Installing Maaslin2 from Bioconductor

Downstream analysis and statistics MaAsLin
1

Dear Maaslin2 developpers and users,

I am experiencing some difficulties installing Maaslin2 using Bioconductor. Basically I got the following error :

Warning message:
package ‘Maaslin2’ is not available (for R version 3.6.1)

This is the output :
sessionInfo()
R version 3.6.1 (2019-07-05)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: macOS Mojave 10.14.6

Matrix products: default
BLAS:   /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libRlapack.dylib

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

loaded via a namespace (and not attached):
[1] BiocManager_1.30.10 compiler_3.6.1      tools_3.6.1
2

I actually had to update BiocManager::install(version = “3.10”)

3

Hi,

Thanks for your post. Yes, to install MaAsLin2 via Bioconductor the version does need to be v3.10 since we did not submit the tool until after the release of v3.10. We are sorry for any confusion! Let us know if you come across any issues while running the tool.

Again, thanks for the feedback!
Best,
Kelsey

4

Dear Kelsey
Is Maaslin2 now available on BiocManager v3.20? R 4.4.2 does not allow usage of BiocManager 3.10 so i seem to be currently unable to install Maaslin2. Is this because Maaslin2 is not on that version of biocmanager or have i made an error?
thanks
Will

5

Hi @WedwardsKent

Unfortunately MaAsLin2 is not available on Bioc v3.20. We are looking into resolving this. In the mean time you can install it directly from Github using devtools with the following commands:

library("devtools")
install_github("biobakery/maaslin2")

Cheers,
Jacob