Hi, Thank you for all the work in this transition Andrzej, Lori, Valerie, Nitesh and Hervé!
I have a few questions about the new system. 1) I already had a github repo (that I manually kept in sync with the subversion one) for the recountWorkflow. Should I just follow the instructions at http://bioconductor.org/developers/how-to/git/sync-existing-repositories/? I guess that I'll need to do this too http://bioconductor.org/developers/how-to/git/abandon-changes/#force-bioconductor--to-github- 2) Is repo/vignettes/.html_output still needed? 3) Related to (2), the .html_output file used to ignore the `output` line in the vignette YAML. I got an email from Lori saying that output: BiocWorkflowTools::f1000_article is not working for recountWorfkflow for now (no html vignette). My guess is that the `output` line now matters, and in my case, that would build a pdf file which is ignored due to https://github.com/LieberInstitute/recountWorkflow/blob/master/.Rbuildignore#L12 in my .Rbuildignore. 4) Related to the last 2. What setup do you recommend so I can maintain a single git repo that produces the files needed for uploading them to F1000research? Before this transition, I had to maintain 3 repos: the subversion one for Bioc, my git copy (well, main), and another one with the files setup for F1000. At some point in the past, Andrzej recommended that I use "output: BiocWorkflowTools::f1000_article" to try to have all the files in 1 place. I imagine that I would still need some ifelse() statements for sentences like the one I have at https://github.com/LieberInstitute/recountWorkflow/blob/master/vignettes/recount-workflow.Rmd#session-information I think that this question could be generalized and documented in the Bioc website. 5) Is there anything else I should be aware of so I can reproduce any errors? In the past, the Bioc workflow system would trigger a build immediately after a new push, and due to the custom way workflows were built (like .html_output), I relied on these builds to check if my changes had worked or not: specially early on where I had issues with figures, links to figures and figure captions. Best, Leo On Mon, Apr 2, 2018 at 7:42 AM, Shepherd, Lori <lori.sheph...@roswellpark.org> wrote: > > For now the page at > > https://www.bioconductor.org/help/workflows/ > > will remain and be updated accordingly however there is discussion about > having this page be removed or redirected. > > > In the next few days I hope to have the new landing pages up and running and > will make an announcement when they are live. The new changes involve having > a link to the workflows on the biocViews page, that will directly link to a > workflow package landing page (like the software, annotation, and experiment > package do). > > > Until the release your changes will be visible in devel which will transition > over to the new release just as done for software packages - > > The workflow are built monday, wednesday, and friday and the new landing > pages will reflect when the package is propagated like the other types of > packages. > http://bioconductor.org/checkResults/3.7/workflows-LATEST/ > > > 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 Aaron Lun > <a...@wehi.edu.au> > Sent: Sunday, April 1, 2018 2:17:09 PM > To: Herv� Pag�s; bioc-devel@r-project.org > Subject: Re: [Bioc-devel] Workflows are now in git (and other Important > workflow-related changes) > > Thanks everybody, this is much appreciated. > > On that note, will the compiled workflows shown at: > > https://www.bioconductor.org/help/workflows/ > > ... be updated to reflect changes in the git repositories for the > workflows? > > Or will the workflow page just directly link to the landing page for > each package? This would be very convenient, not least because it will > avoid me having to make pull requests to the bioconductor.org > repository every time I want to change my workflow blurb. > > I'm in the process of fixing and updating my various workflows, and I'm > wondering when/how my changes will be visible to users. > > Cheers, > > Aaron > > On Fri, 2018-03-30 at 13:10 -0700, Herv� Pag�s wrote: > > To the authors/maintainers of the workflows: > > > > > > Following the svn-to-git migration of the software and data > > experiment > > packages last summer, we've completed the migration of the workflow > > packages. > > > > The canonical location for the workflow source code now is > > git.bioconductor.org > > > > Please use your git client to access/maintain your workflow the same > > way you would do it for a software or data-experiment package. > > > > We've also migrated the workflows to our in-house build system. > > Starting with Bioc 3.7, the build report for the devel versions of > > the workflows can be found here: > > > > https://bioconductor.org/checkResults/devel/workflows-LATEST/ > > > > We run these builds every other day (Mondays, Wednesdays, Fridays). > > Because of limited build resources, we now run the data-experiment > > builds on Sundays, Tuesdays, and Thursdays only (instead of daily). > > > > The links to the package landing pages are not working yet. This > > will be addressed in the next few days. > > > > Please address any error you see on the report for the workflow > > you maintain. > > > > Note that, from now on, we're also following the same version scheme > > for these packages as for the software and data-experiment packages. > > That is, we're using an even y (in x.y.z) in release and an odd y in > > devel. We'll take care of bumping y at release time (like we do for > > software and data-experiment packages). > > > > After the next Bioconductor release (scheduled for May 1), we'll > > start > > building the release versions of the workflows in addition to the > > devel versions. The build report for the release versions will be > > here: > > > > https://bioconductor.org/checkResults/release/workflows-LATEST/ > > > > Finally, please note that with the latest version of BiocInstaller > > (1.29.5), workflow packages can be installed with biocLite(), like > > any other Bioconductor package. We'll deprecate the old mechanism > > (workflowInstall()) at some point in the future. > > > > Thanks to Andrzej, Lori, Nitesh, and Valerie for working on this > > migration. > > > > Let us know if you have any question about this. > > > > H. > > > > > > _______________________________________________ > 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. > [[alternative HTML version deleted]] > > > _______________________________________________ > Bioc-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/bioc-devel > _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
