[Rd] Compilation error Mac binary
Hello, the compilation of the GUTS package on CRAN for Mac produces the following error messages: http://www.r-project.org/nosvn/R.check/r-release-macosx-ix86/GUTS-00install.html I guess it is some namespace collision, but I can not reproduce it on my machine, it compiles fine here. What is the cause and which setup do I need to reproduce the errors? R: version platform i386-apple-darwin9.8.0 arch i386 os darwin9.8.0 system i386, darwin9.8.0 status major 2 minor 13.0 year 2011 month 04 day13 svn rev55427 language R version.string R version 2.13.0 (2011-04-13) I ~ $: gcc --version i686-apple-darwin10-gcc-4.2.1 (GCC) 4.2.1 (Apple Inc. build 5666) (dot 3) Copyright (C) 2007 Free Software Foundation, Inc. This is free software; see the source for copying conditions. There is NO warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. I ~ $: less /opt/local/include/boost/version.hpp // Boost version.hpp configuration header file --// [...] #define BOOST_VERSION 104601 #define BOOST_LIB_VERSION 1_46_1 [...] __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] Compilation error Mac binary
On Jun 29, 2011, at 5:33 AM, soeren.vo...@uzh.ch wrote: Hello, the compilation of the GUTS package on CRAN for Mac produces the following error messages: http://www.r-project.org/nosvn/R.check/r-release-macosx-ix86/GUTS-00install.html I guess it is some namespace collision, but I can not reproduce it on my machine, it compiles fine here. What is the cause and which setup do I need to reproduce the errors? I was going to suggest you take this up with the maintainers... but you _are_ one of the maintainers. Here is the output from an attempt to compile from source, version 0.1.45, with a relatively recent version of R 2.13.0 (but not the most recent and I still use Mac OSX 10.5.8). Perhaps its brevity will be helpful, and the fact that it seems to identify different error than those flagged in the log at CRAN. trying URL 'http://lib.stat.cmu.edu/R/CRAN/src/contrib/GUTS_0.1.45.tar.gz' Content type 'application/x-gzip' length 9842 bytes opened URL == downloaded 9842 bytes Loading required package: lattice Loading required package: sos Loading required package: brew [1] 2011-06-29 09:40:18 EDT * installing *source* package ‘GUTS’ ... ** libs *** arch - i386 g++ -arch i386 -I/Library/Frameworks/R.framework/Resources/include -I/ Library/Frameworks/R.framework/Resources/include/i386 -I/opt/local/ include -I/usr/local/include -I/Library/Frameworks/R.framework/ Versions/2.13/Resources/library/Rcpp/include -fPIC -g -O2 -c GUTS.cpp -o GUTS.o In file included from GUTS.cpp:12: GUTS.h:21:28: error: boost/random.hpp: No such file or directory GUTS.h:22:40: error: boost/math/distributions.hpp: No such file or directory GUTS.cpp: In function ‘void to_print(double)’: GUTS.cpp:277: error: ‘cout’ was not declared in this scope GUTS.cpp: In member function ‘void GUTS::showObject()’: GUTS.cpp:281: error: ‘cout’ is not a member of ‘std’ GUTS.cpp:284: error: ‘cout’ was not declared in this scope make: *** [GUTS.o] Error 1 ERROR: compilation failed for package ‘GUTS’ * removing ‘/Library/Frameworks/R.framework/Versions/2.13/Resources/ library/GUTS’ sessionInfo() R version 2.13.0 beta (2011-04-04 r55296) Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit) locale: [1] en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8 attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] mgcv_1.7-6 sos_1.3-0 brew_1.0-6 lattice_0.19-26 loaded via a namespace (and not attached): [1] grid_2.13.0Matrix_0.999375-50 nlme_3.1-101 tools_2.13.0 -- David. R: version platform i386-apple-darwin9.8.0 arch i386 os darwin9.8.0 system i386, darwin9.8.0 status major 2 minor 13.0 year 2011 month 04 day13 svn rev55427 language R version.string R version 2.13.0 (2011-04-13) I ~ $: gcc --version i686-apple-darwin10-gcc-4.2.1 (GCC) 4.2.1 (Apple Inc. build 5666) (dot 3) Copyright (C) 2007 Free Software Foundation, Inc. This is free software; see the source for copying conditions. There is NO warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. I ~ $: less /opt/local/include/boost/version.hpp // Boost version.hpp configuration header file --// [...] #define BOOST_VERSION 104601 #define BOOST_LIB_VERSION 1_46_1 [...] __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel David Winsemius, MD West Hartford, CT __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] Compilation error Mac binary
Hello David On 29.06.2011, at 15:56, David Winsemius wrote: On Jun 29, 2011, at 5:33 AM, soeren.vo...@uzh.ch wrote: Hello, the compilation of the GUTS package on CRAN for Mac produces the following error messages: http://www.r-project.org/nosvn/R.check/r-release-macosx-ix86/GUTS-00install.html I guess it is some namespace collision, but I can not reproduce it on my machine, it compiles fine here. What is the cause and which setup do I need to reproduce the errors? I was going to suggest you take this up with the maintainers... but you _are_ one of the maintainers. :-) Here is the output from an attempt to compile from source, version 0.1.45, with a relatively recent version of R 2.13.0 (but not the most recent and I still use Mac OSX 10.5.8). Perhaps its brevity will be helpful, and the fact that it seems to identify different error than those flagged in the log at CRAN. Thanks for your answer. The failure on your side is clear to me: there is no installation of the boost C++ library in any of the standard include locations. I have added /opt/local/include in Makevars (Mac Ports installation of C source packages), however, I know I should but still I am reluctant to write a configure script that could circumvent non-standard installations of boost on UNIX machines. So thanks for the output, but the CRAN messages must point to something different... Regards Sören trying URL 'http://lib.stat.cmu.edu/R/CRAN/src/contrib/GUTS_0.1.45.tar.gz' Content type 'application/x-gzip' length 9842 bytes opened URL == downloaded 9842 bytes Loading required package: lattice Loading required package: sos Loading required package: brew [1] 2011-06-29 09:40:18 EDT * installing *source* package ‘GUTS’ ... ** libs *** arch - i386 g++ -arch i386 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -I/opt/local/include -I/usr/local/include -I/Library/Frameworks/R.framework/Versions/2.13/Resources/library/Rcpp/include -fPIC -g -O2 -c GUTS.cpp -o GUTS.o In file included from GUTS.cpp:12: GUTS.h:21:28: error: boost/random.hpp: No such file or directory GUTS.h:22:40: error: boost/math/distributions.hpp: No such file or directory GUTS.cpp: In function ‘void to_print(double)’: GUTS.cpp:277: error: ‘cout’ was not declared in this scope GUTS.cpp: In member function ‘void GUTS::showObject()’: GUTS.cpp:281: error: ‘cout’ is not a member of ‘std’ GUTS.cpp:284: error: ‘cout’ was not declared in this scope make: *** [GUTS.o] Error 1 ERROR: compilation failed for package ‘GUTS’ * removing ‘/Library/Frameworks/R.framework/Versions/2.13/Resources/library/GUTS’ sessionInfo() R version 2.13.0 beta (2011-04-04 r55296) Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit) locale: [1] en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8 attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] mgcv_1.7-6 sos_1.3-0 brew_1.0-6 lattice_0.19-26 loaded via a namespace (and not attached): [1] grid_2.13.0Matrix_0.999375-50 nlme_3.1-101 tools_2.13.0 -- David. R: version platform i386-apple-darwin9.8.0 arch i386 os darwin9.8.0 system i386, darwin9.8.0 status major 2 minor 13.0 year 2011 month 04 day13 svn rev55427 language R version.string R version 2.13.0 (2011-04-13) I ~ $: gcc --version i686-apple-darwin10-gcc-4.2.1 (GCC) 4.2.1 (Apple Inc. build 5666) (dot 3) Copyright (C) 2007 Free Software Foundation, Inc. This is free software; see the source for copying conditions. There is NO warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. I ~ $: less /opt/local/include/boost/version.hpp // Boost version.hpp configuration header file --// [...] #define BOOST_VERSION 104601 #define BOOST_LIB_VERSION 1_46_1 [...] __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel David Winsemius, MD West Hartford, CT __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] Compilation error Mac binary
Looks like a different boost version than the one you require. I'd suggest to talk to the Mac maintainer, Simon Urbanek (CCing). Best, Uwe Ligges On 29.06.2011 17:14, soeren.vo...@uzh.ch wrote: Hello David On 29.06.2011, at 15:56, David Winsemius wrote: On Jun 29, 2011, at 5:33 AM, soeren.vo...@uzh.ch wrote: Hello, the compilation of the GUTS package on CRAN for Mac produces the following error messages: http://www.r-project.org/nosvn/R.check/r-release-macosx-ix86/GUTS-00install.html I guess it is some namespace collision, but I can not reproduce it on my machine, it compiles fine here. What is the cause and which setup do I need to reproduce the errors? I was going to suggest you take this up with the maintainers... but you _are_ one of the maintainers. :-) Here is the output from an attempt to compile from source, version 0.1.45, with a relatively recent version of R 2.13.0 (but not the most recent and I still use Mac OSX 10.5.8). Perhaps its brevity will be helpful, and the fact that it seems to identify different error than those flagged in the log at CRAN. Thanks for your answer. The failure on your side is clear to me: there is no installation of the boost C++ library in any of the standard include locations. I have added /opt/local/include in Makevars (Mac Ports installation of C source packages), however, I know I should but still I am reluctant to write a configure script that could circumvent non-standard installations of boost on UNIX machines. So thanks for the output, but the CRAN messages must point to something different... Regards Sören trying URL 'http://lib.stat.cmu.edu/R/CRAN/src/contrib/GUTS_0.1.45.tar.gz' Content type 'application/x-gzip' length 9842 bytes opened URL == downloaded 9842 bytes Loading required package: lattice Loading required package: sos Loading required package: brew [1] 2011-06-29 09:40:18 EDT * installing *source* package ‘GUTS’ ... ** libs *** arch - i386 g++ -arch i386 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -I/opt/local/include -I/usr/local/include -I/Library/Frameworks/R.framework/Versions/2.13/Resources/library/Rcpp/include -fPIC -g -O2 -c GUTS.cpp -o GUTS.o In file included from GUTS.cpp:12: GUTS.h:21:28: error: boost/random.hpp: No such file or directory GUTS.h:22:40: error: boost/math/distributions.hpp: No such file or directory GUTS.cpp: In function ‘void to_print(double)’: GUTS.cpp:277: error: ‘cout’ was not declared in this scope GUTS.cpp: In member function ‘void GUTS::showObject()’: GUTS.cpp:281: error: ‘cout’ is not a member of ‘std’ GUTS.cpp:284: error: ‘cout’ was not declared in this scope make: *** [GUTS.o] Error 1 ERROR: compilation failed for package ‘GUTS’ * removing ‘/Library/Frameworks/R.framework/Versions/2.13/Resources/library/GUTS’ sessionInfo() R version 2.13.0 beta (2011-04-04 r55296) Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit) locale: [1] en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8 attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] mgcv_1.7-6 sos_1.3-0 brew_1.0-6 lattice_0.19-26 loaded via a namespace (and not attached): [1] grid_2.13.0Matrix_0.999375-50 nlme_3.1-101 tools_2.13.0 -- David. R: version platform i386-apple-darwin9.8.0 arch i386 os darwin9.8.0 system i386, darwin9.8.0 status major 2 minor 13.0 year 2011 month 04 day13 svn rev55427 language R version.string R version 2.13.0 (2011-04-13) I ~ $: gcc --version i686-apple-darwin10-gcc-4.2.1 (GCC) 4.2.1 (Apple Inc. build 5666) (dot 3) Copyright (C) 2007 Free Software Foundation, Inc. This is free software; see the source for copying conditions. There is NO warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. I ~ $: less /opt/local/include/boost/version.hpp // Boost version.hpp configuration header file --// [...] #define BOOST_VERSION 104601 #define BOOST_LIB_VERSION 1_46_1 [...] __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel David Winsemius, MD West Hartford, CT __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] Compilation error Mac binary
On Jun 29, 2011, at 1:12 PM, Uwe Ligges wrote: Looks like a different boost version than the one you require. I'd suggest to talk to the Mac maintainer, Simon Urbanek (CCing). GUTS doesn't specify any system requirements, so obviously it has no business trying to use boost from the system. Also note boost is inlined in the vast majority of cases, so most packages simply supply the headers inside as to guarantee the required version is used (which I would certainly expect GUTS to do since it doesn't depend on boost according to the DESCRIPTION). Cheers, Simon On 29.06.2011 17:14, soeren.vo...@uzh.ch wrote: Hello David On 29.06.2011, at 15:56, David Winsemius wrote: On Jun 29, 2011, at 5:33 AM, soeren.vo...@uzh.ch wrote: Hello, the compilation of the GUTS package on CRAN for Mac produces the following error messages: http://www.r-project.org/nosvn/R.check/r-release-macosx-ix86/GUTS-00install.html I guess it is some namespace collision, but I can not reproduce it on my machine, it compiles fine here. What is the cause and which setup do I need to reproduce the errors? I was going to suggest you take this up with the maintainers... but you _are_ one of the maintainers. :-) Here is the output from an attempt to compile from source, version 0.1.45, with a relatively recent version of R 2.13.0 (but not the most recent and I still use Mac OSX 10.5.8). Perhaps its brevity will be helpful, and the fact that it seems to identify different error than those flagged in the log at CRAN. Thanks for your answer. The failure on your side is clear to me: there is no installation of the boost C++ library in any of the standard include locations. I have added /opt/local/include in Makevars (Mac Ports installation of C source packages), however, I know I should but still I am reluctant to write a configure script that could circumvent non-standard installations of boost on UNIX machines. So thanks for the output, but the CRAN messages must point to something different... Regards Sören trying URL 'http://lib.stat.cmu.edu/R/CRAN/src/contrib/GUTS_0.1.45.tar.gz' Content type 'application/x-gzip' length 9842 bytes opened URL == downloaded 9842 bytes Loading required package: lattice Loading required package: sos Loading required package: brew [1] 2011-06-29 09:40:18 EDT * installing *source* package ‘GUTS’ ... ** libs *** arch - i386 g++ -arch i386 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -I/opt/local/include -I/usr/local/include -I/Library/Frameworks/R.framework/Versions/2.13/Resources/library/Rcpp/include -fPIC -g -O2 -c GUTS.cpp -o GUTS.o In file included from GUTS.cpp:12: GUTS.h:21:28: error: boost/random.hpp: No such file or directory GUTS.h:22:40: error: boost/math/distributions.hpp: No such file or directory GUTS.cpp: In function ‘void to_print(double)’: GUTS.cpp:277: error: ‘cout’ was not declared in this scope GUTS.cpp: In member function ‘void GUTS::showObject()’: GUTS.cpp:281: error: ‘cout’ is not a member of ‘std’ GUTS.cpp:284: error: ‘cout’ was not declared in this scope make: *** [GUTS.o] Error 1 ERROR: compilation failed for package ‘GUTS’ * removing ‘/Library/Frameworks/R.framework/Versions/2.13/Resources/library/GUTS’ sessionInfo() R version 2.13.0 beta (2011-04-04 r55296) Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit) locale: [1] en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8 attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] mgcv_1.7-6 sos_1.3-0 brew_1.0-6 lattice_0.19-26 loaded via a namespace (and not attached): [1] grid_2.13.0Matrix_0.999375-50 nlme_3.1-101 tools_2.13.0 -- David. R: version platform i386-apple-darwin9.8.0 arch i386 os darwin9.8.0 system i386, darwin9.8.0 status major 2 minor 13.0 year 2011 month 04 day13 svn rev55427 language R version.string R version 2.13.0 (2011-04-13) I ~ $: gcc --version i686-apple-darwin10-gcc-4.2.1 (GCC) 4.2.1 (Apple Inc. build 5666) (dot 3) Copyright (C) 2007 Free Software Foundation, Inc. This is free software; see the source for copying conditions. There is NO warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. I ~ $: less /opt/local/include/boost/version.hpp // Boost version.hpp configuration header file --// [...] #define BOOST_VERSION 104601 #define BOOST_LIB_VERSION 1_46_1 [...] __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel David Winsemius, MD West Hartford, CT __
Re: [Rd] Compilation error Mac binary
BTW: the build result is at http://www.r-project.org/nosvn/R.check/r-release-macosx-ix86/GUTS-00install.html so you may want to have a look. I'm not a C++ expert so you may want to ask on the Rcpp list since it appears to be some issue triggered by Rcpp includes - as if boost and tr1 and somehow define the same things but differently ... Since Dirk uses the same boost (1.43 here) successfully in QuantLib he may know more ... Cheers, Simon On Jun 29, 2011, at 2:05 PM, Simon Urbanek wrote: On Jun 29, 2011, at 1:12 PM, Uwe Ligges wrote: Looks like a different boost version than the one you require. I'd suggest to talk to the Mac maintainer, Simon Urbanek (CCing). GUTS doesn't specify any system requirements, so obviously it has no business trying to use boost from the system. Also note boost is inlined in the vast majority of cases, so most packages simply supply the headers inside as to guarantee the required version is used (which I would certainly expect GUTS to do since it doesn't depend on boost according to the DESCRIPTION). Cheers, Simon On 29.06.2011 17:14, soeren.vo...@uzh.ch wrote: Hello David On 29.06.2011, at 15:56, David Winsemius wrote: On Jun 29, 2011, at 5:33 AM, soeren.vo...@uzh.ch wrote: Hello, the compilation of the GUTS package on CRAN for Mac produces the following error messages: http://www.r-project.org/nosvn/R.check/r-release-macosx-ix86/GUTS-00install.html I guess it is some namespace collision, but I can not reproduce it on my machine, it compiles fine here. What is the cause and which setup do I need to reproduce the errors? I was going to suggest you take this up with the maintainers... but you _are_ one of the maintainers. :-) Here is the output from an attempt to compile from source, version 0.1.45, with a relatively recent version of R 2.13.0 (but not the most recent and I still use Mac OSX 10.5.8). Perhaps its brevity will be helpful, and the fact that it seems to identify different error than those flagged in the log at CRAN. Thanks for your answer. The failure on your side is clear to me: there is no installation of the boost C++ library in any of the standard include locations. I have added /opt/local/include in Makevars (Mac Ports installation of C source packages), however, I know I should but still I am reluctant to write a configure script that could circumvent non-standard installations of boost on UNIX machines. So thanks for the output, but the CRAN messages must point to something different... Regards Sören trying URL 'http://lib.stat.cmu.edu/R/CRAN/src/contrib/GUTS_0.1.45.tar.gz' Content type 'application/x-gzip' length 9842 bytes opened URL == downloaded 9842 bytes Loading required package: lattice Loading required package: sos Loading required package: brew [1] 2011-06-29 09:40:18 EDT * installing *source* package ‘GUTS’ ... ** libs *** arch - i386 g++ -arch i386 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -I/opt/local/include -I/usr/local/include -I/Library/Frameworks/R.framework/Versions/2.13/Resources/library/Rcpp/include -fPIC -g -O2 -c GUTS.cpp -o GUTS.o In file included from GUTS.cpp:12: GUTS.h:21:28: error: boost/random.hpp: No such file or directory GUTS.h:22:40: error: boost/math/distributions.hpp: No such file or directory GUTS.cpp: In function ‘void to_print(double)’: GUTS.cpp:277: error: ‘cout’ was not declared in this scope GUTS.cpp: In member function ‘void GUTS::showObject()’: GUTS.cpp:281: error: ‘cout’ is not a member of ‘std’ GUTS.cpp:284: error: ‘cout’ was not declared in this scope make: *** [GUTS.o] Error 1 ERROR: compilation failed for package ‘GUTS’ * removing ‘/Library/Frameworks/R.framework/Versions/2.13/Resources/library/GUTS’ sessionInfo() R version 2.13.0 beta (2011-04-04 r55296) Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit) locale: [1] en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8 attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] mgcv_1.7-6 sos_1.3-0 brew_1.0-6 lattice_0.19-26 loaded via a namespace (and not attached): [1] grid_2.13.0Matrix_0.999375-50 nlme_3.1-101 tools_2.13.0 -- David. R: version platform i386-apple-darwin9.8.0 arch i386 os darwin9.8.0 system i386, darwin9.8.0 status major 2 minor 13.0 year 2011 month 04 day13 svn rev55427 language R version.string R version 2.13.0 (2011-04-13) I ~ $: gcc --version i686-apple-darwin10-gcc-4.2.1 (GCC) 4.2.1 (Apple Inc. build 5666) (dot 3) Copyright (C) 2007 Free Software Foundation, Inc. This is free software; see the source for copying conditions. There is NO
Re: [Rd] Compilation error Mac binary
Thanks Simon, Uwe and David for your helpful answers. English is not my primary language, so I was hypothesising a bit about the correct interpretation of inlining and supply inside. I thought it meant copying the headers inside the package. I was already inspecting RQuantlib but I did, so far, not get smarter. I think I will setup a VMware OS X 10.5 with an older boost. This approach seems more reliable to me than just trying around with a configure script which, eventually, I don't understand fully. Yet, interesting that GUTS builds on Win and Linux, but not on the CRAN OS X. Anyway, thanks for your help. Best Sören On 29.06.2011, at 20:05, Simon Urbanek wrote: On Jun 29, 2011, at 1:12 PM, Uwe Ligges wrote: Looks like a different boost version than the one you require. I'd suggest to talk to the Mac maintainer, Simon Urbanek (CCing). GUTS doesn't specify any system requirements, so obviously it has no business trying to use boost from the system. Also note boost is inlined in the vast majority of cases, so most packages simply supply the headers inside as to guarantee the required version is used (which I would certainly expect GUTS to do since it doesn't depend on boost according to the DESCRIPTION). Cheers, Simon On 29.06.2011 17:14, soeren.vo...@uzh.ch wrote: Hello David On 29.06.2011, at 15:56, David Winsemius wrote: On Jun 29, 2011, at 5:33 AM, soeren.vo...@uzh.ch wrote: Hello, the compilation of the GUTS package on CRAN for Mac produces the following error messages: http://www.r-project.org/nosvn/R.check/r-release-macosx-ix86/GUTS-00install.html I guess it is some namespace collision, but I can not reproduce it on my machine, it compiles fine here. What is the cause and which setup do I need to reproduce the errors? I was going to suggest you take this up with the maintainers... but you _are_ one of the maintainers. :-) Here is the output from an attempt to compile from source, version 0.1.45, with a relatively recent version of R 2.13.0 (but not the most recent and I still use Mac OSX 10.5.8). Perhaps its brevity will be helpful, and the fact that it seems to identify different error than those flagged in the log at CRAN. Thanks for your answer. The failure on your side is clear to me: there is no installation of the boost C++ library in any of the standard include locations. I have added /opt/local/include in Makevars (Mac Ports installation of C source packages), however, I know I should but still I am reluctant to write a configure script that could circumvent non-standard installations of boost on UNIX machines. So thanks for the output, but the CRAN messages must point to something different... Regards Sören trying URL 'http://lib.stat.cmu.edu/R/CRAN/src/contrib/GUTS_0.1.45.tar.gz' Content type 'application/x-gzip' length 9842 bytes opened URL == downloaded 9842 bytes Loading required package: lattice Loading required package: sos Loading required package: brew [1] 2011-06-29 09:40:18 EDT * installing *source* package ‘GUTS’ ... ** libs *** arch - i386 g++ -arch i386 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -I/opt/local/include -I/usr/local/include -I/Library/Frameworks/R.framework/Versions/2.13/Resources/library/Rcpp/include -fPIC -g -O2 -c GUTS.cpp -o GUTS.o In file included from GUTS.cpp:12: GUTS.h:21:28: error: boost/random.hpp: No such file or directory GUTS.h:22:40: error: boost/math/distributions.hpp: No such file or directory GUTS.cpp: In function ‘void to_print(double)’: GUTS.cpp:277: error: ‘cout’ was not declared in this scope GUTS.cpp: In member function ‘void GUTS::showObject()’: GUTS.cpp:281: error: ‘cout’ is not a member of ‘std’ GUTS.cpp:284: error: ‘cout’ was not declared in this scope make: *** [GUTS.o] Error 1 ERROR: compilation failed for package ‘GUTS’ * removing ‘/Library/Frameworks/R.framework/Versions/2.13/Resources/library/GUTS’ sessionInfo() R version 2.13.0 beta (2011-04-04 r55296) Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit) locale: [1] en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8 attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] mgcv_1.7-6 sos_1.3-0 brew_1.0-6 lattice_0.19-26 loaded via a namespace (and not attached): [1] grid_2.13.0Matrix_0.999375-50 nlme_3.1-101 tools_2.13.0 -- David. R: version platform i386-apple-darwin9.8.0 arch i386 os darwin9.8.0 system i386, darwin9.8.0 status major 2 minor 13.0 year 2011 month 04 day13 svn rev55427 language R version.string R version 2.13.0 (2011-04-13) I ~ $: gcc --version i686-apple-darwin10-gcc-4.2.1
Re: [Rd] Compilation error Mac binary
On Jun 29, 2011, at 2:39 PM, soeren.vo...@uzh.ch wrote: Thanks Simon, Uwe and David for your helpful answers. English is not my primary language, so I was hypothesising a bit about the correct interpretation of inlining and supply inside. I thought it meant copying the headers inside the package. Yes, that is what I meant- pick the part of boost that you use and include it (boost has many parts so that's another reason to do that). I was already inspecting RQuantlib but I did, so far, not get smarter. The two comments were unrelated ;). I was just pointing out that Dirk has C++ expertise, uses boots himself and is the author of Rcpp so he may possibly know what the error is about. I did not have RQuantLib in mind for you to look at the boost inclusion - RQuantLib needs QuantLib in addition to boost, so it is not surprising that he doesn't include boost inside as he has additional dependencies (and he does declare them correctly). I think I will setup a VMware OS X 10.5 with an older boost. This approach seems more reliable to me than just trying around with a configure script which, eventually, I don't understand fully. Yet, interesting that GUTS builds on Win and Linux, but not on the CRAN OS X. Anyway, thanks for your help. It is a side-effect that GUTS builds at all, because the only reason it does is that some other package has probably required boost before. If that was not the case, your package would fail everywhere. [That is not the answer to the Mac error since the same applies - your failure to declare the dependency is masked by the fact that other packages do need boost. I suspect the answer will be in the interaction of tr1/boost/Rcpp, but your should fix GUTS regardless] Cheers, Simon On 29.06.2011, at 20:05, Simon Urbanek wrote: On Jun 29, 2011, at 1:12 PM, Uwe Ligges wrote: Looks like a different boost version than the one you require. I'd suggest to talk to the Mac maintainer, Simon Urbanek (CCing). GUTS doesn't specify any system requirements, so obviously it has no business trying to use boost from the system. Also note boost is inlined in the vast majority of cases, so most packages simply supply the headers inside as to guarantee the required version is used (which I would certainly expect GUTS to do since it doesn't depend on boost according to the DESCRIPTION). Cheers, Simon On 29.06.2011 17:14, soeren.vo...@uzh.ch wrote: Hello David On 29.06.2011, at 15:56, David Winsemius wrote: On Jun 29, 2011, at 5:33 AM, soeren.vo...@uzh.ch wrote: Hello, the compilation of the GUTS package on CRAN for Mac produces the following error messages: http://www.r-project.org/nosvn/R.check/r-release-macosx-ix86/GUTS-00install.html I guess it is some namespace collision, but I can not reproduce it on my machine, it compiles fine here. What is the cause and which setup do I need to reproduce the errors? I was going to suggest you take this up with the maintainers... but you _are_ one of the maintainers. :-) Here is the output from an attempt to compile from source, version 0.1.45, with a relatively recent version of R 2.13.0 (but not the most recent and I still use Mac OSX 10.5.8). Perhaps its brevity will be helpful, and the fact that it seems to identify different error than those flagged in the log at CRAN. Thanks for your answer. The failure on your side is clear to me: there is no installation of the boost C++ library in any of the standard include locations. I have added /opt/local/include in Makevars (Mac Ports installation of C source packages), however, I know I should but still I am reluctant to write a configure script that could circumvent non-standard installations of boost on UNIX machines. So thanks for the output, but the CRAN messages must point to something different... Regards Sören trying URL 'http://lib.stat.cmu.edu/R/CRAN/src/contrib/GUTS_0.1.45.tar.gz' Content type 'application/x-gzip' length 9842 bytes opened URL == downloaded 9842 bytes Loading required package: lattice Loading required package: sos Loading required package: brew [1] 2011-06-29 09:40:18 EDT * installing *source* package ‘GUTS’ ... ** libs *** arch - i386 g++ -arch i386 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -I/opt/local/include -I/usr/local/include -I/Library/Frameworks/R.framework/Versions/2.13/Resources/library/Rcpp/include -fPIC -g -O2 -c GUTS.cpp -o GUTS.o In file included from GUTS.cpp:12: GUTS.h:21:28: error: boost/random.hpp: No such file or directory GUTS.h:22:40: error: boost/math/distributions.hpp: No such file or directory GUTS.cpp: In function ‘void to_print(double)’: GUTS.cpp:277: error: ‘cout’ was not declared in this scope GUTS.cpp: In member function ‘void GUTS::showObject()’: GUTS.cpp:281: error: ‘cout’
Re: [Rd] Compilation error Mac binary
On 29 June 2011 at 14:17, Simon Urbanek wrote: | BTW: the build result is at | | http://www.r-project.org/nosvn/R.check/r-release-macosx-ix86/GUTS-00install.html | | so you may want to have a look. I'm not a C++ expert so you may want to ask on the Rcpp list since it appears to be some issue triggered by Rcpp includes - as if boost and tr1 and somehow define the same things but differently ... Since Dirk uses the same boost (1.43 here) successfully in QuantLib he may know more ... Well, I already told Soeren over there on rcpp-devel that his issues are a) totally homegrown (as he continues to ignore configure issues and just assumes things would work because they do on his), b) hence unrelated to Rcpp (as he just throws '#include boost/...' in his code without testing c) almost entirely solvable by copy-and-paste as e.g. my RQuantLib has a configure script using boost-config he could copy (but I acknowldged that the configure script does more and is hence not the easiest possible). Now, I do admit that learning configure is a bit of a pain, but that is the price of admission of CRAN if you use Boost -- or you choose the frequently done but very inelegant route of copying all your Boost headers into your package. My RcppBDT package does that too. Some of us have talked about creating a 'boost-headers' package for CRAN that the couple of Boost-using packages could have a 'Depends:' and 'LinkingTo:' on. Then his issues would be solved -- but we're not there yet. Soeren just shown resilience and persistence in getting his package written, built and now onto CRAN. The remaining step is to learn more about cross-platform build issues. Because that is the (high) standard of CRAN, and if you want to be part of it, you are expected to conform. No shortcuts. Dirk | Cheers, | Simon | | | On Jun 29, 2011, at 2:05 PM, Simon Urbanek wrote: | | | On Jun 29, 2011, at 1:12 PM, Uwe Ligges wrote: | | Looks like a different boost version than the one you require. | I'd suggest to talk to the Mac maintainer, Simon Urbanek (CCing). | | | GUTS doesn't specify any system requirements, so obviously it has no business trying to use boost from the system. Also note boost is inlined in the vast majority of cases, so most packages simply supply the headers inside as to guarantee the required version is used (which I would certainly expect GUTS to do since it doesn't depend on boost according to the DESCRIPTION). | | Cheers, | Simon | | | | On 29.06.2011 17:14, soeren.vo...@uzh.ch wrote: | Hello David | | On 29.06.2011, at 15:56, David Winsemius wrote: | | On Jun 29, 2011, at 5:33 AM, soeren.vo...@uzh.ch wrote: | | Hello, the compilation of the GUTS package on CRAN for Mac produces the following error messages: | | http://www.r-project.org/nosvn/R.check/r-release-macosx-ix86/GUTS-00install.html | | I guess it is some namespace collision, but I can not reproduce it on my machine, it compiles fine here. What is the cause and which setup do I need to reproduce the errors? | | I was going to suggest you take this up with the maintainers... but you _are_ one of the maintainers. | | :-) | | Here is the output from an attempt to compile from source, version 0.1.45, with a relatively recent version of R 2.13.0 (but not the most recent and I still use Mac OSX 10.5.8). Perhaps its brevity will be helpful, and the fact that it seems to identify different error than those flagged in the log at CRAN. | | Thanks for your answer. The failure on your side is clear to me: there is no installation of the boost C++ library in any of the standard include locations. I have added /opt/local/include in Makevars (Mac Ports installation of C source packages), however, I know I should but still I am reluctant to write a configure script that could circumvent non-standard installations of boost on UNIX machines. | | So thanks for the output, but the CRAN messages must point to something different... | | Regards | Sören | | trying URL 'http://lib.stat.cmu.edu/R/CRAN/src/contrib/GUTS_0.1.45.tar.gz' | Content type 'application/x-gzip' length 9842 bytes | opened URL | == | downloaded 9842 bytes | | Loading required package: lattice | Loading required package: sos | Loading required package: brew | [1] 2011-06-29 09:40:18 EDT | * installing *source* package ‘GUTS’ ... | ** libs | *** arch - i386 | g++ -arch i386 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -I/opt/local/include -I/usr/local/include -I/Library/Frameworks/R.framework/Versions/2.13/Resources/library/Rcpp/include -fPIC -g -O2 -c GUTS.cpp -o GUTS.o | In file included from GUTS.cpp:12: | GUTS.h:21:28: error: boost/random.hpp: No such file or directory | GUTS.h:22:40: error: boost/math/distributions.hpp: No such file or directory |
Re: [Rd] Compilation error Mac binary
On 29.06.2011, at 21:19, Dirk Eddelbuettel wrote: Soeren just shown resilience and persistence in getting his package written, built and now onto CRAN. The remaining step is to learn more about cross-platform build issues. Because that is the (high) standard of CRAN, and if you want to be part of it, you are expected to conform. No shortcuts. Hehehe :-D Okay, Dirk, I'll try my best :-)! Cheers Sören __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
