[Bioc-devel] "Reviving" an existing workflow

[Bernd Klaus]

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.klaus using 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-bounces using r-project.org> on behalf of
> > > Bernd Klaus <bernd.klaus using 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
> > > 
> > >   
> > > 
> > > _______________________________________________
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> > > https://stat.ethz.ch/mailman/listinfo/bioc-devel
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