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

[Oleksii Nikolaienko]

https://nonstationarity.sciencesconf.org/resource/page/id/7
That is, perhaps, not surprising...

Package seems to be too good to be abandoned. I wonder if anyone from their
lab <https://modalx.parisnanterre.fr/membres> 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>
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>
> 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> on behalf of
>> Oleksii Nikolaienko <oleksii.nikolaienko using gmail.com>
>> *Sent:* Thursday, June 29, 2023 5:36 AM
>> *To:* Sokratis Kariotis <sokratiskariotis using gmail.com>
>> *Cc:* bioc-devel using r-project.org <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>
>> 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)
>> > Twitter: @s_kariotis <
>> https://secure-web.cisco.com/1EqWv8V2N5hRbw3HmoPEY8RdpEeWxqDoUa71DV8jQUiygXZiRjRxTOSFFWWDUSN7nw3Aviue7E_1xQuvbY4J8O3un4nvR0wtrlQUjMbs1vFGt5o9bI_InwlMvRWb2dhIe9ic0_2ugbdCwXwW_RGN1G4LJxUxm_yO9EkGSnc10bfG2fjit4oALm7Y8gMqnFusMJfqR3j-IKbu0Hem-jPRYXIeAurGmn1l7FvPYk9Pi6MHnOl1RN-5x19R655qOhP8vtsh9q-qwvckAbwuklQvq6lo0zKstGTdB6JkFCIIHswJrur4WrdjGMtwrYkWwOAQs/https%3A%2F%2Ftwitter.com%2Fs_kariotis
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>
> --
> Cheers,
> Sokratis Kariotis
> PhD Student
> University of Sheffield, Medical School
> MedTech <https://www.facebook.com/medtechsheffield/>President
> Twitter: @s_kariotis <https://twitter.com/s_kariotis>
> LinkedIn: http://www.linkedin.com/in/sokratiskariotis
>

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