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List: bioc-devel
Subject: Re: [Bioc-devel] "git push upstream master" does not work
From: "Neumann, Steffen" <sneumann () ipb-halle ! de>
Date: 2020-02-17 7:59:16
Message-ID: 4f6541677b3f0bdc8cae0534eeb7dadd598cabed.camel () ipb-halle ! de
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Hi,
the source package on 3.11/bioc/html/atSNP.html
will only be updated with a new one if all checks succeed.
This prevents that you download a broken package.
Nowadays one would call that a continuous integration pipeline,
but the BioC team already does that since, um, more than a decade ;-)
Yours,
Steffen
On Mon, 2020-02-17 at 07:44 +0000, Shin, Sunyoung wrote:
> Hello Steffen,
>
> Thank you for the response. You are right, and I also recognized it.
> However, I don't see the updates from the source package I downloaded
> from the package webpage at
> http://bioconductor.org/packages/3.11/bioc/html/atSNP.html. I updated
> both DESCRIPTION and graphic.R, but neither were updated.
>
>
> Best,
> Sunyoung
>
> > On Feb 17, 2020, at 1:38 AM, Neumann, Steffen <
> > sneumann@ipb-halle.de> wrote:
> >
> > Hi,
> >
> > please have a look at the build report first:
> >
https://nam02.safelinks.protection.outlook.com/?url=http%3A%2F%2Fbioconductor.org%2Fch \
eckResults%2Fdevel%2Fbioc-LATEST%2FatSNP%2F&data=02%7C01%7CSunyoung.Shin%40utdalla \
s.edu%7C5f2f92f942374791fab308d7b37c5b94%7C8d281d1d9c4d4bf7b16e032d15de9f6c%7C0%7C1%7C \
637175219027370173&sdata=ygVFK7QyLbTTmaq3%2B54W5%2Fg7CL2w0YBMdJf4ZgHImCw%3D&reserved=0
> >
> > where your commit 2020-02-12 has been picked up.
> > The check has an ERROR, most likely in the examples
> > to plotMotifMatch().
> >
> > Also, I guess the version 1.3.0 was the version number
> > bumped after the last BioC release, so consider
> > to bump atSNP to 1.3.1 with you next commit.
> >
> > Hope that helped,
> >
> > Yours,
> > Steffen
> >
> >
> > On Mon, 2020-02-17 at 05:10 +0000, Shin, Sunyoung wrote:
> > > Dear all,
> > >
> > > I used "git push upstream master" to commit changes for atSNP
> > > package
> > > to Bioconductor 4 days ago. But, Bioconductor does not take the
> > > updated version, but sticks with the old version of the package,
> > > which I committed in October. Does someone have an idea about how
> > > to
> > > fix it? Thanks.
> > >
> > >
> > > Best,
> > > Sunyoung
> > > _______________________________________________
> > > Bioc-devel@r-project.org mailing list
> > >
https://nam02.safelinks.protection.outlook.com/?url=https%3A%2F%2Fstat.ethz.ch%2Fmailm \
an%2Flistinfo%2Fbioc-devel&data=02%7C01%7CSunyoung.Shin%40utdallas.edu%7C5f2f92f94 \
2374791fab308d7b37c5b94%7C8d281d1d9c4d4bf7b16e032d15de9f6c%7C0%7C1%7C637175219027370173&sdata=nB10%2BrZJCkXf5CWqHXyQxqaQgIUvP4%2FnkRhLzAwiLnE%3D&reserved=0
> > --
> >
> > Current bits of interest:
> >
> > * Computational Metabolomics PhD Position @ IPB
> >
> >
https://nam02.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.ipb-halle.de%2Fe \
n%2Fcareer%2Fjob-vacancies%2Fjoboffer-detail%2Fwissenschaftlichen-mitarbeiterin-doktor \
andin-bioinformatikmetabolomics-mwd%2F&data=02%7C01%7CSunyoung.Shin%40utdallas.edu \
%7C5f2f92f942374791fab308d7b37c5b94%7C8d281d1d9c4d4bf7b16e032d15de9f6c%7C0%7C1%7C63717 \
5219027370173&sdata=5ukkqm7owpb0KVwgtS8loZvZ7WmuLKmgfwzgrkihVb0%3D&reserved=0
> >
> >
> > * Leibniz Plant Biochemistry Symposium, 14./15.05.2020, Halle
> >
> > https://nam02.safelinks.protection.outlook.com/?url=https%3A%2F%2Fevents.ipb-halle \
> > .de%2Fevent%2F60%2F&data=02%7C01%7CSunyoung.Shin%40utdallas.edu%7C5f2f92f94237 \
> > 4791fab308d7b37c5b94%7C8d281d1d9c4d4bf7b16e032d15de9f6c%7C0%7C1%7C6371752190273701 \
> > 73&sdata=%2Bjxec3fj9e%2F%2Fd7CvOueC%2FAWZ%2BGYiRC7Xpx9%2FSanT5P4%3D&reserved=0
> >
> > * HUPO PSI spring meeting, 23.-25.03.2020, San Diego, CA
> >
> > https://nam02.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.psidev.info%2 \
> > Fhupo-psi-meeting-2020&data=02%7C01%7CSunyoung.Shin%40utdallas.edu%7C5f2f92f94 \
> > 2374791fab308d7b37c5b94%7C8d281d1d9c4d4bf7b16e032d15de9f6c%7C0%7C1%7C6371752190273 \
> > 70173&sdata=cAjXisCXzOCA9z%2FUXbSi%2F2Oz83vC6fEMlRL6WBH1uTQ%3D&reserved=0 \
> >
> > ---
> > IPB Halle AG Massenspektrometrie & Bioinformatik
> > Dr. Steffen Neumann
> > https://nam02.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.IPB-Halle.DE& \
> > amp;data=02%7C01%7CSunyoung.Shin%40utdallas.edu%7C5f2f92f942374791fab308d7b37c5b94 \
> > %7C8d281d1d9c4d4bf7b16e032d15de9f6c%7C0%7C1%7C637175219027370173&sdata=3jUg1A%2B3n8KpUR%2FBJEwQVQ%2FRcjf6KU4Ilm2kQUl3XP0%3D&reserved=0
> > Weinberg 3 Tel. +49 (0) 345 5582 - 1470
> > 06120 Halle +49 (0) 345 5582 - 0
> > sneumann(at)IPB-Halle.DE Fax. +49 (0) 345 5582 - 1409
>
>
--
Current bits of interest:
* Computational Metabolomics PhD Position @ IPB
https://www.ipb-halle.de/en/career/job-vacancies/joboffer-detail/wissenschaftlichen-mitarbeiterin-doktorandin-bioinformatikmetabolomics-mwd/
* Leibniz Plant Biochemistry Symposium, 14./15.05.2020, Halle
https://events.ipb-halle.de/event/60/
* HUPO PSI spring meeting, 23.-25.03.2020, San Diego, CA
http://www.psidev.info/hupo-psi-meeting-2020
---
IPB Halle AG Massenspektrometrie & Bioinformatik
Dr. Steffen Neumann http://www.IPB-Halle.DE
Weinberg 3 Tel. +49 (0) 345 5582 - 1470
06120 Halle +49 (0) 345 5582 - 0
sneumann(at)IPB-Halle.DE Fax. +49 (0) 345 5582 - 1409
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