[MOAB-dev] Build failed in Jenkins: moab_serial #343

Thu Jun 12 16:15:53 CDT 2014

Please make sure to do a make check before commits. Failures in master
branch should not happen. If these are evolving commits part of a larger
feature addition, create a feature branch separately.

Vijay
On Jun 12, 2014 4:03 PM, <jenkins-ci at mcs.anl.gov> wrote:

> See <https://jenkins-ci.mcs.anl.gov/job/moab_serial/343/changes>
>
> Changes:
>
> [wuda] Renamed a few member functions of NCHelper classes (e.g.
> read_variable_setup => read_variables_setup).
>
> ------------------------------------------
> [...truncated 112 lines...]
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> checking whether the g++ linker (/usr/bin/ld -m elf_x86_64) supports
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> checking if g++ PIC flag -fPIC -DPIC works... yes
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> checking dynamic linker characteristics... (cached) GNU/Linux ld.so
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> checking dynamic linker characteristics... (cached) GNU/Linux ld.so
> checking how to hardcode library paths into programs... immediate
> checking for known C compilers... GNU
> checking for known compiler/OS combinations... GNU:x86_64
> checking for known c++ compilers... GNU
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> checking if g++ works... yes
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> checking for Fortran libraries of gfortran...
>  -L/usr/lib/gcc/x86_64-linux-gnu/4.6
> -L/usr/lib/gcc/x86_64-linux-gnu/4.6/../../../x86_64-linux-gnu
> -L/usr/lib/gcc/x86_64-linux-gnu/4.6/../../../../lib -L/lib/x86_64-linux-gnu
> -L/lib/../lib -L/usr/lib/x86_64-linux-gnu -L/usr/lib/../lib
> -L/usr/lib/gcc/x86_64-linux-gnu/4.6/../../.. -lgfortran -lm -lquadmath
> checking for dummy main to link with Fortran libraries... none
> checking for Fortran name-mangling scheme... lower case, underscore, no
> extra underscore
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> checking for Fortran 77 compiler flag for Cray-style pointer...
> -fcray-pointer
> checking whether Fortran 90 supports Cray-style pointer... yes
> checking for Fortran 90 compiler flag for Cray-style pointer...
> -fcray-pointer
> checking for vsnprintf... yes
> checking if std::vector has templatized insert method... yes
> checking if std::copy must be old SGI format... no
> checking for inttypes.h... (cached) yes
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> checking size of void *... 8
> checking for size_t... yes
> checking for ptrdiff_t... yes
> checking size of EntityHandle... 8
> checking if iMesh support is to be built... yes
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> configure: creating ./config.lt
> config.lt: creating libtool
> checking ieeefp.h usability... no
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> checking unsuccessful, Ccmio support disabled...
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> configure: WARNING: CGNS header not found.
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> configure: WARNING: "CGNS support disabled"
> checking for doxygen... /usr/bin/doxygen
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> configure: creating ./config.status
> config.status: creating Makefile
> config.status: creating moab.make
> config.status: creating MOABConfig.cmake
> config.status: creating src/Makefile
> config.status: creating src/io/Makefile
> config.status: creating src/io/mhdf/Makefile
> config.status: creating src/LocalDiscretization/Makefile
> config.status: creating src/parallel/Makefile
> config.status: creating src/oldinc/Makefile
> config.status: creating test/Makefile
> config.status: creating test/dagmc/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 test/perf/point_location/Makefile
> config.status: creating test/io/Makefile
> config.status: creating test/parallel/Makefile
> config.status: creating test/oldinc/Makefile
> config.status: creating itaps/iBase_f.h
> config.status: creating itaps/Makefile
> config.status: creating itaps/imesh/Makefile
> config.status: creating itaps/imesh/iMesh-Defs.inc
> config.status: creating itaps/igeom/Makefile
> config.status: creating itaps/igeom/FBiGeom-Defs.inc
> config.status: creating tools/Makefile
> config.status: creating tools/refiner/Makefile
> config.status: creating tools/mbcoupler/Makefile
> config.status: creating tools/mbcslam/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/dagmc/Makefile
> config.status: creating tools/vtkMOABReader/CMakeLists.txt
> config.status: creating tools/vtkMOABReaderNew/CMakeLists.txt
> config.status: creating doc/Makefile
> config.status: creating doc/user.dox
> config.status: creating doc/config.tex
> config.status: creating MeshFiles/Makefile
> config.status: creating MeshFiles/unittest/Makefile
> config.status: creating MeshFiles/unittest/io/Makefile
> config.status: creating MeshFiles/unittest/iGeom/Makefile
> config.status: creating MeshFiles/unittest/dagmc/Makefile
> config.status: creating config.h
> config.status: config.h is unchanged
> config.status: creating src/moab/Version.h
> config.status: src/moab/Version.h is unchanged
> config.status: creating src/moab/EntityHandle.hpp
> config.status: src/moab/EntityHandle.hpp is unchanged
> config.status: creating src/parallel/moab_mpi_config.h
> config.status: src/parallel/moab_mpi_config.h is unchanged
> config.status: creating src/FCDefs.h
> config.status: src/FCDefs.h is unchanged
> config.status: executing depfiles commands
> config.status: executing libtool commands
> config.status: executing src/MOAB_FCDefs.h commands
> C:   gcc  -Wall -pipe -pedantic -Wno-long-long -Wextra -Wcast-align
>  -Wpointer-arith -Wformat -Wformat-security -Wshadow -Wunused-parameter -O2
> -DNDEBUG  -DUNORDERED_MAP_NS=std::tr1
> -DHAVE_UNORDERED_MAP=tr1/unordered_map
> -DHAVE_UNORDERED_SET=tr1/unordered_set
> C++: g++  -Wall -pipe -pedantic -Wno-long-long -Wextra -Wcast-align
>  -Wpointer-arith -Wformat -Wformat-security -Wshadow -Wunused-parameter -O2
> -DNDEBUG  -DUNORDERED_MAP_NS=std::tr1
> -DHAVE_UNORDERED_MAP=tr1/unordered_map
> -DHAVE_UNORDERED_SET=tr1/unordered_set
> Fortran90: gfortran   -O2 -fcray-pointer
> Fortran77: f77   -O2 -fcray-pointer
> + make
> make  all-recursive
> make[1]: Entering directory `<
> https://jenkins-ci.mcs.anl.gov/job/moab_serial/ws/'>
> Making all in src
> make[2]: Entering directory `<
> https://jenkins-ci.mcs.anl.gov/job/moab_serial/ws/src'>
> (CDPATH="${ZSH_VERSION+.}:" && cd .. && /bin/sh <
> https://jenkins-ci.mcs.anl.gov/job/moab_serial/ws/config/missing> --run
> autoheader)
> rm -f stamp-h5
> touch FCDefs.h.in
> cd .. && /bin/sh ./config.status src/FCDefs.h
> config.status: creating src/FCDefs.h
> config.status: src/FCDefs.h is unchanged
> make  all-recursive
> make[3]: Entering directory `<
> https://jenkins-ci.mcs.anl.gov/job/moab_serial/ws/src'>
> Making all in io
> make[4]: Entering directory `<
> https://jenkins-ci.mcs.anl.gov/job/moab_serial/ws/src/io'>
> Making all in mhdf
> make[5]: Entering directory `<
> https://jenkins-ci.mcs.anl.gov/job/moab_serial/ws/src/io/mhdf'>
> make[5]: Nothing to be done for `all'.
> make[5]: Leaving directory `<
> https://jenkins-ci.mcs.anl.gov/job/moab_serial/ws/src/io/mhdf'>
> Making all in .
> make[5]: Entering directory `<
> https://jenkins-ci.mcs.anl.gov/job/moab_serial/ws/src/io'>
> /bin/sh ../../libtool  --tag=CXX   --mode=compile g++ -DHAVE_CONFIG_H -I.
> -I../.. -I../../src/moab -I../../src/parallel -I../../src
>  -I/homes/fathom/3rdparty/netcdf/4.3.2/gnu/include
> -I/homes/fathom/3rdparty/zlib/1.2.8/gcc/include
> -I/homes/fathom/3rdparty/hdf5/1.8.12/gnu/include
>  -I/homes/fathom/3rdparty/hdf5/1.8.12/gnu/include -isystem
> /homes/fathom/3rdparty/hdf5/1.8.12/gnu/include  -DTEMPLATE_SPECIALIZATION
> -DTEMPLATE_FUNC_SPECIALIZATION -DHAVE_VSNPRINTF -D_FILE_OFFSET_BITS=64
> -DHDF5_FILE -DNETCDF_FILE -DIS_BUILDING_MB -I.. -I./.. -I./../parallel
>  -I./mhdf/include  -DUNORDERED_MAP_NS=std::tr1
> -DHAVE_UNORDERED_MAP=tr1/unordered_map
> -DHAVE_UNORDERED_SET=tr1/unordered_set  -Wall -pipe -pedantic
> -Wno-long-long -Wextra -Wcast-align  -Wpointer-arith -Wformat
> -Wformat-security -Wshadow -Wunused-parameter -O2 -DNDEBUG -MT ReadNC.lo
> -MD -MP -MF .deps/ReadNC.Tpo -c -o ReadNC.lo ReadNC.cpp
> libtool: compile:  g++ -DHAVE_CONFIG_H -I. -I../.. -I../../src/moab
> -I../../src/parallel -I../../src
> -I/homes/fathom/3rdparty/netcdf/4.3.2/gnu/include
> -I/homes/fathom/3rdparty/zlib/1.2.8/gcc/include
> -I/homes/fathom/3rdparty/hdf5/1.8.12/gnu/include
> -I/homes/fathom/3rdparty/hdf5/1.8.12/gnu/include -isystem
> /homes/fathom/3rdparty/hdf5/1.8.12/gnu/include -DTEMPLATE_SPECIALIZATION
> -DTEMPLATE_FUNC_SPECIALIZATION -DHAVE_VSNPRINTF -D_FILE_OFFSET_BITS=64
> -DHDF5_FILE -DNETCDF_FILE -DIS_BUILDING_MB -I.. -I./.. -I./../parallel
> -I./mhdf/include -DUNORDERED_MAP_NS=std::tr1
> -DHAVE_UNORDERED_MAP=tr1/unordered_map
> -DHAVE_UNORDERED_SET=tr1/unordered_set -Wall -pipe -pedantic -Wno-long-long
> -Wextra -Wcast-align -Wpointer-arith -Wformat -Wformat-security -Wshadow
> -Wunused-parameter -O2 -DNDEBUG -MT ReadNC.lo -MD -MP -MF .deps/ReadNC.Tpo
> -c ReadNC.cpp -o ReadNC.o
> mv -f .deps/ReadNC.Tpo .deps/ReadNC.Plo
> /bin/sh ../../libtool  --tag=CXX   --mode=compile g++ -DHAVE_CONFIG_H -I.
> -I../.. -I../../src/moab -I../../src/parallel -I../../src
>  -I/homes/fathom/3rdparty/netcdf/4.3.2/gnu/include
> -I/homes/fathom/3rdparty/zlib/1.2.8/gcc/include
> -I/homes/fathom/3rdparty/hdf5/1.8.12/gnu/include
>  -I/homes/fathom/3rdparty/hdf5/1.8.12/gnu/include -isystem
> /homes/fathom/3rdparty/hdf5/1.8.12/gnu/include  -DTEMPLATE_SPECIALIZATION
> -DTEMPLATE_FUNC_SPECIALIZATION -DHAVE_VSNPRINTF -D_FILE_OFFSET_BITS=64
> -DHDF5_FILE -DNETCDF_FILE -DIS_BUILDING_MB -I.. -I./.. -I./../parallel
>  -I./mhdf/include  -DUNORDERED_MAP_NS=std::tr1
> -DHAVE_UNORDERED_MAP=tr1/unordered_map
> -DHAVE_UNORDERED_SET=tr1/unordered_set  -Wall -pipe -pedantic
> -Wno-long-long -Wextra -Wcast-align  -Wpointer-arith -Wformat
> -Wformat-security -Wshadow -Wunused-parameter -O2 -DNDEBUG -MT NCHelper.lo
> -MD -MP -MF .deps/NCHelper.Tpo -c -o NCHelper.lo NCHelper.cpp
> libtool: compile:  g++ -DHAVE_CONFIG_H -I. -I../.. -I../../src/moab
> -I../../src/parallel -I../../src
> -I/homes/fathom/3rdparty/netcdf/4.3.2/gnu/include
> -I/homes/fathom/3rdparty/zlib/1.2.8/gcc/include
> -I/homes/fathom/3rdparty/hdf5/1.8.12/gnu/include
> -I/homes/fathom/3rdparty/hdf5/1.8.12/gnu/include -isystem
> /homes/fathom/3rdparty/hdf5/1.8.12/gnu/include -DTEMPLATE_SPECIALIZATION
> -DTEMPLATE_FUNC_SPECIALIZATION -DHAVE_VSNPRINTF -D_FILE_OFFSET_BITS=64
> -DHDF5_FILE -DNETCDF_FILE -DIS_BUILDING_MB -I.. -I./.. -I./../parallel
> -I./mhdf/include -DUNORDERED_MAP_NS=std::tr1
> -DHAVE_UNORDERED_MAP=tr1/unordered_map
> -DHAVE_UNORDERED_SET=tr1/unordered_set -Wall -pipe -pedantic -Wno-long-long
> -Wextra -Wcast-align -Wpointer-arith -Wformat -Wformat-security -Wshadow
> -Wunused-parameter -O2 -DNDEBUG -MT NCHelper.lo -MD -MP -MF
> .deps/NCHelper.Tpo -c NCHelper.cpp -o NCHelper.o
> NCHelper.cpp: In static member function 'static moab::NCHelper*
> moab::NCHelper::get_nc_helper(moab::ReadNC*, int, const moab::FileOptions&,
> moab::EntityHandle)':
> NCHelper.cpp:51:75: error: cannot allocate an object of abstract type
> 'moab::NCHelperMPAS'
> NCHelperMPAS.hpp:17:7: note:   because the following virtual functions are
> pure within 'moab::NCHelperMPAS':
> NCHelper.hpp:206:21: note:      virtual moab::ErrorCode
> moab::UcdNCHelper::read_ucd_variables_to_nonset(std::vector<moab::ReadNC::VarData>&,
> std::vector<int>&)
> make[5]: *** [NCHelper.lo] Error 1
> make[5]: Leaving directory `<
> https://jenkins-ci.mcs.anl.gov/job/moab_serial/ws/src/io'>
> make[4]: *** [all-recursive] Error 1
> make[4]: Leaving directory `<
> https://jenkins-ci.mcs.anl.gov/job/moab_serial/ws/src/io'>
> make[3]: *** [all-recursive] Error 1
> make[3]: Leaving directory `<
> https://jenkins-ci.mcs.anl.gov/job/moab_serial/ws/src'>
> make[2]: *** [all] Error 2
> make[2]: Leaving directory `<
> https://jenkins-ci.mcs.anl.gov/job/moab_serial/ws/src'>
> make[1]: *** [all-recursive] Error 1
> make[1]: Leaving directory `<
> https://jenkins-ci.mcs.anl.gov/job/moab_serial/ws/'>
> make: *** [all] Error 2
> Build step 'Execute shell' marked build as failure
>
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