[Bioc-devel] updated package but the Multiple platform for BioC 3.11 is still using the previous one
Paola Rancoita
r@nco|t@@p@o|@ @end|ng |rom gm@||@com
Mon Jan 13 06:35:01 CET 2020
Dear Martin,
thanks a lot for the explanation. I verified and in the last run the
system used the updated package. The package did not get any error so
that it is now in the new version of bioconductor.
Thanks a lot,
Paola
Il 12/01/2020 08:31, Martin Morgan ha scritto:
> The build report says (left-hand side) that the build is based on the repo status as of 16:45 on Fri 10 Jan
>
> Snapshot Date: 2020-01-10 16:45:16 -0500 (Fri, 10 Jan 2020)
> URL: https://git.bioconductor.org/packages/mBPCR
> Branch: master
> Last Commit: 93a2ff2
> Last Changed Date: 2019-10-29 13:35:04 -0500 (Tue, 29 Oct 2019)
>
> And git log shows (printing from the 'Last Commit' shown above to the most recent commit)
>
> mBPCR master$ git log --format="%h %cd" 93a2ff2^..HEAD
> e5aae6f Sat Jan 11 07:59:19 2020 +0100
> 5d577db Sat Jan 11 07:57:36 2020 +0100
> fd3b974 Sat Jan 11 07:53:06 2020 +0100
> 802d7ee Sat Jan 11 07:50:53 2020 +0100
> 2fe29a6 Sat Jan 11 07:50:17 2020 +0100
> 2d04f13 Sat Jan 11 07:48:28 2020 +0100
> 51176e1 Sat Jan 11 07:47:03 2020 +0100
> 44abd70 Sat Jan 11 07:46:17 2020 +0100
> a730736 Sat Jan 11 07:45:21 2020 +0100
> dd25165 Sat Jan 11 07:44:26 2020 +0100
> 9fb05f5 Sat Jan 11 07:42:37 2020 +0100
> 44aebc0 Sat Jan 11 07:39:33 2020 +0100
> 93a2ff2 Tue Oct 29 13:35:04 2019 -0400
>
> So your commits missed the start of the build -- they will be picked up in the next builds, which are running now and will presumably post at about noon US Eastern time on Sunday. (I'm not sure what to specify to get the time offset to correctly match the build report...)
>
> It is a mystery why on the landing page the 'Details' section lists
>
> Version 1.41.1
>
> ...
>
> Martin
>
> On 1/12/20, 1:22 AM, "Bioc-devel on behalf of Paola Rancoita" <bioc-devel-bounces using r-project.org on behalf of rancoita.paola using gmail.com> wrote:
>
> Dear all,
>
> I am the maintainer of the package mBPCR. I was asked to update the
> package due to the deprecation of another package that I was using in my
> code. I updated the package (the new version is mBPCR 1.41.1) and I
> pushed the changes on both GitHub and Bioconductor. The Bioconductor
> devel page of the package now correctly reports the information of the
> updated package
> http://bioconductor.org/packages/3.11/bioc/html/mBPCR.html.
> Nevertheless, the build report of yesterday still reports errors because
> it refers to the older version of the package 1.41.0
> (http://bioconductor.org/checkResults/devel/bioc-LATEST/mBPCR/),
> although I updated the code several hours before all checks ran.
>
> I would like to know if it is simply an issue related to the
> synchronization (and thus today the system will check the correct
> version of the package) or I missed/did wrong some steps when I pushed
> the changes.
>
> Thanks in advanced.
>
> Best regards,
>
> Paola
>
>
>
>
> -------- Messaggio Inoltrato --------
> Oggetto: Re: Bioconductor mBPCR
> Data: Sat, 11 Jan 2020 15:31:28 +0100
> Mittente: Paola Rancoita <rancoita.paola using gmail.com>
> A: Shepherd, Lori <Lori.Shepherd using RoswellPark.org>
>
>
>
> Dear Prof. Sheperd,
>
> I would like to advise you that I changed the code (and updated the
> other files coherently) in order to avoid the usage of the package
> SNPchip. I updated both the versions of the package in GitHub and
> Bioconductor. I am only waiting for the results of the checks on the
> three platforms (on my computer the updated package passed all checks).
>
> Best regards,
>
> Paola
>
>
> Il 14/12/2019 12:21, Shepherd, Lori ha scritto:
> > Yes I can extend to January 12.� If you have any troubles please feel
> > free to ask on the bioc-devel using r-project.org Mailing list.
> > There are useful git help guides for updating your package
> > http://bioconductor.org/developers/how-to/git/
> >
> > Get Outlook for Android <https://aka.ms/ghei36>
> >
> > ------------------------------------------------------------------------
> > *From:* Paola Rancoita <rancoita.paola using gmail.com>
> > *Sent:* Friday, December 13, 2019 9:37:29 PM
> > *To:* Shepherd, Lori <Lori.Shepherd using RoswellPark.org>
> > *Cc:* marcus.hutter using anu.edu.au <marcus.hutter using anu.edu.au>
> > *Subject:* Re: Bioconductor mBPCR
> >
> > Dear Prof. Sheperd,
> >
> > I am sorry not having answering you before. Somehow the previous
> > emails were filtered by my mail account and I did not realized it.
> >
> > I surely want to maintain my package, but I need some time to
> > understand how I can fix the issues. I will try to do it as soon as
> > possible but this is a very busy period for me.
> >
> > Moreover, I need to understand how the new procedure for updating the
> > code works since last time I used SVN.� Can you extend my deadline to
> > January 12th?
> >
> > Thank you in advanced.
> >
> > Best regards,
> >
> > Paola
> >
> >
> > Il 13/12/2019 15:35, Shepherd, Lori ha scritto:
> >> This is your second warning. �If the package is not fixed by the end
> >> of the month we will begin the deprecation process for your package.
> >>
> >>
> >> Lori Shepherd
> >>
> >> Bioconductor Core Team
> >>
> >> Roswell Park Comprehensive Cancer Center
> >>
> >> Department of Biostatistics & Bioinformatics
> >>
> >> Elm & Carlton Streets
> >>
> >> Buffalo, New York 14263
> >>
> >> ------------------------------------------------------------------------
> >> *From:* Shepherd, Lori
> >> *Sent:* Monday, November 18, 2019 11:03 AM
> >> *To:* rancoita.paola using gmail.com <mailto:rancoita.paola using gmail.com>
> >> <rancoita.paola using gmail.com> <mailto:rancoita.paola using gmail.com>;
> >> marcus.hutter using anu.edu.au <mailto:marcus.hutter using anu.edu.au>
> >> <marcus.hutter using anu.edu.au> <mailto:marcus.hutter using anu.edu.au>
> >> *Subject:* Bioconductor mBPCR
> >> Please be advised your package is failing on all three platforms in
> >> devel 3.11
> >> http://bioconductor.org/checkResults/devel/bioc-LATEST/mBPCR
> >>
> >> The package SNPchip has been user requested deprecated in
> >> Bioconductor 3.10. �You will have to alter your package to not
> >> utilize SNPchip to avoid your own package being deprecated. �We made
> >> you aware of this deprecation back in May and the SNPchip packages
> >> has had a deprecation since then as well.
> >>
> >> The other alternative is to take over maintainership of SNPchip
> >> package but you will need to reach out to the maintainer of the
> >> package to formalize this request.
> >>
> >> Cheers,
> >>
> >> Lori Shepherd
> >>
> >> Bioconductor Core Team
> >>
> >> Roswell Park Comprehensive Cancer Center
> >>
> >> Department of Biostatistics & Bioinformatics
> >>
> >> Elm & Carlton Streets
> >>
> >> Buffalo, New York 14263
> >>
> >>
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