[Bioc-devel] "Reviving" an existing workflow

[Shepherd, Lori]

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/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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> > https://stat.ethz.ch/mailman/listinfo/bioc-devel
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