[Bioc-devel] "Reviving" an existing workflow

[Bernd Klaus]

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-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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