Update the pkg in Bioc devel

[antagomir]

For the named package maintainer:

Time to make sure that the latest updates to Bioc packages are pushed to Bioc devel branch (note the approaching DLs):
https://www.bioconductor.org/developers/release-schedule/

And checked for builds
https://bioconductor.org/checkResults/devel/bioc-LATEST/miaSim/lconway-buildsrc.html

See "Sync an existing GitHub repository with Bioconductor" in
https://contributions.bioconductor.org/git-version-control.html#sync-existing-repositories

[YagmurSimsekk]

Thanks for reminding! Both repositories (github and bioc) are already up to date.

[antagomir]

Next update after the submission-related changes and at the latest in March 2023, so we can have them before the next (April) release cycle.

[antagomir]

@YagmurSimsekk could this be done now?

[YagmurSimsekk]

@antagomir Thank you for reminding. Changes are merged now.

[antagomir]

Ok. Have you also updated this to Bioconductor?

[YagmurSimsekk]

Yes, Bioconductor branch is in sync with the main branch.

[antagomir]

The main branch version is 1.7.2 according to DESCRIPTION file:
https://github.com/microbiome/miaSim/blob/main/DESCRIPTION

The Bioc devel branch check system is at 1.7.0:
https://www.bioconductor.org/checkResults/devel/bioc-LATEST/miaSim/

This suggests that the latest main branch in Github has not been synced to the Bioc build system.

Are you sure the Bioconductor branch is in sync with the main branch? How does it relate to the above?

[YagmurSimsekk]

I just realized that I updated Bioc master branch instead of Bioc devel. Now I updated both devel and Bioc devel branches, and they are synchronized. However, I am still seeing the version 1.7.0 displayed on the check system. Could this be due to a delay in the check page updating its information?

[antagomir]

Yes, in my experience there can be 1-3 days delay before it shows in the check/build system.

[antagomir]

If you could follow up on this and close when ready that would be great.

[YagmurSimsekk]

The check page is updated with the latest version, but there are some warnings due to function that was there before, now it is removed, but one of the vignette is still using the function. I assigned "eval = False" but that should be fixed in a better way.

[antagomir]

Which vignette and function?

[YagmurSimsekk]

It is phyloseq/caseStudy2-NutrientThreshold.Rmd vignette and generateSimulations function.

[antagomir]

Ok thanks! I will open an issue on this.

[antagomir]

#82

[antagomir]

The Bioc devel branch check system still has some warnings and errors:
https://www.bioconductor.org/checkResults/devel/bioc-LATEST/miaSim/

-> @YagmurSimsekk are you able to have a look and fix these as the pkg maintainer?

The generateSimulations issue is OK to solve with eval=FALSE and someone can solve that issue #82 separately later. But it is essential make this pass the tests so that it remains in Bioc.

[YagmurSimsekk]

They are fixed now. This issue can be closed.

[antagomir]

Excellent!