From murdoch.duncan at gmail.com  Wed Oct  2 16:50:55 2013
From: murdoch.duncan at gmail.com (Duncan Murdoch)
Date: Wed, 02 Oct 2013 10:50:55 -0400
Subject: [Rd] C++ debugging help needed
Message-ID: <524C32CF.2060307@gmail.com>

I've had reports lately about segfaults in the rgl package.  I've only 
been able to reproduce these on Linux.   I am not so familiar with C++ 
details, so I have a couple of questions way down below. But first some 
background info.

  One recipe to recreate the crash works with a new version 5.0-1 of the 
mixOmics package:

 > library(mixOmics)
 > example(pca)

This crashes with messages like this:

Program received signal SIGSEGV, Segmentation fault.
0x00007ffff28aafd9 in __exchange_and_add (__mem=0x7f7fffff7f7ffff7,
     __val=<optimized out>) at /usr/include/c++/4.7/ext/atomicity.h:48
48        { return __atomic_fetch_add(__mem, __val, __ATOMIC_ACQ_REL); }

The call stack ends with this:

#0  0x00007ffff28aafd9 in __exchange_and_add (__mem=0x7f7fffff7f7ffff7,
     __val=<optimized out>) at /usr/include/c++/4.7/ext/atomicity.h:48
#1  __exchange_and_add_dispatch (__mem=0x7f7fffff7f7ffff7,
     __val=<optimized out>) at /usr/include/c++/4.7/ext/atomicity.h:81
#2  _M_dispose (__a=..., this=0x7f7fffff7f7fffe7)
     at /usr/include/c++/4.7/bits/basic_string.h:242
#3  ~basic_string (this=0x15f8770, __in_chrg=<optimized out>)
     at /usr/include/c++/4.7/bits/basic_string.h:536
#4  Shape::~Shape (this=0x15f8760, __in_chrg=<optimized out>) at 
Shape.cpp:13
#5  0x00007ffff22df50b in ~Background (this=0x15f8760,
     __in_chrg=<optimized out>) at Background.hpp:15
#6  Background::~Background (this=0x15f8760, __in_chrg=<optimized out>)
     at Background.hpp:15

Up to entry #4 this all looks normal.  If I go into that stack frame, I 
see this:


(gdb) up
#4  Shape::~Shape (this=0x15f8760, __in_chrg=<optimized out>) at 
Shape.cpp:13
warning: Source file is more recent than executable.
13        blended(in_material.isTransparent())
(gdb) p this
$9 = (Shape * const) 0x15f8760
(gdb) p *this
$10 = {_vptr.Shape = 0x7ffff2d8e290, mName = 6, mType = {
     static npos = <optimized out>,
     _M_dataplus = {<std::allocator<char>> = 
{<__gnu_cxx::new_allocator<char>> =
{<No data fields>}, <No data fields>},
       _M_p = 0x7f7fffff7f7fffff <Address 0x7f7fffff7f7fffff out of 
bounds>}},
   mShapeColor = {mRed = -1.4044474254567505e+306,
     mGreen = -1.4044477603031902e+306, mBlue = 4.24399170841135e-314,
     mTransparent = 0}, mSpecularReflectivity = 0.0078125,
   mSpecularSize = 1065353216, mDiffuseReflectivity = 0.007812501848093234,
   mAmbientReflectivity = 0}

The things displayed in *this are all wrong.  Those field names come 
from the Shape object in the igraph package, not the Shape object in the 
rgl package.   The mixOmics package uses both.

My questions:

- Has my code somehow got mixed up with the igraph code, so I really do 
have a call out to igraph's Shape::~Shape instead of rgl's 
Shape::~Shape, or is this just bad info being given to me by gdb?

- If I really do have calls to the wrong destructor in there, how do I 
avoid this?

Duncan Murdoch



[Rd] C++ debugging help needed
Duncan Murdoch