RMAGEML 2.14.0
Steffen Durinck
| Snapshot Date: 2008-08-08 00:12:03 -0700 (Fri, 08 Aug 2008) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_2/madman/Rpacks/RMAGEML | | Last Changed Rev: 31430 / Revision: 33132 | | Last Changed Date: 2008-04-29 16:50:18 -0700 (Tue, 29 Apr 2008) |
| lamb1 | Linux (SUSE 10.1) / x86_64 | [ ERROR ] | skipped | |
| wilson2 | Linux (openSUSE 10.3) / x86_64 | OK | OK | |
| wellington | Linux (openSUSE 10.3) / i686 | OK | OK | |
| liverpool | Windows Server 2003 R2 (32-bit) / x64 | N O T S U P P O R T E D |
| pitt | Mac OS X Tiger (10.4.11) / i386 | N O T S U P P O R T E D |
* checking for file 'RMAGEML/DESCRIPTION' ... OK
* preparing 'RMAGEML':
* checking DESCRIPTION meta-information ... OK
* cleaning src
* installing the package to re-build vignettes
* Installing *source* package 'RMAGEML' ...
configure: creating ./config.status
config.status: creating src/Makevars
** libs
gcc -std=gnu99 -I/home/biocbuild/bbs-2.2-bioc/R/include -I/usr/lib64/jvm/java/include -I/usr/lib64/jvm/java/include/linux -I/usr/local/include -fpic -g -O2 -Wall -c rmageml.c -o rmageml.o
rmageml.c: In function 'arji_createJVM':
rmageml.c:65: warning: dereferencing type-punned pointer will break strict-aliasing rules
rmageml.c: In function 'destroyOM':
rmageml.c:92: warning: dereferencing type-punned pointer will break strict-aliasing rules
rmageml.c: In function 'newRMAGESTK':
rmageml.c:109: warning: dereferencing type-punned pointer will break strict-aliasing rules
rmageml.c: In function 'importFeatures':
rmageml.c:134: warning: dereferencing type-punned pointer will break strict-aliasing rules
rmageml.c: In function 'getGridDimensions':
rmageml.c:169: warning: dereferencing type-punned pointer will break strict-aliasing rules
rmageml.c: In function 'selectQTypesDeriv':
rmageml.c:211: warning: dereferencing type-punned pointer will break strict-aliasing rules
rmageml.c: In function 'getSizeDED':
rmageml.c:245: warning: dereferencing type-punned pointer will break strict-aliasing rules
rmageml.c: In function 'selectQTypes':
rmageml.c:295: warning: dereferencing type-punned pointer will break strict-aliasing rules
rmageml.c: In function 'getExternalData':
rmageml.c:349: warning: dereferencing type-punned pointer will break strict-aliasing rules
rmageml.c: In function 'getQuantitationTypes':
rmageml.c:394: warning: dereferencing type-punned pointer will break strict-aliasing rules
rmageml.c: In function 'getQTypeDescription':
rmageml.c:432: warning: dereferencing type-punned pointer will break strict-aliasing rules
rmageml.c: In function 'createNewQTDim':
rmageml.c:464: warning: dereferencing type-punned pointer will break strict-aliasing rules
rmageml.c: In function 'addQuantitationTypeInfo':
rmageml.c:490: warning: dereferencing type-punned pointer will break strict-aliasing rules
rmageml.c: In function 'createNewMBASet':
rmageml.c:525: warning: dereferencing type-punned pointer will break strict-aliasing rules
rmageml.c: In function 'setMBA':
rmageml.c:549: warning: dereferencing type-punned pointer will break strict-aliasing rules
rmageml.c: In function 'updateMAGEML':
rmageml.c:582: warning: dereferencing type-punned pointer will break strict-aliasing rules
rmageml.c:599: warning: cast from pointer to integer of different size
rmageml.c: In function 'writeMAGEML':
rmageml.c:629: warning: dereferencing type-punned pointer will break strict-aliasing rules
rmageml.c: In function 'getVoidArrayInt':
rmageml.c:659: warning: dereferencing type-punned pointer will break strict-aliasing rules
rmageml.c: In function 'getVoidArrayStr':
rmageml.c:694: warning: dereferencing type-punned pointer will break strict-aliasing rules
rmageml.c: In function 'getVoidStr':
rmageml.c:728: warning: dereferencing type-punned pointer will break strict-aliasing rules
rmageml.c: In function 'getVoidVoid':
rmageml.c:751: warning: dereferencing type-punned pointer will break strict-aliasing rules
rmageml.c: In function 'destroyOM':
rmageml.c:95: warning: control reaches end of non-void function
rmageml.c: At top level:
rmageml.c:17: warning: 'JavaMethod_type_tag' defined but not used
gcc -std=gnu99 -shared -L/usr/local/lib64 -o RMAGEML.so rmageml.o -L/usr/lib64/jvm/java/jre/lib/amd64 -L/usr/lib64/jvm/java/jre/lib/i386 -ljava -L/usr/lib64/jvm/java/jre/lib/amd64/server -L/usr/lib64/jvm/java/jre/lib/i386/client -ljvm
** R
** inst
** preparing package for lazy loading
Loading required package: marray
Loading required package: limma
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)'.
** help
>>> Building/Updating help pages for package 'RMAGEML'
Formats: text html latex example
JavaVMRef-class text html latex
MEXP14 text html latex
addDerivedData text html latex example
addNormToMAGEML text html latex example
getArrayID text html latex example
getArrayLayout text html latex example
getArrayLayoutLimma text html latex example
getGnames text html latex example
getNumberOfFeatures text html latex example
getOrganization text html latex example
getQTDimensions text html latex example
getQTypeDescription text html latex example
getQuantitationTypes text html latex example
getSubmitterAddress text html latex example
importMAGEML text html latex example
importMAGEOM text html latex example
makeEset text html latex example
makeMarrayRaw text html latex example
makeRG text html latex example
reset text html latex example
writeMAGEML text html latex example
** building package indices ...
* DONE (RMAGEML)
* creating vignettes ...sh: line 1: 8759 Segmentation fault '/home/biocbuild/bbs-2.2-bioc/R/bin/R' --vanilla --no-save --quiet </tmp/Rin748290333 >/tmp/Rout748269747 2>&1
ERROR
Loading required package: marray
Loading required package: limma
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)'.
*** caught segfault ***
address (nil), cause 'memory not mapped'
Traceback:
1: .Call("getVoidVoid", "init", mageOM, ..rmagemlJVM@jvmptr, PACKAGE = "RMAGEML")
2: importMAGEML(directory = datadir, package = "marray", arrayID = "A-MEXP-14", DED = "DED:707", QTD = "QTD:707", name.Rf = "QT:F635 Mean", name.Rb = "QT:B635 Median", name.Gf = "QT:F532 Mean", name.Gb = "QT:B532 Median")
3: eval.with.vis(expr, .GlobalEnv, baseenv())
4: doTryCatch(return(expr), name, parentenv, handler)
5: tryCatchOne(expr, names, parentenv, handlers[[1]])
6: tryCatchList(expr, classes, parentenv, handlers)
7: 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"))})
8: try(.Internal(eval.with.vis(expr, .GlobalEnv, baseenv())), silent = TRUE)
9: evalFunc(ce, options)
10: driver$runcode(drobj, chunk, chunkopts)
11: utils::Sweave(f, quiet = quiet)
12: doTryCatch(return(expr), name, parentenv, handler)
13: tryCatchOne(expr, names, parentenv, handlers[[1]])
14: tryCatchList(expr, classes, parentenv, handlers)
15: 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)})
16: buildVignettes(dir = ".")
aborting ...