mercredi 2 mars 2016

Rcpp::IntegerVector creation gives segmentation fault

Some RCpp example code works smooth within RStudio. In the C++ IDE Qt Creator segmentation faults (SIGSEGV) occur instead, despite having fresh repositories, a modern GNU/Linux distro and modern g++ version.

This code works fine under RStudio, and gives me a segmentation fault in Qt Creator:

//main.cpp
#include <Rcpp.h>

int main() {
  Rcpp::IntegerVector v(3);
}

Not just this code, but also code copied from the Rcpp test suites like, for example:

DataFrame createTwo(){
    IntegerVector v = IntegerVector::create(1,2,3);
        std::vector<std::string> s(3);
        s[0] = "a";
        s[1] = "b";
        s[2] = "c";
        return DataFrame::create(Named("a")=v, Named("b")=s);
}

I use qmake to create a Makefile, and use the code suggested by Dirk Eddelbuettel and Romain Francois as well:

## -*- mode: Makefile; c-indent-level: 4; c-basic-offset: 4;  tab-width: 8; -*-
##
## Qt usage example for RInside, inspired by the standard 'density
## sliders' example for other GUI toolkits
##
## This file can be used across operating systems as qmake selects appropriate
## values as needed, as do the R and R-related calls below. See the thread at
##     http://ift.tt/1LUvmOj
## for discussion specific to Windows.
##
## Copyright (C) 2012  Dirk Eddelbuettel and Romain Francois

## build an app based on the one headers and two source files
TEMPLATE =      app

## beyond the default configuration, also use SVG graphics
QT +=           svg

## comment this out if you need a different version of R,
## and set set R_HOME accordingly as an environment variable
R_HOME =        $$system(R RHOME)
#message("R_HOME is" $$R_HOME)

## include headers and libraries for R
RCPPFLAGS =         $$system($$R_HOME/bin/R CMD config --cppflags)
RLDFLAGS =      $$system($$R_HOME/bin/R CMD config --ldflags)
RBLAS =         $$system($$R_HOME/bin/R CMD config BLAS_LIBS)
RLAPACK =       $$system($$R_HOME/bin/R CMD config LAPACK_LIBS)

## if you need to set an rpath to R itself, also uncomment
RRPATH =        -Wl,-rpath,$$R_HOME/lib

## include headers and libraries for Rcpp interface classes
## note that RCPPLIBS will be empty with Rcpp (>= 0.11.0) and can be omitted
RCPPINCL =      $$system($$R_HOME/bin/Rscript -e \"Rcpp:::CxxFlags\(\)\")
RCPPLIBS =      $$system($$R_HOME/bin/Rscript -e \"Rcpp:::LdFlags\(\)\")

## for some reason when building with Qt we get this each time
##   /usr/local/lib/R/site-library/Rcpp/include/Rcpp/module/Module_generated_ctor_signature.h:25: warning: unused parameter ‘classname
## so we turn unused parameter warnings off
## no longer needed with Rcpp 0.9.3 or later
#RCPPWARNING =      -Wno-unused-parameter

## include headers and libraries for RInside embedding classes
RINSIDEINCL =       $$system($$R_HOME/bin/Rscript -e \"RInside:::CxxFlags\(\)\")
RINSIDELIBS =       $$system($$R_HOME/bin/Rscript -e \"RInside:::LdFlags\(\)\")

## compiler etc settings used in default make rules
QMAKE_CXXFLAGS +=   $$RCPPWARNING $$RCPPFLAGS $$RCPPINCL $$RINSIDEINCL
QMAKE_LIBS +=           $$RLDFLAGS $$RBLAS $$RLAPACK $$RINSIDELIBS $$RCPPLIBS

## addition clean targets
QMAKE_CLEAN +=      qtdensity Makefile

## My personal additions    

QMAKE_CXXFLAGS += -Wall -Wextra -Weffc++ -std=c++11
QT       += core
QT       -= gui
TEMPLATE = app

SOURCES = main.cpp

Note that I use the C++11 standard with the QMAKE_CXXFLAGS += -std=c++11 flag. Removing this does not solve the problem.

As I said, the code passes all RStudio tests, but will crash on the same code with a segmentation fault in Qt Creator. All Rcpp repositories are fresh.

My G++ version is also the newest version under Lubuntu:

richel@druten:~/GitHubs/RibiLibraries$ g++ -v
Using built-in specs.
COLLECT_GCC=g++
COLLECT_LTO_WRAPPER=/usr/lib/gcc/i686-linux-gnu/5/lto-wrapper
Target: i686-linux-gnu
Configured with: ../src/configure -v --with-pkgversion='Ubuntu 5.2.1-22ubuntu2' --with-bugurl=file:///usr/share/doc/gcc-5/README.Bugs --enable-languages=c,ada,c++,java,go,d,fortran,objc,obj-c++ --prefix=/usr --program-suffix=-5 --enable-shared --enable-linker-build-id --libexecdir=/usr/lib --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --with-sysroot=/ --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-gnu-unique-object --disable-vtable-verify --enable-libmpx --enable-plugin --with-system-zlib --disable-browser-plugin --enable-java-awt=gtk --enable-gtk-cairo --with-java-home=/usr/lib/jvm/java-1.5.0-gcj-5-i386/jre --enable-java-home --with-jvm-root-dir=/usr/lib/jvm/java-1.5.0-gcj-5-i386 --with-jvm-jar-dir=/usr/lib/jvm-exports/java-1.5.0-gcj-5-i386 --with-arch-directory=i386 --with-ecj-jar=/usr/share/java/eclipse-ecj.jar --enable-objc-gc --enable-targets=all --enable-multiarch --disable-werror --with-arch-32=i686 --with-multilib-list=m32,m64,mx32 --enable-multilib --with-tune=generic --enable-checking=release --build=i686-linux-gnu --host=i686-linux-gnu --target=i686-linux-gnu
Thread model: posix
gcc version 5.2.1 20151010 (Ubuntu 5.2.1-22ubuntu2) 

My distro:

richel@druten:~/GitHubs/RibiLibraries$ uname -a
Linux druten 4.2.0-30-generic #36-Ubuntu SMP Fri Feb 26 00:57:19 UTC 2016 i686 athlon i686 GNU/Linux

Here I somewhat construct a stack trace, the debugger takes me to level 3:

0   ??          0xb7d10668  
1   Rf_allocVector3         0xb7d11727  
2   Rf_allocVector          0xb7d023be  
3   Rcpp::Vector<13, Rcpp::PreserveStorage>::Vector Vector.h    129  0x804b214 <- Debugger takes me here
4   main    main.cpp    5   0x804ac40   

The critical piece of code is:

Vector( const int& size ) {
    Storage::set__( Rf_allocVector( RTYPE, size) ) ; // <-- This line
    init() ;
}

What could have gone wrong?

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