I have now got two "solutions" to this. The rgl version currently on
CRAN does a simple rename to avoid the name clash. A later version,
still only on R-forge, puts most objects into a namespace called "rgl".
(The old code had two small namespaces "gui" and "lib"; they are gone now.)
I am not yet confident that the current version with namespaces will
compile on all platforms; it seems much more fragile this way, with
errors showing up on Linux that were not errors on Windows. (E.g.
sometimes I included a header with declarations in the rgl namespace
followed by system header files, and the latter acted differently than
they did when placed before the rgl header file, apparently declaring
the system functions to be in a new anonymous namespace.)
rgl also includes some C code from the gl2ps project and some C++ code
from FTGL; I didn't put those into the rgl namespace. So there are
still possibilities for clashes if anyone else uses those.
I'm still surprised that anything with plugins works on Unix-alike
systems with such bizarre linking rules. This is one of those few cases
where the Windows design seems clearly superior.
Duncan Murdoch
On 02/10/2013 10:50 AM, Duncan Murdoch wrote:
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
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