Hello Lori, thanks for your support! The workflow package is now on the tracker:
https://github.com/Bioconductor/Contributions/issues/765 Cheers, Bernd On Di, 2018-06-05 at 15:33 +0000, Shepherd, Lori wrote: > Excellent news! The RAM requirement was a legacy from the old > builders and we have since improved the capabilities so you should be > alright with the package as is. I will look at updating the > documentation on the website and thank you for bringing it to our > attention. > > We look forward to your submission on the tracker. > > Cheers, > > Lori Shepherd > Bioconductor Core Team > Roswell Park Cancer Institute > Department of Biostatistics & Bioinformatics > Elm & Carlton Streets > Buffalo, New York 14263 > From: Bernd Klaus <bernd.kl...@embl.de> > Sent: Tuesday, June 5, 2018 2:53:41 AM > To: Shepherd, Lori; bioc-devel > Cc: Stefanie Reisenauer > Subject: Re: [Bioc-devel] "Reviving" an existing workflow > > 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/simpleSingleCel > l. > 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. > > 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. 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