Fix for issue #162: Replace is() with inherits when class2 is a vector

[zeehio]

This pull request fixes failures on R-devel 4.2 as described on:

• Failures on R-devel (4.2) #162

I basically replace is() with inherits() when class2 is a vector

This is the R source commit where is() became more stringent (January 2022):

• wch/r-source@e0fa9f3

Looking forward for a merge, since some other packages I maintain fail because of this error in bioconductor.

Thanks for your time!

[zeehio]

The CI is failing in the "Notify slack" stage.

Also I would like to know if there is a timeline for a fix for this issue. The Bioconductor 3.15 freeze is April 11th, in a bit more than two weeks, and if mixOmics can't be ready and with this fix released by then (or before, since I need a bit of time to adapt) I will have to remove it from my package dependencies.

I would rather avoid having to rush at the last minute, that's why I am asking. I can adapt anyway.

[Max-Bladen]

@aljabadi @lecaolab

This pull request has passed all checks save for the 'Notify Slack' action. This action has not failed on any other PR prior or since this so I don't believe it's an issue to worry about. Please advise as to whether this is ready to merge with master.

[Max-Bladen]

Hi @zeehio

Once my supervisors see that this is more an error of the GitHub actions rather than your code adjustments, it will be merged and deployed to Bioc. I wouldn't think it would take more than a few days.

Let me know if theres anything else I can do for you

[zeehio]

Thanks for offering a fix soon!

There is one more thing you could do :-) Please revert 8fc6d96 since that prevents you from testing on the development version of R and Bioconductor packages, hiding this issue in your CI.

Thanks again!

[Max-Bladen]

I'll have to wait for @aljabadi to help out in that regard @zeehio. We made changes 8fc6d96 as all our github actions were failing due to using the devel version

[zeehio]

Sure, take your time and feel free to discuss it 👍

In January there was a change in the behaviour of the is() function in R-devel (linked above) where the second argument of is() (named class2) must be a scalar string of length 1 (not a vector). You use a vector in class2 so you have seen that error in some of your issues.

Your R devel builds started to fail by then. The reaction in 8fc6d96 seems to be "R-devel" may have a bug, let's disable it for now (at least the commit and pull request point in that direction) and we will enable it again later. It is reasonable to think that because regressions in R-devel have happened in the past, especially at the beginning of a new development cycle.

In reality the error was because of a breaking change in R-devel, and not a regression there. We are close to the release of R-devel, so that's why I believe the chances of a regression are rather low and the need for testing compatibility with R-devel is now higher.

[zeehio]

Hi again,

Sorry for being pushy. Would it be possible to at least cherry-pick this bugfix on the current bioconductor master branch? Ideally then the the package would build at https://bioconductor.org/packages/devel/bioc/html/mixOmics.html or http://bioconductor.org/checkResults/devel/bioc-LATEST/mixOmics/ and I would be able to avoid the ERRORs in my bioconductor package, where the checks are failing because your package returns the error addressed in this issue.

I understand that you want to push a new version with very interesting new features, but it would be fantastic if until that happens we could at least get mixOmics in Bioconductor-devel into a working state, so packages that depend on it do not ERROR as well.

Beware of the 3.15 release schedule. https://bioconductor.org/developers/release-schedule/ I would rather not have mixOmics and my package deprecated from Bioconductor because of this issue.

If you can't make it, please say so and I will workaround the test or the issue in my package, so I don't get deprecated/removed from Bioconductor.

[aljabadi]

Thanks @zeehio and sorry it took a while to action this, I was a bit late to see this and this is now fixed in the latest GitHub version. It will also be fixed on bioc devel in the next build before the next release.