Re: [Bioc-devel] shiny, Bioconductor, and reproducible research

2013-07-29 Thread Tim Triche, Jr.
Yeah I'm good like that. What I was looking for is capture.output() capture.output({ # {{{ clusts <- suppressWarnings(heatmap.3(t(tmp), scale="none", trace="none", color.FUN=get(col.fun), dendrogram='none', labCol=snps, kr

Re: [Bioc-devel] shiny, Bioconductor, and reproducible research

2013-07-29 Thread Dan Tenenbaum
Hi Winston, On Mon, Jul 29, 2013 at 2:39 PM, Winston Chang wrote: > Hi everyone - > > Great to hear from you all on your thoughts about Shiny. I've tried to > answer some of Dan's questions below... > > >>> >>> 1) Testing shiny apps >>> >>> Typically, bioconductor packages have man page example

Re: [Bioc-devel] shiny, Bioconductor, and reproducible research

2013-07-29 Thread Steve Lianoglou
Hi, On Mon, Jul 29, 2013 at 1:38 PM, Tim Triche, Jr. wrote: > So here is something I came across in my code: > > > > --t ... you came across a blank line or two? Fascinating ... :-) -steve -- Steve Lianoglou Computational Biologist Bioinformatics and Computational Biology Genentech _

Re: [Bioc-devel] shiny, Bioconductor, and reproducible research

2013-07-29 Thread Tim Triche, Jr.
So here is something I came across in my code: --t On Jul 29, 2013, at 2:08 PM, Kasper Daniel Hansen wrote: > My perspective, > > Clearly we are very interested in supporting reproducible research in > Bioconductor. Indeed, it is a core mission of the project. However, I > feel that Dan i

Re: [Bioc-devel] shiny, Bioconductor, and reproducible research

2013-07-29 Thread Dan Tenenbaum
Hi Kasper, On Mon, Jul 29, 2013 at 12:08 PM, Kasper Daniel Hansen wrote: > My perspective, > > Clearly we are very interested in supporting reproducible research in > Bioconductor. Indeed, it is a core mission of the project. However, I > feel that Dan is placing a very high burden of proof o

Re: [Bioc-devel] shiny, Bioconductor, and reproducible research

2013-07-29 Thread Kasper Daniel Hansen
My perspective, Clearly we are very interested in supporting reproducible research in Bioconductor. Indeed, it is a core mission of the project. However, I feel that Dan is placing a very high burden of proof on shiny apps in his email, since it essentially says "because it is possible to potent

Re: [Bioc-devel] Running Time of readBamGappedAlignmentPairs

2013-07-29 Thread Hervé Pagès
On 07/29/2013 12:00 AM, Dario Strbenac wrote: Because I only allowed unique mappings, the ratio is 2. After installing the development package versions, I only got a 10% improvement. Mmmh that's disappointing. Can you put the file somewhere so I can have a look? Thanks. H. user system

Re: [Bioc-devel] [devteam-bioc] Error in findOverlaps

2013-07-29 Thread Ou, Jianhong
Dear Hervé Pagès, Thank you very much for your email. This make me clear about the exactly mean of maxgap and minoverlap. Previous what I think is that maxgap is the max gap between the both ends of query and subject. Now I understand this only is the situation when we set the parameter type="all"

[Bioc-devel] programmaticallly get unused disk space

2013-07-29 Thread Michael Stadler
Dear list, I am looking for a way to programmatically get the unused disk space in R, ideally in a portable way that works on windows/linux/os x. I have come across OS specific solutions for C (e.g. using statvfs for linux), but I wonder if I am missing something simpler. Thank you for any help,

Re: [Bioc-devel] Running Time of readBamGappedAlignmentPairs

2013-07-29 Thread Dario Strbenac
Because I only allowed unique mappings, the ratio is 2. After installing the development package versions, I only got a 10% improvement. user system elapsed 1681.36 65.79 1752.10 From: Pages, Herve [hpa...@fhcrc.org] Sent: Monday, 29 July 2013 3:29