graphite 1.4.0
Gabriele Sales
| Snapshot Date: 2013-03-24 16:21:20 -0700 (Sun, 24 Mar 2013) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_11/madman/Rpacks/graphite | | Last Changed Rev: 70050 / Revision: 74773 | | Last Changed Date: 2012-10-01 15:16:24 -0700 (Mon, 01 Oct 2012) |
| lamb1 | Linux (openSUSE 12.1) / x86_64 | [ ERROR ] | skipped | |
| moscato1 | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | OK | OK | OK |
| perceval | Mac OS X Leopard (10.5.8) / i386 | OK | OK | OK |
* checking for file ‘graphite/DESCRIPTION’ ... OK
* preparing ‘graphite’:
* checking DESCRIPTION meta-information ... OK
* installing the package to re-build vignettes
* creating vignettes ...sh: line 1: 10287 Segmentation fault '/home/biocbuild/bbs-2.11-bioc/R/bin/Rscript' --vanilla --default-packages= -e "tools::buildVignettes(dir = '.')" > '/tmp/RtmpjPxqHP/xshell27b47892fc2' 2>&1
ERROR
Loading required package: graph
Loading required package: DBI
Loading required package: AnnotationDbi
Loading required package: BiocGenerics
Attaching package: ‘BiocGenerics’
The following object(s) are masked from ‘package:stats’:
xtabs
The following object(s) are masked from ‘package:base’:
Filter, Find, Map, Position, Reduce, anyDuplicated, cbind,
colnames, duplicated, eval, get, intersect, lapply, mapply, mget,
order, paste, pmax, pmax.int, pmin, pmin.int, rbind, rep.int,
rownames, sapply, setdiff, table, tapply, union, unique
Loading required package: Biobase
Welcome to Bioconductor
Vignettes contain introductory material; view with
‘browseVignettes()’. To cite Bioconductor, see
‘citation("Biobase")’, and for packages ‘citation("pkgname")’.
Loading required package: org.Hs.eg.db
Loading required package: R.utils
Loading required package: R.oo
Loading required package: R.methodsS3
R.methodsS3 v1.4.2 (2012-06-22) successfully loaded. See ?R.methodsS3 for help.
R.oo v1.13.0 (2013-03-08) successfully loaded. See ?R.oo for help.
Attaching package: ‘R.oo’
The following object(s) are masked from ‘package:methods’:
getClasses, getMethods
The following object(s) are masked from ‘package:base’:
attach, detach, gc, load, save
R.utils v1.19.5 (2013-01-11) successfully loaded. See ?R.utils for help.
Attaching package: ‘R.utils’
The following object(s) are masked from ‘package:utils’:
timestamp
The following object(s) are masked from ‘package:base’:
cat, commandArgs, getOption, inherits, isOpen, parse, warnings
Warning in .simpleDuplicateClass(def, prev) :
A specification for S3 class “AsIs” in package ‘XMLRPC’ seems equivalent to one from package ‘IRanges’ and is not turning on duplicate class definitions for this class
Scalable Robust Estimators with High Breakdown Point (version 1.3-02)
Loading required package: gRbase
Loading required package: MASS
Attaching package: ‘MASS’
The following object(s) are masked from ‘package:AnnotationDbi’:
select
Loading required package: Rcpp
Loading required package: RcppEigen
Loading required package: Matrix
Loading required package: lattice
Loading required package: RcppArmadillo
Attaching package: ‘RcppArmadillo’
The following object(s) are masked from ‘package:RcppEigen’:
fastLm, fastLmPure
Loading required package: igraph
Attaching package: ‘igraph’
The following object(s) are masked from ‘package:R.oo’:
hierarchy
The following object(s) are masked from ‘package:graphite’:
edges
The following object(s) are masked from ‘package:graph’:
degree, edges
Loading required package: RBGL
Attaching package: ‘RBGL’
The following object(s) are masked from ‘package:igraph’:
transitivity
Attaching package: ‘gRbase’
The following object(s) are masked from ‘package:R.oo’:
compile
The following object(s) are masked from ‘package:Biobase’:
description<-
Loading required package: qpgraph
Loading required package: fields
Loading required package: spam
Spam version 0.29-2 (2012-08-17) is loaded.
Type ‘help( Spam)’ or ‘demo( spam)’ for a short introduction
and overview of this package.
Help for individual functions is also obtained by adding the
suffix ‘.spam’ to the function name, e.g. ‘help( chol.spam)’.
Attaching package: ‘spam’
The following object(s) are masked from ‘package:RBGL’:
bandwidth
The following object(s) are masked from ‘package:R.utils’:
cleanup
The following object(s) are masked from ‘package:base’:
backsolve, forwardsolve
*** caught segfault ***
address 0x4, cause ‘memory not mapped’
Traceback:
1: sp_moralize(amat)
2: moralizeMAT_spC(amat)
3: moralizeMAT(graphNEL2dgCMatrix(object), result = result)
4: moralize.graphNEL(dag)
5: moralize(dag)
6: .processGraph(dag)
7: .procParams(exp1, exp2, dag)
8: test(exp1, exp2, g, ...)
9: runTopologyGSA(p, "var", exp1, exp2, 0.05)
10: eval(expr, envir, enclos)
11: eval(expr, .GlobalEnv)
12: withVisible(eval(expr, .GlobalEnv))
13: doTryCatch(return(expr), name, parentenv, handler)
14: tryCatchOne(expr, names, parentenv, handlers[[1L]])
15: tryCatchList(expr, classes, parentenv, handlers)
16: tryCatch(expr, error = function(e) { call <- conditionCall(e) if (!is.null(call)) { if (identical(call[[1L]], quote(doTryCatch))) call <- sys.call(-4L) dcall <- deparse(call)[1L] prefix <- paste("Error in", dcall, ": ") LONG <- 75L msg <- conditionMessage(e) sm <- strsplit(msg, "\n")[[1L]] w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w") if (is.na(w)) w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L], type = "b") if (w > LONG) prefix <- paste0(prefix, "\n ") } else prefix <- "Error : " msg <- paste0(prefix, conditionMessage(e), "\n") .Internal(seterrmessage(msg[1L])) if (!silent && identical(getOption("show.error.messages"), TRUE)) { cat(msg, file = stderr()) .Internal(printDeferredWarnings()) } invisible(structure(msg, class = "try-error", condition = e))})
17: try(withVisible(eval(expr, .GlobalEnv)), silent = TRUE)
18: evalFunc(ce, options)
19: driver$runcode(drobj, chunk, chunkopts)
20: utils::Sweave(f, quiet = quiet)
21: doTryCatch(return(expr), name, parentenv, handler)
22: tryCatchOne(expr, names, parentenv, handlers[[1L]])
23: tryCatchList(expr, classes, parentenv, handlers)
24: 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)})
25: tools::buildVignettes(dir = ".")
aborting ...