[Bioc-devel] Omada package failing due to removed dependency
Sokratis Kariotis
@okr@t|@k@r|ot|@ @end|ng |rom gm@||@com
Mon Jul 31 13:27:21 CEST 2023
Tried but its Already up to date.
On Mon, 31 Jul 2023, 7:22 pm Martin Grigorov, <martin.grigorov using gmail.com>
wrote:
> 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 <
> sokratiskariotis using 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 <grimbough using 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 <
>> > sokratiskariotis using 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.Shepherd using 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 <sokratiskariotis using gmail.com>
>> >> > *Sent:* Monday, July 10, 2023 10:27 AM
>> >> > *To:* Kern, Lori <Lori.Shepherd using RoswellPark.org>
>> >> > *Cc:* Oleksii Nikolaienko <oleksii.nikolaienko using gmail.com>;
>> >> > bioc-devel using r-project.org <bioc-devel using 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.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:
>> >> >
>> >>
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>> >> > >
>> >> > > [[alternative HTML version deleted]]
>> >> > >
>> >> > > _______________________________________________
>> >> > > Bioc-devel using r-project.org mailing list
>> >> > >
>> >> >
>> >>
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>> >> > >
>> >> >
>> >> > [[alternative HTML version deleted]]
>> >> >
>> >> > _______________________________________________
>> >> > Bioc-devel using r-project.org mailing list
>> >> >
>> >> >
>> >>
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>> >> >
>> >> >
>> >> > This email message may contain legally privileged and/or confidential
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>> >> >
>> >> >
>> >> > --
>> >> > Cheers,
>> >> > Sokratis Kariotis
>> >> > PhD Student
>> >> > University of Sheffield, Medical School
>> >> > MedTech
>> >> > <
>> >>
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>> >> >
>> >> > 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
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>> employee
>> >> or
>> >> > agent responsible for the delivery of this message to the intended
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>> >> > 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/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
>> >> > <
>> >>
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>> >> >
>> >> >
>> >> > This email message may contain legally privileged and/or confidential
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>> employee
>> >> or
>> >> > agent responsible for the delivery of this message to the intended
>> >> > recipient(s), you are hereby notified that any disclosure, copying,
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>> >> > 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 using 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
>>
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>>
>> _______________________________________________
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