Not able to install clusterProfiler on Colab

[pmhchang]

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]

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

[pmhchang]

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 ? — Reply to this email directly, view it on GitHub <#665 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/BF5SKTF3IGCMDX32PSJ3WU3YSRWAJAVCNFSM6AAAAABC2VH7OKVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTSMZTGQZTKMZVGI> . You are receiving this because you authored the thread.Message ID: ***@***.***>

[pmhchang]

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")