<atomic> is not implemented

Hi,

I am trying to install Hijing from : cholm.web.cern.ch/cholm/root/#thijing

The instructions from the downloaded file to install Hijing:

  1. cd' to the directory containing the package's source code and type./configure’ to configure the package for your system.

    Running `configure’ might take a while. While running, it prints
    some messages telling which features it is checking for.

  2. Type `make’ to compile the package.

In the 2. step ‘make’ several errors occurs :

/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../include/c++/v1/atomic:543:2: error: <atomic> is not implemented #error <atomic> is not implemented ^ In file included from THijing.cxx:30: In file included from ../libroot-hijing/THijing.h:33: In file included from /Users/zakig/Documents/root/include/TGenerator.h:138: In file included from /Users/zakig/Documents/root/include/TNamed.h:26: In file included from /Users/zakig/Documents/root/include/TObject.h:31: /Users/zakig/Documents/root/include/Rtypes.h:226:14: error: no type named 'atomic' in namespace 'std' typedef std::atomic<TClass*> atomic_TClass_ptr; ~~~~~^ /Users/zakig/Documents/root/include/Rtypes.h:226:20: error: expected unqualified-id typedef std::atomic<TClass*> atomic_TClass_ptr;

I tried to search for previous posts for solutions and I found: Correct way to replace rootcint in makefile

I am not that good at programming to understand the post. Hope someone can help.

Thanks.

Hi,

Could you tell us which version of ROOT, on which platform, with which compiler?

Cheers, Bertrand.

[quote=“bellenot”]Hi,
Could you tell us which version of ROOT, on which platform, with which compiler?
[/quote]

The OP should really provide these pieces of information, but guessing from the quoted output, I’d say it’s a MacOSX machine (references to XCode!).

Also, the OP should, as given in the the INSTALL instructions of the thijing package post the content of config.log.

Now, the referred package thijing is really old, and the configure script may not be up to date to properly discover the use of Clang rather than GCC on MacOSX. Perhaps OP can try to

autoreconf -i -f 
./configure 
make 
make install

to see if that helps. If there’s still no luck, try

./configure CC=`root-config -cc` CXX=`root-config --cxx` CFLAGS=`root-config --cflags | sed 's/-[ID][-a-zA-Z0-9/"]*//g'` CXXFLAGS=`root-config --cflags | sed 's/-[ID][-a-zA-Z0-9/"]*//g'` CPPFLAGS=`root-config --cflags | sed 's/\(-[ID][-a-zA-Z0-9/"]*\)/\1/g'`

If that doesn’t do it, then you can build the library from the sources like

$ gfortran -fPIC -c hijing1.383.f
$ gfortran -fPIC -c hipyset1.35.f
$ c++ -fPIC -c ran.cxx 
$ c++ -fPIC -c `root-config --cflags` TRanMar.cxx
$ c++ -fPIC -c `root-config --cflags` THijingPara.cxx
$ c++ -fPIC -c `root-config --cflags` THijingMinBias.cxx
$ c++ -fPIC -c `root-config --cflags` THijingFlow.cxx
$ c++ -fPIC -c `root-config --cflags` THijing.cxx
$ rootcint -f HijingDoct.cxx -c -I. THijing.h THijingFlow.h THijingHeader.h THijingMinBias.h THijingPara.h TRanMar.h LinkDef.h 
$ c++ -fPIC -c `root-config --cflags` HijingDict.cxx 
$ c++ -shared -o libTHijing.so *.o

Note, the exact command lines may differ on your system - I know very little of the XCode suite.

Alternatively, you can try to make an XCode project specifying the source files (minus runFlow.C runHijing.C and main.cxx) as input, and make a rule for making the dictionary (HijingDict.cxx and HijingDict.h) using rootcint. Make sure the target is a shared (dynamic) library.

Yours,

Christian

Thanks for the replies Bertrand and Christian.

As I mentioned before I am not that good at programming, and I sorry for the lack of informations.

Yes it is a ROOT 6.04/08, Mac OS 10.10.5 and I am using Xcode.

After typing “autoreconf -i -f ” I got the following error:

configure.ac:44: error: possibly undefined macro: AC_DISABLE_STATIC If this token and others are legitimate, please use m4_pattern_allow. See the Autoconf documentation. configure.ac:45: error: possibly undefined macro: AC_PROG_LIBTOOL autoreconf: /usr/local/Cellar/autoconf/2.69/bin/autoconf failed with exit status: 1

For the second suggestion, I get this error:

Zakis-MacBook-Pro:libroot-hijing-1.7 zakig$ ./configure CC=`root-config -c` CXX=`root-config --cxx` CFLAGS=`root-config --cflags | sed 's/-[ID][-a-zA-Z0-9/"]*//g'` CXXFLAGS=`root-config --cflags | sed 's/-[ID][-a-zA-Z0-9/"]*//g'` CPPFLAGS=`root-config --cflags | sed 's/\(-[ID][-a-zA-Z0-9/"]*\)/\1/g'` Unknown argument "-c"! Usage: root-config [--prefix[=DIR]] [--exec-prefix[=DIR]] [--version] [--cflags] [--auxcflags] [--ldflags] [--new] [--nonew] [--libs] [--glibs] [--evelibs] [--bindir] [--libdir] [--incdir] [--etcdir] [--noauxcflags] [--noauxlibs] [--noldflags] [--has-<feature>] [--arch] [--platform] [--config] [--features] [--ncpu] [--git-revision] [--python-version] [--cc] [--cxx] [--f77] [--ld ] [--help] configure: error: unrecognized option: `-stdlib=libc++' Try `./configure --help' for more information

Now I get this new error message, when I type “make”:

Zakis-MacBook-Pro:libroot-hijing-1.7 zakig$ make cd . && automake-1.15 --gnu configure.ac:27: error: required file 'config/compile' not found configure.ac:27: 'automake --add-missing' can install 'compile' Makefile.am:26: warning: subst -,_,$(distdir: non-POSIX variable name Makefile.am:26: (probably a GNU make extension) libroot-hijing/Makefile.am:25: warning: patsubst hijing%.f,%, $(HIJING_F: non-POSIX variable name libroot-hijing/Makefile.am:25: (probably a GNU make extension) libroot-hijing/Makefile.am:75: warning: wildcard *~: non-POSIX variable name libroot-hijing/Makefile.am:75: (probably a GNU make extension) libroot-hijing/Makefile.am:75: warning: wildcard *_C.so: non-POSIX variable name libroot-hijing/Makefile.am:75: (probably a GNU make extension) libroot-hijing/Makefile.am:75: warning: wildcard *.root: non-POSIX variable name libroot-hijing/Makefile.am:75: (probably a GNU make extension) libroot-hijing/Makefile.am:32: error: Libtool library used but 'LIBTOOL' is undefined libroot-hijing/Makefile.am:32: The usual way to define 'LIBTOOL' is to add 'LT_INIT' libroot-hijing/Makefile.am:32: to 'configure.ac' and run 'aclocal' and 'autoconf' again. libroot-hijing/Makefile.am:32: If 'LT_INIT' is in 'configure.ac', make sure libroot-hijing/Makefile.am:32: its definition is in aclocal's search path. make: *** [Makefile.in] Error 1

The config.log output:

[code]This file contains any messages produced by compilers while
running configure, to aid debugging if configure makes a mistake.

It was created by ROOT interface to Hijing configure 1.7, which was
generated by GNU Autoconf 2.69. Invocation command line was

$ ./configure

---------

Platform.

---------

hostname = Zakis-MacBook-Pro.local
uname -m = x86_64
uname -r = 14.5.0
uname -s = Darwin
uname -v = Darwin Kernel Version 14.5.0: Mon Jan 11 18:48:35 PST 2016; root:xnu-2782.50.2~1/RELEASE_X86_64

/usr/bin/uname -p = i386
/bin/uname -X = unknown

/bin/arch = unknown
/usr/bin/arch -k = unknown
/usr/convex/getsysinfo = unknown
/usr/bin/hostinfo = Mach kernel version:
Darwin Kernel Version 14.5.0: Mon Jan 11 18:48:35 PST 2016; root:xnu-2782.50.2~1/RELEASE_X86_64
Kernel configured for up to 4 processors.
2 processors are physically available.
4 processors are logically available.
Processor type: x86_64h (Intel x86-64h Haswell)
Processors active: 0 1 2 3
Primary memory available: 8.00 gigabytes
Default processor set: 213 tasks, 859 threads, 4 processors
Load average: 1.73, Mach factor: 2.26
/bin/machine = unknown
/usr/bin/oslevel = unknown
/bin/universe = unknown

PATH: /Users/zakig/Documents/root/bin
PATH: /usr/local/bin
PATH: /usr/bin
PATH: /bin
PATH: /usr/sbin
PATH: /sbin
PATH: /opt/X11/bin
PATH: /Library/TeX/texbin

-----------

Core tests.

-----------

configure:1972: checking for a BSD-compatible install
configure:2040: result: /usr/bin/install -c
configure:2051: checking whether build environment is sane
configure:2106: result: yes
configure:2144: WARNING: ‘missing’ script is too old or missing
configure:2257: checking for a thread-safe mkdir -p
configure:2296: result: config/install-sh -c -d
configure:2303: checking for gawk
configure:2333: result: no
configure:2303: checking for mawk
configure:2333: result: no
configure:2303: checking for nawk
configure:2333: result: no
configure:2303: checking for awk
configure:2319: found /usr/bin/awk
configure:2330: result: awk
configure:2341: checking whether make sets $(MAKE)
configure:2363: result: yes
configure:2392: checking whether make supports nested variables
configure:2409: result: yes
configure:2583: checking for gcc
configure:2599: found /usr/bin/gcc
configure:2610: result: gcc
configure:2839: checking for C compiler version
configure:2848: gcc --version >&5
Apple LLVM version 7.0.2 (clang-700.1.81)
Target: x86_64-apple-darwin14.5.0
Thread model: posix
Configured with: --prefix=/Applications/Xcode.app/Contents/Developer/usr --with-gxx-include-dir=/usr/include/c++/4.2.1
configure:2859: $? = 0
configure:2848: gcc -v >&5
Configured with: --prefix=/Applications/Xcode.app/Contents/Developer/usr --with-gxx-include-dir=/usr/include/c++/4.2.1
Apple LLVM version 7.0.2 (clang-700.1.81)
Target: x86_64-apple-darwin14.5.0
Thread model: posix
configure:2859: $? = 0
configure:2848: gcc -V >&5
clang: error: argument to ‘-V’ is missing (expected 1 value)
clang: error: no input files
configure:2859: $? = 1
configure:2848: gcc -qversion >&5
clang: error: unknown argument: '-qversion’
clang: error: no input files
configure:2859: $? = 1
configure:2879: checking whether the C compiler works
configure:2901: gcc conftest.c >&5
configure:2905: $? = 0
configure:2953: result: yes
configure:2956: checking for C compiler default output file name
configure:2958: result: a.out
configure:2964: checking for suffix of executables
configure:2971: gcc -o conftest conftest.c >&5
configure:2975: $? = 0
configure:2997: result:
configure:3019: checking whether we are cross compiling
configure:3027: gcc -o conftest conftest.c >&5
configure:3031: $? = 0
configure:3038: ./conftest
configure:3042: $? = 0
configure:3057: result: no
configure:3062: checking for suffix of object files
configure:3084: gcc -c conftest.c >&5
configure:3088: $? = 0
configure:3109: result: o
configure:3113: checking whether we are using the GNU C compiler
configure:3132: gcc -c conftest.c >&5
configure:3132: $? = 0
configure:3141: result: yes
configure:3150: checking whether gcc accepts -g
configure:3170: gcc -c -g conftest.c >&5
configure:3170: $? = 0
configure:3211: result: yes
configure:3228: checking for gcc option to accept ISO C89
configure:3291: gcc -c -g -O2 conftest.c >&5
configure:3291: $? = 0
configure:3304: result: none needed
configure:3329: checking whether gcc understands -c and -o together
configure:3351: gcc -c conftest.c -o conftest2.o
configure:3354: $? = 0
configure:3351: gcc -c conftest.c -o conftest2.o
configure:3354: $? = 0
configure:3366: result: yes
configure:3394: checking for style of include used by make
configure:3422: result: GNU
configure:3448: checking dependency style of gcc
configure:3559: result: gcc3
configure:3632: checking for g++
configure:3648: found /usr/bin/g++
configure:3659: result: g++
configure:3686: checking for C++ compiler version
configure:3695: g++ --version >&5
Apple LLVM version 7.0.2 (clang-700.1.81)
Target: x86_64-apple-darwin14.5.0
Thread model: posix
Configured with: --prefix=/Applications/Xcode.app/Contents/Developer/usr --with-gxx-include-dir=/usr/include/c++/4.2.1
configure:3706: $? = 0
configure:3695: g++ -v >&5
Configured with: --prefix=/Applications/Xcode.app/Contents/Developer/usr --with-gxx-include-dir=/usr/include/c++/4.2.1
Apple LLVM version 7.0.2 (clang-700.1.81)
Target: x86_64-apple-darwin14.5.0
Thread model: posix
configure:3706: $? = 0
configure:3695: g++ -V >&5
clang: error: argument to ‘-V’ is missing (expected 1 value)
clang: error: no input files
configure:3706: $? = 1
configure:3695: g++ -qversion >&5
clang: error: unknown argument: '-qversion’
clang: error: no input files
configure:3706: $? = 1
configure:3710: checking whether we are using the GNU C++ compiler
configure:3729: g++ -c conftest.cpp >&5
configure:3729: $? = 0
configure:3738: result: yes
configure:3747: checking whether g++ accepts -g
configure:3767: g++ -c -g conftest.cpp >&5
configure:3767: $? = 0
configure:3808: result: yes
configure:3833: checking dependency style of g++
configure:3944: result: gcc3
configure:4012: checking for g77
configure:4042: result: no
configure:4012: checking for xlf
configure:4042: result: no
configure:4012: checking for f77
configure:4042: result: no
configure:4012: checking for frt
configure:4042: result: no
configure:4012: checking for pgf77
configure:4042: result: no
configure:4012: checking for cf77
configure:4042: result: no
configure:4012: checking for fort77
configure:4042: result: no
configure:4012: checking for fl32
configure:4042: result: no
configure:4012: checking for af77
configure:4042: result: no
configure:4012: checking for xlf90
configure:4042: result: no
configure:4012: checking for f90
configure:4042: result: no
configure:4012: checking for pgf90
configure:4042: result: no
configure:4012: checking for pghpf
configure:4042: result: no
configure:4012: checking for epcf90
configure:4042: result: no
configure:4012: checking for gfortran
configure:4028: found /usr/local/bin/gfortran
configure:4039: result: gfortran
configure:4065: checking for Fortran 77 compiler version
configure:4074: gfortran --version >&5
GNU Fortran (Homebrew gcc 5.2.0) 5.2.0
Copyright © 2015 Free Software Foundation, Inc.

GNU Fortran comes with NO WARRANTY, to the extent permitted by law.
You may redistribute copies of GNU Fortran
under the terms of the GNU General Public License.
For more information about these matters, see the file named COPYING

configure:4085: $? = 0
configure:4074: gfortran -v >&5
Using built-in specs.
COLLECT_GCC=gfortran
COLLECT_LTO_WRAPPER=/usr/local/Cellar/gcc/5.2.0/libexec/gcc/x86_64-apple-darwin14.5.0/5.2.0/lto-wrapper
Target: x86_64-apple-darwin14.5.0
Configured with: …/configure --build=x86_64-apple-darwin14.5.0 --prefix=/usr/local/Cellar/gcc/5.2.0 --libdir=/usr/local/Cellar/gcc/5.2.0/lib/gcc/5 --enable-languages=c,c++,objc,obj-c++,fortran --program-suffix=-5 --with-gmp=/usr/local/opt/gmp --with-mpfr=/usr/local/opt/mpfr --with-mpc=/usr/local/opt/libmpc --with-isl=/usr/local/opt/isl --with-system-zlib --enable-libstdcxx-time=yes --enable-stage1-checking --enable-checking=release --enable-lto --with-build-config=bootstrap-debug --disable-werror --with-pkgversion=‘Homebrew gcc 5.2.0’ --with-bugurl=https://github.com/Homebrew/homebrew/issues --enable-plugin --disable-nls --enable-multilib --with-native-system-header-dir=/usr/include --with-sysroot=/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk
Thread model: posix
gcc version 5.2.0 (Homebrew gcc 5.2.0)
configure:4085: $? = 0
configure:4074: gfortran -V >&5
gfortran: error: unrecognized command line option '-V’
gfortran: fatal error: no input files
compilation terminated.
configure:4085: $? = 1
configure:4074: gfortran -qversion >&5
gfortran: error: unrecognized command line option '-qversion’
gfortran: fatal error: no input files
compilation terminated.
configure:4085: $? = 1
configure:4094: checking whether we are using the GNU Fortran 77 compiler
configure:4107: gfortran -c conftest.F >&5
configure:4107: $? = 0
configure:4116: result: yes
configure:4122: checking whether gfortran accepts -g
configure:4133: gfortran -c -g conftest.f >&5
configure:4133: $? = 0
configure:4141: result: yes
configure:4171: checking whether we have newer GFortran
configure:4182: result: no
configure:4189: checking build system type
configure:4203: result: i386-apple-darwin14.5.0
configure:4223: checking host system type
configure:4236: result: i386-apple-darwin14.5.0
configure:4261: checking how to get verbose linking output from gfortran
configure:4271: gfortran -c -g -O2 -fno-automatic -finit-local-zero -ffixed-line-length-132 conftest.f >&5
configure:4271: $? = 0
configure:4289: gfortran -o conftest -g -O2 -fno-automatic -finit-local-zero -ffixed-line-length-132 -v conftest.f
Using built-in specs.
Target: x86_64-apple-darwin14.5.0
Thread model: posix
gcc version 5.2.0 (Homebrew gcc 5.2.0)
/usr/local/Cellar/gcc/5.2.0/libexec/gcc/x86_64-apple-darwin14.5.0/5.2.0/f951 conftest.f -ffixed-form -fPIC -feliminate-unused-debug-symbols -quiet -dumpbase conftest.f -mmacosx-version-min=10.10.5 -mtune=core2 -auxbase conftest -g -O2 -version -fno-automatic -finit-local-zero -ffixed-line-length-132 -fintrinsic-modules-path /usr/local/Cellar/gcc/5.2.0/lib/gcc/5/gcc/x86_64-apple-darwin14.5.0/5.2.0/finclude -o /var/folders/5d/tlqg90_x7l940r5gc8zrcw5h0000gn/T//ccJZV41W.s
GNU Fortran (Homebrew gcc 5.2.0) version 5.2.0 (x86_64-apple-darwin14.5.0)
compiled by GNU C version 5.2.0, GMP version 6.0.0, MPFR version 3.1.3-p2, MPC version 1.0.3
GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072
GNU Fortran2008 (Homebrew gcc 5.2.0) version 5.2.0 (x86_64-apple-darwin14.5.0)
compiled by GNU C version 5.2.0, GMP version 6.0.0, MPFR version 3.1.3-p2, MPC version 1.0.3
GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072
as -arch x86_64 -force_cpusubtype_ALL -o /var/folders/5d/tlqg90_x7l940r5gc8zrcw5h0000gn/T//ccrPY07T.o /var/folders/5d/tlqg90_x7l940r5gc8zrcw5h0000gn/T//ccJZV41W.s
Reading specs from /usr/local/Cellar/gcc/5.2.0/lib/gcc/5/gcc/x86_64-apple-darwin14.5.0/5.2.0/…/…/…/libgfortran.spec
rename spec lib to liborig
/usr/local/Cellar/gcc/5.2.0/libexec/gcc/x86_64-apple-darwin14.5.0/5.2.0/collect2 -dynamic -arch x86_64 -macosx_version_min 10.10.5 -syslibroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk -weak_reference_mismatches non-weak -o conftest -L/usr/local/Cellar/gcc/5.2.0/lib/gcc/5/gcc/x86_64-apple-darwin14.5.0/5.2.0 -L/usr/local/Cellar/gcc/5.2.0/lib/gcc/5/gcc/x86_64-apple-darwin14.5.0/5.2.0/…/…/… /var/folders/5d/tlqg90_x7l940r5gc8zrcw5h0000gn/T//ccrPY07T.o -lgfortran -no_compact_unwind -lSystem -lgcc_ext.10.5 -lgcc -lquadmath -lm -lgcc_ext.10.5 -lgcc -lSystem -v -idsym -dsym
collect2 version 5.2.0
/usr/bin/ld -dynamic -arch x86_64 -macosx_version_min 10.10.5 -syslibroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk -weak_reference_mismatches non-weak -o conftest -L/usr/local/Cellar/gcc/5.2.0/lib/gcc/5/gcc/x86_64-apple-darwin14.5.0/5.2.0 -L/usr/local/Cellar/gcc/5.2.0/lib/gcc/5/gcc/x86_64-apple-darwin14.5.0/5.2.0/…/…/… /var/folders/5d/tlqg90_x7l940r5gc8zrcw5h0000gn/T//ccrPY07T.o -lgfortran -no_compact_unwind -lSystem -lgcc_ext.10.5 -lgcc -lquadmath -lm -lgcc_ext.10.5 -lgcc -lSystem -v
@(#)PROGRAM:ld PROJECT:ld64-253.9
configured to support archs: armv6 armv7 armv7s arm64 i386 x86_64 x86_64h armv6m armv7k armv7m armv7em (tvOS)
Library search paths:
/usr/local/Cellar/gcc/5.2.0/lib/gcc/5/gcc/x86_64-apple-darwin14.5.0/5.2.0
/usr/local/Cellar/gcc/5.2.0/lib/gcc/5
Framework search paths:
ld: library not found for -lSystem
collect2: error: ld returned 1 exit status
configure:4372: result: -v
configure:4374: checking for Fortran 77 libraries of gfortran
configure:4397: gfortran -o conftest -g -O2 -fno-automatic -finit-local-zero -ffixed-line-length-132 -v conftest.f
Using built-in specs.
Target: x86_64-apple-darwin14.5.0
Thread model: posix
gcc version 5.2.0 (Homebrew gcc 5.2.0)
/usr/local/Cellar/gcc/5.2.0/libexec/gcc/x86_64-apple-darwin14.5.0/5.2.0/f951 conftest.f -ffixed-form -fPIC -feliminate-unused-debug-symbols -quiet -dumpbase conftest.f -mmacosx-version-min=10.10.5 -mtune=core2 -auxbase conftest -g -O2 -version -fno-automatic -finit-local-zero -ffixed-line-length-132 -fintrinsic-modules-path /usr/local/Cellar/gcc/5.2.0/lib/gcc/5/gcc/x86_64-apple-darwin14.5.0/5.2.0/finclude -o /var/folders/5d/tlqg90_x7l940r5gc8zrcw5h0000gn/T//ccgxBBjv.s
GNU Fortran (Homebrew gcc 5.2.0) version 5.2.0 (x86_64-apple-darwin14.5.0)
compiled by GNU C version 5.2.0, GMP version 6.0.0, MPFR version 3.1.3-p2, MPC version 1.0.3
GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072
GNU Fortran2008 (Homebrew gcc 5.2.0) version 5.2.0 (x86_64-apple-darwin14.5.0)
compiled by GNU C version 5.2.0, GMP version 6.0.0, MPFR version 3.1.3-p2, MPC version 1.0.3
GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072
as -arch x86_64 -force_cpusubtype_ALL -o /var/folders/5d/tlqg90_x7l940r5gc8zrcw5h0000gn/T//ccZopDof.o /var/folders/5d/tlqg90_x7l940r5gc8zrcw5h0000gn/T//ccgxBBjv.s
Reading specs from /usr/local/Cellar/gcc/5.2.0/lib/gcc/5/gcc/x86_64-apple-darwin14.5.0/5.2.0/…/…/…/libgfortran.spec
rename spec lib to liborig
/usr/local/Cellar/gcc/5.2.0/libexec/gcc/x86_64-apple-darwin14.5.0/5.2.0/collect2 -dynamic -arch x86_64 -macosx_version_min 10.10.5 -syslibroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk -weak_reference_mismatches non-weak -o conftest -L/usr/local/Cellar/gcc/5.2.0/lib/gcc/5/gcc/x86_64-apple-darwin14.5.0/5.2.0 -L/usr/local/Cellar/gcc/5.2.0/lib/gcc/5/gcc/x86_64-apple-darwin14.5.0/5.2.0/…/…/… /var/folders/5d/tlqg90_x7l940r5gc8zrcw5h0000gn/T//ccZopDof.o -lgfortran -no_compact_unwind -lSystem -lgcc_ext.10.5 -lgcc -lquadmath -lm -lgcc_ext.10.5 -lgcc -lSystem -v -idsym -dsym
collect2 version 5.2.0
/usr/bin/ld -dynamic -arch x86_64 -macosx_version_min 10.10.5 -syslibroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk -weak_reference_mismatches non-weak -o conftest -L/usr/local/Cellar/gcc/5.2.0/lib/gcc/5/gcc/x86_64-apple-darwin14.5.0/5.2.0 -L/usr/local/Cellar/gcc/5.2.0/lib/gcc/5/gcc/x86_64-apple-darwin14.5.0/5.2.0/…/…/… /var/folders/5d/tlqg90_x7l940r5gc8zrcw5h0000gn/T//ccZopDof.o -lgfortran -no_compact_unwind -lSystem -lgcc_ext.10.5 -lgcc -lquadmath -lm -lgcc_ext.10.5 -lgcc -lSystem -v
@(#)PROGRAM:ld PROJECT:ld64-253.9
configured to support archs: armv6 armv7 armv7s arm64 i386 x86_64 x86_64h armv6m armv7k armv7m armv7em (tvOS)
Library search paths:
/usr/local/Cellar/gcc/5.2.0/lib/gcc/5/gcc/x86_64-apple-darwin14.5.0/5.2.0
/usr/local/Cellar/gcc/5.2.0/lib/gcc/5
Framework search paths:
ld: library not found for -lSystem
collect2: error: ld returned 1 exit status
configure:4593: result: -L/usr/local/Cellar/gcc/5.2.0/lib/gcc/5/gcc/x86_64-apple-darwin14.5.0/5.2.0 -L/usr/local/Cellar/gcc/5.2.0/lib/gcc/5/gcc/x86_64-apple-darwin14.5.0/5.2.0/…/…/… -lgfortran -lquadmath -lm
configure:4624: checking for root-config
configure:4642: found /Users/zakig/Documents/root/bin/root-config
configure:4655: result: /Users/zakig/Documents/root/bin/root-config
configure:4665: checking for root
configure:4683: found /Users/zakig/Documents/root/bin/root
configure:4696: result: /Users/zakig/Documents/root/bin/root
configure:4706: checking for rootcint
configure:4724: found /Users/zakig/Documents/root/bin/rootcint
configure:4737: result: /Users/zakig/Documents/root/bin/rootcint
configure:4760: checking wether ROOT version >= 3.03
configure:4769: result: yes
configure:4803: checking whether to make debug objects
configure:4828: result: 'CFLAGS=-g -O2’
configure:4841: checking for optimiztion level
configure:4866: result: 'CFLAGS=-g -O2’
configure:4871: checking for perl
configure:4889: found /usr/bin/perl
configure:4901: result: /usr/bin/perl
configure:4911: checking for doxygen
configure:4944: result: no
configure:4961: checking for dot
configure:4994: result: no
configure:5006: checking for doxygen
configure:5039: result: no
configure:5203: checking that generated files are newer than configure
configure:5209: result: done
configure:5244: creating ./config.status

----------------------

Running config.status.

----------------------

This file was extended by ROOT interface to Hijing config.status 1.7, which was
generated by GNU Autoconf 2.69. Invocation command line was

CONFIG_FILES =
CONFIG_HEADERS =
CONFIG_LINKS =
CONFIG_COMMANDS =
$ ./config.status

on Zakis-MacBook-Pro.local

config.status:817: creating Makefile
config.status:817: creating .rootrc
config.status:817: creating libroot-hijing/Makefile
config.status:817: creating example/Makefile
config.status:817: creating doc/Makefile
config.status:817: creating doc/header.html
config.status:817: creating doc/doxyconfig
config.status:989: executing depfiles commands

----------------

Cache variables.

----------------

ac_cv_build=i386-apple-darwin14.5.0
ac_cv_c_compiler_gnu=yes
ac_cv_cxx_compiler_gnu=yes
ac_cv_env_CCC_set=
ac_cv_env_CCC_value=
ac_cv_env_CC_set=
ac_cv_env_CC_value=
ac_cv_env_CFLAGS_set=
ac_cv_env_CFLAGS_value=
ac_cv_env_CPPFLAGS_set=
ac_cv_env_CPPFLAGS_value=
ac_cv_env_CXXFLAGS_set=
ac_cv_env_CXXFLAGS_value=
ac_cv_env_CXX_set=
ac_cv_env_CXX_value=
ac_cv_env_DOXYGEN_set=
ac_cv_env_DOXYGEN_value=
ac_cv_env_F77_set=
ac_cv_env_F77_value=
ac_cv_env_FFLAGS_set=
ac_cv_env_FFLAGS_value=
ac_cv_env_LDFLAGS_set=
ac_cv_env_LDFLAGS_value=
ac_cv_env_LIBS_set=
ac_cv_env_LIBS_value=
ac_cv_env_build_alias_set=
ac_cv_env_build_alias_value=
ac_cv_env_host_alias_set=
ac_cv_env_host_alias_value=
ac_cv_env_target_alias_set=
ac_cv_env_target_alias_value=
ac_cv_f77_compiler_gnu=yes
ac_cv_f77_libs=’ -L/usr/local/Cellar/gcc/5.2.0/lib/gcc/5/gcc/x86_64-apple-darwin14.5.0/5.2.0 -L/usr/local/Cellar/gcc/5.2.0/lib/gcc/5/gcc/x86_64-apple-darwin14.5.0/5.2.0/…/…/… -lgfortran -lquadmath -lm’
ac_cv_host=i386-apple-darwin14.5.0
ac_cv_objext=o
ac_cv_path_PERL=/usr/bin/perl
ac_cv_path_ROOTCINT=/Users/zakig/Documents/root/bin/rootcint
ac_cv_path_ROOTCONF=/Users/zakig/Documents/root/bin/root-config
ac_cv_path_ROOTEXEC=/Users/zakig/Documents/root/bin/root
ac_cv_path_install=’/usr/bin/install -c’
ac_cv_prog_AWK=awk
ac_cv_prog_ac_ct_CC=gcc
ac_cv_prog_ac_ct_CXX=g++
ac_cv_prog_ac_ct_F77=gfortran
ac_cv_prog_cc_c89=
ac_cv_prog_cc_g=yes
ac_cv_prog_cxx_g=yes
ac_cv_prog_f77_g=yes
ac_cv_prog_f77_v=-v
ac_cv_prog_make_make_set=yes
am_cv_CC_dependencies_compiler_type=gcc3
am_cv_CXX_dependencies_compiler_type=gcc3
am_cv_make_support_nested_variables=yes
am_cv_prog_cc_c_o=yes

-----------------

Output variables.

-----------------

ACLOCAL=‘aclocal-1.15’
AMDEPBACKSLASH=’‘
AMDEP_FALSE=’#‘
AMDEP_TRUE=’‘
AMTAR=’$${TAR-tar}‘
AM_BACKSLASH=’‘
AM_DEFAULT_V=’$(AM_DEFAULT_VERBOSITY)‘
AM_DEFAULT_VERBOSITY=‘1’
AM_V=’$(V)‘
AUTOCONF=‘autoconf’
AUTOHEADER=‘autoheader’
AUTOMAKE=‘automake-1.15’
AWK=‘awk’
CC=‘gcc’
CCDEPMODE=‘depmode=gcc3’
CFLAGS=’-g -O2’
CPPFLAGS=’‘
CXX=‘g++‘
CXXDEPMODE=‘depmode=gcc3’
CXXFLAGS=’-g -O2’
CYGPATH_W=‘echo’
DEFS=’-DPACKAGE_NAME=“ROOT\ interface\ to\ Hijing” -DPACKAGE_TARNAME=“libroot-hijing” -DPACKAGE_VERSION=“1.7” -DPACKAGE_STRING=“ROOT\ interface\ to\ Hijing\ 1.7” -DPACKAGE_BUGREPORT="cholm@nbi.dk" -DPACKAGE_URL="" -DPACKAGE=“libroot-hijing” -DVERSION=“1.7”‘
DEPDIR=’.deps’
DOC_KEYWORDS=‘ROOT,TGenerator,Hijing,THijing,Event,Generator’
DOT=’‘
DOT_PATH=’‘
DOXYGEN=’‘
ECHO_C=’\c’
ECHO_N=’‘
ECHO_T=’‘
EXEEXT=’‘
F77=‘gfortran’
FFLAGS=’-g -O2 -fno-automatic -finit-local-zero -ffixed-line-length-132’
FLIBS=’ -L/usr/local/Cellar/gcc/5.2.0/lib/gcc/5/gcc/x86_64-apple-darwin14.5.0/5.2.0 -L/usr/local/Cellar/gcc/5.2.0/lib/gcc/5/gcc/x86_64-apple-darwin14.5.0/5.2.0/…/…/… -lgfortran -lquadmath -lm’
HAVE_DOT=‘NO’
HAVE_DOXYGEN_FALSE=’‘
HAVE_DOXYGEN_TRUE=’#‘
INSTALL_DATA=’${INSTALL} -m 644’
INSTALL_PROGRAM=’${INSTALL}‘
INSTALL_SCRIPT=’${INSTALL}‘
INSTALL_STRIP_PROGRAM=’$(install_sh) -c -s’
LDFLAGS=’‘
LIBOBJS=’‘
LIBS=’‘
LTLIBOBJS=’‘
MAKEINFO=‘makeinfo’
MKDIR_P=‘config/install-sh -c -d’
OBJEXT=‘o’
PACKAGE=‘libroot-hijing’
PACKAGE_BUGREPORT=‘cholm@nbi.dk’
PACKAGE_NAME=‘ROOT interface to Hijing’
PACKAGE_STRING=‘ROOT interface to Hijing 1.7’
PACKAGE_TARNAME=‘libroot-hijing’
PACKAGE_URL=’‘
PACKAGE_VERSION=‘1.7’
PATH_SEPARATOR=’:‘
PERL=’/usr/bin/perl’
ROOTAUXCFLAGS=’-pthread -stdlib=libc++ -std=c++11 -m64’
ROOTAUXLIBS=’-lpthread -stdlib=libc++ -lm -ldl’
ROOTCFLAGS=’-I/Users/zakig/Documents/root/include’
ROOTCINT=’/Users/zakig/Documents/root/bin/rootcint’
ROOTCONF=’/Users/zakig/Documents/root/bin/root-config’
ROOTEXEC=’/Users/zakig/Documents/root/bin/root’
ROOTGLIBS=’-lGui -lCore -lRIO -lNet -lHist -lGraf -lGraf3d -lGpad -lTree -lRint -lPostscript -lMatrix -lPhysics -lMathCore -lThread’
ROOTINCDIR=’/Users/zakig/Documents/root/include’
ROOTLIBDIR=’/Users/zakig/Documents/root/lib’
ROOTLIBS=’-lCore -lRIO -lNet -lHist -lGraf -lGraf3d -lGpad -lTree -lRint -lPostscript -lMatrix -lPhysics -lMathCore -lThread’
ROOTPLUGINDIR=’/Users/zakig/Documents/root/lib’
ROOTRPATH=’/Users/zakig/Documents/root/lib’
SET_MAKE=’‘
SHELL=’/bin/sh’
STRIP=’‘
VERSION=‘1.7’
ac_ct_CC=‘gcc’
ac_ct_CXX=‘g++‘
ac_ct_F77=‘gfortran’
am__EXEEXT_FALSE=’‘
am__EXEEXT_TRUE=’#‘
am__fastdepCC_FALSE=’#‘
am__fastdepCC_TRUE=’‘
am__fastdepCXX_FALSE=’#‘
am__fastdepCXX_TRUE=’‘
am__include=‘include’
am__isrc=’‘
am__leading_dot=’.‘
am__nodep=’_no’
am__quote=’‘
am__tar=’$${TAR-tar} chof - “$$tardir”‘
am__untar=’$${TAR-tar} xf -‘
bindir=’${exec_prefix}/bin’
build=‘i386-apple-darwin14.5.0’
build_alias=’‘
build_cpu=‘i386’
build_os=‘darwin14.5.0’
build_vendor=‘apple’
datadir=’${datarootdir}‘
datarootdir=’${prefix}/share’
docdir=’${datarootdir}/doc/${PACKAGE_TARNAME}‘
dvidir=’${docdir}‘
exec_prefix=’${prefix}‘
host=‘i386-apple-darwin14.5.0’
host_alias=’‘
host_cpu=‘i386’
host_os=‘darwin14.5.0’
host_vendor=‘apple’
htmldir=’${docdir}‘
includedir=’${prefix}/include’
infodir=’${datarootdir}/info’
install_sh=’${SHELL} /Users/zakig/Desktop/libroot-hijing-1.7/config/install-sh’
libdir=’${exec_prefix}/lib’
libexecdir=’${exec_prefix}/libexec’
localedir=’${datarootdir}/locale’
localstatedir=’${prefix}/var’
mandir=’${datarootdir}/man’
mkdir_p=’$(MKDIR_P)‘
oldincludedir=’/usr/include’
pdfdir=’${docdir}‘
prefix=’/Users/zakig’
program_transform_name=‘s,x,x,‘
psdir=’${docdir}‘
sbindir=’${exec_prefix}/sbin’
sharedstatedir=’${prefix}/com’
sysconfdir=’${prefix}/etc’
target_alias=’’

-----------

confdefs.h.

-----------

/* confdefs.h */
#define PACKAGE_NAME “ROOT interface to Hijing”
#define PACKAGE_TARNAME “libroot-hijing”
#define PACKAGE_VERSION “1.7”
#define PACKAGE_STRING “ROOT interface to Hijing 1.7”
#define PACKAGE_BUGREPORT "cholm@nbi.dk"
#define PACKAGE_URL “”
#define PACKAGE “libroot-hijing”
#define VERSION “1.7”

configure: exit 0
[/code]

I was facing the same issue. The problem lies in not using C++11 by default.

For fixing this, try the following.

  1. Download both these files. http://www.gnu.org/software/autoconf-archive/ax_cxx_compile_stdcxx.html and http://www.gnu.org/software/autoconf-archive/ax_cxx_compile_stdcxx_11.html.

  2. Add to configure.ac.AX_CXX_COMPILE_STDCXX_11

  3. Run autoconf -f ./configure make make install

I hope this works.

Cheers,
Ankit