On 20 August 2018 at 15:35, Iñaki Ucar wrote:
| El lun., 20 ago. 2018 a las 9:01, Jan van der Laan
| (<rh...@eoos.dds.nl>) escribió:
| >
| >
| > One of my packges gives a message with the undefined behaviour sanitiser
| > (UBSAN). I have difficulty tracking down/understanding the cause of this
| > message. However, I have been able to create a small example that
| > generates the same warning. The mail below is a bit on the long side,
| > and, I hope it is readable as it mixes quite a lot code with text. I am
| > sorry for that. A probably better readable version can be found at
| > https://github.com/djvanderlaan/lvec_ubsan where also the complete
| > source code and the docker image used for testing can be found.
| >
| > My example consists of two packages: pkg1 and pkg2. The package pkg2
| > links to pkg1. Package pkg1 defines a template class `FooBar<T>` which
| > inherits from virtual class `Foo`. Pointers to the these objects are
| > passed back to R using a `Rcpp:XPtr` object:
| >
| > ========== pkg1/src/construct.cpp ================
| > #include "../inst/include/pkg1.h"
| >
| > // [[Rcpp::export]]
| > RcppExport SEXP new_foobar(int i) {
| > BEGIN_RCPP
| > FooBar<int>* x = new FooBar<int>(i);
| > return Rcpp::XPtr<Foo>(x, true);
| > END_RCPP
| > }
|
| Note that RcppExport SEXP should be just SEXP. BEGIN_RCPP and END_RCPP
| should be dropped too.
+1
Or else don't use [[Rcpp::export]] and Rcpp::compileAttributes().
Dirk
| > // [[Rcpp::export]]
| > RcppExport SEXP new_foobard(double i) {
| > BEGIN_RCPP
| > FooBar<double>* x = new FooBar<double>(i);
| > return Rcpp::XPtr<Foo>(x, true);
| > END_RCPP
| > }
| > ========== END pkg1/src/construct.cpp ================
| >
| > All headers of pkg1 are `inst/include`; these are included by `pkg2`:
| >
| > ========== pkg1/inst/include/pkg1.h ================
| > #include <Rcpp.h>
| >
| > // ==== VISITOR
| > template<typename T> class FooBar;
| >
| > class FooBarVisitor {
| > public:
| > virtual void visit(FooBar<double>& vec) = 0;
| > virtual void visit(FooBar<int>& vec) = 0;
| > };
| >
| > // ==== FOO
| > class Foo {
| > public:
| > Foo() {};
| > virtual ~Foo() {};
| >
| > virtual void visit(FooBarVisitor* visitor) = 0;
| > };
| >
| > // ==== FOOBAR
| > template<typename T>
| > class FooBar : public Foo {
| > public:
| > FooBar(T i = 0) : Foo(), i_(i) {};
| > ~FooBar() {};
| >
| > T i() const { return i_;}
| > void i(T i) { i_ = i;}
| >
| > void visit(FooBarVisitor* visitor) {
| > visitor->visit(*this);
| > }
| > private:
| > T i_;
| > };
| > #endif
| > ========== END pkg1/inst/include/pkg1.h ================
| >
| > The XPtr is passed to c++ code in pkg2 and methods of the Foo object are
| > called:
| >
| > ========== pkg2/src/construct.cpp ================
| > #include <Rcpp.h>
| > #include <pkg1.h>
| >
| > // [[Rcpp::export]]
| > RcppExport int get_foobar(SEXP xp) {
| > Rcpp::XPtr<Foo> x(xp);
| > Foo* y1 = x;
| > FooBar<int>* y2 = dynamic_cast<FooBar<int>*>(y1);
| > return y2->i();
| > }
| > ========== END pkg2/src/construct.cpp ================
| >
| > This generates the following UBSAN messages:
| >
| >
| > ========== WARNING MESSAGES ================
| > Testing pkg2
| > <U+221A> | OK F W S | Context
| > / | 0 | fooconstruct.cpp:9:21: runtime error: <null> address
| > 0x000003c21810 which does not point to an object of type 'Foo'
| > 0x000003c21810: note: object is of type 'FooBar<int>'
| > 00 00 00 00 58 1c 79 fd 48 7f 00 00 0a 00 00 00 00 00 00 00 20
| > 00 00 00 00 00 00 00 01 03 00 00
| > ^~~~~~~~~~~~~~~~~~~~~~~
| > vptr for 'FooBar<int>'
| > construct.cpp:10:14: runtime error: member call on address
| > 0x000003c21810 which does not point to an object of type 'FooBar<int>'
| > 0x000003c21810: note: object is of type 'FooBar<int>'
| > 00 00 00 00 58 1c 79 fd 48 7f 00 00 0a 00 00 00 00 00 00 00 20
| > 00 00 00 00 00 00 00 01 03 00 00
| > ^~~~~~~~~~~~~~~~~~~~~~~
| > vptr for 'FooBar<int>'
| > /usr/local/lib/R/library/pkg1/include/pkg1.h:33:26: runtime error:
| > member access within address 0x000003c21810 which does not point to an
| > object of type 'const FooBar<int>'
| > 0x000003c21810: note: object is of type 'FooBar<int>'
| > 00 00 00 00 58 1c 79 fd 48 7f 00 00 0a 00 00 00 00 00 00 00 20
| > 00 00 00 00 00 00 00 01 03 00 00
| > ^~~~~~~~~~~~~~~~~~~~~~~
| > vptr for 'FooBar<int>'
| > <U+221A> | 1 | foo
| > ========== END WARNING MESSAGES ================
| >
| >
| > I have had real problem reproducing this error. Also searching for the
| > error give little clues as to what the problem is. The following message
| > on the Rcpp-devel list seems somewhat similar:
| >
http://lists.r-forge.r-project.org/pipermail/rcpp-devel/2017-July/009656.html.
| > I thought that it might be caused by the fact that I am passing pointers
| > to template classes between libraries. I also couldn't find much about
| > that. I did find some messages on passing pointers to STL objects
| > between libraries. That should be ok, as long as the same compiler is
| > used for both libraries. Although that might technically still make it
| > undefined behaviour.
|
| pkg2 compiles a shared library using pkg1's headers, but it does not
| link against libpkg1.so (in general, this is not possible in R). So
| both libpkg2.so and libpkg1.so define two copies of the same types,
| Foo and FooBar. pkg2 allocates FooBar from libpkg1.so and then
| dynamically casts it as FooBar from libpkg2.so. This is why clang
| complains. It has to do with how RTTI comparisons are done across
| dynamic objects (see, e.g.,
| https://whatofhow.wordpress.com/2015/03/17/odr-rtti-dso/).
|
| I'd say that these errors can be safely ignored, because types are
| exactly the same. Anyway, shouldn't it be easier to export get_foobar
| in pkg1?
The only thought I had so far (and I had no time to play with the code) is to
maybe wrap Rcpp::Shield<> around the XPtr object.
Dirk
|
| Iñaki
|
| >
| > So, help!?
| >
| > Jan
| >
| >
| >
| >
| >
| > _______________________________________________
| > Rcpp-devel mailing list
| > Rcpp-devel@lists.r-forge.r-project.org
| > https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/rcpp-devel
|
|
|
| --
| Iñaki Ucar
| _______________________________________________
| Rcpp-devel mailing list
| Rcpp-devel@lists.r-forge.r-project.org
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--
http://dirk.eddelbuettel.com | @eddelbuettel | e...@debian.org
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