[R] Error on start R in server
Martin Morgan
mtmorgan at fhcrc.org
Mon Feb 8 21:01:59 CET 2010
On 02/08/2010 12:51 AM, Jiiindo wrote:
>
> Hello all,
> (Thank for your reply)
> I have a web-application in Apache Tomcat, when i start R in this
> application,
> I used packe RSJava
> Code
> ROmegahatInterpreter interp;
> String [] rargs = {"--no-save"};
> REvaluator e;
> interp = new ROmegahatInterpreter (
> ROmegahatInterpreter.fixArgs(rargs),false );
> e =new REvaluator ();
>
>
> Errors
> ================
> R version 2.10.1 (2009-12-14)
> Copyright (C) 2009 The R Foundation for Statistical Computing
> ISBN 3-900051-07-0
>
> R is free software and comes with ABSOLUTELY NO WARRANTY.
> You are welcome to redistribute it under certain conditions.
> Type 'license()' or 'licence()' for distribution details.
>
> Natural language support but running in an English locale
>
> R is a collaborative project with many contributors.
> Type 'contributors()' for more information and
> 'citation()' on how to cite R or R packages in publications.
>
> Type 'demo()' for some demos, 'help()' for on-line help, or
> 'help.start()' for an HTML browser interface to help.
> Type 'q()' to quit R.
>
>
> *** caught segfault ***
> address 0x4, cause 'memory not mapped'
> Warning: stack imbalance in 'if', 153 then 154
> Warning: stack imbalance in '{', 151 then 152
Probably additional information is needed. What version of SJava? In an
R session:
> library(SJava)
> sessionInfo()
Try to start R with fewer packages (and more quietly) with
String rargs[] = {"--quiet", "--vanilla"};
Can you get as far as
String [] rargs = {"--quiet", "--vanilla"};
ROmegahatInterpreter interp = new ROmegahatInterpreter (
ROmegahatInterpreter.fixArgs(rargs),false );
REvaluator e =new REvaluator ();
tryCatch({
e.voidEval("library(SJava)");
e.voidEval("print(sessionInfo())");
} catch (Exception ex) {
e.printStackTrack();
}
?
Martin
> Warning: stack imbalance in '<-', 145 then 146
> Warning: stack imbalance in 'if', 143 then 145
> Warning: stack imbalance in '{', 141 then 142
> Warning: stack imbalance in '<-', 135 then 137
> Warning: stack imbalance in 'if', 146 then 148
> Warning: stack imbalance in 'is.list', 163 then 164
> Warning: stack imbalance in '{', 144 then 145
> Warning: stack imbalance in '<-', 138 then 139
> Warning: stack imbalance in 'if', 136 then 143
> Warning: stack imbalance in 'lazyLoadDBfetch', 140 then 138
> Warning: stack imbalance in '{', 147 then 146
> Warning: stack imbalance in '||', 140 then 139
> Warning: stack imbalance in 'if', 138 then 137
> Warning: stack imbalance in '{', 133 then 135
> Warning: stack imbalance in 'if', 127 then 129
> Warning: stack imbalance in '{', 125 then 127
> Warning: stack imbalance in '[', 142 then 146
> Warning: stack imbalance in 'lazyLoadDBfetch', 128 then 138
> Warning: stack imbalance in 'lazyLoadDBfetch', 87 then 88
> Warning: stack imbalance in 'if', 112 then 111
> Warning: stack imbalance in 'inherits', 122 then 121
> Warning: stack imbalance in '.Internal', 121 then 120
> Warning: stack imbalance in 'if', 111 then 110
> Warning: stack imbalance in 'match', 110 then 108
> Warning: stack imbalance in '.Internal', 109 then 107
> Warning: stack imbalance in '<-', 103 then 100
> Warning: stack imbalance in '>', 109 then 110
> Warning: stack imbalance in '&&', 102 then 103
> Warning: stack imbalance in 'if', 100 then 101
> Warning: stack imbalance in '{', 101 then 98
> Warning: stack imbalance in 'if', 99 then 97
> Warning: stack imbalance in '<-', 84 then 85
> Warning: stack imbalance in '{', 82 then 84
> Warning: stack imbalance in 'if', 80 then 82
>
> Traceback:
> 1: .getClassFromCache(Class, where)
> 2: getClassDef(cl)
> 3: methods:::is(genfun, "genericFunction")
> 4: registerS3methods(nsInfo$S3methods, package, env)
> 5: loadNamespace(package, c(which.lib.loc, lib.loc), keep.source =
> keep.source)
> 6: doTryCatch(return(expr), name, parentenv, handler)
> 7: tryCatchOne(expr, names, parentenv, handlers[[1L]])
> 8: tryCatchList(expr, classes, parentenv, handlers)
> 9: 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 <- paste(prefix, "\n ", sep =
> "") } else prefix <- "Error : " msg <- paste(prefix,
> conditionMessage(e), "\n", sep = "") .Internal(seterrmessage(msg[1L]))
> if (!silent && identical(getOption("show.error.messages"), TRUE)) {
> cat(msg, file = stderr()) .Internal(printDeferredWarnings()) }
> invisible(structure(msg, class = "try-error"))})
> 10: try({ ns <- loadNamespace(package, c(which.lib.loc, lib.loc),
> keep.source = keep.source) dataPath <- file.path(which.lib.loc, package,
> "data") env <- attachNamespace(ns, pos = pos, dataPath = dataPath)})
> 11: library(package, lib.loc = lib.loc, character.only = TRUE,
> logical.return = TRUE, warn.conflicts = warn.conflicts, keep.source =
> keep.source)
> 12: require(pkg, quietly = TRUE, warn.conflicts = FALSE, character.only =
> TRUE, save = FALSE)
> 13: .First.sys()
>
> Possible actions:
> 1: abort (with core dump, if enabled)
> 2: normal R exit
> 3: exit R without saving workspace
> 4: exit R saving workspace
>
> *** caught segfault ***
> address 0x4, cause 'memory not mapped'
>
> Traceback:
> 1: nchar(dcall, type = "w")
> 2: value[[3L]](cond)
> 3: tryCatchOne(expr, names, parentenv, handlers[[1L]])
> 4: tryCatchList(expr, classes, parentenv, handlers)
> 5: 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 <- paste(prefix, "\n ", sep =
> "") } else prefix <- "Error : " msg <- paste(prefix,
> conditionMessage(e), "\n", sep = "") .Internal(seterrmessage(msg[1L]))
> if (!silent && identical(getOption("show.error.messages"), TRUE)) {
> cat(msg, file = stderr()) .Internal(printDeferredWarnings()) }
> invisible(structure(msg, class = "try-error"))})
> 6: try({ ns <- loadNamespace(package, c(which.lib.loc, lib.loc),
> keep.source = keep.source) dataPath <- file.path(which.lib.loc, package,
> "data") env <- attachNamespace(ns, pos = pos, dataPath = dataPath)})
> 7: library(package, lib.loc = lib.loc, character.only = TRUE,
> logical.return = TRUE, warn.conflicts = warn.conflicts, keep.source =
> keep.source)
> 8: require(pkg, quietly = TRUE, warn.conflicts = FALSE, character.only =
> TRUE, save = FALSE)
> 9: .First.sys()
>
> Possible actions:
> 1: abort (with core dump, if enabled)
> 2: normal R exit
> 3: exit R without saving workspace
> 4: exit R saving workspace
> Error in get(Info[i, 1], envir = env) : invalid 'inherits' argument
> During startup - Warning message:
> package stats in options("defaultPackages") was not found
> Selection: readline: readline_callback_read_char() called with no handler!
> 1
> bash: 1: command not found
>
--
Martin Morgan
Computational Biology / Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N.
PO Box 19024 Seattle, WA 98109
Location: Arnold Building M1 B861
Phone: (206) 667-2793
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