Re: [Bioc-devel] Announcing Docker containers for Bioconductor

Hi BioC team, I'd like to report the progress on the metabolomics docker image. We now have a fork of https://github.com/Bioconductor/bioc_docker on https://github.com/phnmnl/bioc_docker which includes the devel_metabolomic image, which build successfully on our jenkins at

Re: [Bioc-devel] Making GenomicAlignments::readGAlignmentPairs() fail fast if given bad seqlevels in `which`

On 03/17/2016 10:35 AM, Martin Morgan wrote: On 03/17/2016 10:29 AM, Peter Hickey wrote: Thanks, Aaron. I implemented a similar workaround, but I think it would be nice to have in the core Bioconductor implementation. I had a quick poke around GenomicAlignments::readGAlignmentPairs(),

Re: [Bioc-devel] Making GenomicAlignments::readGAlignmentPairs() fail fast if given bad seqlevels in `which`

Thanks, Aaron. I implemented a similar workaround, but I think it would be nice to have in the core Bioconductor implementation. I had a quick poke around GenomicAlignments::readGAlignmentPairs(), however, but it looked like I'd have to learn a bit too much about the underlying

Re: [Bioc-devel] Issues uploading our updated package (CausalR)

Sounds good. Thanks for fixing it. Valerie On 03/16/2016 08:58 AM, Glyn Bradley wrote: > Hi Valarie > OK , thanks for your detailed reply. > I thought we had cleared all errors before commit (another colleague has > actually been doing it, not me) but obviously we missed the namespaceExport >

Re: [Bioc-devel] Issues uploading our updated package (CausalR)

Thanks, we’ve already read that. I was more hoping for a response from the Bioconductor team Glyn From: Kasper Daniel Hansen [mailto:kasperdanielhan...@gmail.com] Sent: 16 March 2016 13:20 To: Glyn Bradley Cc: bioc-devel@r-project.org Subject: Re: [Bioc-devel] Issues uploading our updated package

Re: [Bioc-devel] Package reference manuals in html

Hi all, I had a discussion earlier today with Martin and Dan on providing online man pages for Bioconductor packages. As we dived into implementation details, it turned out that this idea is a little bit more complex and resource-intensive than originally anticipated. The main problem in

[Bioc-devel] Making GenomicAlignments::readGAlignmentPairs() fail fast if given bad seqlevels in `which`

Hi, GenomicAlignments::readGAlignmentPairs() can take a while to (correctly) fail if the `which` parameter contains a "bad" seqlevel. It'd be great if it failed early in the following scenario (just experienced). An example BAM is available from

Re: [Bioc-devel] Making GenomicAlignments::readGAlignmentPairs() fail fast if given bad seqlevels in `which`

Hi Peter, GenomicAlignments::readGAlignmentPairs() can take a while to (correctly) fail if the `which` parameter contains a "bad" seqlevel. It'd be great if it failed early in the following scenario (just experienced). I had the same problem a while ago and solved it by first reading only the

Re: [Bioc-devel] Issues uploading our updated package (CausalR)

Hi Glyn, On 03/16/2016 03:20 AM, Glyn Bradley wrote: > Hi All, > > Our package, CausalR, broke when igraph was updated last year. We have now > fixed this, but are having problems uploading the > new version. The package had become depreciated in devel, but there's still a > landing page in

Re: [Bioc-devel] Issues uploading our updated package (CausalR)

I don't know much about deprecated packages and how to deal with them, but for your svn questions, start by reading the howto: https://www.bioconductor.org/developers/source-control/ Kasper On Wed, Mar 16, 2016 at 6:19 AM, Glyn Bradley wrote: > Hi All, > > Our

Re: [Bioc-devel] Package reference manuals in html

Dear Andrzej Thank you. If automagic resolution of cross-links is the one and major bottleneck, then maybe we can drop this? (The perfect being the enemy of the good…). Assuming a universal namespace, i.e. where symbols are mapped to other packages and where this is considered to be universal

Re: [Bioc-devel] Announcing Docker containers for Bioconductor

Sure, send a pull request. Pushing is done automatically. https://github.com/Bioconductor/bioc_docker/blob/master/Rakefile#L98-L102 Dan - Original Message - > From: "Steffen Neumann" > To: "bioc-devel" > Sent: Friday, March 18, 2016

Re: [Bioc-devel] Making GenomicAlignments::readGAlignmentPairs() fail fast if given bad seqlevels in `which`

Wonderful. Thanks, Martin > in svn at 1.23.5, and in Bioc-devel hopefully after tonight's build. > > Martin ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel