[Bioc-devel] Omada package failing due to removed dependency

Fri Jul 28 15:12:27 CEST 2023

The package code needs to be pushed to git.bioconductor.org  not github.  Just wanted to be sure you are trying to push to the right place.  Could you please show the commands you are using with full output along with a git remote -v to make sure that is all set up correctly.
There are useful git workflows and help listed at:
 http://contributions.bioconductor.org/git-version-control.html#essential-work-flow

If you are using a ssh key that was set up on github and reutilized for our credentials, that would be the passphrase you initially set up and not of our control.  If you cannot remember it you will have to create a new ssh key and upload it to the BiocCredentials app.  See some other possibilities at (specifically number 16)
http://contributions.bioconductor.org/git-version-control.html#faq

Cheers,

Lori Shepherd - Kern

Bioconductor Core Team

Roswell Park Comprehensive Cancer Center

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263

________________________________
From: Sokratis Kariotis <sokratiskariotis using gmail.com>
Sent: Friday, July 28, 2023 2:31 AM
To: Kern, Lori <Lori.Shepherd using RoswellPark.org>
Cc: Oleksii Nikolaienko <oleksii.nikolaienko using gmail.com>; bioc-devel using r-project.org <bioc-devel using r-project.org>
Subject: Re: [Bioc-devel] Omada package failing due to removed dependency

Hey both,

I have edited the package code but I'm having some difficulties pushing it to trigger another build (github passphrase). Is there another way to trigger the build? Thanks!

Cheers,
Sokratis

On Wed, Jul 12, 2023 at 1:43 AM Kern, Lori <Lori.Shepherd using roswellpark.org<mailto:Lori.Shepherd using roswellpark.org>> wrote:
We can give you a little more time (a few weeks) to fix the package but please fix as soon as possible to avoid deprecation.

Cheers,

Lori Shepherd - Kern

Bioconductor Core Team

Roswell Park Comprehensive Cancer Center

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263

________________________________
From: Sokratis Kariotis <sokratiskariotis using gmail.com<mailto:sokratiskariotis using gmail.com>>
Sent: Monday, July 10, 2023 10:27 AM
To: Kern, Lori <Lori.Shepherd using RoswellPark.org>
Cc: Oleksii Nikolaienko <oleksii.nikolaienko using gmail.com<mailto:oleksii.nikolaienko using gmail.com>>; bioc-devel using r-project.org<mailto:bioc-devel using r-project.org> <bioc-devel using r-project.org<mailto:bioc-devel using r-project.org>>
Subject: Re: [Bioc-devel] Omada package failing due to removed dependency

Hey both,

I have checked the package license (GPL) and it should be fine to use the code. However, I am having difficulty finding the actual code to calculate the internal metrics I am using (used in Omada's function cluster_voting.R). I can only find the wrapper function but not the ones that actually calculate the metrics. I am not sure how to proceed with this in time, so the Omada package won't get deprecated.

Regards,
Sokratis

On Fri, Jul 7, 2023 at 1:03 AM Kern, Lori <Lori.Shepherd using roswellpark.org<mailto:Lori.Shepherd using roswellpark.org>> wrote:
We would not hunt down the lab especially for CRAN packages,  but you could reach out if you like.  That would probably be a recommended action to either ask someone from their lab to maintain or if you are willing and you really want the package around you could ask the lab if they mind you volunteering to be the new maintainer.

There could see two options for rewriting/maintaining.

1. Take over maintenance of the package and resubmit to CRAN
It's a little tricky cause this is a CRAN package so I'm not sure on their exact policy of taking over an abandoned package. If this is desired,  I would reach out to CRAN to find out their exact policy
2. Move needed code to your Bioconductor package
You'll have to check the original package license to make sure this is allowed under the license of the package. You will still want to give the original authors/maintainer credit. I would say to be safe I would include them as contributors/authors in the DESCRITPION Authors using R field and in the R code I would add a comment above the code to reference original package citation and stating it was copied from there.  I'm not a lawyer or license/copy right expert so not sure if that would be good enough but that would be my take on it.

Lori Shepherd - Kern

Bioconductor Core Team

Roswell Park Comprehensive Cancer Center

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263

________________________________
From: Oleksii Nikolaienko <oleksii.nikolaienko using gmail.com<mailto:oleksii.nikolaienko using gmail.com>>
Sent: Thursday, July 6, 2023 1:58 AM
To: Sokratis Kariotis <sokratiskariotis using gmail.com<mailto:sokratiskariotis using gmail.com>>
Cc: Kern, Lori <Lori.Shepherd using RoswellPark.org>; bioc-devel using r-project.org<mailto:bioc-devel using r-project.org> <bioc-devel using r-project.org<mailto:bioc-devel using r-project.org>>
Subject: Re: [Bioc-devel] Omada package failing due to removed dependency

https://nonstationarity.sciencesconf.org/resource/page/id/7<https://secure-web.cisco.com/1pCvxIL3lfzw2yMAoq1pXQ5JiavYeyZHI2qtDauHw4xwZZBxaV-dAKGWcVKgwz09vF4YJJGVvkcQloDj0mJOUxj7BI3WPu_1Ze3vDW0a9syxuRsiQNOGsRkJ8BaWBdlxOdRBAw39KujDDGqb_DPfL6IsjHK5UCqoCpzw39GduVcBLFIutoPM8Nqjgp8ArDuh-oK-Bxe-huDYCoLXUX5GyU_fEG81AEtF-osCFtJNLRiQBggrsxcViF8mNihzVj8-UT4cNawHmz7xye_KNs45WZOxnVljiq5QQHuIGCeXRkbYBUvrpcEoTootlVxLloYK0/https%3A%2F%2Fnonstationarity.sciencesconf.org%2Fresource%2Fpage%2Fid%2F7>
That is, perhaps, not surprising...

Package seems to be too good to be abandoned. I wonder if anyone from their lab<https://secure-web.cisco.com/1IisY82Mh0-7_0tTgq7v7MgjvGFKIBucg15oqE_SNpUPzwuvYYaCPgz427Efo9Xga7j3PYM6msIsM8GJAK7ofsjmhrfAG3_kBGCmTdF0gVYBUz17CdZjNygLUpDMXPSt6h5CfKAjX_SrymhwTWvvEuyH1cH3nCYhVkVd5xfdd2W5azA0g9MJ4bPASnxJwY9quFxu_6CAIuYXkkO_DqiO9NC6Nb22USMev1V4qh5A3IX2kg6l60sRbM9gDQWjNwbJAPSnWq9G5setIw9CNP8avnjON5nhm_cjNhhn6s6kY07wwiSQ4sSQqsekskzOjhbm1/https%3A%2F%2Fmodalx.parisnanterre.fr%2Fmembres> could take over maintenance, if you still bother to ask...

Best,
Oleksii

On Thu, 6 Jul 2023 at 06:23, Sokratis Kariotis <sokratiskariotis using gmail.com<mailto:sokratiskariotis using gmail.com>> wrote:
Hey,

I haven't received any responses from the maintainer of ClusterCrit so I guess I will have to re-write the code used. How can I properly go about this and credit the authors as well? Thanks!

Cheers,
Sokratis

On Thu, Jun 29, 2023 at 7:38 PM Kern, Lori <Lori.Shepherd using roswellpark.org<mailto:Lori.Shepherd using roswellpark.org>> wrote:
We do not allow archived packages to be used.  All dependencies must be on CRAN or Bioconductor. So yes if you can get them to reinstate the package on CRAN that would be ideal.  If not you will have to remove the package from the dependency list and either re-write the code used (giving original clusterCrit authors credit) or remove the functionality used from that package.

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<mailto:bioc-devel-bounces using r-project.org>> on behalf of Oleksii Nikolaienko <oleksii.nikolaienko using gmail.com<mailto:oleksii.nikolaienko using gmail.com>>
Sent: Thursday, June 29, 2023 5:36 AM
To: Sokratis Kariotis <sokratiskariotis using gmail.com<mailto:sokratiskariotis using gmail.com>>
Cc: bioc-devel using r-project.org<mailto:bioc-devel using r-project.org> <bioc-devel using r-project.org<mailto:bioc-devel using r-project.org>>
Subject: Re: [Bioc-devel] Omada package failing due to removed dependency

Hi,
in this case maybe it's worth reaching out to the maintainer of
clusterCrit. It was removed from CRAN because of (seems-to-be) minor
warnings, which can be addressed by the clusterCrit developer in no time...

Best,
Oleksii

On Thu, 29 Jun 2023 at 08:44, Sokratis Kariotis <sokratiskariotis using gmail.com<mailto:sokratiskariotis using gmail.com>>
wrote:

> Dear Bioconductor team,
>
> I received an email that my package "Omada" is failing in release and
> devel. I had a look and the problem seems to be: *ERROR: dependency
> ‘clusterCrit’ is not available for package ‘omada’*. So the package
> clusterCrit was removed. Is there a way I can use a archived version of it
> (or something similar) so I don't have to rewrite code based on new
> packages to avoid potentially inconsistencies? Please advise, thank you!
>
> Cheers,
> Dr. Sokratis Kariotis (PhD)
> Agency for Science, Technology and Research (A*STAR)
> Singapore Immunology Network (SIgN)
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