Closed Vinalti closed 2 years ago
We've been experiencing some issues due to KEGGREST. Can you check your version of KEGGREST
?
If it's out-of-date, please update via:
devtools::install_github("Bioconductor/KEGGREST")
Indeed, my KEGGREST version was:
KEGGREST_1.30.1
The command devtools::install_github("Bioconductor/KEGGREST")
installed the version 1.37.3
Then I had to reload the module with library('KEGGREST')
And now it works, Thanks for the help ! ✅
Describe the bug When running the command
run_pathfindR(RA_processed, pin_name_path='STRING', search_method = 'SA')
on my data, I get results, but the diagrams don't get downloaded. It seem that the Image URL is empty :'url' must be a length-one character vector
When looking at
tcpdump
I can notice traffic leaving my computer forrest.kegg.jp
andwww.kegg.jp
and some response coming.To Reproduce Steps to reproduce the behavior:
Expected behavior The images should be downloaded. As they actually exist on the KEGG website.
Screenshots If applicable, add screenshots to help explain your problem.![image](https://user-images.githubusercontent.com/22568112/179935929-fc9ad14e-329a-43c8-88af-bae22a3d4102.png)
Desktop (please complete the following information):
R Session Information: Please provide the R session information (by running
sessionInfo()
)Additional context Add any other context about the problem here. While pathfindR is an R package, the active subnetwork search functionality is written in Java. If you suspect any issue regarding java please provide your Java version (by running
java --version
)