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Trouble Installing ggpicrust2 #139

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mwhite942 opened this issue Feb 18, 2025 · 1 comment
Closed

Trouble Installing ggpicrust2 #139

mwhite942 opened this issue Feb 18, 2025 · 1 comment

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@mwhite942
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I am trying to install ggpicrust2 for use in RStudio. The install.packages("ggpicrust2") command didn't find the package, but I was sort of expecting this because of the note on the main page of the GitHub about it currently not being available from CRAN. Next, I tried the method listed in that notice to install the development version from GitHub:
devtools::install_github("cafferychen777/ggpicrust2")

This seemed to be working, but then at the end gave the following error:
`ERROR: dependencies 'edgeR', 'lefser', 'limma', 'Maaslin2', 'metagenomeSeq' are not available for package 'ggpicrust2'

  • removing 'C:/Users/Me/AppData/Local/R/win-library/4.4/ggpicrust2'
    Warning message:
    In i.p(...) :
    installation of package ‘C:/Users/Me/AppData/Local/Temp/RtmpEzVdY9/file9504ee1596f/ggpicrust2_1.7.4.tar.gz’ had non-zero exit status
    And running library(ggpicrust2) gives the error that there is no package called 'ggpicrust2', like you get if you haven't installed a package yet.

I tried to install edgeR, lefser, limma, Maaslin2, and metagenomeSeq, and while edgeR installed successfully, the others didn't seem to have packages for the version of R I'm running. How can I get ggpicrust2 to install?

(I'm using R version 4.4.1)

@mwhite942
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I was able to resolve this by using
BiocManager::install(c( "ALDEx2", "DESeq2", "edgeR", "limma", "Maaslin2", "metagenomeSeq", "SummarizedExperiment", "phyloseq", "biomformat", "lefser" ))
from another post in this help forum (#2) to install the packages that were causing the issue.

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