[Bioc-devel] Repitools Bioconductor

[Mark D. Robinson]

Sorry for the delay; I have the fix for this problem now ..

But my Bioc git account in a bit mangled because they recently shut off my mark.robinson using imls.uzh.ch<mailto:mark.robinson using imls.uzh.ch> account (I have literally no way to access it) in favour of this mark.robinson using mls account .. but unfortunately that is not the account that is attached to the BioC packages ..

In particular, the @imls account is listed here:
https://www.bioconductor.org/packages/release/bioc/html/Repitools.html

When I try to register the new email address, I get:

mark.robinson using mls.uzh.ch is not associated with a maintainer of a Bioconductor package. Please check the spelling or contact bioc-devel using r-project.org for help.

Can someone sort me out, please?

Thanks, Mark


-----
Prof. Mark D. Robinson
Statistical Bioinformatics DMLS+SIB
https://robinsonlabuzh.github.io/

On 13 Mar 2024, at 12:32, CoreTeam Bioconductor <bioconductorcoreteam using gmail.com> wrote:

Per the original email send:

We would like to bring to your attention that your package is failing in devel across all platforms. This is very problematic. Please investigate the issues and fix the package to avoid deprecation.

https://bioconductor.org/checkResults/devel/bioc-LATEST/
<https://bioconductor.org/checkResults/3.17/workflows-LATEST/TCGAWorkflow>

If you have further questions or concerns please reach out on the bioc-devel using r-project.org<mailto:bioc-devel using r-project.org>

We appreciate your quick attention to this matter

The Ringo package that is missing was deprecated in Bioconductor 3.18 and removed in 3.19.  You will have to adjust your package to not depend on Ringo.

Cheers,
On behalf of the Bioconductor Core Team

On Wed, Mar 13, 2024 at 3:50 AM Mark D. Robinson <mark.robinson using mls.uzh.ch<mailto:mark.robinson using mls.uzh.ch>> wrote:

Right. Ringo is deprecated. I’ll try and figure out what we imported from there ..

Mark


-----
Prof. Mark D. Robinson
Statistical Bioinformatics DMLS+SIB
https://robinsonlabuzh.github.io/

On 13 Mar 2024, at 08:49, Mark Robinson <mark.robinson using mls.uzh.ch<mailto:mark.robinson using mls.uzh.ch>> wrote:


I haven’t had a chance to look at it. When are the deadlines?

The error seems to be:

ERROR: dependency ‘Ringo’ is not available for package ‘Repitools’

.. which is not actually a Repitools error.

Mark

-----
Prof. Mark D. Robinson
Statistical Bioinformatics DMLS+SIB
https://robinsonlabuzh.github.io/

On 12 Mar 2024, at 14:28, CoreTeam Bioconductor <bioconductorcoreteam using gmail.com<mailto:bioconductorcoreteam using gmail.com>> wrote:

Hi Mark,

I'm hoping you can give an update on Repitools?  The next release is fast approaching and the package continues to fail.  I will be deprecating it shortly if it is not fixed.


On Thu, Feb 29, 2024 at 12:19 PM CoreTeam Bioconductor <bioconductorcoreteam using gmail.com<mailto:bioconductorcoreteam using gmail.com>> wrote:
It has been over a month and the package continues to fail.  Can we expect updates soon or should we continue with deprecation of the package?

On Tue, Jan 16, 2024 at 10:07 AM CoreTeam Bioconductor <bioconductorcoreteam using gmail.com<mailto:bioconductorcoreteam using gmail.com>> wrote:
Please update yourself when you make changes to the package.  We use whatever email is listed in the DESCRIPTION of the package.

On Mon, Jan 15, 2024 at 3:30 AM Mark D. Robinson <mark.robinson using mls.uzh.ch<mailto:mark.robinson using mls.uzh.ch>> wrote:
Dear BioC core team,

Can you change my email address to mark.robinson using mls.uzh.ch<mailto:mark.robinson using mls.uzh.ch> (not @imls), please? .. then I will also try to deal with the Ringo dependency.

Thanks!

Best, Mark

-----
Prof. Mark D. Robinson
Statistical Bioinformatics DMLS+SIB
https://robinsonlabuzh.github.io/

On 14 Jan 2024, at 20:55, Andrea Riebler <andrea.riebler using ntnu.no<mailto:andrea.riebler using ntnu.no>> wrote:

Dear Mark,

Happy new year and congratulations on being a full professor!!! 😊 That is really great and well deserved.

I hope you and your family are doing fine. Here, there is not so much new.

Probably you have already seen that there seems to be an issue with Repitools. I attach you below an email I have received from Bioconductor.

Maybe it works out to see you soon in person again 😊

Best wishes from Trondheim,
Andrea

From: CoreTeam Bioconductor <bioconductorcoreteam using gmail.com<mailto:bioconductorcoreteam using gmail.com>>
Date: Friday, 12 January 2024 at 13:38
To: Dario Strbenac <dario.strbenac using sydney.edu.au<mailto:dario.strbenac using sydney.edu.au>>, a.statham using garvan.org.au<mailto:a.statham using garvan.org.au> <a.statham using garvan.org.au<mailto:a.statham using garvan.org.au>>, Andrea Riebler <andrea.riebler using ntnu.no<mailto:andrea.riebler using ntnu.no>>
Subject: Fwd: Repitools Bioconductor

You are currently listed as an Author of the Repitools package.   I tried to send the following email to the listed maintainer of the Repitools package
Maintainer: Mark Robinson <mark.robinson using imls.uzh.ch<mailto:mark.robinson using imls.uzh.ch>>
But received an email address is not found.
If you still have contact with Mark Robinson could you please forward and let him know your package is at risk for deprecation if the package is not fix and if the maintainer email is not updated to a reachable address.

Thank you
On behalf of the Bioconductor Core Team


---------- Forwarded message ---------
From: CoreTeam Bioconductor <bioconductorcoreteam using gmail.com<mailto:bioconductorcoreteam using gmail.com>>
Date: Thu, Jan 11, 2024 at 9:36 AM
Subject: Repitools Bioconductor
To: <mark.robinson using imls.uzh.ch<mailto:mark.robinson using imls.uzh.ch>>

We would like to bring to your attention that your package is failing in devel across all platforms. This is very problematic. Please investigate the issues and fix the package to avoid deprecation.

https://bioconductor.org/checkResults/devel/bioc-LATEST/

If you have further questions or concerns please reach out on the bioc-devel using r-project.org<mailto:bioc-devel using r-project.org>

We appreciate your quick attention to this matter

The Ringo package that is missing was deprecated in Bioconductor 3.18 and removed in 3.19.  You will have to adjust your package to not depend on Ringo.

Cheers,
On behalf of the Bioconductor Core Team





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