Question

Not able to install clusterProfiler

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Snehal • 0

@5a65f5e9

Last seen 14 months ago

India


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

BiocManager::install("clusterProfiler")

clusterProfiler • 2.3k views

ADD COMMENT • link updated 9 months ago by Perry • 0 • written 16 months ago by Snehal • 0

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You do not provide any clue to find a solution, a minimum would be to add the error message you have after running this code

ADD REPLY • link 16 months ago Basti ▴ 780

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I have trouble install the "clusterProfiler" on Google colab. It was working until 1 weeks ago. Here is the error message:

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

BiocManager::install("clusterProfiler") output 'getOption("repos")' replaces Bioconductor standard repositories, see 'help("repositories", package = "BiocManager")' for details. Replacement repositories: CRAN: https://cran.rstudio.com

Bioconductor version 3.18 (BiocManager 1.30.22), R 4.3.2 (2023-10-31)

Installing package(s) 'clusterProfiler'

also installing the dependencies 'tidygraph', 'graphlayouts', 'ggraph', 'enrichplot', 'igraph'

Warning message in install.packages(...): "installation of package 'igraph' had non-zero exit status" Warning message in install.packages(...): "installation of package 'tidygraph' had non-zero exit status" Warning message in install.packages(...): "installation of package 'graphlayouts' had non-zero exit status" Warning message in install.packages(...): "installation of package 'ggraph' had non-zero exit status" Warning message in install.packages(...): "installation of package 'enrichplot' had non-zero exit status" Warning message in install.packages(...): "installation of package 'clusterProfiler' had non-zero exit status" Old packages: 'textshaping'

ADD REPLY • link updated 9 months ago by James W. MacDonald 67k • written 9 months ago by Perry • 0

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Found the solution by manually install "igraph" and "tidygraph"

download.file("https://cran.r-project.org/src/contrib/Archive/igraph/igraph_1.6.0.tar.gz", "igraph_1.6.0.tar.gz") install.packages("igraph_1.6.0.tar.gz", repos = NULL, type = "source")

download.file("https://cran.r-project.org/src/contrib/Archive/tidygraph/tidygraph_1.3.0.tar.gz", "tidygraph_1.3.0.tar.gz") install.packages("tidygraph_1.3.0.tar.gz", repos = NULL, type = "source")

ADD REPLY • link 9 months ago Perry • 0