> temp <- getGmt("Human_NetPath_September_01_2016_Entrezgene.gmt",geneIdType=EntrezIdentifier())
Error in doWithOneRestart(return(expr), restart) : bad error message

the failure is because .warningf() is called with more than one string as its second argument. Changing R/getObjects.R with the following diff corrects this error:

--- r-bioc-gseabase-1.34.0.orig/R/getObjects.R
+++ r-bioc-gseabase-1.34.0/R/getObjects.R
@@ -168,7 +168,7 @@
     }, dups)
     if (length(dups))
         .warningf("%d record(s) contain duplicate ids: %s",
-                  length(dups), selectSome(sort(ls(dups))))
+                  length(dups), paste(collapse=", ",selectSome(sort(ls(dups)))))
     GeneSetCollection(lapply(lines, function(line) {
         GeneSet(unlist(line[-(1:2)]),
                 geneIdType=geneIdType,

Thanks, this has been fixed in GSEABase 1.34.1 (release) and 1.35.4 (devel).