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YuLab-SMU / clusterProfiler

:bar_chart: A universal enrichment tool for interpreting omics data
https://yulab-smu.top/biomedical-knowledge-mining-book/
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Not able to install clusterProfiler on Colab #665

Open pmhchang opened 5 months ago

pmhchang commented 5 months ago

Not able to install clusterProfiler on Colab

install.packages("BiocManager") BiocManager::install("clusterProfiler")

Installing package into ‘/usr/local/lib/R/site-library’ (as ‘lib’ is unspecified)

'getOption("repos")' replaces Bioconductor standard repositories, see 'help("repositories", package = "BiocManager")' for details. Replacement repositories: BioCsoft: https://bioconductor.org/packages/3.18/bioc BioCann: https://bioconductor.org/packages/3.18/data/annotation BioCexp: https://bioconductor.org/packages/3.18/data/experiment BioCworkflows: https://bioconductor.org/packages/3.18/workflows BioCbooks: https://bioconductor.org/packages/3.18/books 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'

HarshKr960 commented 5 months ago

I am having the same issue. Did you find out how to fix it ?

pmhchang commented 5 months ago

Not yet, still struggling with the same issue. Let me know if you find anything!

On Thu, Feb 8, 2024 at 12:28 AM HarshKr960 @.***> wrote:

I am having the same issue. Did you find out how to fix it ?

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pmhchang commented 4 months ago

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")