Re: [Bioc-devel] "git push upstream master" does not work

2020-02-16 Thread Neumann, Steffen 
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 +, 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 <
> > sneum...@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%2FcheckResults%2Fdevel%2Fbioc-LATEST%2FatSNP%2Fdata=02%7C01%7CSunyoung.Shin%40utdallas.edu%7C5f2f92f942374791fab308d7b37c5b94%7C8d281d1d9c4d4bf7b16e032d15de9f6c%7C0%7C1%7C637175219027370173sdata=ygVFK7QyLbTTmaq3%2B54W5%2Fg7CL2w0YBMdJf4ZgHImCw%3Dreserved=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 +, 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%2Fmailman%2Flistinfo%2Fbioc-develdata=02%7C01%7CSunyoung.Shin%40utdallas.edu%7C5f2f92f942374791fab308d7b37c5b94%7C8d281d1d9c4d4bf7b16e032d15de9f6c%7C0%7C1%7C637175219027370173sdata=nB10%2BrZJCkXf5CWqHXyQxqaQgIUvP4%2FnkRhLzAwiLnE%3Dreserved=0
> >  -- 
> > 
> > Current bits of interest:
> > 
> > * Computational Metabolomics PhD Position @ IPB
> > 
> > 
https://nam02.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.ipb-halle.de%2Fen%2Fcareer%2Fjob-vacancies%2Fjoboffer-detail%2Fwissenschaftlichen-mitarbeiterin-doktorandin-bioinformatikmetabolomics-mwd%2Fdata=02%7C01%7CSunyoung.Shin%40utdallas.edu%7C5f2f92f942374791fab308d7b37c5b94%7C8d281d1d9c4d4bf7b16e032d15de9f6c%7C0%7C1%7C637175219027370173sdata=5ukkqm7owpb0KVwgtS8loZvZ7WmuLKmgfwzgrkihVb0%3Dreserved=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%2Fdata=02%7C01%7CSunyoung.Shin%40utdallas.edu%7C5f2f92f942374791fab308d7b37c5b94%7C8d281d1d9c4d4bf7b16e032d15de9f6c%7C0%7C1%7C637175219027370173sdata=%2Bjxec3fj9e%2F%2Fd7CvOueC%2FAWZ%2BGYiRC7Xpx9%2FSanT5P4%3Dreserved=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%2Fhupo-psi-meeting-2020data=02%7C01%7CSunyoung.Shin%40utdallas.edu%7C5f2f92f942374791fab308d7b37c5b94%7C8d281d1d9c4d4bf7b16e032d15de9f6c%7C0%7C1%7C637175219027370173sdata=cAjXisCXzOCA9z%2FUXbSi%2F2Oz83vC6fEMlRL6WBH1uTQ%3Dreserved=0
> > 
> > ---
> > IPB HalleAG Massenspektrometrie & Bioinformatik
> > Dr. Steffen Neumann  
> > https://nam02.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.IPB-Halle.DEdata=02%7C01%7CSunyoung.Shin%40utdallas.edu%7C5f2f92f942374791fab308d7b37c5b94%7C8d281d1d9c4d4bf7b16e032d15de9f6c%7C0%7C1%7C637175219027370173sdata=3jUg1A%2B3n8KpUR%2FBJEwQVQ%2FRcjf6KU4Ilm2kQUl3XP0%3Dreserved=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 HalleAG Massenspektrometrie & Bioinformatik
Dr. Steffen Neumann  http://www.IPB-Halle.DE
Weinberg 3   Tel.

Re: [Bioc-devel] "git push upstream master" does not work

2020-02-16 Thread Shin, Sunyoung 
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 
mailto:sneum...@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%2FcheckResults%2Fdevel%2Fbioc-LATEST%2FatSNP%2Fdata=02%7C01%7CSunyoung.Shin%40utdallas.edu%7C5f2f92f942374791fab308d7b37c5b94%7C8d281d1d9c4d4bf7b16e032d15de9f6c%7C0%7C1%7C637175219027370173sdata=ygVFK7QyLbTTmaq3%2B54W5%2Fg7CL2w0YBMdJf4ZgHImCw%3Dreserved=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 +, 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
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--

Current bits of interest:

* Computational Metabolomics PhD Position @ IPB

https://nam02.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.ipb-halle.de%2Fen%2Fcareer%2Fjob-vacancies%2Fjoboffer-detail%2Fwissenschaftlichen-mitarbeiterin-doktorandin-bioinformatikmetabolomics-mwd%2Fdata=02%7C01%7CSunyoung.Shin%40utdallas.edu%7C5f2f92f942374791fab308d7b37c5b94%7C8d281d1d9c4d4bf7b16e032d15de9f6c%7C0%7C1%7C637175219027370173sdata=5ukkqm7owpb0KVwgtS8loZvZ7WmuLKmgfwzgrkihVb0%3Dreserved=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%2Fdata=02%7C01%7CSunyoung.Shin%40utdallas.edu%7C5f2f92f942374791fab308d7b37c5b94%7C8d281d1d9c4d4bf7b16e032d15de9f6c%7C0%7C1%7C637175219027370173sdata=%2Bjxec3fj9e%2F%2Fd7CvOueC%2FAWZ%2BGYiRC7Xpx9%2FSanT5P4%3Dreserved=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%2Fhupo-psi-meeting-2020data=02%7C01%7CSunyoung.Shin%40utdallas.edu%7C5f2f92f942374791fab308d7b37c5b94%7C8d281d1d9c4d4bf7b16e032d15de9f6c%7C0%7C1%7C637175219027370173sdata=cAjXisCXzOCA9z%2FUXbSi%2F2Oz83vC6fEMlRL6WBH1uTQ%3Dreserved=0

---
IPB HalleAG Massenspektrometrie & Bioinformatik
Dr. Steffen Neumann  
https://nam02.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.IPB-Halle.DEdata=02%7C01%7CSunyoung.Shin%40utdallas.edu%7C5f2f92f942374791fab308d7b37c5b94%7C8d281d1d9c4d4bf7b16e032d15de9f6c%7C0%7C1%7C637175219027370173sdata=3jUg1A%2B3n8KpUR%2FBJEwQVQ%2FRcjf6KU4Ilm2kQUl3XP0%3Dreserved=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


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Re: [Bioc-devel] "git push upstream master" does not work

2020-02-16 Thread Neumann, Steffen 
Hi,

please have a look at the build report first:
http://bioconductor.org/checkResults/devel/bioc-LATEST/atSNP/

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 +, 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://stat.ethz.ch/mailman/listinfo/bioc-devel
-- 

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 HalleAG 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
___
Bioc-devel@r-project.org mailing list
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[Bioc-devel] "git push upstream master" does not work

2020-02-16 Thread Shin, Sunyoung 
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
___
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Re: [Bioc-devel] Updates to SingleCellExperiment class structure - no action required

2020-02-16 Thread Aaron Lun 

That would be correct.

On 2/16/20 6:38 AM, Kasper Daniel Hansen wrote:
It sounds to me that the class definition / structure is updated. You 
should also have an associated updateObject() method to deal with this; 
that's tradition. Of course, you may already have addressed this and 
just not written about it in your email.


On Sun, Feb 16, 2020 at 3:51 AM Aaron Lun 
> wrote:


Dear list,

As of version 1.9.2, the SingleCellExperiment class structure has been
updated so that "sizeFactors()<-" will store values in a "sizeFactor"
field in the "colData()", rather than the internal metadata. This aims
to improve interoperability of the SCE size factors with functions that
retrieve information from the column metadata; see GitHub for details.

This change occurs under the hood in the "sizeFactors()" getter and
setter functions, so no action should be required from users who were
already using those functions to manipulate the SCE size factors.
Nonetheless, downstream developers should keep an eye on their unit
tests as some of the more fragile checks may fail, e.g., if they
hard-coded the expected column names of the "colData" of an SCE.

Version 1.9.2. also removes a bunch of deprecated functionality from
the
package, which may cause unrelated failures; though this was pretty
esoteric stuff that didn't see a lot of use in the first place.

Best,

-A

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--
Best,
Kasper


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Re: [Bioc-devel] Updates to SingleCellExperiment class structure - no action required

2020-02-16 Thread Kasper Daniel Hansen 
It sounds to me that the class definition / structure is updated. You
should also have an associated updateObject() method to deal with this;
that's tradition. Of course, you may already have addressed this and just
not written about it in your email.

On Sun, Feb 16, 2020 at 3:51 AM Aaron Lun <
infinite.monkeys.with.keyboa...@gmail.com> wrote:

> Dear list,
>
> As of version 1.9.2, the SingleCellExperiment class structure has been
> updated so that "sizeFactors()<-" will store values in a "sizeFactor"
> field in the "colData()", rather than the internal metadata. This aims
> to improve interoperability of the SCE size factors with functions that
> retrieve information from the column metadata; see GitHub for details.
>
> This change occurs under the hood in the "sizeFactors()" getter and
> setter functions, so no action should be required from users who were
> already using those functions to manipulate the SCE size factors.
> Nonetheless, downstream developers should keep an eye on their unit
> tests as some of the more fragile checks may fail, e.g., if they
> hard-coded the expected column names of the "colData" of an SCE.
>
> Version 1.9.2. also removes a bunch of deprecated functionality from the
> package, which may cause unrelated failures; though this was pretty
> esoteric stuff that didn't see a lot of use in the first place.
>
> Best,
>
> -A
>
> ___
> Bioc-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>


-- 
Best,
Kasper

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