Hello, I am trying to use the "WebGestaltR" package in CRAN (https://cran.r-project.org/web/packages/WebGestaltR/index.html) and I prepared a txt file of the DEG list with only one column.

However, there was an error message as "For the user ID list, please upload a 'txt' file with only one column". I would appreciate it if you could inform me of how to cope with this problem.

install.packages("WebGestaltR")
install.packages("systemfonts") 
library(systemfonts)
library(WebGestaltR)
geneFile <- system.file("2flyDEG2.txt", package="WebGestaltR")
outputDirectory <- getwd()
enrichResult <- WebGestaltR(enrichMethod="ORA",organism="dmelanogaster", enrichDatabase="pathway_KEGG",interestGeneFile=geneFile,interestGeneType="genesymbol", isOutput=TRUE,outputDirectory=outputDirectory, projectName=NULL)

Loading the functional categories...
Loading the ID list...                                                                       
Error in formatCheck(dataType = dataType, inputGeneFile = inputGeneFile,  : 
  ERROR: For the user ID list, please upload a 'txt' file with only one column.

Since WebGestaltR isn't a Bioconductor package this isn't really the appropriate place to ask for help with that package. You might get a better response either contacting the authors directly on Github (https://github.com/bzhanglab/WebGestaltR) or at a more general support site like BioStars (https://www.biostars.org/).

However, I suspect your issue is because you're not actually passing the path to your 2flyDEG2.txt file. The system.file() function looks for a file within a specific package. If I run that code I get back nothing:

system.file("2flyDEG2.txt", package="WebGestaltR")
#> [1] ""

I suspect the error message should really be "can not find that file" rather than mentioning the number of columns. You probably want something like geneFile <- "/path/to/2flyDEG2.txt" (you should change that to the location of the file on your own computer).

You can always look for help on a function using ? e.g. ?system.file.