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

[Henrik Bengtsson]

On Tue, Oct 11, 2016 at 6:05 PM, Dan Tenenbaum <dtenenba at fredhutch.org> wrote:
>
>
> ----- 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.

... 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 <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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