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

[Kasper Daniel Hansen]

I am happy to see it now lists C++11 under SystemRequirements.

On Tue, Oct 11, 2016 at 9:05 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.
> 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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> >
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> > https://stat.ethz.ch/mailman/listinfo/bioc-devel
>

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