Re: [Bioc-devel] Extending Views to support GRanges (and possibly BigWig files)

Yes, I am generally in favor of the GViews, and I've been a fan of Views since they were invented. Was just pointing out that we can do a lot with Lists these days. On Tue, Jun 28, 2016 at 4:56 PM, Hervé Pagès wrote: > On 06/28/2016 05:43 AM, Michael Lawrence wrote: >> >>

Re: [Bioc-devel] Extending Views to support GRanges (and possibly BigWig files)

On 06/28/2016 03:54 AM, Johnston, Jeffrey wrote: During the BioC developer day, Hervé brought up the idea of possibly extending the concept of GenomicViews to other use cases. I'd like to share how we currently use GenomicRanges, Views and RleLists to perform certain analyses, and hopefully

[Bioc-devel] Survey results

The results are at https://www.surveymonkey.com/results/SM-FKMZZ2QT/ Martin This email message may contain legally privileged and/or...{{dropped:2}} ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel

Re: [Bioc-devel] NotNeeded in build report RSS feeds

Hi Antti, I'm not sure I follow. NotNeeded is a status seen in the INSTALL phase of the build, and it means your package did not need to be installed because no other package built by the build system depends on it. This status should not change from one day to the next. (It would change if

Re: [Bioc-devel] Confusion on biocLite() with github and annotation data repo

I think you need to add the dependencies=TRUE argument which gets passed to devtools::install_github() and thence to devtools::install(). Dan - Original Message - > From: "Martin Morgan" > To: "James W. MacDonald" , "Sean

Re: [Bioc-devel] Confusion on biocLite() with github and annotation data repo

I had a similar experience, where the dependencies were not found upon installation. I didn't do anything to fix it - instead it seemed that just re-running biocLite after the initial failed install ended up working. Maybe the same will work for you? Best, Jim On Mon, Jun 27, 2016 at 5:03

Re: [Bioc-devel] Extending Views to support GRanges (and possibly BigWig files)

Thanks for these use cases. I've been wondering about the usefulness of Views given how far along Lists have come since the invention of Views. Instead of viewSums(Views(cov, gr)) we could just do sum(cov[gr]). The latter works today. The difference between the Views and List approach is that the

[Bioc-devel] NotNeeded in build report RSS feeds

Would it be possible to change the build report RSS feed generation to treat "NotNeeded" similarly as "OK"? This would make the feed more useful for spotting real problems. Thanks! Antti ___ Bioc-devel@r-project.org mailing list

[Bioc-devel] Extending Views to support GRanges (and possibly BigWig files)

During the BioC developer day, Hervé brought up the idea of possibly extending the concept of GenomicViews to other use cases. I'd like to share how we currently use GenomicRanges, Views and RleLists to perform certain analyses, and hopefully demonstrate that a way to directly use Views with