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

[Dan Tenenbaum]

----- Original Message -----
> From: "Kasper Daniel Hansen" <kasperdanielhansen at gmail.com>
> To: "Mike" <wjiang2 at fhcrc.org>
> Cc: "bioc-devel" <bioc-devel at 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 <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’
>>>
>>>
>>
> 
>	[[alternative HTML version deleted]]
> 
> _______________________________________________
> Bioc-devel at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel