Re: [Bioc-devel] Duplicated method names in purrr and GenomicRanges

On this topic, one way of staying abreast of conflicts as you introduce them during the evolution of a project through use of the `conflicted` library toward the top of your project, usage modelled as follows: ``` ## Force use of package prefixes for ALL conflicting function names ## lacking

Re: [Bioc-devel] IGV - a new package in preparation

Hi, > -Original Message- > From: Bioc-devel On Behalf Of > Michael Lawrence > Sent: Friday, March 09, 2018 1:49 PM > To: Paul Shannon > Cc: Gabe Becker ; bioc-devel@r-project.org > Subject: Re:

Re: [Bioc-devel] IGV - a new package in preparation

Hello, Jumping in the conversation perhaps late. If it helps the effort, below are some IGV related R functions I've used in the past to good effect communicating with IGV running on local/remote host and issuing GOTO and Save Snapshot commands. They use utils::write.socket One things that

Re: [Bioc-devel] as.list of a GRanges

Hi, Can I ask, is this change under discussion in current release or so far in Bioconductor devel only (my assumption)? > On 02/15/2018 08:37 AM, Michael Lawrence wrote: > > So is as.list() no longer supported for GRanges objects? I have found it > > useful in places. > > Very few places.

Re: [Bioc-devel] systemPipeR error - Error in NSBS(i, x, exact = exact, upperBoundIsStrict = !allow.append) :

> -Original Message- > From: Bioc-devel [mailto:bioc-devel-boun...@r-project.org] On Behalf Of > Hervé Pagès > Sent: Monday, October 26, 2015 12:39 PM > To: Thomas Girke ; Arora, Sonali > ; bioc-devel@r-project.org > Subject: Re:

[Bioc-devel] BUG: emacs orgmode ob-R.el function org-babel-R-evaluate-session over aggressively performs "; ; cleanup extra prompts left in output" and a possible workaround

Hello , I am not sure what the best solution is, but, in my hands using Org-mode version 8.3.2-elpa org-20150929 the reg-expt used to "cleanup extra prompts left in output" is over-aggressive and will trim session :output at lines consisting exclusively of blanks and periods such as produced

Re: [Bioc-devel] Adding a lengths() method to List class

Yay m- thx From: Michael Lawrence [mailto:lawrence.mich...@gene.com] Sent: Tuesday, September 29, 2015 11:16 AM To: Cook, Malcolm <m...@stowers.org> Cc: Michael Lawrence <lawrence.mich...@gene.com>; Peter Hickey <peter.hic...@gmail.com>; bioc-devel@r-project.org Subject: Re: [

Re: [Bioc-devel] Adding a lengths() method to List class

Dumb question (?) follows in line: > That is the plan. Note that we already have elementLengths() that serves the > same purpose. It was the direct inspiration for lengths(). Why have both? > > On Mon, Sep 28, 2015 at 9:41 PM, Peter Hickey > wrote: > > > The

Re: [Bioc-devel] 'semantically rich' subsetting of SummarizedExperiments

Hi, https://github.com/vjcitn/biocMultiAssay/blob/master/vignettes/SEresolver.Rnw shows some modifications to [ that allow subsetting of SE by gene or pathway name Without reading the code, do you intend that SE[i,j] will , if i is provided as vector of string, will subset those rows where

Re: [Bioc-devel] Bug tracker for Bioconductor?

Great. It sounds like promoting this in http://www.bioconductor.org/developers/package-guidelines/ might be the path of least pain/most gain. The BioConductor project _could_ at some point as a service choose to host a single bug/issue tracking system which individual package developers could

Re: [Bioc-devel] Bug tracker for Bioconductor?

Martin, I'm sure you're watching this thread. Can we take it as some feedback from other developers that you requested way back in https://stat.ethz.ch/pipermail/bioc- devel/2011-October/002854.html when I wished for similar I don't really have anything constructive to

Re: [Bioc-devel] Bug tracker for Bioconductor?

Martin, I'm sure you're watching this thread. Can we take it as some feedback from other developers that you requested way back in https://stat.ethz.ch/pipermail/bioc-devel/2011-October/002854.html when I wished for similar In any case, +1, Malcolm -Original Message-

Re: [Bioc-devel] Bug tracker for Bioconductor?

your question “do we really need...”, I’d vote +2 !Malcolm From: Michael Lawrence [mailto:lawrence.mich...@gene.com] Sent: Friday, May 23, 2014 1:31 PM To: Cook, Malcolm Cc: Keith Hughitt; Nicolas Delhomme; Martin Morgan; bioc-devel@r-project.org Subject: Re: [Bioc-devel] Bug tracker

Re: [Bioc-devel] [BioC] granges() method for GenomicRanges objects akin to ranges()...

Wondering, Is it too off the beaten track to expect `mcols-`(x,NULL) to work? hint: it does not -Original Message- From: bioc-devel-boun...@r-project.org [mailto:bioc-devel-boun...@r-project.org] On Behalf Of Hervé Pagès Sent: Monday, May 05, 2014 1:28 PM To: Kasper Daniel

Re: [Bioc-devel] [BioC] granges() method for GenomicRanges objects akin to ranges()...

On 05/05/2014 01:00 PM, Cook, Malcolm wrote: Wondering, Is it too off the beaten track to expect `mcols-`(x,NULL) args(`mcols-`) function (x, ..., value) Arguments after the ellipsis must be named: `mcols-`(x, value=NULL) Herve - Great - of course - so - does

[Bioc-devel] rJava .jpackage(RDAVIDWebService) segfaults in restored R session

Hi, I'm having trouble making a minimal reproducible example, but, pretty reliably I get the following segfault calling DAVIDWebService in a restored R session: david-DAVIDWebService$new(email=m...@stowers.org) *** caught segfault *** address 0x7f5b1bd0e000, cause 'invalid permissions'

Re: [Bioc-devel] BigWigViews

Hi, I just went through this approach in yeast, regions = gene promoters assays = H3K3ME1, H3K3ME2, H3K3ME3 ChipSeq experimental conditions: 7 recombinant knock-outs and knock-ins of different domains of different genes. two replicates So, what I first

Re: [Bioc-devel] SRAdb listSRAfile returns empty datatable with filetype='fastq' (rasko) (SUB#832914)

14, 2013 6:54 AM .To: Cook, Malcolm .Cc: bioc-devel@r-project.org; zhuj...@mail.nih.gov .Subject: RE: [Bioc-devel] SRAdb listSRAfile returns empty datatable with filetype='fastq' (rasko) (SUB#832914) . .Dear Malcolm, . .We have reverted minor differences in the reports for submitted

Re: [Bioc-devel] SRAdb listSRAfile returns empty datatable with filetype='fastq' (rasko) (SUB#832914)

Fix confirmed. Thanks very much. .-Original Message- .From: datas...@ebi.ac.uk [mailto:datas...@ebi.ac.uk] .Sent: Thursday, February 14, 2013 10:04 AM .To: Cook, Malcolm .Cc: bioc-devel@r-project.org; zhuj...@mail.nih.gov .Subject: RE: [Bioc-devel] SRAdb listSRAfile returns empty

Re: [Bioc-devel] SRAdb listSRAfile returns empty datatable with filetype='fastq'

...@r-project.org] On Behalf Of Cook, Malcolm .Sent: Wednesday, February 13, 2013 5:18 PM .To: 'bioc-devel@r-project.org'; 'zhuj...@mail.nih.gov' .Subject: [Bioc-devel] SRAdb listSRAfile returns empty datatable with filetype='fastq' . .Hi Jack, . .Do you happen to know if EBI is refreshing

Re: [Bioc-devel] [GenomicFeatures] no pkgName found. makeTxDbPackage() called after txdb created from GFF3 file

.Hi Tengfei, . .Yes that looks like an oversight. Thanks for reporting that! I will .extend makeTxDbPackage so that it's more accommodating of these newer .transcriptDbs. If you want to help me out, you could call saveDb() on .your gmax189 object and send me the .sqlite file that you save