Entering edit mode
Paul Shannon
▴
750
@paul-shannon-5161
Last seen 10.2 years ago
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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