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.sheph...@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@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.nikolaie...@gmail.com> > *Sent:* Thursday, July 6, 2023 1:58 AM > *To:* Sokratis Kariotis <sokratiskario...@gmail.com> > *Cc:* Kern, Lori <lori.sheph...@roswellpark.org>; bioc-devel@r-project.org > <bioc-devel@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 <sokratiskario...@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.sheph...@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-boun...@r-project.org> on behalf of > Oleksii Nikolaienko <oleksii.nikolaie...@gmail.com> > *Sent:* Thursday, June 29, 2023 5:36 AM > *To:* Sokratis Kariotis <sokratiskario...@gmail.com> > *Cc:* bioc-devel@r-project.org <bioc-devel@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 < > sokratiskario...@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@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@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. 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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. 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