ken_lee
2002-Apr-25 07:20 UTC
[R] An unexpected exception has been detected in native code outside the VM
Dear all:
I have a problem with calling R from Java,
It was ok at the first time,but the error message "An unexpected exception
has been detected in native code outside the VM. "
will appear. What is the issue of "native code"?
Could somebody help me ?
Thanks,
ken
This is the log I obtained:
executing: source('/export/home/users/ruser/java/Rmain.R')
Loading RInterpreter library
R : Copyright 2002, The R Development Core Team
Version 1.4.1 (2002-01-30)
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.
R is a collaborative project with many contributors.
Type `contributors()' for more information.
Type `demo()' for some demos, `help()' for on-line help, or
`help.start()' for a HTML browser interface to help.
Type `q()' to quit R.
[Previously saved workspace restored]
now dyn.load(/usr/local/lib/R/library/ctest/libs/ctest.so)..
`envir' chosen:<environment: R_GlobalEnv>
--> parsed 1 expressions; now eval(.)ing them:
>>>> eval(expression_nr. 1 )
================> rmain <- function(Rvals = NULL) {
library(SJava)
library(nlme)
library(ctest)
print(Rvals)
file <- "zz"
dev <- "png"
print .... [TRUNCATED]
curr.fun: symbol <-
.. after `expression(rmain <- function(Rvals = NULL) { library(SJava)
library(nlme) library(ctest) print(Rvals) file <- "zz"
dev <- "png" print(dev) draw <-
"pairs_corr_scatter" if (draw == "pairs_corr_scatter") {
source("/export/home/users/ruser/rsc/pcscatter01.R") NODE =
rnorm(77) RSM2 = rnorm(77) CADT = rnorm(77) VTS = c(NODE -
c(rnorm(12), rep(0, 65))) xRS = c(NODE - c(rnorm(27), rep(0, 50)))
reda <- data.frame(NODE = NODE, RSM2 = RSM2, CADT = CADT, VTS =
VTS, xRS = xRS) pcscatter01(file = file, dev = dev, reda = reda, title =
"title", footnote = "aaa") } print(file)
val <- 1 val})'
now dyn.load(/usr/local/lib/R/library/SJava/libs/SJava.so)..
Garbage collection 1 = 0+0+1 (level 2) ...
146961 cons cells free (36%)
5.7 Mbytes of heap free (95%)
Loading required package: nls
Garbage collection 2 = 1+0+1 (level 0) ...
85806 cons cells free (21%)
5.5 Mbytes of heap free (92%)
now dyn.load(/usr/local/lib/R/library/nls/libs/nls.so)..
now dyn.load(/usr/local/lib/R/library/nlme/libs/nlme.so)..
`envir' chosen:<environment: R_GlobalEnv>
--> parsed 1 expressions; now eval(.)ing them:
>>>> eval(expression_nr. 1 )
================> pcscatter01 <- function(file = NULL, dev, reda, title,
footnote, width = 10, height = 7) {
tmp <- paste(file, dev, sep = "_pcscatter.")
c .... [TRUNCATED]
curr.fun: symbol <-
.. after `expression(pcscatter01 <- function(file = NULL, dev, reda, title,
footnote, width = 10, height = 7) { tmp <- paste(file, dev, sep =
"_pcscatter.") cmd <- paste("| gs -dNOPAUSE -dBATCH -q
-sDEVICE=png256 -r90 -g900x630 -sOutputFile=", tmp, " -",
sep = "") postscript(file = cmd, width = width, height = height,
pointsize = 10.5, paper = "special", horizontal = F)
invisible() par(mar = c(5, 4, 4, 2)) title <- list(title, col =
"red", cex = 1.5) panel.cor <- function(x, y, digits = 2, prefix
= "", cex.cor) { usr <- par("usr")
on.exit(par(usr)) par(usr = c(0, 1, 0, 1)) r <- abs(cor(x, y))
txt <- format(c(r, 0.123456789), digits = digits)[1] txt <-
paste(prefix, txt, sep = "") if (missing(cex.cor))
cex <- 0.8/strwidth(txt) text(0.5, 0.5, txt, cex = cex * r) }
pairs(reda, lower.panel = panel.smooth, upper.panel = panel.cor) title(main =
title, line = 2) graphics.off()})'
Garbage collection 3 = 2+0+1 (level 0) ...
83676 cons cells free (20%)
5.5 Mbytes of heap free (91%)
executing: source('/export/home/users/ruser/java/Rmain.R')
R : Copyright 2002, The R Development Core Team
Version 1.4.1 (2002-01-30)
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.
R is a collaborative project with many contributors.
Type `contributors()' for more information.
Type `demo()' for some demos, `help()' for on-line help, or
`help.start()' for a HTML browser interface to help.
Type `q()' to quit R.
An unexpected exception has been detected in native code outside the VM.
<=====ERROR MESSAGE===Unexpected Signal : 11 occurred at PC=0xf27e2440
Function name=do_dump
Library=/usr/local/lib/R/bin/libR.so
Current Java thread:
at org.omegahat.R.Java.ROmegahatInterpreter.initR(Native Method)
at
org.omegahat.R.Java.ROmegahatInterpreter.<init>(ROmegahatInterpreter.java:65)
at com.tynesys.common.cpc01Action.perform(cpc01Action.java:231)
at
org.apache.struts.action.ActionServlet.processActionPerform(ActionServlet.java:1787)
at org.apache.struts.action.ActionServlet.process(ActionServlet.java:1586)
at org.apache.struts.action.ActionServlet.doPost(ActionServlet.java:510)
at javax.servlet.http.HttpServlet.service(HttpServlet.java:760)
at javax.servlet.http.HttpServlet.service(HttpServlet.java:853)
at
org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:247)
at
org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:193)
at
org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:243)
at
org.apache.catalina.core.StandardPipeline.invokeNext(StandardPipeline.java:566)
at org.apache.catalina.core.StandardPipeline.invoke(StandardPipeline.java:472)
at org.apache.catalina.core.ContainerBase.invoke(ContainerBase.java:943)
at
org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:190)
at
org.apache.catalina.core.StandardPipeline.invokeNext(StandardPipeline.java:566)
at org.apache.catalina.core.StandardPipeline.invoke(StandardPipeline.java:472)
at org.apache.catalina.core.ContainerBase.invoke(ContainerBase.java:943)
at org.apache.catalina.core.StandardContext.invoke(StandardContext.java:2343)
at
org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:180)
at
org.apache.catalina.core.StandardPipeline.invokeNext(StandardPipeline.java:566)
at
org.apache.catalina.valves.ErrorDispatcherValve.invoke(ErrorDispatcherValve.java:170)
at
org.apache.catalina.core.StandardPipeline.invokeNext(StandardPipeline.java:564)
at
org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:170)
at
org.apache.catalina.core.StandardPipeline.invokeNext(StandardPipeline.java:564)
at org.apache.catalina.valves.AccessLogValve.invoke(AccessLogValve.java:468)
at
org.apache.catalina.core.StandardPipeline.invokeNext(StandardPipeline.java:564)
at org.apache.catalina.core.StandardPipeline.invoke(StandardPipeline.java:472)
at org.apache.catalina.core.ContainerBase.invoke(ContainerBase.java:943)
at
org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.java:174)
at
org.apache.catalina.core.StandardPipeline.invokeNext(StandardPipeline.java:566)
at org.apache.catalina.core.StandardPipeline.invoke(StandardPipeline.java:472)
at org.apache.catalina.core.ContainerBase.invoke(ContainerBase.java:943)
at
org.apache.catalina.connector.http.HttpProcessor.process(HttpProcessor.java:1012)
at
org.apache.catalina.connector.http.HttpProcessor.run(HttpProcessor.java:1107)
at java.lang.Thread.run(Thread.java:479)
Dynamic libraries:
0x10000 /usr/java/bin/../bin/sparc/native_threads/java
0xff350000 /usr/lib/libthread.so.1
0xff390000 /usr/lib/libdl.so.1
0xff200000 /usr/lib/libc.so.1
0xff330000 /usr/platform/SUNW,Ultra-60/lib/libc_psr.so.1
0xfe480000 /usr/j2se/jre/lib/sparc/client/libjvm.so
0xff2e0000 /usr/lib/libCrun.so.1
0xff1e0000 /usr/lib/libsocket.so.1
0xff100000 /usr/lib/libnsl.so.1
0xff0d0000 /usr/lib/libm.so.1
0xff310000 /usr/lib/libw.so.1
0xff0b0000 /usr/lib/libmp.so.2
0xff080000 /usr/j2se/jre/lib/sparc/native_threads/libhpi.so
0xff050000 /usr/j2se/jre/lib/sparc/libverify.so
0xfe440000 /usr/j2se/jre/lib/sparc/libjava.so
0xff020000 /usr/j2se/jre/lib/sparc/libzip.so
0xfaed0000 /usr/j2se/jre/lib/sparc/libnet.so
0xfacd0000 /usr/lib/nss_files.so.1
0xf3ee0000 /usr/local/lib/R/library/SJava/libs/SJava.so
0xf3ec0000 /usr/local/lib/R/library/SJava/libs/libRSNativeJava.so
0xf2780000 /usr/local/lib/R/bin/libR.so
0xf3ea0000 /usr/local/lib/libgcc_s.so.1
0xf3dd0000 /usr/lib/libz.so.1
0xf3c30000 /usr/lib/libcurses.so.1
0xf3db0000 /usr/local/lib/R/library/ctest/libs/ctest.so
0xf3c10000 /usr/local/lib/R/library/nls/libs/nls.so
0xf3b50000 /usr/local/lib/R/library/nlme/libs/nlme.so
Local Time = Thu Apr 25 11:18:04 2002
Elapsed Time = 51
#
# The exception above was detected in native code outside the VM
#
# Java VM: Java HotSpot(TM) Client VM (1.3.1_03-b03 mixed mode)
#
# An error report file has been saved as hs_err_pid6344.log.
# Please refer to the file for further information.
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A.J. Rossini
2002-Apr-25 07:31 UTC
[R] An unexpected exception has been detected in native code outside the VM
>>>>> "ken" == ken lee <ken_lee> writes:ken> Dear all: ken> I have a problem with calling R from Java, ken> It was ok at the first time,but the error message "An unexpected exception has been detected in native code outside the VM. " ken> will appear. What is the issue of "native code"? It refers to the R shared library, being loaded in using JNI. The message is quite clear about this: ken> An unexpected exception has been detected in native code outside the VM. <=====ERROR MESSAGE=== ken> Unexpected Signal : 11 occurred at PC=0xf27e2440 ken> Function name=do_dump ken> Library=/usr/local/lib/R/bin/libR.so Good luck with that! I've had better luck the other way (Java within R). Not perfect luck, but usually acceptable. Cool! Servlet processing. You'll need luck, then... best, -tony -- A.J. Rossini Rsrch. Asst. Prof. of Biostatistics U. of Washington Biostatistics rossini at u.washington.edu FHCRC/SCHARP/HIV Vaccine Trials Net rossini at scharp.org -------------- http://software.biostat.washington.edu/ ---------------- FHCRC: M-W: 206-667-7025 (fax=4812)|Voicemail is pretty sketchy/use Email UW: Th: 206-543-1044 (fax=3286)|Change last 4 digits of phone to FAX (my friday location is usually completely unpredictable.) -.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.- r-help mailing list -- Read http://www.ci.tuwien.ac.at/~hornik/R/R-FAQ.html Send "info", "help", or "[un]subscribe" (in the "body", not the subject !) To: r-help-request at stat.math.ethz.ch _._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._