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

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

Thread (6 messages)