issues installing pathfindR package
Hi
I am trying to use the pathfindR package to do enrichment analysis on my data. According to the vignette the package is downloaded from CRAN by
install.packages("pathfindR")
this gives the following output
Installing package into ��
(as �lib� is unspecified)
Warning in install.packages :
dependencies ‘org.Hs.eg.db’, ‘KEGGREST’, ‘KEGGgraph’ are not available
trying URL 'https://cran.rstudio.com/bin/windows/contrib/4.0/pathfindR_1.6.0.zip'
Content type 'application/zip' length 2782854 bytes (2.7 MB)
downloaded 2.7 MB
package ‘pathfindR’ successfully unpacked and MD5 sums checked
so I believe the package has been installed successfully. However, when I call the package by
library(pathfindR)
I get
#Error in library("pathfindR") : there is no package called ‘pathfindR’
Any thoughts/suggestions?
• 428 views
Hey!
A bit late but I had the same issue today, and I resolved it installing separately the 2 packages using bioconductor
if (!requireNamespace("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("KEGGgraph")
and
if (!requireNamespace("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("KEGGREST")
Then I faced the same issue with Java, so I just downloaded on my mac oracle JDK and java 8, and eventually the pathfindR package was installed
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