[Rcpp-devel] package install problem
Søren Højsgaard
sorenh at math.aau.dk
Wed Feb 22 01:05:04 CET 2012
Dear Dirk,
It might be an Rtools-issue. I use the new Rtools because on the Rtools page it says
"R-patched subsequent to Jan 22, 2012, R-devel, and releases after 2.14.1 will use a new toolchain based on pre-4.6.3 gcc, put together by Prof. Brian Ripley and available as multi.zip on his web page. Rtools 2.15 includes this toolchain. It uses the same gcc version for both 32 and 64 bit builds. Separate versions of the gdb debugger are also included for each archtecture. "
Maybe R.2.14.1-patches are not totally "up to" the the new R-tools after all? (I've also noticed that patches (R-2.14.2) are not available these days, so there may be something going on elsewhere...)
Regards
Søren
-----Oprindelig meddelelse-----
Fra: Dirk Eddelbuettel [mailto:edd at debian.org]
Sendt: 22. februar 2012 00:55
Til: Søren Højsgaard
Cc: Dirk Eddelbuettel; rcpp-devel at lists.r-forge.r-project.org
Emne: Re: SV: [Rcpp-devel] package install problem
On 21 February 2012 at 23:39, Søren Højsgaard wrote:
| Dear list,
|
| I get what I believe to be similar errors on R.2.14.1, but things work on R-devel; please see transcript below.
Hm. It could be an issue with Rtools. R-devel NEWS (derived from the NEWS file in SVN) had this too the other day:
2.14.2 PACKAGE INSTALLATION (Windows)
The preferred toolchain has changed since the one used for R 2.12.0 to
2.14.1: see the‘R Installation and Administration manual’. Compiled code
(except DLLs) may be incompatible with previous toolchains (and compiled C++
code almost certainly will be: users of ‘Rcpp’ take care).
So make sure you don't mix compilers -- but I think this refers to Rtools 2.15.
For what it is worth, I just re-ran things on a virtual machine with plain old R 2.14.1 and (I think) Rtools 2.14 and it all worked.
Dirk
| Regards
| Søren
|
|
|
| ==== R 2.14.1 ====
|
| > library(Rcpp)
| > library(inline)
| >
| > src <- '
| + Rcpp::NumericMatrix Am(A);
| + int nrows = Am.nrow();
| + int ncolumns = Am.ncol();
| + for (int i = 0; i < ncolumns; i++) {
| + for (int j = 1; j < nrows; j++) {
| + Am(j,i) = Am(j,i) + Am(j-1,i);
| + }
| + }
| + return Am;
| + '
| > fun <- cxxfunction(signature(A = "numeric"), body = src,
| > plugin="Rcpp")
| c:/programs/rtools/gcc-4.6.3/bin/../lib/gcc/i686-w64-mingw32/4.6.3/../../../../lib/libstdc++.a(stdexcept.o):(.text$_ZNSt11range_errorD0Ev+0x0): multiple definition of `std::range_error::~range_error()'
| C:/programs/R/current/library/Rcpp/lib/i386/libRcpp.a(RcppCommon.o):Rc
| ppCommon.cpp:(.text$_ZNSt11range_errorD0Ev[std::range_error::~range_er
| ror()]+0x0): first defined here
| c:/programs/rtools/gcc-4.6.3/bin/../lib/gcc/i686-w64-mingw32/4.6.3/../../../../lib/libstdc++.a(stdexcept.o):(.text$_ZNSt11range_errorD2Ev+0x0): multiple definition of `std::range_error::~range_error()'
| C:/programs/R/current/library/Rcpp/lib/i386/libRcpp.a(RcppCommon.o):Rc
| ppCommon.cpp:(.text$_ZNSt11range_errorD1Ev[std::range_error::~range_er
| ror()]+0x0): first defined here
| C:/programs/R/current/library/Rcpp/lib/i386/libRcpp.a(exceptions.o):exceptions.cpp:(.text+0x392): undefined reference to `_Unwind_Resume'
| C:/programs/R/current/library/Rcpp/lib/i386/libRcpp.a(exceptions.o):exceptions.cpp:(.text+0x44e): undefined reference to `_Unwind_Resume'
| C:/programs/R/current/library/Rcpp/lib/i386/libRcpp.a(exceptions.o):exceptions.cpp:(.text+0x519): undefined reference to `_Unwind_Resume'
| C:/programs/R/current/library/Rcpp/lib/i386/libRcpp.a(exceptions.o):exceptions.cpp:(.text+0x6f1): undefined reference to `_Unwind_Resume'
| C:/programs/R/current/library/Rcpp/lib/i386/libRcpp.a(exceptions.o):exceptions.cpp:(.eh_frame+0x12): undefined reference to `__gxx_personality_v0'
| C:/programs/R/current/library/Rcpp/lib/i386/libRcpp.a(RcppCommon.o):RcppCommon.cpp:(.text+0x72b): undefined reference to `_Unwind_Resume'
| C:/programs/R/current/library/Rcpp/lib/i386/libRcpp.a(RcppCommon.o):RcppCommon.cpp:(.text+0x777): undefined reference to `_Unwind_Resume'
| C:/programs/R/current/library/Rcpp/lib/i386/libRcpp.a(RcppCommon.o):RcppCommon.cpp:(.eh_frame+0x12): undefined reference to `__gxx_personality_v0'
| C:/programs/R/current/library/Rcpp/lib/i386/libRcpp.a(RObject.o):RObject.cpp:(.text+0x409): undefined reference to `_Unwind_Resume'
| C:/programs/R/current/library/Rcpp/lib/i386/libRcpp.a(RObject.o):RObject.cpp:(.text+0x7c0): undefined reference to `_Unwind_Resume'
| C:/programs/R/current/library/Rcpp/lib/i386/libRcpp.a(RObject.o):RObject.cpp:(.text$_ZNSt6vectorISsSaISsEE13_M_insert_auxEN9__gnu_cxx17__normal_iteratorIPSsS1_EERKSs[std::vector<std::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::allocator<std::basic_string<char, std::char_traits<char>, std::allocator<char> > > >::_M_insert_aux(__gnu_cxx::__normal_iterator<std::basic_string<char, std::char_traits<char>, std::allocator<char> >*, std::vector<std::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::allocator<std::basic_string<char, std::char_traits<char>, std::allocator<char> > > > >, std::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)]+0x361): undefined reference to `_Unwind_Resume'
| C:/programs/R/current/library/Rcpp/lib/i386/libRcpp.a(RObject.o):RObject.cpp:(.text$_ZNSt6vectorISsSaISsEE13_M_insert_auxEN9__gnu_cxx17__normal_iteratorIPSsS1_EERKSs[std::vector<std::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::allocator<std::basic_string<char, std::char_traits<char>, std::allocator<char> > > >::_M_insert_aux(__gnu_cxx::__normal_iterator<std::basic_string<char, std::char_traits<char>, std::allocator<char> >*, std::vector<std::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::allocator<std::basic_string<char, std::char_traits<char>, std::allocator<char> > > > >, std::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)]+0x370): undefined reference to `_Unwind_Resume'
| C:/programs/R/current/library/Rcpp/lib/i386/libRcpp.a(RObject.o):RObject.cpp:(.eh_frame+0x12): undefined reference to `__gxx_personality_v0'
| C:/programs/R/current/library/Rcpp/lib/i386/libRcpp.a(r_cast.o):r_cast.cpp:(.text+0x4b9): undefined reference to `_Unwind_Resume'
| C:/programs/R/current/library/Rcpp/lib/i386/libRcpp.a(r_cast.o):r_cast.cpp:(.text$_ZN4Rcpp14not_compatibleC1ERKSs[Rcpp::not_compatible::not_compatible(std::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)]+0x43): undefined reference to `_Unwind_Resume'
| C:/programs/R/current/library/Rcpp/lib/i386/libRcpp.a(r_cast.o):r_cast.cpp:(.eh_frame+0x12): undefined reference to `__gxx_personality_v0'
| C:/programs/R/current/library/Rcpp/lib/i386/libRcpp.a(debugging.o):debugging.cpp:(.text+0x6b4): undefined reference to `_Unwind_Resume'
| C:/programs/R/current/library/Rcpp/lib/i386/libRcpp.a(debugging.o):debugging.cpp:(.text+0x6d7): undefined reference to `_Unwind_Resume'
| C:/programs/R/current/library/Rcpp/lib/i386/libRcpp.a(debugging.o):debugging.cpp:(.eh_frame+0x12): undefined reference to `__gxx_personality_v0'
| C:/programs/R/current/library/Rcpp/lib/i386/libRcpp.a(Evaluator.o):Evaluator.cpp:(.text+0x21f): undefined reference to `_Unwind_Resume'
| C:/programs/R/current/library/Rcpp/lib/i386/libRcpp.a(Evaluator.o):Evaluator.cpp:(.text+0x23c): undefined reference to `_Unwind_Resume'
| C:/programs/R/current/library/Rcpp/lib/i386/libRcpp.a(Evaluator.o):Evaluator.cpp:(.text+0x2d3): undefined reference to `_Unwind_Resume'
| C:/programs/R/current/library/Rcpp/lib/i386/libRcpp.a(Evaluator.o):Evaluator.cpp:(.text+0x35a): undefined reference to `_Unwind_Resume'
| C:/programs/R/current/library/Rcpp/lib/i386/libRcpp.a(Evaluator.o):Evaluator.cpp:(.text$_ZStplIcSt11char_traitsIcESaIcEESbIT_T0_T1_ERKS6_PKS3_[std::basic_string<char, std::char_traits<char>, std::allocator<char> > std::operator+<char, std::char_traits<char>, std::allocator<char> >(std::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, char const*)]+0x53): undefined reference to `_Unwind_Resume'
| C:/programs/R/current/library/Rcpp/lib/i386/libRcpp.a(Evaluator.o):Evaluator.cpp:(.eh_frame+0x12): undefined reference to `__gxx_personality_v0'
| C:/programs/R/current/library/Rcpp/lib/i386/libRcpp.a(Environment.o):Environment.cpp:(.text+0x147): undefined reference to `_Unwind_Resume'
| C:/programs/R/current/library/Rcpp/lib/i386/libRcpp.a(Environment.o):Environment.cpp:(.text+0x204): undefined reference to `_Unwind_Resume'
| C:/programs/R/current/library/Rcpp/lib/i386/libRcpp.a(Environment.o):Environment.cpp:(.text+0x693): undefined reference to `_Unwind_Resume'
| C:/programs/R/current/library/Rcpp/lib/i386/libRcpp.a(Environment.o):Environment.cpp:(.text+0x6dc): undefined reference to `_Unwind_Resume'
| C:/programs/R/current/library/Rcpp/lib/i386/libRcpp.a(Environment.o):Environment.cpp:(.text+0xd4f): undefined reference to `_Unwind_Resume'
| C:/programs/R/current/library/Rcpp/lib/i386/libRcpp.a(Environment.o):E
| nvironment.cpp:(.text+0xe31): more undefined references to
| `_Unwind_Resume' follow
| C:/programs/R/current/library/Rcpp/lib/i386/libRcpp.a(Environment.o):Environment.cpp:(.eh_frame+0x12): undefined reference to `__gxx_personality_v0'
| collect2: ld returned 1 exit status
|
|
| > sessionInfo()
| R version 2.14.1 Patched (2012-01-27 r58216)
| Platform: i386-pc-mingw32/i386 (32-bit)
|
| locale:
| [1] LC_COLLATE=Danish_Denmark.1252 LC_CTYPE=Danish_Denmark.1252 LC_MONETARY=Danish_Denmark.1252 LC_NUMERIC=C LC_TIME=Danish_Denmark.1252
|
| attached base packages:
| [1] stats graphics grDevices utils datasets methods base
|
| other attached packages:
| [1] inline_0.3.8 Rcpp_0.9.10 SHDtools_1.0
|
| loaded via a namespace (and not attached):
| [1] tools_2.14.1
|
| ==== R devel ====
|
|
| > library(Rcpp)
| > library(inline)
| >
| > src <- '
| + Rcpp::NumericMatrix Am(A);
| + int nrows = Am.nrow();
| + int ncolumns = Am.ncol();
| + for (int i = 0; i < ncolumns; i++) {
| + for (int j = 1; j < nrows; j++) {
| + Am(j,i) = Am(j,i) + Am(j-1,i);
| + }
| + }
| + return Am;
| + '
| > fun <- cxxfunction(signature(A = "numeric"), body = src,
| > plugin="Rcpp")
| > sessionInfo()
| R Under development (unstable) (2012-02-16 r58364)
| Platform: i386-pc-mingw32/i386 (32-bit)
|
| locale:
| [1] LC_COLLATE=Danish_Denmark.1252 LC_CTYPE=Danish_Denmark.1252 LC_MONETARY=Danish_Denmark.1252 LC_NUMERIC=C LC_TIME=Danish_Denmark.1252
|
| attached base packages:
| [1] stats graphics grDevices utils datasets methods base
|
| other attached packages:
| [1] inline_0.3.8 Rcpp_0.9.10 SHDtools_1.0
|
| loaded via a namespace (and not attached):
| [1] tools_2.15.0
|
|
|
|
| -----Oprindelig meddelelse-----
| Fra: rcpp-devel-bounces at r-forge.wu-wien.ac.at
| [mailto:rcpp-devel-bounces at r-forge.wu-wien.ac.at] På vegne af Dirk
| Eddelbuettel
| Sendt: 21. februar 2012 22:56
| Til: Dirk Eddelbuettel
| Cc: rcpp-devel at lists.r-forge.r-project.org
| Emne: Re: [Rcpp-devel] package install problem
|
|
| On 21 February 2012 at 12:55, Dirk Eddelbuettel wrote:
| | For what it is worth, a package of mine just built fine on
| | win-builder in for both r-devel and r-release. I use this as
| | src/Makevars.win
|
| David reported (off-list) that win-builder and another machine also worked for him.
|
| So far, this looks like it is a local issue, possibly a mix-up between different Rtools versions, rather than something wrong with Rcpp 0.9.10.
|
| Dirk
|
| --
| "Outside of a dog, a book is a man's best friend. Inside of a dog, it
| is too dark to read." -- Groucho Marx
| _______________________________________________
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--
"Outside of a dog, a book is a man's best friend. Inside of a dog, it is too dark to read." -- Groucho Marx
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