Re: [Bioc-devel] Missed deadline

ONE more note that Gabe reminded me of! As soon as your package is accepted into bioc-devel, it will be accessible via https://bioconductor.org/packages/mypackage/. Once it enters the release branch, that URL will instead point to the release page. On Tue, Apr 3, 2018 at 11:56 AM, Gabe Becker

Re: [Bioc-devel] Missed deadline

Indeed, and to be a bit more explicit about Levi's point, you *can* publish your package to bioconductor any time after the deadline, it will simply go to the development repo for ~6 months, which, as he points out, may not be a bad thing if it's not ready yet. On Tue, Apr 3, 2018 at 8:06 AM,

Re: [Bioc-devel] vignette problems

Please use 'reply all' so that the mailing list remains engaged. Check out the release schedule http://bioconductor.org/developers/release-schedule/ in particular Wednesday April 25 - Deadline for packages passing ‘‘R CMD build’’ and ‘‘R CMD check’’ without errors or warnings. so you

Re: [Bioc-devel] Missed deadline

On Tue, Apr 3, 2018 at 5:32 AM, Kenneth Condon wrote: > Have I missed the deadline for the latest release? I have created a > package, that runs great but there are a number of errors still from R CMD > check that I am sorting out. > > This is my first R package so I'm not

[Bioc-devel] Bioconductor 3.7 annotation deadlines

Hello all! The deadline for contributed annotations for the upcoming Bioconductor 3.7 release is April 16th. db0 packages will be available by April 9th. This email message may contain legally privileged and/or confidential information. If you are not the intended recipient(s), or the

[Bioc-devel] Workflow package landing pages

As mentioned last week the workflow packages are now in git. We have also updated the workflow landing pages. There is now an entry in the biocViews for workflows that lists all workflows and have landing pages similar to those for the software/annotation/experiment packages (note this is

Re: [Bioc-devel] RareVariantVis failed

hi Tomasz, regarding the warning caused by GenomicScores: > Warning in scores(phastCons100way.UCSC.hg19, scores.only = TRUE, > GRanges(seqnames = paste0("chr", : >The 'scores()' method has been deprecated and will become defunct in > the next release version of Biocondcutor 3.8. Please use

Re: [Bioc-devel] Workflows are now in git (and other Important workflow-related changes)

It would also be nice to have a mechanism to obtain the underlying *.md files used to generate the compiled workflow HTMLs. I've been using this to check that the results have not changed since the last run. Of course, I could also do this locally, but it would be reassuring to confirm that the

Re: [Bioc-devel] Missed deadline

The deadline to submit new packages for this release was yesterday. You could still submit the package for review but there is no guarantee it will make it through the review process in time to be included as reviewers will focus on packages that made the deadline. The last day for the newly

[Bioc-devel] RareVariantVis failed

Dear bioc-devel, My package RareVariantVis currently failed check because of examples warnings/error. I am not able to reproduce this on my system, despite updating R and Bioconductor. It seems that recent changes in dependencies are causing this trouble. Should I go for useDevel() to

Re: [Bioc-devel] Workflows are now in git (and other Important workflow-related changes)

Dear Leo, thanks for you inquiry. Re points 2-4: there is no need to use the token file .html_output anymore. This was an intermediate solution meant for the transition period to new output format. Now all workflow vignettes for the the website are build using this new format, regardless the

[Bioc-devel] Missed deadline

Hello, Have I missed the deadline for the latest release? I have created a package, that runs great but there are a number of errors still from R CMD check that I am sorting out. This is my first R package so I'm not sure if development is far enough along, although I suspect it might be. Could

Re: [Bioc-devel] Release of R package

Hi, You package is currently only available in the developmental branch of Bioconductor as it was accepted within the current six-monthly release cycle. The build report for the developmental version is available at http://bioconductor.org/checkResults/devel/bioc-LATEST/MAGeCKFlute/ The

[Bioc-devel] CfH: mzR 2.13.5 on macOS duplicated symbols from HDF5

Hi, this is a Call for Help (CfH) to fix mzR. There has been a report of a build failure on macOS. We're tracking this in https://github.com/sneumann/mzR/issues/152 but were unable to reproduce so far, it works on build machines and the macs we have access to. The underlying issue is that for