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

Thanks, Gabe. You make an excellent point: bioc objects get first class support. In some instance, base R data types deserve that also, and data.frames lead the list for me, being useful, concise, universally available, expressive. So perhaps not “data.frames replaced by” but “accompanied b

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

Paul, Sounds cool! My one note after a quick first pass is that here: On Wed, Mar 7, 2018 at 2:15 PM, Paul Shannon wrote: > > Note that though igv.js typically gets its track data from CORS/indexed > webservers, the IGV package will also support locally created R data.frames > describing either

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

To avoid duplication of effort, and perhaps to attract some early reviewers, I figure I’d let this group know that I plan to submit a new package “IGV” for inclusion in the next Bioconductor release. The package will provide an interface to the excellent and quite new browser-based genome viewe

[Bioc-devel] Cleanup of Bioconductor organization on Github

Hi Developers and Maintainers, We are cleaning up our Bioconductor organization on Github to make sure the organization stays secure, and access is limited to members to repositories as needed. If anyone is removed from a repository, or lost access to something, please reply back to this threa

Re: [Bioc-devel] Duplicate commits in mimager package

Hi Aaron, As Johannes said, your have to fix the repo yourself. Your duplicate commits are non-contiguous which is surprising. It’s almost as if the commit dates were changed somehow. Once you fix the repo on Github, please send me the link and I can force push to Bioconductor. Best, Nites

Re: [Bioc-devel] Duplicate commits in mimager package

Thanks, Nitesh. I’ve already gone through the process of fixing the duplicate commits and force pushed the cleaned history to GitHub (https://github.com/aaronwolen/mimager). No idea why the duplicates appeared out of order but I did verify the dates/times were unchanged by comparing to a backup

Re: [Bioc-devel] Duplicate commits in mimager package

Thanks for the information, Jo. Sounds like a very similar issue—even down to the potentially faulty git-svn setup. Glad to hear Nitesh was able to copy over your cleaned history to Bioconductor. Hopefully we can do the same for mimamger. On Mar 7, 2018, 1:26 AM -0500, Rainer Johannes , wrote:

Re: [Bioc-devel] Daily build

Hi Nicolas, This is the last commit I see in the master branch for ChIPSeqSpike: commit abce855631cb5689bd345df41e71cfee356a1c6f (HEAD -> master, origin/master, origin/HEAD) Author: kitano902 Date: Fri Jan 26 14:29:26 2018 -0500 remove '{' in count.Rd

[Bioc-devel] Daily build

Dear community, When my package ChIPSeqSpike was accepted, I have been noticed that no further action was required regarding my github ( https://github.com/descostesn/ChIPSeqSpike). I did two commits with version bump yesterday and I did not receive any notification. I checked the version at http