[Bioc-devel] flowCore fails with GCC 4.4.7 on RHEL 6.0

[Mike]

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/compiler/gcc/4.4.7/R/3.3.x/lib64/R/include 
> -DNDEBUG -I../inst/include/  -I/usr/local/include 
> -I"/jhpce/shared/community/compiler/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/compiler/gcc/4.4.7/R/3.3.x/lib64/R/include 
> -DNDEBUG -I../inst/include/  -I/usr/local/include 
> -I"/jhpce/shared/community/compiler/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/compiler/gcc/4.4.7/R/3.3.x/lib64/R/include 
> -DNDEBUG -I../inst/include/  -I/usr/local/include 
> -I"/jhpce/shared/community/compiler/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/compiler/gcc/4.4.7/R/3.3.x/lib64/R/include 
> -DNDEBUG -I../inst/include/  -I/usr/local/include 
> -I"/jhpce/shared/community/compiler/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/compiler/gcc/4.4.7/R/3.3.x/lib64/R/include 
> -DNDEBUG -I../inst/include/  -I/usr/local/include 
> -I"/jhpce/shared/community/compiler/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/compiler/gcc/4.4.7/R/3.3.x/lib64/R/include 
> -DNDEBUG -I../inst/include/  -I/usr/local/include 
> -I"/jhpce/shared/community/compiler/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’
>