On Tue, Oct 11, 2016 at 6:05 PM, Dan Tenenbaum <dtene...@fredhutch.org> wrote: > > > ----- Original Message ----- >> From: "Kasper Daniel Hansen" <kasperdanielhan...@gmail.com> >> To: "Mike" <wjia...@fhcrc.org> >> Cc: "bioc-devel" <bioc-devel@r-project.org> >> Sent: Tuesday, October 11, 2016 5:57:02 PM >> Subject: Re: [Bioc-devel] flowCore fails with GCC 4.4.7 on RHEL 6.0 > >> Two things. >> >> 1. You might be surprised how many HPC facilities uses older versions of >> GCC for stability. We do, and many others I know of. >> 2. In my opinion, you should have a configure script check for newer >> versions of GCC or document it elsewhere. I don't see that. >> > > flowCore does mention SystemRequirements: C++11 as it is supposed do.
... since ~8 hours ;) https://github.com/Bioconductor-mirror/flowCore/commit/4ce445b24c0e48d9c33d8d5a6e8d33bb6dabc2e3 /Henrik > Dan > > >> Best, >> Kasper >> >> On Tue, Oct 11, 2016 at 3:07 PM, Mike <wjia...@fhcrc.org> wrote: >> >>> It does use some c++11 code and I think it is reasonable to expect >>> relative newer gcc (>=4.8.4) to be installed. >>> >>> >>> >>> On 10/10/2016 05:42 PM, Kasper Daniel Hansen wrote: >>> >>>> Latest version (1.39.11). >>>> >>>> My guess is that this is a case of the author using C++ stuff which is >>>> not support on 4.4.7. >>>> >>>> ** libs >>>> /usr/bin/g++ -std=c++0x -I/jhpce/shared/community/comp >>>> iler/gcc/4.4.7/R/3.3.x/lib64/R/include -DNDEBUG -I../inst/include/ >>>> -I/usr/local/include -I"/jhpce/shared/community/com >>>> piler/gcc/4.4.7/R/3.3.x/lib64/R/site-library/Rcpp/include" >>>> -I"/jhpce/shared/community/compiler/gcc/4.4.7/R/3.3.x/lib64/R/site-library/BH/include" >>>> -fpic -g -O2 -march=amdfam10 -c FastLogicle.cpp -o FastLogicle.o >>>> /usr/bin/g++ -std=c++0x -I/jhpce/shared/community/comp >>>> iler/gcc/4.4.7/R/3.3.x/lib64/R/include -DNDEBUG -I../inst/include/ >>>> -I/usr/local/include -I"/jhpce/shared/community/com >>>> piler/gcc/4.4.7/R/3.3.x/lib64/R/site-library/Rcpp/include" >>>> -I"/jhpce/shared/community/compiler/gcc/4.4.7/R/3.3.x/lib64/R/site-library/BH/include" >>>> -fpic -g -O2 -march=amdfam10 -c Hyperlog.cpp -o Hyperlog.o >>>> /usr/bin/g++ -std=c++0x -I/jhpce/shared/community/comp >>>> iler/gcc/4.4.7/R/3.3.x/lib64/R/include -DNDEBUG -I../inst/include/ >>>> -I/usr/local/include -I"/jhpce/shared/community/com >>>> piler/gcc/4.4.7/R/3.3.x/lib64/R/site-library/Rcpp/include" >>>> -I"/jhpce/shared/community/compiler/gcc/4.4.7/R/3.3.x/lib64/R/site-library/BH/include" >>>> -fpic -g -O2 -march=amdfam10 -c Logicle.cpp -o Logicle.o >>>> /usr/bin/g++ -std=c++0x -I/jhpce/shared/community/comp >>>> iler/gcc/4.4.7/R/3.3.x/lib64/R/include -DNDEBUG -I../inst/include/ >>>> -I/usr/local/include -I"/jhpce/shared/community/com >>>> piler/gcc/4.4.7/R/3.3.x/lib64/R/site-library/Rcpp/include" >>>> -I"/jhpce/shared/community/compiler/gcc/4.4.7/R/3.3.x/lib64/R/site-library/BH/include" >>>> -fpic -g -O2 -march=amdfam10 -c RcppExports.cpp -o RcppExports.o >>>> /usr/bin/g++ -std=c++0x -I/jhpce/shared/community/comp >>>> iler/gcc/4.4.7/R/3.3.x/lib64/R/include -DNDEBUG -I../inst/include/ >>>> -I/usr/local/include -I"/jhpce/shared/community/com >>>> piler/gcc/4.4.7/R/3.3.x/lib64/R/site-library/Rcpp/include" >>>> -I"/jhpce/shared/community/compiler/gcc/4.4.7/R/3.3.x/lib64/R/site-library/BH/include" >>>> -fpic -g -O2 -march=amdfam10 -c biexponential.cpp -o biexponential.o >>>> /usr/bin/g++ -std=c++0x -I/jhpce/shared/community/comp >>>> iler/gcc/4.4.7/R/3.3.x/lib64/R/include -DNDEBUG -I../inst/include/ >>>> -I/usr/local/include -I"/jhpce/shared/community/com >>>> piler/gcc/4.4.7/R/3.3.x/lib64/R/site-library/Rcpp/include" >>>> -I"/jhpce/shared/community/compiler/gcc/4.4.7/R/3.3.x/lib64/R/site-library/BH/include" >>>> -fpic -g -O2 -march=amdfam10 -c convertRawBytes.cpp -o convertRawBytes.o >>>> convertRawBytes.cpp: In function ‘std::vector<double, >>>> std::allocator<double> > convertRawBytes(BYTES, bool, std::vector<short >>>> unsigned int, std::allocator<short unsigned int> >, short unsigned int, >>>> bool)’: >>>> convertRawBytes.cpp:48: error: expected initializer before ‘:’ token >>>> convertRawBytes.cpp:53: error: expected primary-expression before ‘auto’ >>>> convertRawBytes.cpp:53: error: expected ‘)’ before ‘auto’ >>>> convertRawBytes.cpp:56: error: ‘nElement’ was not declared in this scope >>>> convertRawBytes.cpp:61: error: ‘nrow’ was not declared in this scope >>>> convertRawBytes.cpp:97: error: call of overloaded ‘to_string(short >>>> unsigned int&)’ is ambiguous >>>> /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/ >>>> c++/4.4.7/bits/basic_string.h:2604: note: candidates are: std::string >>>> std::to_string(long long int) >>>> /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/ >>>> c++/4.4.7/bits/basic_string.h:2610: note: std::string >>>> std::to_string(long long unsigned int) >>>> /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/ >>>> c++/4.4.7/bits/basic_string.h:2616: note: std::string >>>> std::to_string(long double) >>>> convertRawBytes.cpp:112: error: call of overloaded ‘to_string(short >>>> unsigned int&)’ is ambiguous >>>> /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/ >>>> c++/4.4.7/bits/basic_string.h:2604: note: candidates are: std::string >>>> std::to_string(long long int) >>>> /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/ >>>> c++/4.4.7/bits/basic_string.h:2610: note: std::string >>>> std::to_string(long long unsigned int) >>>> /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/ >>>> c++/4.4.7/bits/basic_string.h:2616: note: std::string >>>> std::to_string(long double) >>>> make: *** [convertRawBytes.o] Error 1 >>>> ERROR: compilation failed for package ‘flowCore’ >>>> * removing ‘/jhpce/shared/community/compiler/gcc/4.4.7/R/3.3.x/lib64/R/ >>>> site-library/flowCore’ >>>> >>>> >>> >> >> [[alternative HTML version deleted]] >> >> _______________________________________________ >> Bioc-devel@r-project.org mailing list >> https://stat.ethz.ch/mailman/listinfo/bioc-devel > > _______________________________________________ > Bioc-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/bioc-devel _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
