bug in graph::addNode() w/ graph::edgeData()
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Paul Shannon ▴ 750
@paul-shannon-5161
Last seen 9.6 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 > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor
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Robert Castelo ★ 3.1k
@rcastelo
Last seen 23 hours ago
Barcelona/Universitat Pompeu Fabra
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 >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor at r-project.org >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor
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