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 at 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 at gmail.com>
*Sent:* Thursday, July 6, 2023 1:58 AM
*To:* Sokratis Kariotis <sokratiskariotis at gmail.com>
*Cc:* Kern, Lori <Lori.Shepherd at RoswellPark.org>; bioc-devel at r-project.org
<bioc-devel at 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 at 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 at 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 at r-project.org> on behalf of
Oleksii Nikolaienko <oleksii.nikolaienko at gmail.com>
*Sent:* Thursday, June 29, 2023 5:36 AM
*To:* Sokratis Kariotis <sokratiskariotis at gmail.com>
*Cc:* bioc-devel at r-project.org <bioc-devel at 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 at 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
(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)
Twitter: @s_kariotis <
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