[MOAB-dev] MOAB check for *x86* failed.

[Nightly Test]

configure: WARNING: unknown Fortran name-mangling scheme
../src/cub_file_test.cc: In function ‘void test_vertices()’:
../src/cub_file_test.cc:197: error: ‘sort’ is not a member of ‘std’
../src/cub_file_test.cc: In function ‘void test_element(const char*, MBEntityType, int, int, const int*)’:
../src/cub_file_test.cc:237: error: ‘sort’ is not a member of ‘std’
../src/cub_file_test.cc: In function ‘int check_geometric_set(MBInterface&, int, int, const int*, int, std::vector<int, std::allocator<int> >)’:
../src/cub_file_test.cc:455: error: ‘sort’ is not a member of ‘std’
../src/cub_file_test.cc:462: error: ‘sort’ is not a member of ‘std’
../src/cub_file_test.cc:468: error: ‘sort’ is not a member of ‘std’
../src/cub_file_test.cc:475: error: ‘sort’ is not a member of ‘std’
make[2]: *** [cub_file_test.o] Error 1
make[2]: *** Waiting for unfinished jobs....
make[1]: *** [check-am] Error 2
make: *** [check-recursive] Error 1
suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether cc accepts -g... yes
checking for cc option to accept ISO C89... none needed
checking dependency style of cc... gcc3
checking how to run the C preprocessor... cc -E
checking for CC... no
checking for aCC... no
checking for cxx... no
checking for xlC_r... no
checking for xlC... no
checking for c++... c++
checking whether we are using the GNU C++ compiler... yes
checking whether c++ accepts -g... yes
checking dependency style of c++... gcc3
checking how to run the C++ preprocessor... c++ -E
checking for gfortran... gfortran
checking whether we are using the GNU Fortran compiler... yes
checking whether gfortran accepts -g... yes
checking for gfortran... gfortran
checking whether we are using the GNU Fortran 77 compiler... yes
checking whether gfortran accepts -g... yes
checking for known C compilers... GNU
checking for known compiler/OS combinations... GNU:x86_64
checking for known c++ compilers... GNU
checking for known compiler/OS combinations... GNU:x86_64
checking whether ln -s works... yes
checking whether make sets $(MAKE)... (cached) yes
checking for a sed that does not truncate output... /bin/sed
checking for grep that handles long lines and -e... /bin/grep
checking for egrep... /bin/grep -E
checking for ld used by cc... /usr/bin/ld
checking if the linker (/usr/bin/ld) is GNU ld... yes
checking for /usr/bin/ld option to reload object files... -r
checking for BSD-compatible nm... /usr/bin/nm -B
checking how to recognize dependent libraries... pass_all
checking for ANSI C header files... yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking dlfcn.h usability... yes
checking dlfcn.h presence... yes
checking for dlfcn.h... yes
checking how to run the C++ preprocessor... c++ -E
checking the maximum length of command line arguments... 98304
checking command to parse /usr/bin/nm -B output from cc object... ok
checking for objdir... .libs
checking for ar... ar
checking for ranlib... ranlib
checking for strip... strip
checking if cc supports -fno-rtti -fno-exceptions... no
checking for cc option to produce PIC... -fPIC
checking if cc PIC flag -fPIC works... yes
checking if cc static flag -static works... yes
checking if cc supports -c -o file.o... yes
checking whether the cc linker (/usr/bin/ld -m elf_i386) supports shared libraries... yes
checking dynamic linker characteristics... GNU/Linux ld.so
checking how to hardcode library paths into programs... immediate
checking whether stripping libraries is possible... yes
checking if libtool supports shared libraries... yes
checking whether to build shared libraries... no
checking whether to build static libraries... yes
configure: creating libtool
appending configuration tag "CXX" to libtool
checking for ld used by c++... /usr/bin/ld -m elf_i386
checking if the linker (/usr/bin/ld -m elf_i386) is GNU ld... yes
checking whether the c++ linker (/usr/bin/ld -m elf_i386) supports shared libraries... yes
checking for c++ option to produce PIC... -fPIC
checking if c++ PIC flag -fPIC works... yes
checking if c++ static flag -static works... yes
checking if c++ supports -c -o file.o... yes
checking whether the c++ linker (/usr/bin/ld -m elf_i386) supports shared libraries... yes
checking dynamic linker characteristics... GNU/Linux ld.so
(cached) (cached) checking how to hardcode library paths into programs... immediate
appending configuration tag "F77" to libtool
checking if libtool supports shared libraries... yes
checking whether to build shared libraries... no
checking whether to build static libraries... yes
checking for gfortran option to produce PIC... -fPIC
checking if gfortran PIC flag -fPIC works... yes
checking if gfortran static flag -static works... yes
checking if gfortran supports -c -o file.o... yes
checking whether the gfortran linker (/usr/bin/ld -m elf_i386) supports shared libraries... yes
checking dynamic linker characteristics... GNU/Linux ld.so
(cached) (cached) checking how to hardcode library paths into programs... immediate
checking for gunzip... gunzip -c
checking for gzip... (cached) gunzip -c
checking for zcat... (cached) gunzip -c
checking if C++ compiler supports template specialization... yes
checking how to get verbose linking output from gfortran... -v
checking for Fortran libraries of gfortran...  -L/usr/lib/gcc/x86_64-linux-gnu/4.3.1 -L/usr/lib/gcc/x86_64-linux-gnu/4.3.1/../../../../lib -L/lib/../lib -L/usr/lib/../lib -L/usr/lib/gcc/x86_64-linux-gnu/4.3.1/../../.. -lgfortranbegin -lgfortran -lm
checking for dummy main to link with Fortran libraries... none
checking for Fortran name-mangling scheme... unknown
checking for inttypes.h... (cached) yes
checking for stdint.h... (cached) yes
checking for sys/types.h... (cached) yes
checking stddef.h usability... yes
checking stddef.h presence... yes
checking for stddef.h... yes
checking for stdlib.h... (cached) yes
checking for size_t... yes
checking for ptrdiff_t... yes
checking ieeefp.h usability... no
checking ieeefp.h presence... no
checking for ieeefp.h... no
checking valgrind/memcheck.h usability... yes
checking valgrind/memcheck.h presence... yes
checking for valgrind/memcheck.h... yes
checking for deflate in -lz... yes
checking for SZ_Decompress in -lsz... no
checking if HDF5 support is enabled... yes
checking hdf5.h usability... yes
checking hdf5.h presence... yes
checking for hdf5.h... yes
checking for H5Fopen in -lhdf5... yes
checking if NetCDF support is enabled... yes
checking strstream.h usability... no
checking strstream.h presence... no
checking for strstream.h... no
checking sstream.h usability... no
checking sstream.h presence... no
checking for sstream.h... no
checking strstream usability... yes
checking strstream presence... yes
checking for strstream... yes
checking netcdf.h usability... yes
checking netcdf.h presence... yes
checking for netcdf.h... yes
checking for netcdf.hh... yes
checking for netcdf_c++ library... yes
checking if mbconvert is to be built... yes
checking if hexmodops is to be built... yes
checking if mbchaco is to be built... no
checking if mbperf is to be built... yes
checking if qvdual is to be built... no
checking if mbsize is to be built... yes
checking if mbskin is to be built... yes
checking if mbtagprop is to be built... yes
checking if mcnpmit is to be built... no
checking if mbcoupler is to be built... no
checking if spheredecomp is to be built... yes
checking if mbsurfplot is to be built... yes
checking if mbzoltan is to be built... no
checking if dagmc is to be built... yes
checking if iMesh support is to be built... yes
checking for /opt/babel-0.10.10-32-c2/bin/babel... yes
configure: creating ./config.status
C:   cc  -Wall -pipe -g -m32
C++: c++  -Wall -pipe -g -m32
Fortran: gfortran -g -O2 -g
 /bin/sh ./config.status
config.status: creating Makefile
config.status: creating moab.make
config.status: creating testdir.h
config.status: creating parallel/Makefile
config.status: creating mhdf/Makefile
config.status: creating test/Makefile
config.status: creating test/h5file/Makefile
config.status: creating test/dual/Makefile
config.status: creating test/obb/Makefile
config.status: creating test/perf/Makefile
config.status: creating tools/Makefile
config.status: creating tools/converter/Makefile
config.status: creating tools/hexmodops/Makefile
config.status: creating tools/iMesh/Makefile
config.status: creating tools/iMesh/iMesh-Defs.inc
config.status: creating tools/iMesh/SIDL/iMesh-SIDL-Defs.inc
config.status: creating tools/iMesh/SIDL/Makefile
config.status: creating tools/iMesh/SIDL/common.make
config.status: creating tools/mbperf/Makefile
config.status: creating tools/mbchaco/Makefile
config.status: creating tools/mbcoupler/Makefile
config.status: creating tools/mbzoltan/Config.moab
config.status: creating tools/mbzoltan/Makefile
config.status: creating tools/mcnpmit/Makefile
config.status: creating tools/qvdual/Makefile
config.status: creating tools/size/Makefile
config.status: creating tools/skin/Makefile
config.status: creating tools/tagprop/Makefile
config.status: creating tools/spheredecomp/Makefile
config.status: creating tools/surfplot/Makefile
config.status: creating tools/dagmc/Makefile
config.status: creating tools/dagmc/dagmc.make
config.status: creating doc/Makefile
config.status: creating doxygen/Makefile
config.status: creating config.h
config.status: config.h is unchanged
config.status: creating MBVersion.h
config.status: MBVersion.h is unchanged
config.status: creating MBEntityHandle.h
config.status: MBEntityHandle.h is unchanged
config.status: creating MBCN_FCDefs.h
config.status: MBCN_FCDefs.h is unchanged
config.status: executing depfiles commands
make  all-recursive
make[1]: Entering directory `/home/jason/moab/test/x86'
Making all in mhdf
make[2]: Entering directory `/home/jason/moab/test/x86/mhdf'
make[2]: Nothing to be done for `all'.
make[2]: Leaving directory `/home/jason/moab/test/x86/mhdf'
Making all in .
make[2]: Entering directory `/home/jason/moab/test/x86'
make[2]: Leaving directory `/home/jason/moab/test/x86'
Making all in test
make[2]: Entering directory `/home/jason/moab/test/x86/test'
Making all in dual
make[3]: Entering directory `/home/jason/moab/test/x86/test/dual'
make[3]: Nothing to be done for `all'.
make[3]: Leaving directory `/home/jason/moab/test/x86/test/dual'
Making all in h5file
make[3]: Entering directory `/home/jason/moab/test/x86/test/h5file'
make[3]: Nothing to be done for `all'.
make[3]: Leaving directory `/home/jason/moab/test/x86/test/h5file'
Making all in obb
make[3]: Entering directory `/home/jason/moab/test/x86/test/obb'
make[3]: Nothing to be done for `all'.
make[3]: Leaving directory `/home/jason/moab/test/x86/test/obb'
Making all in perf
make[3]: Entering directory `/home/jason/moab/test/x86/test/perf'
make[3]: Nothing to be done for `all'.
make[3]: Leaving directory `/home/jason/moab/test/x86/test/perf'
make[3]: Entering directory `/home/jason/moab/test/x86/test'
make[3]: Nothing to be done for `all-am'.
make[3]: Leaving directory `/home/jason/moab/test/x86/test'
make[2]: Leaving directory `/home/jason/moab/test/x86/test'
Making all in tools
make[2]: Entering directory `/home/jason/moab/test/x86/tools'
Making all in iMesh
make[3]: Entering directory `/home/jason/moab/test/x86/tools/iMesh'
Making all in .
make[4]: Entering directory `/home/jason/moab/test/x86/tools/iMesh'
make[4]: Nothing to be done for `all-am'.
make[4]: Leaving directory `/home/jason/moab/test/x86/tools/iMesh'
Making all in SIDL
make[4]: Entering directory `/home/jason/moab/test/x86/tools/iMesh/SIDL'
if test "xyes" = "xyes"; then \
	  (cd mserver && make -f ../../../../../src/tools/iMesh/SIDL/mserver.make all) && \
	  (cd Cclient && make -f ../../../../../src/tools/iMesh/SIDL/Cclient.make all) && \
	  (cd Fclient && make -f ../../../../../src/tools/iMesh/SIDL/Fclient.make all) ; \
	fi
make[5]: Entering directory `/home/jason/moab/test/x86/tools/iMesh/SIDL/mserver'
make[5]: Nothing to be done for `all'.
make[5]: Leaving directory `/home/jason/moab/test/x86/tools/iMesh/SIDL/mserver'
make[5]: Entering directory `/home/jason/moab/test/x86/tools/iMesh/SIDL/Cclient'
make[5]: Nothing to be done for `all'.
make[5]: Leaving directory `/home/jason/moab/test/x86/tools/iMesh/SIDL/Cclient'
make[5]: Entering directory `/home/jason/moab/test/x86/tools/iMesh/SIDL/Fclient'
make[5]: Nothing to be done for `all'.
make[5]: Leaving directory `/home/jason/moab/test/x86/tools/iMesh/SIDL/Fclient'
make[4]: Leaving directory `/home/jason/moab/test/x86/tools/iMesh/SIDL'
make[3]: Leaving directory `/home/jason/moab/test/x86/tools/iMesh'
Making all in converter
make[3]: Entering directory `/home/jason/moab/test/x86/tools/converter'
make[3]: Nothing to be done for `all'.
make[3]: Leaving directory `/home/jason/moab/test/x86/tools/converter'
Making all in hexmodops
make[3]: Entering directory `/home/jason/moab/test/x86/tools/hexmodops'
make[3]: Nothing to be done for `all'.
make[3]: Leaving directory `/home/jason/moab/test/x86/tools/hexmodops'
Making all in mbperf
make[3]: Entering directory `/home/jason/moab/test/x86/tools/mbperf'
make[3]: Nothing to be done for `all'.
make[3]: Leaving directory `/home/jason/moab/test/x86/tools/mbperf'
Making all in size
make[3]: Entering directory `/home/jason/moab/test/x86/tools/size'
make[3]: Nothing to be done for `all'.
make[3]: Leaving directory `/home/jason/moab/test/x86/tools/size'
Making all in skin
make[3]: Entering directory `/home/jason/moab/test/x86/tools/skin'
make[3]: Nothing to be done for `all'.
make[3]: Leaving directory `/home/jason/moab/test/x86/tools/skin'
Making all in tagprop
make[3]: Entering directory `/home/jason/moab/test/x86/tools/tagprop'
make[3]: Nothing to be done for `all'.
make[3]: Leaving directory `/home/jason/moab/test/x86/tools/tagprop'
Making all in spheredecomp
make[3]: Entering directory `/home/jason/moab/test/x86/tools/spheredecomp'
make[3]: Nothing to be done for `all'.
make[3]: Leaving directory `/home/jason/moab/test/x86/tools/spheredecomp'
Making all in surfplot
make[3]: Entering directory `/home/jason/moab/test/x86/tools/surfplot'
make[3]: Nothing to be done for `all'.
make[3]: Leaving directory `/home/jason/moab/test/x86/tools/surfplot'
Making all in dagmc
make[3]: Entering directory `/home/jason/moab/test/x86/tools/dagmc'
make[3]: Nothing to be done for `all'.
make[3]: Leaving directory `/home/jason/moab/test/x86/tools/dagmc'
make[3]: Entering directory `/home/jason/moab/test/x86/tools'
make[3]: Nothing to be done for `all-am'.
make[3]: Leaving directory `/home/jason/moab/test/x86/tools'
make[2]: Leaving directory `/home/jason/moab/test/x86/tools'
Making all in doc
make[2]: Entering directory `/home/jason/moab/test/x86/doc'
make[2]: Nothing to be done for `all'.
make[2]: Leaving directory `/home/jason/moab/test/x86/doc'
Making all in doxygen
make[2]: Entering directory `/home/jason/moab/test/x86/doxygen'
make[2]: Nothing to be done for `all'.
make[2]: Leaving directory `/home/jason/moab/test/x86/doxygen'
make[1]: Leaving directory `/home/jason/moab/test/x86'
Making check in mhdf
make[1]: Entering directory `/home/jason/moab/test/x86/mhdf'
make[1]: Nothing to be done for `check'.
make[1]: Leaving directory `/home/jason/moab/test/x86/mhdf'
Making check in .
make[1]: Entering directory `/home/jason/moab/test/x86'
make  moab_test homxform_test scdseq_test tqdcfr test_adj seq_man_test geom_util_test xform_test obb_test vtk_test adaptive_kd_tree_tests bsp_tree_test file_options_test kd_tree_test var_len_test var_len_test_no_template tag_test mesh_set_test cub_file_test kd_tree_tool kd_tree_time
make[2]: Entering directory `/home/jason/moab/test/x86'
c++ -DTEMPLATE_SPECIALIZATION -DHDF5_FILE -DNETCDF_FILE -DNETCDF_FILE -DIS_BUILDING_MB -I. -I../src -I. -I../src/mhdf/include  -I/opt/netcdf-3.6.1-32-c2/include  -I/opt/hdf5-1.6.5-32-c2/include  -DVALGRIND -DSRCDIR=../src -DTEST_TQDCFR -Wall -pipe -g -m32 -Wall -pipe -g -m32 -MT tqdcfr-Tqdcfr.o -MD -MP -MF .deps/tqdcfr-Tqdcfr.Tpo -c -o tqdcfr-Tqdcfr.o `test -f 'Tqdcfr.cpp' || echo '../src/'`Tqdcfr.cpp
c++ -DTEMPLATE_SPECIALIZATION -DHDF5_FILE -DNETCDF_FILE -DNETCDF_FILE -DIS_BUILDING_MB -I. -I../src -I. -I../src/mhdf/include  -I/opt/netcdf-3.6.1-32-c2/include  -I/opt/hdf5-1.6.5-32-c2/include  -DVALGRIND -DSRCDIR=../src  -Wall -pipe -g -m32 -MT TestTypeSequenceManager.o -MD -MP -MF .deps/TestTypeSequenceManager.Tpo -c -o TestTypeSequenceManager.o ../src/TestTypeSequenceManager.cpp
c++ -DTEMPLATE_SPECIALIZATION -DHDF5_FILE -DNETCDF_FILE -DNETCDF_FILE -DIS_BUILDING_MB -I. -I../src -I. -I../src/mhdf/include  -I/opt/netcdf-3.6.1-32-c2/include  -I/opt/hdf5-1.6.5-32-c2/include  -DVALGRIND -DSRCDIR=../src  -Wall -pipe -g -m32 -MT GeomUtilTests.o -MD -MP -MF .deps/GeomUtilTests.Tpo -c -o GeomUtilTests.o ../src/GeomUtilTests.cpp
c++ -DTEMPLATE_SPECIALIZATION -DHDF5_FILE -DNETCDF_FILE -DNETCDF_FILE -DIS_BUILDING_MB -I. -I../src -I. -I../src/mhdf/include  -I/opt/netcdf-3.6.1-32-c2/include  -I/opt/hdf5-1.6.5-32-c2/include  -DVALGRIND -DSRCDIR=../src  -Wall -pipe -g -m32 -MT bsp_tree_test.o -MD -MP -MF .deps/bsp_tree_test.Tpo -c -o bsp_tree_test.o ../src/bsp_tree_test.cpp
make[2]: `file_options_test' is up to date.
c++ -DTEMPLATE_SPECIALIZATION -DHDF5_FILE -DNETCDF_FILE -DNETCDF_FILE -DIS_BUILDING_MB -I. -I../src -I. -I../src/mhdf/include  -I/opt/netcdf-3.6.1-32-c2/include  -I/opt/hdf5-1.6.5-32-c2/include  -DVALGRIND -DSRCDIR=../src  -Wall -pipe -g -m32 -MT VarLenTagTest.o -MD -MP -MF .deps/VarLenTagTest.Tpo -c -o VarLenTagTest.o ../src/VarLenTagTest.cpp
c++ -DTEMPLATE_SPECIALIZATION -DHDF5_FILE -DNETCDF_FILE -DNETCDF_FILE -DIS_BUILDING_MB -I. -I../src -I. -I../src/mhdf/include  -UTEMPLATE_SPECIALIZATION -DVALGRIND -DSRCDIR=../src  -Wall -pipe -g -m32 -MT var_len_test_no_template-VarLenTagTest.o -MD -MP -MF .deps/var_len_test_no_template-VarLenTagTest.Tpo -c -o var_len_test_no_template-VarLenTagTest.o `test -f 'VarLenTagTest.cpp' || echo '../src/'`VarLenTagTest.cpp
c++ -DTEMPLATE_SPECIALIZATION -DHDF5_FILE -DNETCDF_FILE -DNETCDF_FILE -DIS_BUILDING_MB -I. -I../src -I. -I../src/mhdf/include  -I/opt/netcdf-3.6.1-32-c2/include  -I/opt/hdf5-1.6.5-32-c2/include  -DVALGRIND -DSRCDIR=../src  -Wall -pipe -g -m32 -MT TagTest.o -MD -MP -MF .deps/TagTest.Tpo -c -o TagTest.o ../src/TagTest.cpp
c++ -DTEMPLATE_SPECIALIZATION -DHDF5_FILE -DNETCDF_FILE -DNETCDF_FILE -DIS_BUILDING_MB -I. -I../src -I. -I../src/mhdf/include  -I/opt/netcdf-3.6.1-32-c2/include  -I/opt/hdf5-1.6.5-32-c2/include  -DVALGRIND -DSRCDIR=../src  -Wall -pipe -g -m32 -MT Test_MBMeshSet.o -MD -MP -MF .deps/Test_MBMeshSet.Tpo -c -o Test_MBMeshSet.o ../src/Test_MBMeshSet.cpp
mv -f .deps/VarLenTagTest.Tpo .deps/VarLenTagTest.Po
c++ -DTEMPLATE_SPECIALIZATION -DHDF5_FILE -DNETCDF_FILE -DNETCDF_FILE -DIS_BUILDING_MB -I. -I../src -I. -I../src/mhdf/include  -I/opt/netcdf-3.6.1-32-c2/include  -I/opt/hdf5-1.6.5-32-c2/include  -DVALGRIND -DSRCDIR=../src  -Wall -pipe -g -m32 -MT cub_file_test.o -MD -MP -MF .deps/cub_file_test.Tpo -c -o cub_file_test.o ../src/cub_file_test.cc
mv -f .deps/var_len_test_no_template-VarLenTagTest.Tpo .deps/var_len_test_no_template-VarLenTagTest.Po
c++ -DTEMPLATE_SPECIALIZATION -DHDF5_FILE -DNETCDF_FILE -DNETCDF_FILE -DIS_BUILDING_MB -I. -I../src -I. -I../src/mhdf/include  -I/opt/netcdf-3.6.1-32-c2/include  -I/opt/hdf5-1.6.5-32-c2/include  -DVALGRIND -DSRCDIR=../src  -Wall -pipe -g -m32 -MT MBTest.o -MD -MP -MF .deps/MBTest.Tpo -c -o MBTest.o ../src/MBTest.cpp
make[2]: `homxform_test' is up to date.
make[2]: `scdseq_test' is up to date.
make[2]: `test_adj' is up to date.
make[2]: `xform_test' is up to date.
make[2]: `obb_test' is up to date.
make[2]: `vtk_test' is up to date.
make[2]: `adaptive_kd_tree_tests' is up to date.
make[2]: `kd_tree_test' is up to date.
mv -f .deps/bsp_tree_test.Tpo .deps/bsp_tree_test.Po
/bin/sh ./libtool --tag=CXX   --mode=link c++  -Wall -pipe -g -m32 -L/opt/netcdf-3.6.1-32-c2/lib   -L/opt/hdf5-1.6.5-32-c2/lib  -lm -o var_len_test VarLenTagTest.o  -lm
mv -f .deps/TestTypeSequenceManager.Tpo .deps/TestTypeSequenceManager.Po
mv -f .deps/GeomUtilTests.Tpo .deps/GeomUtilTests.Po
c++ -Wall -pipe -g -m32 -o var_len_test VarLenTagTest.o  -L/opt/netcdf-3.6.1-32-c2/lib -L/opt/hdf5-1.6.5-32-c2/lib -lm  
mv -f .deps/Test_MBMeshSet.Tpo .deps/Test_MBMeshSet.Po
mv -f .deps/TagTest.Tpo .deps/TagTest.Po
mv -f .deps/tqdcfr-Tqdcfr.Tpo .deps/tqdcfr-Tqdcfr.Po
mv -f .deps/MBTest.Tpo .deps/MBTest.Po
make[2]: Leaving directory `/home/jason/moab/test/x86'
make[1]: Leaving directory `/home/jason/moab/test/x86'