Error in read file, access ing directory

[cjwilli98]

Error in file(filename, "r", encoding = encoding) :
cannot open the connection

The ssgsea_gui.R is saved in the same directory as my .GCT file and GMT file. Does this read file command need to be updated on my part using the built in R function update.packages() or am I doing something fundamentally wrong? I click source-->select directory contining my .GCT files, ("........Thesis lab\proteomics data\GO analysis\SPHKAP Kv1.2 Data.gct") select my GMT as ".........Thesis lab\proteomics data\GO analysis\c1.all.v7.0.symbols.gmt". The location of the ssgea_gui.R script is "...........Thesis lab\proteomics data\GO analysis\ssgsea-gui.R"
In addition: Warning messages:
1: package ‘pacman’ was built under R version 4.3.3
2: In file(filename, "r", encoding = encoding) :
cannot open file 'C:/Users/chris/Desktop/Rotation4_Thesis lab/proteomics data/GO analysis/src/ssGSEA2.0.R': No such file or directory

[wcorinne]

Hello! Rather than moving the ssgsea_gui.R script into the same directory as the GCT files, you'll want to keep it in its original directory-structure. The script assumes it will be able to find the other scripts in the git repository (e.g. the src/ssGSEA2.0.R script, in this case), and therefore breaks if it is run standalone.

The script will prompt you to select the folder with your GCT files, so it is fine to have them in a separate folders.