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

[Paul Shannon]

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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