Packages for microbiome data analysis

[Bettya]

Hi everyone
I have this package called DESeq2, I need it along with other packages for microbiome data analysis workflow. I was unable to install it on my R Studio. It gave the warning:
"package ‘DESeq2’ was built under R version 4.0.3"
I have the latest R Studio (R version 4.1.0 (2021-05-18)) and I have to follow a tutorial for the analysis of microbiome data.
I will accept help from this forum.

Regards.

[andresrcs]

@Bettya

"package ‘DESeq2’ was built under R version 4.0.3"

This is not necessarily a problem but it can have unexpected consequences, try to update/reinstall
DESeq2 so you can get a version that has been compiled for your R version

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

BiocManager::install("DESeq2")

@Bettya

I have the latest R Studio (R version 4.1.0

Be aware that the latest R version is 4.1.3

[Bettya]

Hi Sustainer

Thank you for your help, it actually works.
Packages suitability is one of the challenges faced by beginners in R studio.
A permanent solution will be a good welcome.

Thank you for your help

Regards.

Betty

[Bettya]

Hi
Based on this notification:

@andresrcs

Be aware that the latest R version is 4.1.3

I updated my R to the latest version but my R Studio still showed R 4.0.2.
Am not sure I know how these versions work. If I can get a good explanation or readings that can help me understand why I have the latest R version and my R Studio showed a different version. Also, note that version 4.0.2 is always quoted when there are package version issues.
Snapshot attached to show my concern.

Regards.
Betty

[andresrcs]

@Bettya

I updated my R to the latest version but my R Studio still showed R 4.0.2.

On Windows, you can set the used R version from the "Tools -> Global Options" menu

[Bettya]

Hi Sustainer

It really works.

Thanks and regards.

Betty

[Jo1984]

Hi,
I work with the version 4.1.3 and I used tis scripts:

.cran_packages <- c("tidyverse", "cowplot", "picante", "vegan", "HMP", "dendextend", "rms", "devtools")
.bioc_packages <- c("phyloseq", "DESeq2", "microbiome", "metagenomeSeq", "ALDEx2")
.inst <- .cran_packages %in% installed.packages()
if(any(!.inst)) {
install.packages(.cran_packages[!.inst])
}
if (!requireNamespace("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install(.bioc_packages, version = "3.14")
devtools::install_github("adw96/breakaway")
devtools::install_github(repo = "malucalle/selbal")
library(DESeq2)