[Debian-med-packaging] [devteam-bioc] Failure in test suite of hypergraph

[Martin Morgan]

On 10/17/2014 07:52 AM, Maintainer wrote:
> Hi,
>
> I'm packaging BioConductor 3.0 modules for Debian (targeting at
> "experimental" distribution since the freeze for the next release is to
> close and we will not manage to reach this unfortunately).  When doing
> so I'm trying to run all test suites and I detected a slight problem in
> hypergraph.  One test out of 13 fails and it boils down to the code in
> file hypergraph/inst/unitTests/hypergraph_test.R.  If I add two simple
> debug lines with print() the problem becomes obvious:

thanks the unit test has been updated in version 1.38.1 of this package. Martin

>
>
> testHyperedges <- function() {
>      nodes <- LETTERS[1:4]
> ##    hEdges <- lapply(list("A", LETTERS[1:2], LETTERS[3:4]), "Hyperedge")
>      eList <- list("A", LETTERS[1:2], LETTERS[3:4])
>      hEdges <- l2hel(eList)
>      hg <- new("Hypergraph", nodes=nodes, hyperedges=hEdges)
>      ## Add "default" labels
>      for (i in 1:length(hEdges)) {
>          he <- hEdges[[i]]
>          label(he) <- as.character(i)
>          hEdges[[i]] <- he
>      }
>      checkEquals(hEdges, hyperedges(hg))
>      names(eList) <- paste("e", 1:length(eList), sep="")
>      hEdges <- l2hel(eList)
>   print(names(eList))
>   print(hyperedgeLabels(hg))
>      checkEquals(names(eList), hyperedgeLabels(hg))
> }
>
> which results in the following output:
>
>
> Loading required package: hypergraph
> Loading required package: graph
>
>
> Executing test function testHyperedges  ... [1] "e1" "e2" "e3"
> [1] "1" "2" "3"
> Timing stopped at: 0.004 0 0.004
> Error in checkEquals(names(eList), hyperedgeLabels(hg)) :
>    3 string mismatches
>   done successfully.
>
> RUNIT TEST PROTOCOL -- Fri Oct 17 16:54:41 2014
> ***********************************************
> Number of test functions: 1
> Number of errors: 0
> Number of failures: 1
>
>
>
> Please check the label code to fix the unit test.
>
> Kind regards
>
>         Andreas.
>
>


-- 
Computational Biology / Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N.
PO Box 19024 Seattle, WA 98109

Location: Arnold Building M1 B861
Phone: (206) 667-2793