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

[Kasper Daniel Hansen]

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.

Best,
Kasper

On Tue, Oct 11, 2016 at 3:07 PM, Mike <wjiang2 at 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’
>>
>>
>

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