[Bioc-devel] "Reviving" an existing workflow

Bernd Klaus bernd.klaus at embl.de
Thu May 3 18:41:32 CEST 2018

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.



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 at r-project.org> on behalf of
> Bernd Klaus <bernd.klaus at 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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