Hello Lori, following up on this, we have now finished the revision of the workflow and are ready to submit it to Bioc:
https://github.com/Steffireise/maEndToEnd However, using a call to gc() at end of the workflow and rendering it via rmarkdown::render gives a memory usage of ~ 4.5 GB, while the guidelines: http://bioconductor.org/developers/how-to/workflows/ say that "The package should require <= 4GB RAM" Is it okay to submit the workflow as it is, or do we have to look into splitting it up as in: http://bioconductor.org/packages/devel/workflows/html/simpleSingleCell. html ? Thanks and best wishes, Bernd On Do, 2018-05-03 at 18:41 +0200, Bernd Klaus wrote: > 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
