[Bioc-devel] "Reviving" an existing workflow

Shepherd, Lori Lori.Shepherd at RoswellPark.org
Thu May 3 17:50:36 CEST 2018

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.


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:

  1.  Add "Workflow: True"  as a field in the DESCRIPTION
  2.  Updating the BiocViews terms to be part of the workflow biocViews: http://bioconductor.org/packages/devel/BiocViews.html#___Workflow
  3.  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.


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

Upon a recent request by the Bioc Team, I changed into a package, which
is now at:


on the Bioconductor git server. Access works fine with my Bioc

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:


and the workflow be published on the Bioc website.

Could you please guide me on how to proceed?

Thanks and best wishes,


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