Hi Sokratis, You need to do "git pull --rebase" before trying to push. Most probably the version has been bumped upstream.
Regards, Martin On Mon, Jul 31, 2023 at 2:16 PM Sokratis Kariotis < sokratiskario...@gmail.com> wrote: > Hey all, > > I created a new key and now I can commit etc but there is a conflict that > is not allowing me to go ahead. > > My commands: > git add . > git commit -m "Update metrics" > git push upstream main:devel > > *The above results in the following error:* > > > > > > > > > > > > > > *Enumerating objects: 19, done.Counting objects: 100% (17/17), done.Delta > compression using up to 16 threadsCompressing objects: 100% (11/11), > done.Writing objects: 100% (11/11), 4.78 KiB | 4.78 MiB/s, done.Total 11 > (delta 7), reused 0 (delta 0), pack-reused 0remote: Error: You cannot push > without resolving merge conflicts.remote:remote: Please check the files in > the commit pushed to the git-serverremote: for merge conflict markers like > '<<<<<<<', '========', '>>>>>>>'.remote:To > git.bioconductor.org:packages/omada ! [remote rejected] main -> devel > (pre-receive hook declined)error: failed to push some refs to > 'git.bioconductor.org:packages/omada'* > > > > On Mon, Jul 31, 2023 at 3:36 PM Mike Smith <grimbo...@gmail.com> wrote: > > > Hi Sokratis, > > > > Everything in Bioconductor is built around the central Bioconductor git > > repositories. The only way to get changes out to users is to commit them > > to git.bioconductor.org and then the build system will pick those up, > run > > the tests and checks, create new versions of packages, and make them > > available for distribution. > > > > Perhaps you can include the git command you're running to submit the > > changes and a copy of the exact error you're receiving. That might help > > the team suggest a solution. > > > > Best regards, > > Mike > > > > On Fri, 28 Jul 2023 at 08:32, Sokratis Kariotis < > > sokratiskario...@gmail.com> wrote: > > > >> 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.sheph...@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 <sokratiskario...@gmail.com> > >> > *Sent:* Monday, July 10, 2023 10:27 AM > >> > *To:* Kern, Lori <lori.sheph...@roswellpark.org> > >> > *Cc:* Oleksii Nikolaienko <oleksii.nikolaie...@gmail.com>; > >> > bioc-devel@r-project.org <bioc-devel@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.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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Thank you. > >> > > >> > > >> > > >> > -- > >> > Cheers, > >> > Sokratis Kariotis > >> > PhD Student > >> > University of Sheffield, Medical School > >> > MedTech > >> > < > >> > https://secure-web.cisco.com/1EbU56JtxgdwdoJoUZSkRfzViaYzT5UpVv7Wn4bHXpw7_iNUn_et52ACzsUWbzs2Du309DRo4wtQgGcVuDWVIPx5vtUsOovTfb6A-HIBq3NSje0v9lBELQCeYZvBzjm0t2kAdce_aXnf8m3mH7-cYUd0C6Wu2R7erAmQwuoI22clJuDcztgq-JhMyIczKcN_UhCUNAzJ-b_kHKI3mxzoO76dg0N8g2MIp_pHBC3x0rVQno00wElfOCtr3poLLQZwpcZCTPoAQmYs-Dfin4Lwoy2-B9Qn5txtHoCygaeneDxgiTHVOAuILij26i2Q9cgAQ/https%3A%2F%2Fwww.facebook.com%2Fmedtechsheffield%2F > >> > > >> > President > >> > Twitter: @s_kariotis > >> > < > >> > https://secure-web.cisco.com/1RhhMUBj_mRXVHCOKQB6We-WITw332tSjBMu7_BVsJxiUs4tE1EO3zyDwMwygB4WIh8AaEo6gPZZcTCl81Qy6PrClu7SxtC3TbzSz30XZlzOjZukAKbowWtBHiJ36lG-a4U_5dYeM6CKUfdb7MaXesg8oLlZscBYO4fVVKMdcjn0NvtsvF-RfOVtu8tVFiOw6yvb3Rt1g-2xPBcrCEEn69L2z59SnUHY8pboO84aP6YBHHPhMHXw1Quz5J7KfGN3qlcX3kehRg0RIISJKLCdu87PnMhtcbODE0T15xmjyc1mUYKmjlmwghgZF4m-UzFoP/https%3A%2F%2Ftwitter.com%2Fs_kariotis > >> > > >> > LinkedIn: http://www.linkedin.com/in/sokratiskariotis > >> > < > >> > http://secure-web.cisco.com/1QlRJ-HwDhYoeQZGt2FCzKpzCEleTeJuBprI0G9qystL3HbJH4unSUkFhwBB5vlm1EWz9u50EG4S0Xnv38OXhu3-ioroUBcS0KG6x7V3cFf73lNR3mJnwnqVqzPtq9gIMtUxwnPPzS6sHVbJhDi2CyejXNt0HoO5oRi4T3Ruca3MN7ZxxXJd2gbyGVGryXBDFLrVBlg3KZ-3_m8AFoTvBpUvWv7fs0vGBQ2lWUXSoQ7JYARZ0vy5mW0a4kK2EzbxCWaOFLR6JcbDwA3T9BO006AtSM2onHVqveK_jx2VZB6CvZsLrR-VJ4j41A8IvYfuQ/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]] > >> > >> _______________________________________________ > >> Bioc-devel@r-project.org mailing list > >> https://stat.ethz.ch/mailman/listinfo/bioc-devel > >> > > > > -- > 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]] > > _______________________________________________ > Bioc-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/bioc-devel > [[alternative HTML version deleted]] _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
