Question: GSEABase getGmt() fails when more than 1 line contains duplicates
0
gravatar for dondelelcaro
3.1 years ago by
dondelelcaro10
USA/Champaign/University of Illinois
dondelelcaro10 wrote:
> 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,

 

gseabase bug • 580 views
ADD COMMENTlink modified 3.1 years ago by Martin Morgan ♦♦ 23k • written 3.1 years ago by dondelelcaro10
Answer: GSEABase getGmt() fails when more than 1 line contains duplicates
1
gravatar for Martin Morgan
3.1 years ago by
Martin Morgan ♦♦ 23k
United States
Martin Morgan ♦♦ 23k wrote:

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

ADD COMMENTlink written 3.1 years ago by Martin Morgan ♦♦ 23k
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