Hello, Here it happens under both 32-bit and 64-bit Fedora 10. Maybe this is a gcc version problem? ________________________________________ Fra: Vincent Carey [stvjc at channing.harvard.edu] Sendt: 19. oktober 2010 19:59 Til: Bernt Guldbrandtsen Cc: bioconductor at stat.math.ethz.ch Emne: Re: [BioC] Compilation problem RBGL_1.26 I could not reproduce this on a 32-bit ubuntu 9.10 with gcc 4.4.1 -- biocLite gave a successful compilation and install. On Tue, Oct 19, 2010 at 10:34 AM, Bernt Guldbrandtsen <bernt.guldbrandtsen at="" agrsci.dk=""> wrote: > Dear Bioconductor, > > I was trying to update to the new release of Bioconductor under R-2.12.0 and ran into the following compilation problem when building RBGL_1.26 during compilation of incrConnComp.cpp under Fedora 10: > --------------------------------------------------------------- > g++ -I/opt/ghpc/R-2.12.0/lib/R/include "-I/opt/ghpc/include" -IboostIncl -fpic -g -O2 -c incrConnComp.cpp -o incrConnComp.o > incrConnComp.cpp: In function 'SEXPREC* BGL_incr_comp_internal(SEXPREC*, SEXPREC*, SEXPREC*, E_IC_METHOD)': > incrConnComp.cpp:65: error: expected initializer before 'j' > incrConnComp.cpp:71: error: 'j' was not declared in this scope > incrConnComp.cpp:71: error: 'struct std::pair<boost::detail::compone nt_index_iterator<__gnu_cxx::__normal_iterator<unsigned="" int*,="" std::vector<unsigned="" int,="" std::allocator<unsigned="" int=""> > > >, boost::d etail::component_index_iterator<__gnu_cxx::__normal_iterator<unsigned int*,="" std::vector<unsigned="" int,="" std::allocator<unsigned="" int=""> > > > >' has no member named 'begin' > incrConnComp.cpp:71: error: 'struct std::pair<boost::detail::compone nt_index_iterator<__gnu_cxx::__normal_iterator<unsigned="" int*,="" std::vector<unsigned="" int,="" std::allocator<unsigned="" int=""> > > >, boost::d etail::component_index_iterator<__gnu_cxx::__normal_iterator<unsigned int*,="" std::vector<unsigned="" int,="" std::allocator<unsigned="" int=""> > > > >' has no member named 'end' > incrConnComp.cpp:76: error: 'struct std::pair<boost::detail::compone nt_index_iterator<__gnu_cxx::__normal_iterator<unsigned="" int*,="" std::vector<unsigned="" int,="" std::allocator<unsigned="" int=""> > > >, boost::d etail::component_index_iterator<__gnu_cxx::__normal_iterator<unsigned int*,="" std::vector<unsigned="" int,="" std::allocator<unsigned="" int=""> > > > >' has no member named 'begin' > incrConnComp.cpp:76: error: 'struct std::pair<boost::detail::compone nt_index_iterator<__gnu_cxx::__normal_iterator<unsigned="" int*,="" std::vector<unsigned="" int,="" std::allocator<unsigned="" int=""> > > >, boost::d etail::component_index_iterator<__gnu_cxx::__normal_iterator<unsigned int*,="" std::vector<unsigned="" int,="" std::allocator<unsigned="" int=""> > > > >' has no member named 'end' > make: *** [incrConnComp.o] Error 1 > ERROR: compilation failed for package 'RBGL' > * removing '/opt/ghpc/R-2.12.0/lib/R/library/RBGL' > * restoring previous '/opt/ghpc/R-2.12.0/lib/R/library/RBGL' > > The downloaded packages are in > '/tmp/RtmpwPfL9j/downloaded_packages' > Updating HTML index of packages in '.Library' > Warning message: > In install.packages("RBGL", rep = biocinstallRepos()) : > installation of package 'RBGL' had non-zero exit status > --------------------------------------------------------------- > About gcc: > --------------------------------------------------------------- > [root at pn01 ~]# gcc -v > Using built-in specs. > Target: i386-redhat-linux > Configured with: ../configure --prefix=/usr --mandir=/usr/share/man --infodir=/usr/share/info --enable-shared --enable-threads=posix --enable-checking=release --with-system-zlib --enable-__cxa_atexit --disable-libunwind-exceptions --enable- languages=c,c++,objc,obj-c++,java,fortran,ada --enable-java-awt=gtk --disable-dssi --enable-plugin --with-java- home=/usr/lib/jvm/java-1.5.0-gcj-1.5.0.0/jre --enable-libgcj-multifile --enable-java-maintainer-mode --with-ecj-jar=/usr/share/java/eclipse- ecj.jar --with-cpu=generic --host=i386-redhat-linux > Thread model: posix > gcc version 4.1.2 20070925 (Red Hat 4.1.2-27) > --------------------------------------------------------------- > Session info is: > --------------------------------------------------------------- >> sessionInfo() > R version 2.12.0 (2010-10-15) > Platform: i686-pc-linux-gnu (32-bit) > > locale: > [1] LC_CTYPE=en_US LC_NUMERIC=C LC_TIME=en_US > [4] LC_COLLATE=en_US LC_MONETARY=C LC_MESSAGES=en_US > [7] LC_PAPER=en_US LC_NAME=C LC_ADDRESS=C > [10] LC_TELEPHONE=C LC_MEASUREMENT=en_US LC_IDENTIFICATION=C > > attached base packages: > [1] stats graphics grDevices utils datasets methods base > > loaded via a namespace (and not attached): > [1] tools_2.12.0 > --------------------------------------------------------------- > > All other R packages are up to date. > > Am I missing something obvious here? > > Kind regards > > > Bernt Guldbrandtsen > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor >

And then, apparently not; compiling with Intel's icc gives a very similar problem: ------------------------------------------------- icc -I/opt/ghpc/R-2.12.0/lib64/R/include "-I/opt/ghpc/include" -IboostIncl -fpic -g -O2 -c incrConnComp.cpp -o incrConnComp.o incrConnComp.cpp(65): error: name followed by "::" must be a class or namespace name Components::value_type::iterator j; ^ incrConnComp.cpp(65): error: expected a ";" Components::value_type::iterator j; ^ incrConnComp.cpp(71): error: identifier "j" is undefined for (j = components[k].begin(); j != components[k].end(); j++ ) ^ incrConnComp.cpp(71): error: class "std::pair<boost::detail::component _index_iterator<__gnu_cxx::__normal_iterator<unsigned="" int="" *,="" std::vector<unsigned="" int,="" std::allocator<unsigned="" int="">>>>, boost::deta il::component_index_iterator<__gnu_cxx::__normal_iterator<unsigned int="" *,="" std::vector<unsigned="" int,="" std::allocator<unsigned="" int="">>>>>" has no member "begin" for (j = components[k].begin(); j != components[k].end(); j++ ) ^ incrConnComp.cpp(71): error: class "std::pair<boost::detail::component _index_iterator<__gnu_cxx::__normal_iterator<unsigned="" int="" *,="" std::vector<unsigned="" int,="" std::allocator<unsigned="" int="">>>>, boost::deta il::component_index_iterator<__gnu_cxx::__normal_iterator<unsigned int="" *,="" std::vector<unsigned="" int,="" std::allocator<unsigned="" int="">>>>>" has no member "end" for (j = components[k].begin(); j != components[k].end(); j++ ) ^ incrConnComp.cpp(76): error: class "std::pair<boost::detail::component _index_iterator<__gnu_cxx::__normal_iterator<unsigned="" int="" *,="" std::vector<unsigned="" int,="" std::allocator<unsigned="" int="">>>>, boost::deta il::component_index_iterator<__gnu_cxx::__normal_iterator<unsigned int="" *,="" std::vector<unsigned="" int,="" std::allocator<unsigned="" int="">>>>>" has no member "begin" for (j = components[k].begin(); j != components[k].end(); j++ ) ^ incrConnComp.cpp(76): error: class "std::pair<boost::detail::component _index_iterator<__gnu_cxx::__normal_iterator<unsigned="" int="" *,="" std::vector<unsigned="" int,="" std::allocator<unsigned="" int="">>>>, boost::deta il::component_index_iterator<__gnu_cxx::__normal_iterator<unsigned int="" *,="" std::vector<unsigned="" int,="" std::allocator<unsigned="" int="">>>>>" has no member "end" for (j = components[k].begin(); j != components[k].end(); j++ ) ^ compilation aborted for incrConnComp.cpp (code 2) make: *** [incrConnComp.o] Error 2 ERROR: compilation failed for package 'RBGL' * removing '/opt/ghpc/R-2.12.0/lib64/R/library/RBGL' * restoring previous '/opt/ghpc/R-2.12.0/lib64/R/library/RBGL' The downloaded packages are in '/tmp/RtmpFDel9f/downloaded_packages' Updating HTML index of packages in '.Library' Warning message: In install.packages(pkgs = pkgs, repos = repos, ...) : installation of package 'RBGL' had non-zero exit status ------------------------------------------------- Best regards, Bernt Guldbrandtsen ________________________________________ Fra: Vincent Carey [stvjc at channing.harvard.edu] Sendt: 19. oktober 2010 19:59 Til: Bernt Guldbrandtsen Cc: bioconductor at stat.math.ethz.ch Emne: Re: [BioC] Compilation problem RBGL_1.26 I could not reproduce this on a 32-bit ubuntu 9.10 with gcc 4.4.1 -- biocLite gave a successful compilation and install. On Tue, Oct 19, 2010 at 10:34 AM, Bernt Guldbrandtsen <bernt.guldbrandtsen at="" agrsci.dk=""> wrote: > Dear Bioconductor, > > I was trying to update to the new release of Bioconductor under R-2.12.0 and ran into the following compilation problem when building RBGL_1.26 during compilation of incrConnComp.cpp under Fedora 10: > --------------------------------------------------------------- > g++ -I/opt/ghpc/R-2.12.0/lib/R/include "-I/opt/ghpc/include" -IboostIncl -fpic -g -O2 -c incrConnComp.cpp -o incrConnComp.o > incrConnComp.cpp: In function 'SEXPREC* BGL_incr_comp_internal(SEXPREC*, SEXPREC*, SEXPREC*, E_IC_METHOD)': > incrConnComp.cpp:65: error: expected initializer before 'j' > incrConnComp.cpp:71: error: 'j' was not declared in this scope > incrConnComp.cpp:71: error: 'struct std::pair<boost::detail::compone nt_index_iterator<__gnu_cxx::__normal_iterator<unsigned="" int*,="" std::vector<unsigned="" int,="" std::allocator<unsigned="" int=""> > > >, boost::d etail::component_index_iterator<__gnu_cxx::__normal_iterator<unsigned int*,="" std::vector<unsigned="" int,="" std::allocator<unsigned="" int=""> > > > >' has no member named 'begin' > incrConnComp.cpp:71: error: 'struct std::pair<boost::detail::compone nt_index_iterator<__gnu_cxx::__normal_iterator<unsigned="" int*,="" std::vector<unsigned="" int,="" std::allocator<unsigned="" int=""> > > >, boost::d etail::component_index_iterator<__gnu_cxx::__normal_iterator<unsigned int*,="" std::vector<unsigned="" int,="" std::allocator<unsigned="" int=""> > > > >' has no member named 'end' > incrConnComp.cpp:76: error: 'struct std::pair<boost::detail::compone nt_index_iterator<__gnu_cxx::__normal_iterator<unsigned="" int*,="" std::vector<unsigned="" int,="" std::allocator<unsigned="" int=""> > > >, boost::d etail::component_index_iterator<__gnu_cxx::__normal_iterator<unsigned int*,="" std::vector<unsigned="" int,="" std::allocator<unsigned="" int=""> > > > >' has no member named 'begin' > incrConnComp.cpp:76: error: 'struct std::pair<boost::detail::compone nt_index_iterator<__gnu_cxx::__normal_iterator<unsigned="" int*,="" std::vector<unsigned="" int,="" std::allocator<unsigned="" int=""> > > >, boost::d etail::component_index_iterator<__gnu_cxx::__normal_iterator<unsigned int*,="" std::vector<unsigned="" int,="" std::allocator<unsigned="" int=""> > > > >' has no member named 'end' > make: *** [incrConnComp.o] Error 1 > ERROR: compilation failed for package 'RBGL' > * removing '/opt/ghpc/R-2.12.0/lib/R/library/RBGL' > * restoring previous '/opt/ghpc/R-2.12.0/lib/R/library/RBGL' > > The downloaded packages are in > '/tmp/RtmpwPfL9j/downloaded_packages' > Updating HTML index of packages in '.Library' > Warning message: > In install.packages("RBGL", rep = biocinstallRepos()) : > installation of package 'RBGL' had non-zero exit status > --------------------------------------------------------------- > About gcc: > --------------------------------------------------------------- > [root at pn01 ~]# gcc -v > Using built-in specs. > Target: i386-redhat-linux > Configured with: ../configure --prefix=/usr --mandir=/usr/share/man --infodir=/usr/share/info --enable-shared --enable-threads=posix --enable-checking=release --with-system-zlib --enable-__cxa_atexit --disable-libunwind-exceptions --enable- languages=c,c++,objc,obj-c++,java,fortran,ada --enable-java-awt=gtk --disable-dssi --enable-plugin --with-java- home=/usr/lib/jvm/java-1.5.0-gcj-1.5.0.0/jre --enable-libgcj-multifile --enable-java-maintainer-mode --with-ecj-jar=/usr/share/java/eclipse- ecj.jar --with-cpu=generic --host=i386-redhat-linux > Thread model: posix > gcc version 4.1.2 20070925 (Red Hat 4.1.2-27) > --------------------------------------------------------------- > Session info is: > --------------------------------------------------------------- >> sessionInfo() > R version 2.12.0 (2010-10-15) > Platform: i686-pc-linux-gnu (32-bit) > > locale: > [1] LC_CTYPE=en_US LC_NUMERIC=C LC_TIME=en_US > [4] LC_COLLATE=en_US LC_MONETARY=C LC_MESSAGES=en_US > [7] LC_PAPER=en_US LC_NAME=C LC_ADDRESS=C > [10] LC_TELEPHONE=C LC_MEASUREMENT=en_US LC_IDENTIFICATION=C > > attached base packages: > [1] stats graphics grDevices utils datasets methods base > > loaded via a namespace (and not attached): > [1] tools_2.12.0 > --------------------------------------------------------------- > > All other R packages are up to date. > > Am I missing something obvious here? > > Kind regards > > > Bernt Guldbrandtsen > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor >