[BioC] bug in graph::addNode() w/ graph::edgeData()

[Robert Castelo]

hi Paul,

excellent news, thanks for the fix!

best regards,
robert.

On 12/21/13 12:46 AM, Paul Shannon wrote:
> Hi Robert,
>
> The graphBAM addNode bug is now finally fixed.  Thanks for your patience.
>
> The fix is available now in devel as graph 1.41.2.   By mid-day Saturday, it will be available in release as graph 1.40.1.
>
> Thanks again for the excellent bug report.
>
>   - Paul
>
> On Nov 7, 2013, at 7:04 AM, Robert Castelo wrote:
>
>> hi,
>>
>> i have found a problem when using the functions addNode() and edgeData() from the graph package, which i believe is a bug and it can be reproduced with the following minimal example:
>>
>> library(graph)
>>
>> ## build a graphBAM object with vertices a, b, d, e and edges a-d, b-e
>> df <- data.frame(from=c("a", "b"),
>>                  to  =c("d", "e"),
>>                  weight=rep(1, 2))
>> g <- graphBAM(df)
>> nodes(g)
>> [1] "a" "b" "d" "e"
>>
>> ## add a numerical attribute to one of the edges
>> edgeDataDefaults(g, "x") <- NA_real_
>> edgeData(g, from="a", to="d", "x") <- 1
>> unlist(edgeData(g, attr="x"))
>> a|d b|e d|a e|b
>>   1  NA   1  NA
>>
>> ## add an extra node f to the graphBAM object and fetch edge attributes
>> gOK <- addNode("f", g)
>> nodes(gOK)
>> [1] "a" "b" "d" "e" "f"
>> unlist(edgeData(gOK, attr="x"))
>> a|d b|e d|a e|b
>>   1  NA   1  NA
>>
>> ## now comes the bug ...
>>
>> ## add an extra node c to the graphBAM object and fetch edge attributes
>> gBUG <- addNode("c", g)
>> nodes(gBUG)
>> [1] "a" "b" "c" "d" "e"
>> unlist(edgeData(gBUG, attr="x"))
>> Error in data.frame(ft, tmp, stringsAsFactors = FALSE) :
>>   arguments imply differing number of rows: 4, 6
>> traceback()
>> 7: stop(gettextf("arguments imply differing number of rows: %s",
>>        paste(unique(nrows), collapse = ", ")), domain = NA)
>> 6: data.frame(ft, tmp, stringsAsFactors = FALSE)
>> 5: .eAttrsFun(self, from = names(edges(self)), attr = attr)
>> 4: as.list(.eAttrsFun(self, from = names(edges(self)), attr = attr))
>> 3: edgeData(gBUG, attr = "x")
>> 2: edgeData(gBUG, attr = "x")
>> 1: unlist(edgeData(gBUG, attr = "x"))
>>
>> from this output, my guess is that the problem is related to the first line of code of the addNode() method in the R/methods-graphBAM.R file:
>>
>> setMethod("addNode",
>>         signature(node="character", object="graphBAM", edges="missing"),
>>         function(node, object) {
>>
>>             nds <- sort(unique(c(nodes(object), node)))
>> [...]
>>
>> because if i simply remove the call to the function sort, i.e., replacing this line by
>>
>>             nds <- unique(c(nodes(object), node))
>>
>> then the problem is solved. however, i don't know whether this has other consequences related to the design of the package. upfront, i do not see a reason why, internally to the package, vertices should be alphabetically ordered.
>>
>> best regards,
>> robert.
>> ps: sessionInfo()
>> R version 3.0.2 (2013-09-25)
>> Platform: x86_64-unknown-linux-gnu (64-bit)
>>
>> locale:
>> [1] LC_CTYPE=en_US.UTF8       LC_NUMERIC=C LC_TIME=en_US.UTF8        LC_COLLATE=en_US.UTF8
>> [5] LC_MONETARY=en_US.UTF8    LC_MESSAGES=en_US.UTF8 LC_PAPER=en_US.UTF8       LC_NAME=C
>> [9] LC_ADDRESS=C              LC_TELEPHONE=C LC_MEASUREMENT=en_US.UTF8 LC_IDENTIFICATION=C
>>
>> attached base packages:
>> [1] stats     graphics  grDevices utils     datasets  methods   base
>>
>> other attached packages:
>> [1] graph_1.40.0   vimcom_0.9-91  setwidth_1.0-3 colorout_1.0-1
>>
>> loaded via a namespace (and not attached):
>> [1] BiocGenerics_0.8.0 parallel_3.0.2     stats4_3.0.2       tools_3.0.2
>>
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