Package: genefilter

Version: 1.15.6

Command: /home/biocbuild/bbs-2.1-bioc/R/bin/R CMD build genefilter

RetCode: 1

Time: 13.5 seconds

Status: ERROR

PackageFile: None

* checking for file 'genefilter/DESCRIPTION' ... OK
* preparing 'genefilter':
* checking DESCRIPTION meta-information ... OK
* cleaning src
* installing the package to re-build vignettes
* Installing *source* package 'genefilter' ...
** libs
g++ -I/home/biocbuild/bbs-2.1-bioc/R/include -I/home/biocbuild/bbs-2.1-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -Wall -c half_range_mode.cpp -o half_range_mode.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.1-bioc/R/include -I/home/biocbuild/bbs-2.1-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -Wall -c init.c -o init.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.1-bioc/R/include -I/home/biocbuild/bbs-2.1-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -Wall -c nd.c -o nd.o
nd.c: In function 'detectTies':
nd.c:70: warning: format '%d' expects type 'int', but argument 3 has type 'RSInt'
nd.c: In function 'gf_dist_binary':
nd.c:242: warning: unused variable 'w2'
nd.c:242: warning: unused variable 'w1'
gcc -std=gnu99 -I/home/biocbuild/bbs-2.1-bioc/R/include -I/home/biocbuild/bbs-2.1-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -Wall -c pAUC.c -o pAUC.o
pAUC.c: In function 'pAUC_c':
pAUC.c:75: warning: operation on 'ta' may be undefined
pAUC.c:78: warning: operation on 'ta' may be undefined
pAUC.c:81: warning: operation on 'ta' may be undefined
pAUC.c: In function 'pAUC':
pAUC.c:141: warning: suggest parentheses around comparison in operand of |
pAUC.c:123: warning: unused variable 'i'
pAUC.c: In function 'pAUC_c':
pAUC.c:22: warning: 'ysum' may be used uninitialized in this function
pAUC.c:22: warning: 'xsum' may be used uninitialized in this function
gcc -std=gnu99 -I/home/biocbuild/bbs-2.1-bioc/R/include -I/home/biocbuild/bbs-2.1-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -Wall -c rowPAUCs.c -o rowPAUCs.o
rowPAUCs.c: In function 'ROCpAUC_c':
rowPAUCs.c:95: warning: operation on 'ta' may be undefined
rowPAUCs.c:98: warning: operation on 'ta' may be undefined
rowPAUCs.c:101: warning: operation on 'ta' may be undefined
rowPAUCs.c:23: warning: 'ysum' may be used uninitialized in this function
rowPAUCs.c:23: warning: 'xsum' may be used uninitialized in this function
gcc -std=gnu99 -I/home/biocbuild/bbs-2.1-bioc/R/include -I/home/biocbuild/bbs-2.1-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -Wall -c rowttests.c -o rowttests.o
gfortran   -fpic  -g -O2 -Wall -c ttest.f -o ttest.o
g++ -shared -L/usr/local/lib64 -o genefilter.so half_range_mode.o init.o nd.o pAUC.o rowPAUCs.o rowttests.o ttest.o  -lgfortran -lm -L/home/biocbuild/bbs-2.1-bioc/R/lib -lR
** R
** data
**  moving datasets to lazyload DB
** inst
** preparing package for lazy loading
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: survival
Loading required package: splines
Creating a new generic function for "plot" in "genefilter"
** help
 >>> Building/Updating help pages for package 'genefilter'
     Formats: text html latex example 
  Anova                             text    html    latex   example
  allNA                             text    html    latex   example
  coxfilter                         text    html    latex   example
  cv                                text    html    latex   example
  dist2                             text    html    latex   example
  eSetFilter                        text    html    latex   example
  filterfun                         text    html    latex   example
  findLargest                       text    html    latex   example
  gapFilter                         text    html    latex   example
  genefilter                        text    html    latex   example
  genefinder                        text    html    latex   example
  genescale                         text    html    latex   example
  half.range.mode                   text    html    latex   example
  kOverA                            text    html    latex   example
  maxA                              text    html    latex   example
  nsFilter                          text    html    latex   example
  pOverA                            text    html    latex   example
  rowFtests                         text    html    latex   example
  rowROC-class                      text    html    latex   example
  rowSds                            text    html    latex   example
  rowpAUCs                          text    html    latex   example
  shorth                            text    html    latex   example
  tdata                             text    html    latex   example
  ttest                             text    html    latex   example
** building package indices ...
* DONE (genefilter)
* creating vignettes ...sh: line 1: 16202 Segmentation fault      '/home/biocbuild/bbs-2.1-bioc/R/bin/R' --vanilla --no-save --quiet </tmp/Rin1586882731 >/tmp/Rout1586880289 2>&1
 ERROR
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: survival
Loading required package: splines

 *** caught segfault ***
address 0xa68028fbf10, cause 'memory not mapped'

Traceback:
 1: .C("gf_distance", X = as.double(X), nr = N, nc = ncol(X), g = as.integer(Genes),     d = as.double(Dists), iRow = as.integer(iRows), nInterest = as.integer(ninterest),     nResults = as.integer(numResults), method = as.integer(method),     weights = as.double(weights), DUP = FALSE, NAOK = TRUE, PACKAGE = "genefilter")
 2: genefinder(exprs(X), ilist, numResults, scale, weights, method = method)
 3: genefinder(exprs(X), ilist, numResults, scale, weights, method = method)
 4: genefinder(sample.ExpressionSet, igenes, 10, method = "euc",     scale = "none")
 5: genefinder(sample.ExpressionSet, igenes, 10, method = "euc",     scale = "none")
 6: eval.with.vis(expr, .GlobalEnv, baseenv())
 7: doTryCatch(return(expr), name, parentenv, handler)
 8: tryCatchOne(expr, names, parentenv, handlers[[1]])
 9: tryCatchList(expr, classes, parentenv, handlers)
10: 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"))})
11: try(.Internal(eval.with.vis(expr, .GlobalEnv, baseenv())), silent = TRUE)
12: evalFunc(ce, options)
13: driver$runcode(drobj, chunk, chunkopts)
14: utils::Sweave(f, quiet = quiet)
15: doTryCatch(return(expr), name, parentenv, handler)
16: tryCatchOne(expr, names, parentenv, handlers[[1]])
17: tryCatchList(expr, classes, parentenv, handlers)
18: 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)})
19: buildVignettes(dir = ".")
aborting ...