biocGraph 1.4.0
Li Long
| Bioconductor Changelog | | Snapshot Date: 2009-04-18 11:27:48 -0700 (Sat, 18 Apr 2009) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_3/madman/Rpacks/biocGraph | | Last Changed Rev: 34811 / Revision: 38965 | | Last Changed Date: 2008-10-21 15:32:58 -0700 (Tue, 21 Oct 2008) |
| wilson2 | Linux (openSUSE 11.1) / x86_64 | [ ERROR ] | skipped | |
| liverpool | Windows Server 2003 R2 (32-bit) / x64 | ERROR | skipped | skipped |
| pitt | Mac OS X Tiger (10.4.11) / i386 | OK | OK | OK |
| pelham | Mac OS X Leopard (10.5.6) / i386 | OK | OK | OK |
* checking for file 'biocGraph/DESCRIPTION' ... OK
* preparing 'biocGraph':
* checking DESCRIPTION meta-information ... OK
* installing the package to re-build vignettes
* Installing *source* package 'biocGraph' ...
** R
** inst
** preparing package for lazy loading
Loading required package: graph
Loading required package: geneplotter
Loading required package: Biobase
Loading required package: tools
Welcome to Bioconductor
Vignettes contain introductory material. To view, type
'openVignette()'. To cite Bioconductor, see
'citation("Biobase")' and for packages 'citation(pkgname)'.
Loading required package: lattice
Loading required package: annotate
Loading required package: AnnotationDbi
Loading required package: xtable
KernSmooth 2.22 installed
Copyright M. P. Wand 1997
Attaching package: 'geneplotter'
The following object(s) are masked from package:lattice :
panel.smoothScatter
Loading required package: Rgraphviz
Loading required package: grid
Attaching package: 'Rgraphviz'
The following object(s) are masked from package:annotate :
toFile
Loading required package: fibroEset
Loading required package: hgu95av2.db
Loading required package: DBI
** help
>>> Building/Updating help pages for package 'biocGraph'
Formats: text html latex example
imageMap text html latex example
** building package indices ...
* DONE (biocGraph)
* creating vignettes ...sh: line 1: 29269 Segmentation fault '/home/biocbuild/bbs-2.3-bioc/R/bin/R' --vanilla --no-save --quiet < /tmp/Rin2912655989 > /tmp/Rout2912604105 2>&1
ERROR
Loading required package: graph
Loading required package: geneplotter
Loading required package: Biobase
Welcome to Bioconductor
Vignettes contain introductory material. To view, type
'openVignette()'. To cite Bioconductor, see
'citation("Biobase")' and for packages 'citation(pkgname)'.
Loading required package: lattice
Loading required package: annotate
Loading required package: AnnotationDbi
Loading required package: xtable
KernSmooth 2.22 installed
Copyright M. P. Wand 1997
Attaching package: 'geneplotter'
The following object(s) are masked from package:lattice :
panel.smoothScatter
Loading required package: Rgraphviz
Loading required package: grid
Attaching package: 'Rgraphviz'
The following object(s) are masked from package:annotate :
toFile
Loading required package: fibroEset
Loading required package: hgu95av2.db
Loading required package: DBI
Error: lost ITGB ITGA edge
Error: lost ITGB ILK edge
Error: lost ITGB CAV edge
*** caught segfault ***
address (nil), cause 'memory not mapped'
Traceback:
1: .Call("Rgraphviz_doLayout", graph, as.integer(type), PACKAGE = "Rgraphviz")
2: graphLayout(g)
3: agopen(IMCAGraph, name = "foo", attrs = list(graph = list(rankdir = "LR", rank = ""), node = list(fixedsize = FALSE)), nodeAttrs = makeNodeAttrs(IMCAGraph), subGList = IMCAAttrs$subGList)
4: eval.with.vis(expr, .GlobalEnv, baseenv())
5: doTryCatch(return(expr), name, parentenv, handler)
6: tryCatchOne(expr, names, parentenv, handlers[[1]])
7: tryCatchList(expr, classes, parentenv, handlers)
8: tryCatch(expr, error = function(e) { call <- conditionCall(e) if (!is.null(call)) { if (identical(call[[1]], quote(doTryCatch))) call <- sys.call(-4) dcall <- deparse(call)[1] prefix <- paste("Error in", dcall, ": ") LONG <- 75 msg <- conditionMessage(e) sm <- strsplit(msg, "\n")[[1]] if (14 + nchar(dcall, type = "w") + nchar(sm[1], type = "w") > LONG) prefix <- paste(prefix, "\n ", sep = "") } else prefix <- "Error : " msg <- paste(prefix, conditionMessage(e), "\n", sep = "") .Internal(seterrmessage(msg[1])) if (!silent && identical(getOption("show.error.messages"), TRUE)) { cat(msg, file = stderr()) .Internal(printDeferredWarnings()) } invisible(structure(msg, class = "try-error"))})
9: try(.Internal(eval.with.vis(expr, .GlobalEnv, baseenv())), silent = TRUE)
10: evalFunc(ce, options)
11: driver$runcode(drobj, chunk, chunkopts)
12: utils::Sweave(f, quiet = quiet)
13: doTryCatch(return(expr), name, parentenv, handler)
14: tryCatchOne(expr, names, parentenv, handlers[[1]])
15: tryCatchList(expr, classes, parentenv, handlers)
16: tryCatch(utils::Sweave(f, quiet = quiet), error = function(e) { stop(gettextf("processing vignette '%s' failed with diagnostics:\n%s", f, conditionMessage(e)), domain = NA, call. = FALSE)})
17: buildVignettes(dir = ".")
aborting ...