issues installing pathfindR package

Question

[peter.berry5]

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?

[GenoMax]

Warning in install.packages :  dependencies ‘org.Hs.eg.db’, ‘KEGGREST’, ‘KEGGgraph’ are not available

So the install was not complete. You should install those packages first.

[peter.berry5]

@GenoMax, thanks, I did wonder about that bit. Any suggestions on how to fix that problem? I understood the dependencies installed automatically and that no action from me was required.

[brunobsouzaa]

Just install the required packages. Those dependencies are not automatically installed!

[peter.berry5]

@GenoMax and Bruno. Have done that and it it's working. Just for info the other issue I had was I needed to install a JRE which I apparently hadn't done before. Thanks for the help. It's appreciated.

[poornemaa]

I have the same problem today!

Error: package or namespace load failed for ‘pathfindR’: .onAttach failed in attachNamespace() for 'pathfindR', details: call: fetch_java_version() error: Java version not detected. Please download and install Java from “https://www.java.com/en/” Error: loading failed Execution halted ERROR: loading failed

Could someone tell me where I am going wrong? I updated my Java and installed KEGGgraph, etc separately as well

Answer 1

[Elie]

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