[Bioc-devel] "Reviving" an existing workflow

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

??