Hi,
I am able to integrate C++ and R through RInside library. However when I
use a jni call as my UI is through java it crashes at C++ side. My files
are
------------------------------------------------
JNICallingClass.C:
JNIEXPORT void JNICALL Java_CallR_run (JNIEnv* env, jobject callr){
std::cout << "Inside JNICALL" << std::endl;
testR();
std::cout << "ENd of JNICALL" << std::endl;
}
-------------------------------------------------
CppCall2R.C
void testR(){
Rcpp::NumericVector vec(1);
cout << "RInside ready" << endl;
}
---------------------------------------------------
JavaClass.java
public class CallR{
static{
try {
System.loadLibrary("callr");
} catch (UnsatisfiedLinkError e) {
System.err.println("Native code library failed to
load.\n" + e);
System.exit(1);
}
}
public native void run();
public static void main(String[] args){
CallR callr = new CallR();
//Runtime.getRuntime().exec("R");
callr.run();
}
}
----------------------------------------------------------------------------
If I just compile the C++ code and invoke it through a main C++ class I get
no error . But when I call the code from Java I get the following error:
#
# A fatal error has been detected by the Java Runtime Environment:
#
# SIGSEGV (0xb) at pc=0x00007f9e6974ba8e, pid=5891, tid=140319087077120
#
# JRE version: 6.0_31-b05
# Java VM: Java HotSpot(TM) 64-Bit Server VM (20.6-b01 mixed mode
linux-amd64 compressed oops)
# Problematic frame:
# C [libR.so+0x11aa8e] R_gc+0x9e
--------------------------------------------------------------------------------------------
The error log is :
Current thread (0x00007f9e90006800): JavaThread "main" [_thread_in_native,
id=5892, stack(0x00007f9e95472000,0x00007f9e95573000)]
siginfo:si_signo=SIGSEGV: si_errno=0, si_code=1 (SEGV_MAPERR),
si_addr=0x0000000000000018
Registers:
RAX=0x0000000000000001, RBX=0x0000000000000030, RCX=0x0000000000000000,
RDX=0x00007f9e900b7588
RSP=0x00007f9e95571580, RBP=0x0000000000000028, RSI=0x0000000000000000,
RDI=0x0000000000000004
R8 =0x00007f9e69af9990, R9 =0x000000000000004f, R10=0x00007f9e69af9850,
R11=0x00000036b327f430
R12=0x00007f9e900b7580, R13=0x0000000000000001, R14=0x0000000000000001,
R15=0x00007f9e69adfc00
RIP=0x00007f9e6974ba8e, EFLAGS=0x0000000000010206,
CSGSFS=0x0000000000000033, ERR=0x0000000000000004
TRAPNO=0x000000000000000e
Top of Stack: (sp=0x00007f9e95571580)
0x00007f9e95571580: 0000000000000000 0000000000000001
0x00007f9e95571590: 000000000000000e 000000077b07d340
0x00007f9e955715a0: 00007f9e95571948 00007f9e6974c9ed
0x00007f9e955715b0: 000000077b07d340 00007f9e95571640
0x00007f9e955715c0: 0000000000000000 00000036b2e14915
0x00007f9e955715d0: 0000000000000001 00000036b32e495d
0x00007f9e955715e0: 00007f9e8c3f2430 000000077b07d340
0x00007f9e955715f0: 00007f9e95571640 0000000000000000
0x00007f9e95571600: 000000077b07d340 00007f9e95571948
0x00007f9e95571610: 00007f9e90006800 00007f9e8c1e9857
0x00007f9e95571620: 00007f9e95571898 00007f9e95571860
0x00007f9e95571630: 00007f9e95572700 000000077b07d340
0x00007f9e95571640: 00007f9e955718b0 00007f9e8c1e94cf
0x00007f9e95571650: 00007f9e6918ba98 0000000000000000
0x00007f9e95571660: 00007f9e6918b990 00007f9e900b5330
0x00007f9e95571670: 00007f9e900b5330 00007f9e900b5330
0x00007f9e95571680: 0000000000000000 0000000000000000
0x00007f9e95571690: 0000000000000000 00007f9e691a1ac0
0x00007f9e955716a0: 0000000000000000 0000000000000000
0x00007f9e955716b0: 0000000000000000 0000000000000000
0x00007f9e955716c0: 0000000000000000 00007f9e900b50f0
0x00007f9e955716d0: 0000000000000001 0000000000000008
0x00007f9e955716e0: 0000000000000000 0000000000000000
0x00007f9e955716f0: 0000003600000000 00007f9e900b5330
0x00007f9e95571700: 0000000000002000 00007f9e00000001
0x00007f9e95571710: 0000000000000000 0000000000000000
0x00007f9e95571720: 0000000000000000 00007f9e691a1f80
0x00007f9e95571730: 0000000000000000 0000000000000000
0x00007f9e95571740: 0000000000000000 0000000000000000
0x00007f9e95571750: 00007f9e6918bac0 0000000000000006
0x00007f9e95571760: 0000000000000000 0000000000001002
0x00007f9e95571770: 0000003600000002 0000000000000000
Instructions: (pc=0x00007f9e6974ba8e)
0x00007f9e6974ba6e: 40 04 01 85 ed 4d 89 60 08 49 89 0c 24 48 8d 0d
0x00007f9e6974ba7e: 6e dc 3a 00 4c 8d 14 01 49 8b 0a 74 4d 44 89 e8
0x00007f9e6974ba8e: 4c 8b 49 18 31 f6 c1 e0 05 89 c7 4c 89 d0 0f 1f
0x00007f9e6974ba9e: 40 00 41 83 00 01 48 89 4a 10 83 c6 01 48 89 51
Register to memory mapping:
RAX=0x0000000000000001 is an unknown value
RBX=0x0000000000000030 is an unknown value
RCX=0x0000000000000000 is an unknown value
RDX=0x00007f9e900b7588 is an unknown value
RSP=0x00007f9e95571580 is pointing into the stack for thread:
0x00007f9e90006800
RBP=0x0000000000000028 is an unknown value
RSI=0x0000000000000000 is an unknown value
RDI=0x0000000000000004 is an unknown value
R8 =0x00007f9e69af9990: <offset 0x4c8990> in /usr/lib64/R/lib/libR.so at
0x00007f9e69631000
R9 =0x000000000000004f is an unknown value
R10=0x00007f9e69af9850: <offset 0x4c8850> in /usr/lib64/R/lib/libR.so at
0x00007f9e69631000
R11=0x00000036b327f430: __libc_malloc+0 in /lib64/libc.so.6 at
0x00000036b3200000
R12=0x00007f9e900b7580 is an unknown value
R13=0x0000000000000001 is an unknown value
R14=0x0000000000000001 is an unknown value
R15=0x00007f9e69adfc00: <offset 0x4aec00> in /usr/lib64/R/lib/libR.so at
0x00007f9e69631000
Stack: [0x00007f9e95472000,0x00007f9e95573000], sp=0x00007f9e95571580,
free space=1021k
Native frames: (J=compiled Java code, j=interpreted, Vv=VM code, C=native
code)
C [libR.so+0x11aa8e] R_gc+0x9e
[error occurred during error reporting (printing native stack), id 0xb]
Java frames: (J=compiled Java code, j=interpreted, Vv=VM code)
j CallR.run()V+0
j CallR.main([Ljava/lang/String;)V+9
v ~StubRoutines::call_stub
Is there a solution for this?
Roy
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