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

Mon Jul 31 09:36:29 CEST 2023

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
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> >
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> > >
> > > _______________________________________________
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> >
> >
> > --
> > 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
> > <
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> >
> >
> >
> > This email message may contain legally privileged and/or confidential
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> > agent responsible for the delivery of this message to the intended
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> >
> >
> >
> > --
> > 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
> > <
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> >
> > LinkedIn: http://www.linkedin.com/in/sokratiskariotis
> > <
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> >
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> > agent responsible for the delivery of this message to the intended
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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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