Maaslin 3 package versioning

Downstream analysis and statistics MaAsLin
1

Hello,

This is a question regarding how versions are handled for the maaslin3 package. I’ve seen that installing maaslin3 from Bioconductor release 3.23 gives maaslin3 version 1.4.0, and installing from Bioconductor 3.22 gives maaslin3 version 1.2.0. But looking at the source code on github, I cannot see any commit at which the decription files shows either of these versions.

This means there is no way to easily install maaslin3 1.2.0 under R 4.6.0 for example, as BiocManager::install("maaslin3", version = "3.22") gives an error with R 4.6.0

With all that said, I am wondering which github version aligns with Bioconductor release 3.22 (maaslin 1.2.0)?

Thanks for all the work you’ve put into this package!

Kind regards,

Eli

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Hi Eli,

It’s not super clean, but if you look at the commit history on the DESCRIPTION file, each time we bump the y in x.y.z should correspond to a BioC release. They require submitting the devel versions with an odd y which automatically gets bumped to the next even number in their release, so our description 1.3.1 corresponds to their release 1.4.0. Bioc release 3.22 should be this commit.

With that said, there shouldn’t be any changes to the statistical methods between the versions, so for the purpose of citing, 1.2 and 1.4 should be equivalent. We updated how the parallelization is handled and swapped out some packages, but otherwise things should’ve stayed the same.

Will

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Hi Will, thanks for the reply! I’m a bit new to bioconductor, thanks for clearing that up for me.

Just for anyone stumbling on this you can also clone bioconductor package versions with git and install locally with pak::pak or remotes::install_local:

git clone --branch RELEASE_3_22 https://git.bioconductor.org/packages/maaslin3 maaslin3

and then in R

pak::pak("path/to/maaslin3")
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