Re: [Bioc-devel] [question about class extension]

[migdal migdal]

Hi Delphine,

I had a similar dilemma while developing midasHLA
 package. There, we wanted to have
unique features names across all experiments and colData as well as
mandatory metadata. To this end I wrote a new class specific to my package
that extends MAE. I had some negative comments
 regarding
this solution (see R code section of the comment by LTLA; it might help you
decide how to approach your particular case), but IMO it works nicely.

Best Maciek

On Wed, 24 Jan 2024 at 14:43, Sean Maden  wrote:

>  There aren't strict standards imposed on many of the packages in
> Bioconductor introducing classes, but many other packages extend and impose
> standards and constraints for given areas/fields/subjects.
>
> If you are considering this route, something like the following could work
> to determine if introducing metadata features and restrictions is the route
> to take:
>
> libraryVector <-
>   c("MultiAssayExperiment", "SummarizedExperiment",
> "SingleCellExperiment", "SpatialExperiment")
>
> # Try something like this to test your candidate data classes:
>
> testClass <- function(libraryName, functionString){
>   # libraryName : valid class library
>   eval(parse(text = paste0(functionString,"(",libraryName,")")))
> }
>
> for(libraryName in libraryVector){
>   testClass(libraryName, "library")
>   testClass(libraryName, "new <- ")
>
>   metadata(new) #
>
>   testClass("new", "rm")
>   testClass(libraryName, "detach")
> }
>
> There may be better ways to harmonize and share the data with collaborators
> as a flat table.
>
> MAE has extensive documentation and there is also a cheatsheet provided to
> help out with tasking.
>
> See also: DOI: 10.18129/B9.bioc.MultiAssayExperiment
>
> Sean
>
> On Tue, Jan 23, 2024 at 5:45 AM Delphine Charif 
> wrote:
>
> > Dear Bioc developer,
> >
> > We are developing a package and have used the MultiAssayExperiment class
> > to manage our data.
> > We need to impose a particular structure on the slot metadata of the MAE
> > object (list => named list)
> > because we havec defined methods that depend on this named list.
> > Is it good practice to extend the MAE class for the specificity of our
> > metadata structure or is it better
> > to define new methods applying to a MAE object  (and check the metadata
> > structure )?
> >
> > Thanks in advance,
> >
> >
> >
> >
> >
> >
> > --
> > Delphine CHARIF
> > +33 (0)1 30 83 35 24
> >
> > IJPB -  INRAE<
> > https://www.inrae.fr/>
> > RD10 - Route de Saint-Cyr
> > 78026 Versailles
> > ---
> > En temps partiel le mercredi
> >
> >
> >
> > [[alternative HTML version deleted]]
> >
> > ___
> > Bioc-devel@r-project.org mailing list
> > https://stat.ethz.ch/mailman/listinfo/bioc-devel
> >
>
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>
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>

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

[migdal migdal]

Thanks again Steffen and Mike for sharing, recently I found some free time
and ended up implementing your suggestions as a GitHub Action.
Maybe this could be of interest to you
https://github.com/Genentech/midasHLA/issues/27#issuecomment-1855795946

Cheers Maciek

On Thu, 16 Nov 2023 at 11:08, Mike Smith  wrote:

> Personally I do as Steffen mentioned, and grab the upstream changes
> manually.  Changes not introduced by me only happen once every 6 months,
> and I'm involved enough with Bioconductor that I generally know when the
> release and version bump has occurred, so it's never quite felt like enough
> work to implement an automatic workflow.  I think I'm just as likely to
> forget to put the changes from GitHub to my local machine, and still end up
> with a merge conflict at some point.
>
> However, I think you should be able to use this action from the
> marketplace to achieve the automatic syncing without too much work creating
> the workflow:
>
> https://github.com/marketplace/actions/upstream-sync
>
> Cheers,
> Mike
>
> On Wed, 15 Nov 2023 at 12:22, migdal migdal  wrote:
>
>> 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]]
>> > >
>> > > ___
>> > > Bioc-devel@r-project.org mailing list
>> > > https://stat.ethz.ch/mailman/listinfo/bioc-devel
>> >
>> > --
>> > Upcoming events:
>> >
>> > * 2nd ELIXIR-DE Hackathon, 11-15 December 2023 in Bielefeld
>> >  https://www.denbi.de/de-nbi-events/1547-biohackathon-germany-2
>> >
>> >
>> > ---
>> > IPB HalleComputational Plant Biochemistry (CPB)
>> > 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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>>
>> ___
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>>
>

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

[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]]
> >
> > ___
> > Bioc-devel@r-project.org mailing list
> > https://stat.ethz.ch/mailman/listinfo/bioc-devel
>
> --
> Upcoming events:
>
> * 2nd ELIXIR-DE Hackathon, 11-15 December 2023 in Bielefeld
>  https://www.denbi.de/de-nbi-events/1547-biohackathon-germany-2
>
>
> ---
> IPB HalleComputational Plant Biochemistry (CPB)
> 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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[Bioc-devel] Diverging version numbering on Bioconductor RELEASE

[migdal migdal]

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

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[Bioc-devel] Query about package submission status

[migdal migdal]

Dear bioc-devel moderators,

I would like to ask about my recent package submission status (
https://github.com/Bioconductor/Contributions/issues/2496). Sorry if I am
impatient here, some time ago I submitted requested fixes and now I noticed
that no one is assigned to my ticket. Please kindly, let me know about my
submission status or if I missed something on my end.

All the best
Maciek

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[Bioc-devel] What is the Timeout limit on R CMD check?

[migdal migdal]

Dear all,

I am currently in the process of submitting my package to Bioconductor and
I got a bit stuck trying to go through the R CMD CHECK. The problem I am
facing at the moment is

TIMEOUT: R CMD check exceeded 14 mins

(here is full report if needed
http://bioconductor.org/spb_reports/midasHLA_buildreport_20210210035124.html)

While the message is obvious, it is unclear to me what is the time
limit for R CMD CHECK? Such that I know what to aim at.

I've found some information here
https://bioconductor.org/developers/how-to/long-tests/, but it says:
"The maximum amount of time that R CMD check is allowed to spend
on each package is 40 min."  Does not really add up with the TIMEOUT
error above, unless I am missing something.

Cheers Maciek

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