Error in rowMeans(GCMat[key_df$gene.1, ]) :

[cdkodira1]

I ran this code with your example files:
netList <- RunMLnet(GCMat, BarCluFile, RecClu, LigClu,
pval, logfc,
LigRecLib, TFTarLib, RecTFLib)

I got this error :

Error in rowMeans(GCMat[key_df$gene.1, ]) :
'x' must be an array of at least two dimensions