----- 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. 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]] > > _______________________________________________ > 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