Re: [Bioc-devel] autonomics : nebbiolo (only) fails to locate weave

2023-11-15 Thread Jennifer Wokaty 
There were some issues with that version of R-devel, so we updated R on Linux 
devel builder yesterday.  The error message that appears today is different for 
autonomics and similar to what is reported on the arm64 linux devel builder. 
I'm updating R on the Mac and Windows devel builders today so the errors may be 
more consistent in the report in the next day or so.

Jennifer Wokaty (they/them)

Waldron Lab at CUNY SPH
Bioconductor Core Team

From: Bioc-devel  on behalf of Aditya Bhagwat 
via Bioc-devel 
Sent: Tuesday, November 14, 2023 4:23 AM
To: bioc-devel@r-project.org 
Subject: [Bioc-devel] autonomics : nebbiolo (only) fails to locate weave

* This email originates from a sender outside of CUNY. Verify the sender before 
replying or clicking on links and attachments. *

Dear BioC devel,

autonomics devel install/build/checks:
https://nam02.safelinks.protection.outlook.com/?url=https%3A%2F%2Furldefense.com%2Fv3%2F__https%3A%2F%2Fbioconductor.org%2FcheckResults%2Fdevel%2Fbioc-LATEST%2Fautonomics%2F__%3B!!PxiZbSOawA!IgmJQYkJiE1CYBM8ZqmpFDAktZXlKG3vQBZ46ZwM4E_ampRc78FQsVYDR1d9ibXt2-afvLKrWo3CZPAd-qfHmd4N1zY07ObozA%24=05%7C01%7Cjennifer.wokaty%40sph.cuny.edu%7C09ae275414054935240008dbe4f3643e%7C6f60f0b35f064e099715989dba8cc7d8%7C0%7C0%7C638355506283269639%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C=XUNdcigTbWuD%2FNTokrj98CUSb98ygmQBopJSE7APe1E%3D=0
fine on palomino3 (win) and merida1 (mac).
'fails to locate weave' on nebbiolo (ubuntu).

Could this be a nebbiolo rather than an autonomics issue?

Thankyou : )

Aditya






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Biological Pharmacological Center � Room A406
Tel.: +49 6421 28 27403


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Translational Proteomics � Philipps-University Marburg
Biological Pharmacological Center � Room A406
Tel.: +49 6421 28 27403

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Re: [Bioc-devel] Build issue on nebbiolo2 for DEWSeq

2023-11-15 Thread Hervé Pagès 
Hi Sudeep,

I don't see magrittr in any of the Depends, Imports, or Suggests field 
of DEWSeq.

Remember that any function or symbol you use from another package 
requires that you declare that package in one of these fields. In this 
case, since you only use %>% in the vignette, then you only need to put 
magrittr in the Suggests field. You don't need to import it.

However, as suggested by Kristian, why not just use R basic pipe "|>" 
instead?

Best,

H.

On 11/14/23 23:23, Biohentze wrote:
> Dear all,
>
> We are facing build issue on nebbiolo2 on our vignette for the package 
> DEWSeq. The issue is that we use magittr pipe (%>%) in the vignette and the 
> issue occurs only on the linux machine.
> Checks, builds and installation completes successfully on windows and mac. 
> Here is the complete build 
> report:https://master.bioconductor.org/checkResults/3.18/bioc-LATEST/DEWSeq/nebbiolo2-checksrc.html
>
>   Could you please look into it  ?
>
> Thank you in advance,
> Sudeep.
>
>   [[alternative HTML version deleted]]
>
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[Bioc-devel] Single Package Builder for new submission

2023-11-15 Thread Kern, Lori via Bioc-devel 
We will be updating the single package builder for new package submissions to 
run on the devel version of Bioconductor (3.19) and R (4.4).  During the update 
period there may be periods of intermittent downtime where build on demand is 
unavailable.  We appreciate your understanding during this time.


Lori Shepherd - Kern

Bioconductor Core Team

Roswell Park Comprehensive Cancer Center

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263


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Re: [Bioc-devel] Diverging version numbering on Bioconductor RELEASE

2023-11-15 Thread migdal migdal 
Awesome, thanks for the response!

I think it should be possible to put what you are doing manually into
GithubActions script, but I am not sure how to do that.

On Wed, Nov 15, 2023, 12:12 Neumann, Steffen  wrote:

> Hi,
>
> so far I am doing this manually, I have my github as remote origin,
> and the bioc git as upstream, and indeed after the releases I pull from
> upstream the changed version number and push it to my origin on github.
>
> Yours,
> Steffen
>
> On Sat, 2023-11-11 at 09:35 +0100, migdal migdal wrote:
> > Hi guys,
> >
> > recently I have realized that the version number in one of my
> > packages does
> > not match with the version in the bioconductor repository (
> > https://github.com/Genentech/midasHLA/issues/27
> > ). The reason is that, while
> > I have been doing no changes past the last few releases a version
> > bump was
> > happening on each Bioconductor RELEASE.
> >
> > Does anyone use some automated way to synchronise between the
> > repositories?
> > GitHub Actions would be an ideal solution.
> >
> > Cheers Maciek
> >
> > [[alternative HTML version deleted]]
> >
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Re: [Bioc-devel] Diverging version numbering on Bioconductor RELEASE

2023-11-15 Thread Neumann, Steffen 
Hi,

so far I am doing this manually, I have my github as remote origin,
and the bioc git as upstream, and indeed after the releases I pull from
upstream the changed version number and push it to my origin on github.

Yours,
Steffen

On Sat, 2023-11-11 at 09:35 +0100, migdal migdal wrote:
> Hi guys,
>
> recently I have realized that the version number in one of my
> packages does
> not match with the version in the bioconductor repository (
> https://github.com/Genentech/midasHLA/issues/27
> ). The reason is that, while
> I have been doing no changes past the last few releases a version
> bump was
> happening on each Bioconductor RELEASE.
>
> Does anyone use some automated way to synchronise between the
> repositories?
> GitHub Actions would be an ideal solution.
>
> Cheers Maciek
>
> [[alternative HTML version deleted]]
>
> ___
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> https://stat.ethz.ch/mailman/listinfo/bioc-devel

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* 2nd ELIXIR-DE Hackathon, 11-15 December 2023 in Bielefeld
 https://www.denbi.de/de-nbi-events/1547-biohackathon-germany-2


---
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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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Re: [Bioc-devel] Build issue on nebbiolo2 for DEWSeq

2023-11-15 Thread Kristian Ullrich 
Dear Sudeep,

Have you tried to use the R basic pipe "|>" instead of the magrittr pipe?

If you use it directly in your R function you could add in the corresponding 
function the following line:

@importFrom magrittr %>%

Best regards

Kristian
-- 
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Max Planck Institute
For Evolutionary Biology

Scientific IT group
Department of Evolutionary Genetics
August Thienemann Str. 2
24306 Plön
Germany
+49 4522 763 313
ullr...@evolbio.mpg.de

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> On 15. Nov 2023, at 08:23, Biohentze  wrote:
> 
> Dear all,
> 
> We are facing build issue on nebbiolo2 on our vignette for the package 
> DEWSeq. The issue is that we use magittr pipe (%>%) in the vignette and the 
> issue occurs only on the linux machine.
> Checks, builds and installation completes successfully on windows and mac. 
> Here is the complete build report: 
> https://master.bioconductor.org/checkResults/3.18/bioc-LATEST/DEWSeq/nebbiolo2-checksrc.html
> 
> Could you please look into it  ?
> 
> Thank you in advance,
> Sudeep.
> 
>   [[alternative HTML version deleted]]
> 
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