[Bioc-devel] Request for undeprecation of motifbreakR

Kern, Lori Lor|@Shepherd @end|ng |rom Ro@we||P@rk@org
Wed Jun 28 13:01:53 CEST 2023

Thank you.  Yes we can undeprecate the package. Please remember to also push your changes to RELEASE_3_17 branch as the package is also failing there.

Lori Shepherd - Kern

Bioconductor Core Team

Roswell Park Comprehensive Cancer Center

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263

From: Bioc-devel <bioc-devel-bounces using r-project.org> on behalf of Coetzee, Simon via Bioc-devel <bioc-devel using r-project.org>
Sent: Wednesday, June 28, 2023 1:05 AM
To: bioc-devel using r-project.org <bioc-devel using r-project.org>
Subject: [Bioc-devel] Request for undeprecation of motifbreakR

Dear bioc-devel,

I am sorry for not being responsive to the error messages related to the building of motifbreakR.

As you can likely see, I was responsive to errors earlier in the year, entering many changes to keep up to date with the changing conditions of the Bioc universe, and bugs that I discovered (with the help of users on my github issues).

Earlier in the year, perhaps as a result of altering my email notifications and organization as a result of going on paternity leave, I somehow lost track of a recurrent error introduced as a response to my most recent change to motifbreakR, despite your repeated emails to that effect. On Tuesday June 27, I got an email from my PI indicating that the package has been depreciated.

It appears as though the errors were from the most recent change altering the examples to a couple of my functions, and I have fixed them on upstream/devel. Additionally, I have made sure that any email filters and organizational changes have been reverted to their previously functional states.

As a result of these remedies, I hope that, once again, motifbreakR can be reinstated to good standing in Bioconductor. Is there anything else that I can do to prove my continued enthusiasm and commitment to the package and community?

Thank you,

Simon Coetzee

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