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

Mon Jul 10 16:27:42 CEST 2023

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>
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>
> *Sent:* Thursday, July 6, 2023 1:58 AM
> *To:* Sokratis Kariotis <sokratiskariotis using gmail.com>
> *Cc:* Kern, Lori <Lori.Shepherd using RoswellPark.org>; bioc-devel using r-project.org
> <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>
> 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
> >
> > LinkedIn:
> http://secure-web.cisco.com/1hrH0VDgCpCKm6BWl_eP9v57iZE2j6Y9RUetJ4RMrKylsFeYV7AWyeBfOewj6SpLxhrD-_JnI4sPdaUJB9Mwxuj-B5ot2FZIu4AU87ty04CdxW8zw9DShqtsaZPm68os9ySeI12kEcN_iujEcY11StQo1_qKeBsQchHO3Vc_qvfAbA2T29jSt4KX0OnG4UZENEfns3cigBqNgiYMOOiCGmz01_nIY5M3cgVbsTmSNA-pov7ZD6si4bOXF6pt-manBCeK0NB13icO5MMlpc8HNxSqkARD7n-R71Sa3ZsGQOIYPgA0uuuIRAR9DbV_F5kSj/http%3A%2F%2Fwww.linkedin.com%2Fin%2Fsokratiskariotis
> >
> >         [[alternative HTML version deleted]]
> >
> > _______________________________________________
> > Bioc-devel using r-project.org mailing list
> >
> https://secure-web.cisco.com/1CoMZlPPSNe-MfqZkOpNFvpMkwbnIVkEbPIxbET9FKoHMGCVzTeeTdPJGpD4PHivCSzZwalSMt8BeA1_Ab8Pa5gS2jCkg9_onfbYE3UAgbywg5GD1CrAN86qgN8FH4tjTwPBq95yDFIvYCamr14TUrSDkZKUvFhtAw7FR6bpJ_Ub9z2fU6f-G3Xw_FHRqcg6aM9xrpq4GmnfMOKO_Jlf10TJsdvhdReM9Phw2lV_EMy55ZjFYD5bteCpN4_qqRQb4_J6IbFYjlRQEi1A0DiwxC67Gzaf0QPTRszxXRxqPy4oancisQKzNmQJod-2cz9Oa/https%3A%2F%2Fstat.ethz.ch%2Fmailman%2Flistinfo%2Fbioc-devel
> >
>
>         [[alternative HTML version deleted]]
>
> _______________________________________________
> Bioc-devel using r-project.org mailing list
>
> https://secure-web.cisco.com/1CoMZlPPSNe-MfqZkOpNFvpMkwbnIVkEbPIxbET9FKoHMGCVzTeeTdPJGpD4PHivCSzZwalSMt8BeA1_Ab8Pa5gS2jCkg9_onfbYE3UAgbywg5GD1CrAN86qgN8FH4tjTwPBq95yDFIvYCamr14TUrSDkZKUvFhtAw7FR6bpJ_Ub9z2fU6f-G3Xw_FHRqcg6aM9xrpq4GmnfMOKO_Jlf10TJsdvhdReM9Phw2lV_EMy55ZjFYD5bteCpN4_qqRQb4_J6IbFYjlRQEi1A0DiwxC67Gzaf0QPTRszxXRxqPy4oancisQKzNmQJod-2cz9Oa/https%3A%2F%2Fstat.ethz.ch%2Fmailman%2Flistinfo%2Fbioc-devel
>
>
> This email message may contain legally privileged and/or confidential
> information. If you are not the intended recipient(s), or the employee or
> agent responsible for the delivery of this message to the intended
> recipient(s), you are hereby notified that any disclosure, copying,
> distribution, or use of this email message is prohibited. If you have
> received this message in error, please notify the sender immediately by
> e-mail and delete this email message from your computer. Thank you.
>
>
>
> --
> Cheers,
> Sokratis Kariotis
> PhD Student
> University of Sheffield, Medical School
> MedTech
> <https://secure-web.cisco.com/1j_t_6XlNHmK_Mlrd4WRabc9QOpzT2OGES5vH7ZXf-zkhvpeT6fGj6r1c6HMwcYrnxIzGZ6HwikAhhXIh8OkaEgWqigSPXAd_m0NPSjZf7cr7xi4b003k8sYSFAOfwcStP8WCMJQEHURgiHkNDvUmrUdfJYydQO9lMNOyfaP6SnxI2mQX21fOBWIj5wlIAVh9_pBFujbt_XfCBhHL495EtB_s0ntbiowBalE7bhEa4FullCdFTSex4VfICmSriWx91cSPmk1TzmAHv6KZtr7XqAgLH4OzGlGEUTMdjmcrYOoLTC5XpKAljIZMsCwu8hDP/https%3A%2F%2Fwww.facebook.com%2Fmedtechsheffield%2F>
> President
> Twitter: @s_kariotis
> <https://secure-web.cisco.com/13IN8xWDrADy-iyp1mknOrX5y2tJixhXPBcywL3EoIE7tOUCkSYs7hbAy2slZfzwMH3Bq9AnScXs3HK_KnDOO2kihBQdfM9nIHxnoa1vAkVFfYH8L_ns7w9KGqC0pzUOOxThE_ZMGVWk1LyQyf-RPrv_HY7RqQZo1IEYNirDTKWBu2lkLCH8qvs8lRMm79wx5eRwdZVYNH0uq7g7EcP_vvK9d8vQ534dzt0hOgHaDByQVi2reoXzwifR0pOYP-6LhdI15nbDtZHxMBmTvueysM77gfHBn7_IUHK6y9-biSIidTmH3GlJMkhk83x7UR5Jk/https%3A%2F%2Ftwitter.com%2Fs_kariotis>
> LinkedIn: http://www.linkedin.com/in/sokratiskariotis
> <http://secure-web.cisco.com/1h1oCsLmDI6MQdDDyPKrhabJrDBtBogVZA8wMdTLiZENtCtnsB9UQqak12XHMegX9sP0mimjSxawrR5u0VlKLv-D4lrX8u8A05PST1zfXM9VJX6E41Hj2-TOTZm9uOWc8hfxBrCT6UPjQ0X5pFh0sQRgC5tqu2Ks1EALVXZvSixGddS_zQ2C0bQhnc9KLJe8J3jtxPOkUz7QqCjcwpfgixL9ls_ysxmn2OGFxfiMwTmWgUXWcfWwvOXy6OhfeAl_IDK9USdONEsQETuVSgt7f2eVi5DJJBy_4eVwIVz3GV6iTGr2VjRBlh98HxZMAr-iP/http%3A%2F%2Fwww.linkedin.com%2Fin%2Fsokratiskariotis>
>
>
> This email message may contain legally privileged and/or confidential
> information. If you are not the intended recipient(s), or the employee or
> agent responsible for the delivery of this message to the intended
> recipient(s), you are hereby notified that any disclosure, copying,
> distribution, or use of this email message is prohibited. If you have
> received this message in error, please notify the sender immediately by
> e-mail and delete this email message from your computer. Thank you.
>

-- 
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

	[[alternative HTML version deleted]]