[Bioc-devel] Question about Access to Bioconductor through Git

Hi Bioc-Devel List, I am having trouble pushing to the git bioconductor repository, most likely due to not requesting for access correctly. I was able to follow the instructions to open a github account and link the github repository to the one on my local machine, and then sync both with the

Re: [Bioc-devel] splitting simpleSingleCell into self-contained vignettes

Thanks for you feedback Aaron! On Tue, Dec 12, 2017 at 9:49 PM, Aaron Lun wrote: > Thanks Andrzej. > > > Thank you. I've edited the workflow index page by introducing a separate > > "Single-cell Workflows" section, and by substituting the previous link to > > your workflow by

Re: [Bioc-devel] splitting simpleSingleCell into self-contained vignettes

Thanks Andrzej. > Thank you. I've edited the workflow index page by introducing a separate > "Single-cell Workflows" section, and by substituting the previous link to > your workflow by links to the individual parts. Great, I'm looking forward to seeing it. Do you know how frequently the index

Re: [Bioc-devel] splitting simpleSingleCell into self-contained vignettes

Hi Aaron, Thank you. I've edited the workflow index page by introducing a separate "Single-cell Workflows" section, and by substituting the previous link to your workflow by links to the individual parts. As discussed during EuroBioc, I'm happy to restructure the index page by grouping workflows

Re: [Bioc-devel] splitting simpleSingleCell into self-contained vignettes

The split-up workflows seem to have built successfully: http://docbuilder.bioconductor.org:8080/job/simpleSingleCell/ Is there something I have to do to get a blurb specific to each vignette, as observed for "Annotation_Resources" vs "Annotating_Genomic_Ranges"? The various vignettes are

Re: [Bioc-devel] splitting simpleSingleCell into self-contained vignettes

The split-up workflows seem to have built successfully: http://docbuilder.bioconductor.org:8080/job/simpleSingleCell/ The various vignettes are ordered pedagogically, so the order in which they are presented in the workflow page might require some manual specification. It would also be nice if

[Bioc-devel] R: DaMiRseq: error while pushing

Hi Nitesh, I read but I just wanted to be sure. So, I typed: git pull upstream master Update the Version in DESCRIPTION git add . git commit -m "new message" git push upstream master and, I hope that everything will be ok now. Many Thanks Nitesh! Mattia Da:

Re: [Bioc-devel] DaMiRseq: error while pushing

Hi Mattia, If you read the “error” and “hint” messages carefully, it says do a > hint: (e.g., 'git pull ...') before pushing again. Did you try that? Best, Nitesh > On Dec 12, 2017, at 10:21 AM, Mattia Chiesa wrote: > > Dear All, > I am the mantainer of the

Re: [Bioc-devel] Version update question and an error?

1. Here is a page that describes versioning: http://bioconductor.org/developers/how-to/version-numbering/ x.y.z When there is a Bioconductor release we bump the 'y' version of the package to even for release and then again in devel so devel is odd and a version above the current

[Bioc-devel] Version update question and an error?

Hi I have had a package quite recently accepted to the bioconductor. I have two questions: 1. My version is listed as 0.99.98 in my local description file, 1.1.0 in my bioconductor development web page, and 1.0.0 in the non development bioconductor web page. Do I bump to 1.1.1 in my next commit

[Bioc-devel] SummarizedExperiment: duplication of metadata, when modifying colData

Hi all, I got a bit of weird behaviour with SummarizedExperiments in Bioc 3.6 and 3.7. I suppose it is a bug, but I might be wrong, since the accession to the SummarizedExperiment object is not really straight forward. Any suggestions? library(GenomicRanges) library(SummarizedExperiment)