the issue for GOexpress now, I realise that the issue is not in GOexpress itself, but actually within the VennDiagram package that GOexpress imports. You actually captured that

[Bioc-devel] Bioconductor 3.5 release: March 31 deadlines

Hi all, Reminder that today (March 31) is the last day for new package submissions. I've run into a few problems generating the db0 annotation packages so unfortunately they won't be ready today - I'm hoping Monday at the latest. http://www.bioconductor.org/developers/release-schedule/

Re: [Bioc-devel] masking functions

That took care of it. Thank you, Vincent. From: Vincent Carey [mailto:st...@channing.harvard.edu] Sent: Friday, March 31, 2017 5:37 AM To: Zimmermann, Michael T., Ph.D. Cc: bioc-devel@r-project.org Subject: Re: [Bioc-devel] masking functions in the NAMESPACE file import(gplots)

Re: [Bioc-devel] Error in veracruz2: object 'R_svmtrain' not found

Hi, Looks like this was a glitch in rtracklayer and has been fixed: r127902 | m.lawrence | 2017-03-31 04:37:23 -0700 (Fri, 31 Mar 2017) | 2 lines do not try to import pmapFromTranscripts from GenomicAlignments My guess is

Re: [Bioc-devel] condition tests on vectors with length greater than 1

Hi Martin, Thanks a lot for systematically identifying the issue. Looking at the issue for GOexpress now, I realise that the issue is not in GOexpress itself, but actually within the VennDiagram package that GOexpress imports. You actually captured that in your report:

Re: [Bioc-devel] Question about R functions

And note the existence of the "Internal" keyword for documentation: http://www.hep.by/gnu/r-patched/r-exts/R-exts_50.html On Fri, Mar 31, 2017 at 5:35 AM, Wolfgang Huber wrote: > > Thanks Juan; the .point used to be a way to do this, but since the > introduction of

Re: [Bioc-devel] masking functions

in the NAMESPACE file import(gplots) import(plotrix, except=plotCI) can help avoid the warning you mention. If this is not a solution for you you will have to provide more details. On Fri, Mar 31, 2017 at 1:07 AM, Zimmermann, Michael T., Ph.D. < zimmermann.mich...@mayo.edu> wrote: > Dear

Re: [Bioc-devel] Cannot find SummarizedExperiment's function assays()

On 03/31/2017 05:29 AM, Sokratis Kariotis wrote: Hey all, Following your advice, the package now builds successfully! However, I got this error while checking: * checking package dependencies ... ERROR Namespace dependency not required: ‘SummarizedExperiment’ Should I add /Imports

Re: [Bioc-devel] Question about R functions

Thanks Juan; the .point used to be a way to do this, but since the introduction of namespaces to R, it is neither necessary nor sufficient for private functions. See e.g. .Hub in the AnnotationHub package, or the .Call function in base. See

Re: [Bioc-devel] Cannot find SummarizedExperiment's function assays()

Hey all, Following your advice, the package now builds successfully! However, I got this error while checking: * checking package dependencies ... ERROR Namespace dependency not required: ‘SummarizedExperiment’ Should I add *Imports :**SummarizedExperiment* in my DESCRIPTION file? Regards,

[Bioc-devel] Error in veracruz2: object 'R_svmtrain' not found

Hi, My package DaMiRseq fails to build in veracruz2 server with this error: Quitting from lines 424-428 (DaMiRseq.Rnw) Error: processing vignette 'DaMiRseq.Rnw' failed with diagnostics: object 'R_svmtrain' not found Moreover, this message appeared in latest nightly builds: No methods found in

[Bioc-devel] segfault when building in veracruz2 for BioC 3.5

Dear All, A package I maintain, ADaCGH2, is failing to build in veracruz2 with a segfault that seems to happen when plotting (in a call to plotting that happens inside a mclapply) http://bioconductor.org/checkResults/devel/bioc-LATEST/ADaCGH2/veracruz2-buildsrc.html these are some of the