Bioconductor install error
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Tess • 0
@tess-24214
Last seen 9 months ago

Trying to install Phyloseq and Bioconductor. I have installed Bioconductor but when I try to install phyloseq it comes up with an error about the BioCManager. I am following instructions from https://www.bioconductor.org/install/ and https://joey711.github.io/phyloseq/install.html

I have updated my R to version 4.0.3 which according to the Bioconductor page is compatible with Bioconductor 3.12 so not sure why it keeps coming up with this issue. Any help appreciated.

> BiocManager::install(version = "3.12")
Bioconductor version 3.12 (BiocManager 1.30.10), R 4.0.3 (2020-10-10)

> source('http://bioconductor.org/biocLite.R')
 Error: With R version 3.5 or greater, install Bioconductor packages using BiocManager; see https://bioconductor.org/install 
> biocLite('phyloseq')
phyloseq Bioconductor • 561 views
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ATpoint ▴ 830
@atpoint-13662
Last seen 1 hour ago
Germany

Here is the installation command: https://www.bioconductor.org/packages/release/bioc/html/phyloseq.html

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("phyloseq")

You should always check the official repositiries rather than years-old GitHub tutorials. As of R > 3.5 biocLite is deprecated and the BiocManager::install() function is the workhorse.

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Thanks so much!

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