[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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