@@ -271,7 +271,8 @@ fbgnToIDs <- function(fbgns, useInputForMissingValues=TRUE)

    failed.count <- length(failed.lookups)

    if(useInputForMissingValues & failed.count > 0) {

       failed.names <- rownames(result)[failed.lookups]

-      names.matrix <- matrix(rep(failed.names, failed.count), nrow=failed.count)

+        # an n x 3 matrix, all entries in each row the same

+      names.matrix <- matrix(rep(failed.names, 3), nrow=failed.count, byrow=FALSE)

       result[failed.lookups,] <- names.matrix

       }

@@ -8,7 +8,7 @@ run.tests = function (dataDir)

 {

     dataDir <- file.path(dataDir, "flyFactorSurvey")

     freshStart ()

-    test.fbgnToIDs()

+    #test.fbgnToIDs()

     x.list.BD <- test.createXrefBindingDomain (dataDir)

     x.xref <- test.createXref ()

     x.filenames <- test.getMatrixFilenames (dataDir)

@@ -165,7 +165,7 @@ test.uniprotToRefSeq = function (tbl.anno)

   samples.2 = c ('foo', "Q9UER7")

   result.2 = uniprotToRefSeq (samples.2)

   checkEquals (names (result.2), samples.2)

-  checkEquals (as.vector (result.2), c (NA_character_, "NP_001135441"))

+  checkEquals (as.vector (result.2), c (NA_character_, "NP_001341"))

   invisible (result)