MaAsLin2 Not Available for R3.6.1?

[Stephanie Dijk]

Hi Everyone,

I'm very new to R, and am learning to use it as I'd like to use MaAsLin2 to analyze some multi-omics data. I'm working through RStudio, but have been hitting an error while trying to install the Maaslin2 package as I follow along with the user guide - I've also got an error on the pbapply package - is there something I'm doing wrong? The rest of the require packages installed no problem.

pbapply error:

 install.packages("pbapply")

"Installing package into ‘C:/Users/Steph/Documents/R/win-library/3.6’ (as ‘lib’ is unspecified)   There is a binary version available but the source version is later:  binary source needs_compilation pbapply  1.4-0  1.4-1             FALSE

installing the source package ‘pbapply’

trying URL 'https://cran.rstudio.com/src/contrib/pbapply_1.4-1.tar.gz' Content type 'application/x-gzip' length 15130 bytes (14 KB) downloaded 14 KB

ERROR: failed to lock directory 'C:/Users/Steph/Documents/R/win-library/3.6' for modifying

Try removing 'C:/Users/Steph/Documents/R/win-library/3.6/00LOCK-pbapply' Warning in install.packages :   installation of package ‘pbapply’ had non-zero exit status

The downloaded source packages are in  'C:\Users\Steph\AppData\Local\Temp\RtmpgxRgGH\downloaded_packages’

Trying to Install MaAsLin2:

> if(!requireNamespace("BiocManager", quietly = TRUE))

+     install.packages("BiocManager")

> BiocManager::install("Maaslin2")

Bioconductor version 3.9 (BiocManager 1.30.4), R 3.6.1 (2019-07-05)

Installing package(s) 'Maaslin2'

Warning message:

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

Any help is much appreciated for a total beginner here! Alternately.... should I just give up and try the Huttenhower lab Galaxy? I really need a stepbystep userguide XD

Stephanie

[Lauren McIver]

Hello XD, We are in the process of submitting Maaslin2 to bioconductor but it is not yet included as a package in their release. If you would use the devtools install method it should resolve the error you are seeing. Please let me know if you have any other issues. http://huttenhower.sph.harvard.edu/maaslin2

Thanks!

Lauren

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[Stephanie Dijk]

That fix worked great, thanks Lauren!

Stephanie

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