Hi,
I am having trouble getting certain packages to work in R snippet nodes in knime on Mac (Mac OS Sequoia 15.6.1). I believe I have downloaded all necessary packages (e.g. Rserve, Cairo). I have inputted the correct R path in my preferences. Base R code runs perfectly fine. Certain packages, such as ‘dplyr’, also load and work fine. However, there are certain packages that cause issues. For example, whenever I try to load the package ‘msigdbr’, I get an error. See the following:
> library(msigdbr)
ERROR: R evaluation failed.: "knime.tmp.ret<-NULL;printError<-function(e) message(paste(‘Error:’,conditionMessage(e)));for(exp in tryCatch(parse(text=knime.tmp.script),error=printError)){tryCatch(knime.tmp.ret<-withVisible(eval(exp)),error=printError)
if(!is.null(knime.tmp.ret)) {if(knime.tmp.ret$visible) tryCatch(print(knime.tmp.ret$value),error=printError)}};rm(knime.tmp.script,exp,printError);knime.tmp.ret$value"ERROR: R evaluation failed.: "knime.tmp.ret<-NULL;printError<-function(e) message(paste(‘Error:’,conditionMessage(e)));for(exp in tryCatch(parse(text=knime.tmp.script),error=printError)){tryCatch(knime.tmp.ret<-withVisible(eval(exp)),error=printError)
if(!is.null(knime.tmp.ret)) {if(knime.tmp.ret$visible) tryCatch(print(knime.tmp.ret$value),error=printError)}};rm(knime.tmp.script,exp,printError);knime.tmp.ret$value"ERROR: eval failedERROR: Could not capture output of command.ERROR: R evaluation failed.: "sink();sink(type=‘message’)
close(knime.stdout.con);close(knime.stderr.con)
knime.output.ret<-c(paste(knime.stdout,collapse=‘\n’), paste(knime.stderr,collapse=‘\n’))
knime.output.ret"ERROR: R evaluation failed.: "sink();sink(type=‘message’)
close(knime.stdout.con);close(knime.stderr.con)
knime.output.ret<-c(paste(knime.stdout,collapse=‘\n’), paste(knime.stderr,collapse=‘\n’))
knime.output.ret"ERROR: eval failedERROR: Could not cleanup after command execution.ERROR: R evaluation failed.: "rm(knime.tmp.ret,knime.output.ret,knime.stdout.con,knime.stderr.con,knime.stdout,knime.stderr)"ERROR: R evaluation failed.: "rm(knime.tmp.ret,knime.output.ret,knime.stdout.con,knime.stderr.con,knime.stdout,knime.stderr)"ERROR: voidEval failedERROR: Could not execute internal command.ERROR: R evaluation failed.: "dev.off()"ERROR: R evaluation failed.: "dev.off()"ERROR: eval failedERROR: Could not execute internal command.ERROR: R evaluation failed.: "ls()"ERROR: R evaluation failed.: "ls()"ERROR: eval failed
I know the package is definitely installed as I see it when I list packages from within the R node. It also loads perfectly fine in my terminal which uses the same R.
Certain other functions also produce the exact same error, for example, doing this:
library(httr)
url ← “https://data.broadinstitute.org/gsea-msigdb/msigdb/release/2025.1.Hs/c5.go.bp.v2025.1.Hs.symbols.gmt”
response ← GET(url)
The httr package seems to load fine, but using the GET command does not work. I am unsure exactly what the issue is and how to solve it, so any help would be greatly appreciated!
