Hello Lori, thanks a lot for your prompt and your constructive feedback!
We will revise the workflow accordingly and then submit it to the submission tracker. Cheers, Bernd On Do, 2018-05-03 at 15:50 +0000, Shepherd, Lori wrote: > Hello Bernd, > > Thanks for reaching out. It looks like the last build on Jenkin's > was two release cycles ago (Oct 2), because of the time lapse and > that there have been quite a few changes to depending packages, and > that it was never "published", we would recommend putting the > workflow on the submission tracker. > > We understand that it isn't a new submission, but this will allow the > debugging process to be separate from the daily builder. > > https://github.com/Bioconductor/Contributions > > > Thank you for converting your workflow to a package. Please also > review > http://bioconductor.org/developers/how-to/workflows/ as it outlines > some important aspects to implement that are new from when the > workflow was originally submitted. > Most Importantly: > Add "Workflow: True" as a field in the DESCRIPTION > Updating the BiocViews terms to be part of the workflow biocViews: ht > tp://bioconductor.org/packages/devel/BiocViews.html#___Workflow > See the consistent formatting section. We will require the vignette > be updated to use BiocStyle and include author and affiliations, > date, and versioning information. > > > I did try to build your package locally and ran into quite a few > issues. > The first run: > Quitting from lines 1510-1512 (MA-Workflow.Rmd) > Error: processing vignette 'MA-Workflow.Rmd' failed with diagnostics: > package Rgraphviz is required > > So it seems like you need to add Rgraphviz > > The second run after installing Rgraphviz: > Quitting from lines 1578-1579 (MA-Workflow.Rmd) > Error: processing vignette 'MA-Workflow.Rmd' failed with diagnostics: > could not find function "enrichMap" > > I think this stems from the fact that DOSE moved a lot of their > plotting functions or the plotting functionality to the enrichplot > package but something that will have to be remedied. > > I also would git rm the vignette/MA-Workflow.html - this should be > generated automatically from the Rmd file and including a version > could result it a stale copy. > > Just on quick glance of the vignette - It seems like you set.seed in > the vignette but that code is not exposed to the user - assuming this > would be important to show so that a user could reproduce your > work. > > We look forward to getting this workflow active again and on the > builder. > > Cheers, > > Lori Shepherd > Bioconductor Core Team > Roswell Park Cancer Institute > Department of Biostatistics & Bioinformatics > Elm & Carlton Streets > Buffalo, New York 14263 > From: Bioc-devel <bioc-devel-boun...@r-project.org> on behalf of > Bernd Klaus <bernd.kl...@embl.de> > Sent: Thursday, May 3, 2018 3:03:20 AM > To: bioc-devel > Subject: [Bioc-devel] "Reviving" an existing workflow > > Dear Bioc Team, > > > I submitted a Microarray workflow some time ago (using SVN / Jenkins) > to Bioconductor, but I never published it at the (now retired) > workflow > page. > > Upon a recent request by the Bioc Team, I changed into a package, > which > is now at: > > packages/maEndToEnd > > on the Bioconductor git server. Access works fine with my Bioc > credentials. > > In the near feature I want to submit a revised version, so it would > be > great if the package could be included in the build reports: > > https://bioconductor.org/checkResults/devel/workflows-LATEST/ > > and the workflow be published on the Bioc website. > > Could you please guide me on how to proceed? > > Thanks and best wishes, > > Bernd > > > > _______________________________________________ > Bioc-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/bioc-devel > > This email message may contain legally privileged and/or confidential > information. If you are not the intended recipient(s), or the > employee or agent responsible for the delivery of this message to the > intended recipient(s), you are hereby notified that any disclosure, > copying, distribution, or use of this email message is prohibited. If > you have received this message in error, please notify the sender > immediately by e-mail and delete this email message from your > computer. Thank you. _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
