[Rcpp-devel] Strange compiler error when using boost uBLAS on Ubuntu 11.04

With
sessionInfo()
R version 2.14.0 Under development (unstable) (2011-05-26 r55995)
Platform: x86_64-unknown-linux-gnu (64-bit)

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8
 [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8
 [7] LC_PAPER=C                 LC_NAME=C
 [9] LC_ADDRESS=C               LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base

other attached packages:
[1] Rcpp_0.9.4.1 inline_0.3.8

loaded via a namespace (and not attached):
[1] tools_2.14.0

and

$ g++ --version
g++ (Ubuntu/Linaro 4.5.2-8ubuntu4) 4.5.2
$ wajig list libboost-dev
ii  libboost-dev                   1.42.0.1ubuntu1
Boost C++ Libraries development files (default version)

I get a strange compiler error when trying to compile the "Hello
World" example of the coordinate_matrix representation from Boost's
uBLAS, as shown in the enclosed.  The first two examples (the
mapped_matrix and the compressed_matrix) compile for me but the third
and the fourth don't.  The error I get is

Error in compileCode(f, code, language = language, verbose = verbose) :
  Compilation ERROR, function(s)/method(s) not created! In file
included from /usr/include/c++/4.5/bits/stl_algo.h:63:0,
                 from /usr/include/c++/4.5/algorithm:63,
                 from
/home/bates/R/x86_64-unknown-linux-gnu-library/2.14/Rcpp/include/RcppCommon.h:121,
                 from
/home/bates/R/x86_64-unknown-linux-gnu-library/2.14/Rcpp/include/Rcpp.h:27,
                 from file6b444b24.cpp:4:
/usr/include/c++/4.5/bits/stl_tempbuf.h: In constructor
?std::_Temporary_buffer<_ForwardIterator,
_Tp>::_Temporary_buffer(_ForwardIterator, _ForwardIterator) [with
_ForwardIterator =
boost::numeric::ublas::indexed_iterator<boost::numeric::ublas::index_triple_array<std::vector<long
unsigned int>, std::vector<long unsigned int>, std::vector<double> >,
std::random_access_iterator_tag>, _Tp =
boost::numeric::ublas::index_triple<boost::numeric::ublas::index_triple_array<std::vector<long
unsigned int>, std::vector<long unsigned int>, std::vector<double> >
]?:
/usr
In addition: Warning message:
running command '/home/bates/build/R-devel/bin/R CMD SHLIB
file6b444b24.cpp 2> file6b444b24.cpp.err.txt' had status 1

Do others get this error for other versions of boost or other compilers?
Can anyone decide what that error means?  I'm perplexed about how
"/usr" ended up in the error message unless it was the name of a file
that somehow got truncated.
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| With
| 
| > sessionInfo()
| R version 2.14.0 Under development (unstable) (2011-05-26 r55995)
| Platform: x86_64-unknown-linux-gnu (64-bit)
| 
| locale:
|  [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
|  [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8
|  [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8
|  [7] LC_PAPER=C                 LC_NAME=C
|  [9] LC_ADDRESS=C               LC_TELEPHONE=C
| [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
| 
| attached base packages:
| [1] stats     graphics  grDevices utils     datasets  methods   base
| 
| other attached packages:
| [1] Rcpp_0.9.4.1 inline_0.3.8
| 
| loaded via a namespace (and not attached):
| [1] tools_2.14.0
| 
| and
| 
| $ g++ --version
| g++ (Ubuntu/Linaro 4.5.2-8ubuntu4) 4.5.2
| $ wajig list libboost-dev
| ii  libboost-dev                   1.42.0.1ubuntu1
| Boost C++ Libraries development files (default version)
| 
| I get a strange compiler error when trying to compile the "Hello
| World" example of the coordinate_matrix representation from Boost's
| uBLAS, as shown in the enclosed.  The first two examples (the
| mapped_matrix and the compressed_matrix) compile for me but the third
| and the fourth don't.  The error I get is
| 
| Error in compileCode(f, code, language = language, verbose = verbose) :
|   Compilation ERROR, function(s)/method(s) not created! In file
| included from /usr/include/c++/4.5/bits/stl_algo.h:63:0,
|                  from /usr/include/c++/4.5/algorithm:63,
|                  from
| /home/bates/R/x86_64-unknown-linux-gnu-library/2.14/Rcpp/include/RcppCommon.h:121,
|                  from
| /home/bates/R/x86_64-unknown-linux-gnu-library/2.14/Rcpp/include/Rcpp.h:27,
|                  from file6b444b24.cpp:4:
| /usr/include/c++/4.5/bits/stl_tempbuf.h: In constructor
| ?std::_Temporary_buffer<_ForwardIterator,
| _Tp>::_Temporary_buffer(_ForwardIterator, _ForwardIterator) [with
| _ForwardIterator =
| boost::numeric::ublas::indexed_iterator<boost::numeric::ublas::index_triple_array<std::vector<long
| unsigned int>, std::vector<long unsigned int>, std::vector<double> >,
| std::random_access_iterator_tag>, _Tp =
| boost::numeric::ublas::index_triple<boost::numeric::ublas::index_triple_array<std::vector<long
| unsigned int>, std::vector<long unsigned int>, std::vector<double> >
| >]?:
| /usr
| In addition: Warning message:
| running command '/home/bates/build/R-devel/bin/R CMD SHLIB
| file6b444b24.cpp 2> file6b444b24.cpp.err.txt' had status 1
| 
| Do others get this error for other versions of boost or other compilers?

Yes, confirmed. Examples one and two build, three and four puke.  

Can you try them without Rcpp to see if there is a side-effect?

Dirk

| Can anyone decide what that error means?  I'm perplexed about how
| "/usr" ended up in the error message unless it was the name of a file
| that somehow got truncated.
| xuntyped binary data, RcppUblas.R    [Click mouse-2 to save to a file]
| _______________________________________________
| Rcpp-devel mailing list
| Rcpp-devel at lists.r-forge.r-project.org
| https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/rcpp-devel
Gauss once played himself in a zero-sum game and won $50.
                      -- #11 at http://www.gaussfacts.com
Sorry to take so long to respond.
On 4 June 2011 at 11:52, Douglas Bates wrote:
| With
|
| > sessionInfo()
| R version 2.14.0 Under development (unstable) (2011-05-26 r55995)
| Platform: x86_64-unknown-linux-gnu (64-bit)
|
| locale:
| ?[1] LC_CTYPE=en_US.UTF-8 ? ? ? LC_NUMERIC=C
| ?[3] LC_TIME=en_US.UTF-8 ? ? ? ?LC_COLLATE=en_US.UTF-8
| ?[5] LC_MONETARY=en_US.UTF-8 ? ?LC_MESSAGES=en_US.UTF-8
| ?[7] LC_PAPER=C ? ? ? ? ? ? ? ? LC_NAME=C
| ?[9] LC_ADDRESS=C ? ? ? ? ? ? ? LC_TELEPHONE=C
| [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
|
| attached base packages:
| [1] stats ? ? graphics ?grDevices utils ? ? datasets ?methods ? base
|
| other attached packages:
| [1] Rcpp_0.9.4.1 inline_0.3.8
|
| loaded via a namespace (and not attached):
| [1] tools_2.14.0
|
| and
|
| $ g++ --version
| g++ (Ubuntu/Linaro 4.5.2-8ubuntu4) 4.5.2
| $ wajig list libboost-dev
| ii ?libboost-dev ? ? ? ? ? ? ? ? ? 1.42.0.1ubuntu1
| Boost C++ Libraries development files (default version)
|
| I get a strange compiler error when trying to compile the "Hello
| World" example of the coordinate_matrix representation from Boost's
| uBLAS, as shown in the enclosed. ?The first two examples (the
| mapped_matrix and the compressed_matrix) compile for me but the third
| and the fourth don't. ?The error I get is
|
| Error in compileCode(f, code, language = language, verbose = verbose) :
| ? Compilation ERROR, function(s)/method(s) not created! In file
| included from /usr/include/c++/4.5/bits/stl_algo.h:63:0,
| ? ? ? ? ? ? ? ? ?from /usr/include/c++/4.5/algorithm:63,
| ? ? ? ? ? ? ? ? ?from
| /home/bates/R/x86_64-unknown-linux-gnu-library/2.14/Rcpp/include/RcppCommon.h:121,
| ? ? ? ? ? ? ? ? ?from
| /home/bates/R/x86_64-unknown-linux-gnu-library/2.14/Rcpp/include/Rcpp.h:27,
| ? ? ? ? ? ? ? ? ?from file6b444b24.cpp:4:
| /usr/include/c++/4.5/bits/stl_tempbuf.h: In constructor
| ?std::_Temporary_buffer<_ForwardIterator,
| _Tp>::_Temporary_buffer(_ForwardIterator, _ForwardIterator) [with
| _ForwardIterator =
| boost::numeric::ublas::indexed_iterator<boost::numeric::ublas::index_triple_array<std::vector<long
| unsigned int>, std::vector<long unsigned int>, std::vector<double> >,
| std::random_access_iterator_tag>, _Tp =
| boost::numeric::ublas::index_triple<boost::numeric::ublas::index_triple_array<std::vector<long
| unsigned int>, std::vector<long unsigned int>, std::vector<double> >
| >]?:
| /usr
| In addition: Warning message:
| running command '/home/bates/build/R-devel/bin/R CMD SHLIB
| file6b444b24.cpp 2> file6b444b24.cpp.err.txt' had status 1
|
| Do others get this error for other versions of boost or other compilers?

Yes, confirmed. Examples one and two build, three and four puke.

Can you try them without Rcpp to see if there is a side-effect?
I did so. Trying to compile the example section of
http://www.boost.org/doc/libs/1_46_1/libs/numeric/ublas/doc/matrix_sparse.htm#coordinate_matrix

produces

$ g++ -O3 -g0 foo.cpp -o foo
In file included from /usr/include/c++/4.5/bits/stl_algo.h:63:0,
                 from /usr/include/c++/4.5/algorithm:63,
                 from /usr/include/boost/utility/swap.hpp:24,
                 from /usr/include/boost/swap.hpp:10,
                 from /usr/include/boost/array.hpp:37,
                 from /usr/include/boost/serialization/array.hpp:26,
                 from /usr/include/boost/numeric/ublas/storage_sparse.hpp:19,
                 from /usr/include/boost/numeric/ublas/vector_sparse.hpp:16,
                 from /usr/include/boost/numeric/ublas/matrix_sparse.hpp:16,
                 from foo.cpp:1:
/usr/include/c++/4.5/bits/stl_tempbuf.h: In constructor
?std::_Temporary_buffer<_ForwardIterator,
_Tp>::_Temporary_buffer(_ForwardIterator, _ForwardIterator) [with
_ForwardIterator =
boost::numeric::ublas::indexed_iterator<boost::numeric::ublas::index_triple_array<boost::numeric::ublas::unbounded_array<long
unsigned int>, boost::numeric::ublas::unbounded_array<long unsigned
int>, boost::numeric::ublas::unbounded_array<double,
std::allocator<double> > >, std::random_access_iterator_tag>, _Tp =
boost::numeric::ublas::index_triple<boost::numeric::ublas::index_triple_array<boost::numeric::ublas::unbounded_array<long
unsigned int>, boost::numeric::ublas::unbounded_array<long unsigned
int>, boost::numeric::ublas::unbounded_array<double,
std::allocator<double> > > >]?:
/usr/include/c++/4.5/bits/stl_algo.h:3084:17:   instantiated from
?void std::inplace_merge(_BIter, _BIter, _BIter) [with _BIter =
boost::numeric::ublas::indexed_iterator<boost::numeric::ublas::index_triple_array<boost::numeric::ublas::unbounded_array<long
unsigned int>, boost::numeric::ublas::unbounded_array<long unsigned
int>, boost::numeric::ublas::unbounded_array<double,
std::allocator<double> > >, std::random_access_iterator_tag>]?
/usr/include/boost/numeric/ublas/matrix_sparse.hpp:4387:17:
instantiated from ?void boost::numeric::ublas::coordinate_matrix<T, L,
IB, IA, TA>::sort() const [with T = double, L =
boost::numeric::ublas::basic_row_major<>, long unsigned int IB = 0ul,
IA = boost::numeric::ublas::unbounded_array<long unsigned int>, TA =
boost::numeric::ublas::unbounded_array<double, std::allocator<double>
]?
/usr/include/boost/numeric/ublas/matrix_sparse.hpp:4174:13:
instantiated from ?const T*
boost::numeric::ublas::coordinate_matrix<T, L, IB, IA,
TA>::find_element(boost::numeric::ublas::coordinate_matrix<T, L, IB,
IA, TA>::size_type, boost::numeric::ublas::coordinate_matrix<T, L, IB,
IA, TA>::size_type) const [with T = double, L =
boost::numeric::ublas::basic_row_major<>, long unsigned int IB = 0ul,
IA = boost::numeric::ublas::unbounded_array<long unsigned int>, TA =
boost::numeric::ublas::unbounded_array<double, std::allocator<double>
, const T* = const double*,
boost::numeric::ublas::coordinate_matrix<T, L, IB, IA, TA>::size_type
= long unsigned int]?
/usr/include/boost/numeric/ublas/matrix_sparse.hpp:4192:49:
instantiated from ?const T&
boost::numeric::ublas::coordinate_matrix<T, L, IB, IA,
TA>::operator()(boost::numeric::ublas::coordinate_matrix<T, L, IB, IA,
TA>::size_type, boost::numeric::ublas::coordinate_matrix<T, L, IB, IA,
TA>::size_type) const [with T = double, L =
boost::numeric::ublas::basic_row_major<>, long unsigned int IB = 0ul,
IA = boost::numeric::ublas::unbounded_array<long unsigned int>, TA =
boost::numeric::ublas::unbounded_array<double, std::allocator<double>
, const T& = const double&,
boost::numeric::ublas::coordinate_matrix<T, L, IB, IA, TA>::size_type
= long unsigned int]?
/usr/include/boost/numeric/ublas/io.hpp:96:17:   instantiated from
?std::basic_ostream<_CharT, _Traits>&
boost::numeric::ublas::operator<<(std::basic_ostream<_CharT,
_Traits>&, const boost::numeric::ublas::matrix_expression<E2>&) [with
E = char, T = std::char_traits<char>, ME =
boost::numeric::ublas::coordinate_matrix<double>]?
foo.cpp:10:18:   instantiated from here
/usr/include/c++/4.5/bits/stl_tempbuf.h:192:6: error: invalid
initialization of non-const reference of type
?boost::numeric::ublas::index_triple<boost::numeric::ublas::index_triple_array<boost::numeric::ublas::unbounded_array<long
unsigned int>, boost::numeric::ublas::unbounded_array<long unsigned
int>, boost::numeric::ublas::unbounded_array<double,
std::allocator<double> > > >&? from an rvalue of type
?boost::numeric::ublas::indexed_iterator<boost::numeric::ublas::index_triple_array<boost::numeric::ublas::unbounded_array<long
unsigned int>, boost::numeric::ublas::unbounded_array<long unsigned
int>, boost::numeric::ublas::unbounded_array<double,
std::allocator<double> > >,
std::random_access_iterator_tag>::reference?
/usr/include/c++/4.5/bits/stl_uninitialized.h:223:5: error: in passing
argument 3 of ?void
std::__uninitialized_construct_range(_ForwardIterator,
_ForwardIterator, _Tp&) [with _ForwardIterator =
boost::numeric::ublas::index_triple<boost::numeric::ublas::index_triple_array<boost::numeric::ublas::unbounded_array<long
unsigned int>, boost::numeric::ublas::unbounded_array<long unsigned
int>, boost::numeric::ublas::unbounded_array<double,
std::allocator<double> > > >*, _Tp =
boost::numeric::ublas::index_triple<boost::numeric::ublas::index_triple_array<boost::numeric::ublas::unbounded_array<long
unsigned int>, boost::numeric::ublas::unbounded_array<long unsigned
int>, boost::numeric::ublas::unbounded_array<double,
std::allocator<double> > > >]?

which answers one of my original questions about the trailing '/usr'.
It resulted from truncation of the messages.

Strangely I can't find other reports of this problem on the ublas or
ubuntu lists.
| Sorry to take so long to respond.

No worries.
| > Can you try them without Rcpp to see if there is a side-effect?
| 
| I did so. Trying to compile the example section of
| http://www.boost.org/doc/libs/1_46_1/libs/numeric/ublas/doc/matrix_sparse.htm#coordinate_matrix
| 
| produces

[...]

Same for me, now that I checked.  

But it may be a Boost issue with that release.  I'll fire up one of the
currently sleeping Debian testing machines when I get home to try Boost 1.46.
What I was able to confirm that with Boost 1.33 (!!) as on a CentOS box, I am
in fact able to build it.

Dirk
Gauss once played himself in a zero-sum game and won $50.
                      -- #11 at http://www.gaussfacts.com
On 7 June 2011 at 12:44, Douglas Bates wrote:
| Sorry to take so long to respond.

No worries.

| On Sat, Jun 4, 2011 at 12:26 PM, Dirk Eddelbuettel <edd at debian.org> wrote:
| > Can you try them without Rcpp to see if there is a side-effect?
|
| I did so. Trying to compile the example section of
| http://www.boost.org/doc/libs/1_46_1/libs/numeric/ublas/doc/matrix_sparse.htm#coordinate_matrix
|
| produces

[...]

Same for me, now that I checked.

But it may be a Boost issue with that release. ?I'll fire up one of the
currently sleeping Debian testing machines when I get home to try Boost 1.46.
What I was able to confirm that with Boost 1.33 (!!) as on a CentOS box, I am
in fact able to build it.
I just tried with boost 1.43.0 and with boost 1.46.1.  In both cases
the error persists.  What would you recommend trying with gcc-4.6.x?
| > But it may be a Boost issue with that release. ?I'll fire up one of the
| > currently sleeping Debian testing machines when I get home to try Boost 1.46.
| > What I was able to confirm that with Boost 1.33 (!!) as on a CentOS box, I am
| > in fact able to build it.
| 
| I just tried with boost 1.43.0 and with boost 1.46.1.  In both cases
| the error persists.  What would you recommend trying with gcc-4.6.x?

Damn. Another bubble burst.

In that case I'd try one of the Boost mailing lists.  It is after all a piece
of documented code which goes belly-up.

Dirk
Gauss once played himself in a zero-sum game and won $50.
                      -- #11 at http://www.gaussfacts.com