=> Bootstrap dependency digest>=20010302: found digest-20111104
=> Bootstrap dependency fetch-[0-9]*: found fetch-1.7
WARNING: [license.mk] Every package should define a LICENSE.
===> Building for py25-pytables-2.2.1nb1
(cd /tmp/pkgsrc/math/py-pytables/work/tables-2.2.1/ && /usr/bin/env USETOOLS=no PTHREAD_CFLAGS=\ -pthread\ PTHREAD_LDFLAGS=\ -pthread PTHREAD_LIBS=-lpthread\ -lrt PTHREADBASE=/usr DL_CFLAGS= DL_LDFLAGS= DL_LIBS= PYTHON=/usr/pkg/bin/python2.5 CC=gcc CFLAGS=-O3\ -pipe\ -fstack-protector\ -Wno-format\ -fno-builtin\ -I/usr/include\ -I/usr/pkg/include CPPFLAGS=-I/usr/include\ -I/usr/pkg/include CXX=g++ CXXFLAGS=-O3\ -pipe\ -fstack-protector\ -Wno-format\ -fno-builtin\ -I/usr/include\ -I/usr/pkg/include COMPILER_RPATH_FLAG=-Wl,-R F77=f77 FC=f77 FFLAGS=-O LANG=C LC_COLLATE=C LC_CTYPE=C LC_MESSAGES=C LC_MONETARY=C LC_NUMERIC=C LC_TIME=C LDFLAGS=-L/usr/lib\ -Wl,-R/usr/lib\ -L/usr/pkg/lib\ -Wl,-R/usr/pkg/lib LINKER_RPATH_FLAG=-R PATH=/tmp/pkgsrc/math/py-pytables/work/.wrapper/bin:/tmp/pkgsrc/math/py-pytables/work/.buildlink/bin:/tmp/pkgsrc/math/py-pytables/work/.gcc/bin:/tmp/pkgsrc/math/py-pytables/work/.tools/bin:/usr/pkg/bin:/bin:/usr/bin:/usr/pkg/bin:/usr/pkg/bin PREFIX=/usr/pkg PKG_SYSCONFDIR=/usr/pkg/etc CXXCPP=cpp HOME=/tmp/pkgsrc/math/py-pytables/work/.home CPP=cpp LINK_ALL_LIBGCC_HACK= LOCALBASE=/usr/pkg NO_WHOLE_ARCHIVE_FLAG=-Wl,--no-whole-archive WHOLE_ARCHIVE_FLAG=-Wl,--whole-archive X11BASE=/usr/pkg X11PREFIX=/usr/pkg PKGMANDIR=share/man PKGINFODIR=share/info MAKECONF=/dev/null OBJECT_FMT=ELF USETOOLS=no BSD_INSTALL_PROGRAM=/usr/bin/install\ -c\ -s\ -o\ pbulk\ -g\ pbulk\ -m\ 755 BSD_INSTALL_SCRIPT=/usr/bin/install\ -c\ -o\ pbulk\ -g\ pbulk\ -m\ 755 BSD_INSTALL_LIB=/usr/bin/install\ -c\ -o\ pbulk\ -g\ pbulk\ -m\ 755 BSD_INSTALL_DATA=/usr/bin/install\ -c\ -o\ pbulk\ -g\ pbulk\ -m\ 644 BSD_INSTALL_MAN=/usr/bin/install\ -c\ -o\ pbulk\ -g\ pbulk\ -m\ 644 BSD_INSTALL=/usr/bin/install BSD_INSTALL_PROGRAM_DIR=/usr/bin/install\ -d\ -o\ pbulk\ -g\ pbulk\ -m\ 755 BSD_INSTALL_SCRIPT_DIR=/usr/bin/install\ -d\ -o\ pbulk\ -g\ pbulk\ -m\ 755 BSD_INSTALL_LIB_DIR=/usr/bin/install\ -d\ -o\ pbulk\ -g\ pbulk\ -m\ 755 BSD_INSTALL_DATA_DIR=/usr/bin/install\ -d\ -o\ pbulk\ -g\ pbulk\ -m\ 755 BSD_INSTALL_MAN_DIR=/usr/bin/install\ -d\ -o\ pbulk\ -g\ pbulk\ -m\ 755 BSD_INSTALL_GAME=/usr/bin/install\ -c\ -s\ -o\ pbulk\ -g\ pbulk\ -m\ 2555 BSD_INSTALL_GAME_DATA=/usr/bin/install\ -c\ -o\ pbulk\ -g\ pbulk\ -m\ 664 BSD_INSTALL_GAME_DIR=/usr/bin/install\ -d\ -o\ pbulk\ -g\ pbulk\ -m\ 775 INSTALL_INFO= MAKEINFO=/tmp/pkgsrc/math/py-pytables/work/.tools/bin/makeinfo PKG_CONFIG= PKG_CONFIG_LIBDIR=/tmp/pkgsrc/math/py-pytables/work/.buildlink/lib/pkgconfig:/tmp/pkgsrc/math/py-pytables/work/.buildlink/share/pkgconfig PKG_CONFIG_LOG=/tmp/pkgsrc/math/py-pytables/work/.pkg-config.log PKG_CONFIG_PATH= WRAPPER_DEBUG=no WRAPPER_UPDATE_CACHE=yes VIEWBASE=/usr/pkg /usr/pkg/bin/python2.5 setup.py build --hdf5=/usr/pkg)
* Found numpy 1.4.1 package installed.
* Found HDF5 headers at ``/usr/pkg/include``, library at ``/usr/pkg/lib``.
.. WARNING:: Could not find the HDF5 runtime.
The HDF5 shared library was *not* found in the default library
paths. In case of runtime problems, please remember to install it.
* Could not find LZO 2 headers and library; disabling support for it.
* Could not find LZO 1 headers and library; disabling support for it.
* Found bzip2 headers at ``/usr/include``, library at ``/usr/lib64``.
running build
running build_py
creating build
creating build/lib.linux-x86_64-2.5
creating build/lib.linux-x86_64-2.5/tables
copying tables/parameters.py -> build/lib.linux-x86_64-2.5/tables
copying tables/description.py -> build/lib.linux-x86_64-2.5/tables
copying tables/atom.py -> build/lib.linux-x86_64-2.5/tables
copying tables/path.py -> build/lib.linux-x86_64-2.5/tables
copying tables/utils.py -> build/lib.linux-x86_64-2.5/tables
copying tables/exceptions.py -> build/lib.linux-x86_64-2.5/tables
copying tables/group.py -> build/lib.linux-x86_64-2.5/tables
copying tables/earray.py -> build/lib.linux-x86_64-2.5/tables
copying tables/table.py -> build/lib.linux-x86_64-2.5/tables
copying tables/_parameters_common.py -> build/lib.linux-x86_64-2.5/tables
copying tables/_table_common.py -> build/lib.linux-x86_64-2.5/tables
copying tables/vlarray.py -> build/lib.linux-x86_64-2.5/tables
copying tables/attributeset.py -> build/lib.linux-x86_64-2.5/tables
copying tables/flavor.py -> build/lib.linux-x86_64-2.5/tables
copying tables/__init__.py -> build/lib.linux-x86_64-2.5/tables
copying tables/node.py -> build/lib.linux-x86_64-2.5/tables
copying tables/_conditions_common.py -> build/lib.linux-x86_64-2.5/tables
copying tables/file.py -> build/lib.linux-x86_64-2.5/tables
copying tables/unimplemented.py -> build/lib.linux-x86_64-2.5/tables
copying tables/filters.py -> build/lib.linux-x86_64-2.5/tables
copying tables/leaf.py -> build/lib.linux-x86_64-2.5/tables
copying tables/undoredo.py -> build/lib.linux-x86_64-2.5/tables
copying tables/req_versions.py -> build/lib.linux-x86_64-2.5/tables
copying tables/link.py -> build/lib.linux-x86_64-2.5/tables
copying tables/expression.py -> build/lib.linux-x86_64-2.5/tables
copying tables/carray.py -> build/lib.linux-x86_64-2.5/tables
copying tables/registry.py -> build/lib.linux-x86_64-2.5/tables
copying tables/array.py -> build/lib.linux-x86_64-2.5/tables
copying tables/conditions.py -> build/lib.linux-x86_64-2.5/tables
creating build/lib.linux-x86_64-2.5/tables/nodes
copying tables/nodes/__init__.py -> build/lib.linux-x86_64-2.5/tables/nodes
copying tables/nodes/filenode.py -> build/lib.linux-x86_64-2.5/tables/nodes
creating build/lib.linux-x86_64-2.5/tables/scripts
copying tables/scripts/__init__.py -> build/lib.linux-x86_64-2.5/tables/scripts
copying tables/scripts/ptrepack.py -> build/lib.linux-x86_64-2.5/tables/scripts
copying tables/scripts/ptdump.py -> build/lib.linux-x86_64-2.5/tables/scripts
creating build/lib.linux-x86_64-2.5/tables/nra
copying tables/nra/__init__.py -> build/lib.linux-x86_64-2.5/tables/nra
copying tables/nra/attributeaccess.py -> build/lib.linux-x86_64-2.5/tables/nra
copying tables/nra/nestedrecords.py -> build/lib.linux-x86_64-2.5/tables/nra
copying tables/nra/nriterators.py -> build/lib.linux-x86_64-2.5/tables/nra
creating build/lib.linux-x86_64-2.5/tables/netcdf3
copying tables/netcdf3/__init__.py -> build/lib.linux-x86_64-2.5/tables/netcdf3
creating build/lib.linux-x86_64-2.5/tables/netcdf3/scripts
copying tables/netcdf3/scripts/nctoh5.py -> build/lib.linux-x86_64-2.5/tables/netcdf3/scripts
copying tables/netcdf3/scripts/__init__.py -> build/lib.linux-x86_64-2.5/tables/netcdf3/scripts
creating build/lib.linux-x86_64-2.5/tables/misc
copying tables/misc/proxydict.py -> build/lib.linux-x86_64-2.5/tables/misc
copying tables/misc/__init__.py -> build/lib.linux-x86_64-2.5/tables/misc
copying tables/misc/lrucache.py -> build/lib.linux-x86_64-2.5/tables/misc
copying tables/misc/enum.py -> build/lib.linux-x86_64-2.5/tables/misc
creating build/lib.linux-x86_64-2.5/tables/tests
copying tables/tests/test_attributes.py -> build/lib.linux-x86_64-2.5/tables/tests
copying tables/tests/common.py -> build/lib.linux-x86_64-2.5/tables/tests
copying tables/tests/test_links.py -> build/lib.linux-x86_64-2.5/tables/tests
copying tables/tests/test_backcompat.py -> build/lib.linux-x86_64-2.5/tables/tests
copying tables/tests/test_tables.py -> build/lib.linux-x86_64-2.5/tables/tests
copying tables/tests/test_numarray.py -> build/lib.linux-x86_64-2.5/tables/tests
copying tables/tests/test_do_undo.py -> build/lib.linux-x86_64-2.5/tables/tests
copying tables/tests/test_create.py -> build/lib.linux-x86_64-2.5/tables/tests
copying tables/tests/test_nestedtypes.py -> build/lib.linux-x86_64-2.5/tables/tests
copying tables/tests/test_queries.py -> build/lib.linux-x86_64-2.5/tables/tests
copying tables/tests/test_garbage.py -> build/lib.linux-x86_64-2.5/tables/tests
copying tables/tests/__init__.py -> build/lib.linux-x86_64-2.5/tables/tests
copying tables/tests/test_carray.py -> build/lib.linux-x86_64-2.5/tables/tests
copying tables/tests/test_basics.py -> build/lib.linux-x86_64-2.5/tables/tests
copying tables/tests/test_array.py -> build/lib.linux-x86_64-2.5/tables/tests
copying tables/tests/test_all.py -> build/lib.linux-x86_64-2.5/tables/tests
copying tables/tests/test_enum.py -> build/lib.linux-x86_64-2.5/tables/tests
copying tables/tests/test_earray.py -> build/lib.linux-x86_64-2.5/tables/tests
copying tables/tests/test_types.py -> build/lib.linux-x86_64-2.5/tables/tests
copying tables/tests/test_tree.py -> build/lib.linux-x86_64-2.5/tables/tests
copying tables/tests/test_timetype.py -> build/lib.linux-x86_64-2.5/tables/tests
copying tables/tests/test_index_backcompat.py -> build/lib.linux-x86_64-2.5/tables/tests
copying tables/tests/test_expression.py -> build/lib.linux-x86_64-2.5/tables/tests
copying tables/tests/test_hdf5compat.py -> build/lib.linux-x86_64-2.5/tables/tests
copying tables/tests/test_numpy.py -> build/lib.linux-x86_64-2.5/tables/tests
copying tables/tests/test_vlarray.py -> build/lib.linux-x86_64-2.5/tables/tests
copying tables/tests/test_tablesMD.py -> build/lib.linux-x86_64-2.5/tables/tests
copying tables/tests/check_leaks.py -> build/lib.linux-x86_64-2.5/tables/tests
copying tables/tests/test_Numeric.py -> build/lib.linux-x86_64-2.5/tables/tests
copying tables/tests/test_lists.py -> build/lib.linux-x86_64-2.5/tables/tests
creating build/lib.linux-x86_64-2.5/tables/nodes/tests
copying tables/nodes/tests/test_filenode.py -> build/lib.linux-x86_64-2.5/tables/nodes/tests
copying tables/nodes/tests/__init__.py -> build/lib.linux-x86_64-2.5/tables/nodes/tests
creating build/lib.linux-x86_64-2.5/tables/netcdf3/tests
copying tables/netcdf3/tests/__init__.py -> build/lib.linux-x86_64-2.5/tables/netcdf3/tests
copying tables/netcdf3/tests/test_netcdf3.py -> build/lib.linux-x86_64-2.5/tables/netcdf3/tests
creating build/lib.linux-x86_64-2.5/tables/nra/tests
copying tables/nra/tests/test_nestedrecords.py -> build/lib.linux-x86_64-2.5/tables/nra/tests
copying tables/nra/tests/__init__.py -> build/lib.linux-x86_64-2.5/tables/nra/tests
copying tables/nra/tests/test_nriterators.py -> build/lib.linux-x86_64-2.5/tables/nra/tests
copying tables/tests/nested-type-with-gaps.h5 -> build/lib.linux-x86_64-2.5/tables/tests
copying tables/tests/elink.h5 -> build/lib.linux-x86_64-2.5/tables/tests
copying tables/tests/slink.h5 -> build/lib.linux-x86_64-2.5/tables/tests
copying tables/tests/smpl_enum.h5 -> build/lib.linux-x86_64-2.5/tables/tests
copying tables/tests/time-table-vlarray-1_x.h5 -> build/lib.linux-x86_64-2.5/tables/tests
copying tables/tests/Tables_lzo2.h5 -> build/lib.linux-x86_64-2.5/tables/tests
copying tables/tests/smpl_f64le.h5 -> build/lib.linux-x86_64-2.5/tables/tests
copying tables/tests/smpl_f64be.h5 -> build/lib.linux-x86_64-2.5/tables/tests
copying tables/tests/ex-noattr.h5 -> build/lib.linux-x86_64-2.5/tables/tests
copying tables/tests/smpl_i32le.h5 -> build/lib.linux-x86_64-2.5/tables/tests
copying tables/tests/Tables_lzo1_shuffle.h5 -> build/lib.linux-x86_64-2.5/tables/tests
copying tables/tests/non-chunked-table.h5 -> build/lib.linux-x86_64-2.5/tables/tests
copying tables/tests/smpl_i64le.h5 -> build/lib.linux-x86_64-2.5/tables/tests
copying tables/tests/blosc_bigendian.h5 -> build/lib.linux-x86_64-2.5/tables/tests
copying tables/tests/test_szip.h5 -> build/lib.linux-x86_64-2.5/tables/tests
copying tables/tests/smpl_compound_chunked.h5 -> build/lib.linux-x86_64-2.5/tables/tests
copying tables/tests/smpl_SDSextendible.h5 -> build/lib.linux-x86_64-2.5/tables/tests
copying tables/tests/zerodim-attrs-1.3.h5 -> build/lib.linux-x86_64-2.5/tables/tests
copying tables/tests/idx-std-1.x.h5 -> build/lib.linux-x86_64-2.5/tables/tests
copying tables/tests/smpl_unsupptype.h5 -> build/lib.linux-x86_64-2.5/tables/tests
copying tables/tests/flavored_vlarrays-format1.6.h5 -> build/lib.linux-x86_64-2.5/tables/tests
copying tables/tests/elink2.h5 -> build/lib.linux-x86_64-2.5/tables/tests
copying tables/tests/smpl_i32be.h5 -> build/lib.linux-x86_64-2.5/tables/tests
copying tables/tests/Tables_lzo1.h5 -> build/lib.linux-x86_64-2.5/tables/tests
copying tables/tests/Tables_lzo2_shuffle.h5 -> build/lib.linux-x86_64-2.5/tables/tests
copying tables/tests/array_mdatom.h5 -> build/lib.linux-x86_64-2.5/tables/tests
copying tables/tests/indexes_2_0.h5 -> build/lib.linux-x86_64-2.5/tables/tests
copying tables/tests/zerodim-attrs-1.4.h5 -> build/lib.linux-x86_64-2.5/tables/tests
copying tables/tests/times-nested-be.h5 -> build/lib.linux-x86_64-2.5/tables/tests
copying tables/tests/attr-u16.h5 -> build/lib.linux-x86_64-2.5/tables/tests
copying tables/tests/smpl_i64be.h5 -> build/lib.linux-x86_64-2.5/tables/tests
copying tables/tests/Table2_1_lzo_nrv2e_shuffle.h5 -> build/lib.linux-x86_64-2.5/tables/tests
copying tables/tests/vlunicode_endian.h5 -> build/lib.linux-x86_64-2.5/tables/tests
copying tables/nodes/tests/test_filenode.dat -> build/lib.linux-x86_64-2.5/tables/nodes/tests
copying tables/nodes/tests/test_filenode.xbm -> build/lib.linux-x86_64-2.5/tables/nodes/tests
copying tables/nodes/tests/test_filenode_v1.h5 -> build/lib.linux-x86_64-2.5/tables/nodes/tests
running build_ext
building 'tables.utilsExtension' extension
C compiler: gcc -DNDEBUG -O3 -pipe -fstack-protector -Wno-format -fno-builtin -I/usr/include -I/usr/pkg/include/db4 -I/usr/pkg/include -I/usr/pkg/include/ncurses -O3 -pipe -fstack-protector -Wno-format -fno-builtin -I/usr/include -I/usr/pkg/include -I/usr/include -I/usr/pkg/include -fPIC
creating build/temp.linux-x86_64-2.5
creating build/temp.linux-x86_64-2.5/tables
creating build/temp.linux-x86_64-2.5/src
creating build/temp.linux-x86_64-2.5/blosc
compile options: '-DNDEBUG=1 -DHAVE_BZ2_LIB=1 -Iblosc -I/usr/pkg/lib/python2.5/site-packages/numpy/core/include -I/usr/pkg/include -I/usr/pkg/include/python2.5 -c'
extra options: '-O3 -pipe -fstack-protector -Wno-format -fno-builtin -I/usr/include -I/usr/pkg/include -Isrc -DH5_USE_16_API'
gcc: src/H5ATTR.c
gcc: src/utils.c
gcc: src/H5ARRAY.c
In file included from /tmp/pkgsrc/math/py-pytables/work/.buildlink/include/python2.5/Python.h:8:0,
from src/utils.h:1,
from src/H5ARRAY.c:4:
/tmp/pkgsrc/math/py-pytables/work/.buildlink/include/python2.5/pyconfig.h:939:0: warning: "_POSIX_C_SOURCE" redefined
/usr/include/features.h:214:0: note: this is the location of the previous definition
gcc: blosc/shuffle.c
gcc: blosc/blosc_filter.c
gcc: blosc/blosclz.c
gcc: blosc/blosc.c
gcc: tables/utilsExtension.c
gcc -pthread -shared -L/tmp/pkgsrc/lang/python25/work/Python-2.5.6 -L/usr/lib -Wl,-R/usr/lib -L/usr/pkg/lib -Wl,-R/usr/pkg/lib -L/usr/lib -Wl,-R/usr/lib -L/usr/pkg/lib -Wl,-R/usr/pkg/lib -O3 -pipe -fstack-protector -Wno-format -fno-builtin -I/usr/include -I/usr/pkg/include -I/usr/include -I/usr/pkg/include build/temp.linux-x86_64-2.5/tables/utilsExtension.o build/temp.linux-x86_64-2.5/src/utils.o build/temp.linux-x86_64-2.5/src/H5ARRAY.o build/temp.linux-x86_64-2.5/src/H5ATTR.o build/temp.linux-x86_64-2.5/blosc/blosc.o build/temp.linux-x86_64-2.5/blosc/blosclz.o build/temp.linux-x86_64-2.5/blosc/shuffle.o build/temp.linux-x86_64-2.5/blosc/blosc_filter.o -L/usr/pkg/lib -L/usr/pkg/lib -lhdf5 -lpython2.5 -o build/lib.linux-x86_64-2.5/tables/utilsExtension.so -L/usr/lib -Wl,-R/usr/lib -L/usr/pkg/lib -Wl,-R/usr/pkg/lib
building 'tables.hdf5Extension' extension
C compiler: gcc -DNDEBUG -O3 -pipe -fstack-protector -Wno-format -fno-builtin -I/usr/include -I/usr/pkg/include/db4 -I/usr/pkg/include -I/usr/pkg/include/ncurses -O3 -pipe -fstack-protector -Wno-format -fno-builtin -I/usr/include -I/usr/pkg/include -I/usr/include -I/usr/pkg/include -fPIC
compile options: '-DNDEBUG=1 -DHAVE_BZ2_LIB=1 -Iblosc -I/usr/pkg/lib/python2.5/site-packages/numpy/core/include -I/usr/pkg/include -I/usr/pkg/include/python2.5 -c'
extra options: '-O3 -pipe -fstack-protector -Wno-format -fno-builtin -I/usr/include -I/usr/pkg/include -Isrc -DH5_USE_16_API'
gcc: tables/hdf5Extension.c
gcc: src/typeconv.c
gcc: src/H5ARRAY-opt.c
gcc: src/H5VLARRAY.c
In file included from /tmp/pkgsrc/math/py-pytables/work/.buildlink/include/python2.5/Python.h:8:0,
from src/utils.h:1,
from src/H5VLARRAY.c:3:
/tmp/pkgsrc/math/py-pytables/work/.buildlink/include/python2.5/pyconfig.h:939:0: warning: "_POSIX_C_SOURCE" redefined
/usr/include/features.h:214:0: note: this is the location of the previous definition
gcc -pthread -shared -L/tmp/pkgsrc/lang/python25/work/Python-2.5.6 -L/usr/lib -Wl,-R/usr/lib -L/usr/pkg/lib -Wl,-R/usr/pkg/lib -L/usr/lib -Wl,-R/usr/lib -L/usr/pkg/lib -Wl,-R/usr/pkg/lib -O3 -pipe -fstack-protector -Wno-format -fno-builtin -I/usr/include -I/usr/pkg/include -I/usr/include -I/usr/pkg/include build/temp.linux-x86_64-2.5/tables/hdf5Extension.o build/temp.linux-x86_64-2.5/src/utils.o build/temp.linux-x86_64-2.5/src/typeconv.o build/temp.linux-x86_64-2.5/src/H5ARRAY.o build/temp.linux-x86_64-2.5/src/H5ARRAY-opt.o build/temp.linux-x86_64-2.5/src/H5VLARRAY.o build/temp.linux-x86_64-2.5/src/H5ATTR.o build/temp.linux-x86_64-2.5/blosc/blosc.o build/temp.linux-x86_64-2.5/blosc/blosclz.o build/temp.linux-x86_64-2.5/blosc/shuffle.o build/temp.linux-x86_64-2.5/blosc/blosc_filter.o -L/usr/pkg/lib -L/usr/pkg/lib -lhdf5 -lpython2.5 -o build/lib.linux-x86_64-2.5/tables/hdf5Extension.so -L/usr/lib -Wl,-R/usr/lib -L/usr/pkg/lib -Wl,-R/usr/pkg/lib
building 'tables.tableExtension' extension
C compiler: gcc -DNDEBUG -O3 -pipe -fstack-protector -Wno-format -fno-builtin -I/usr/include -I/usr/pkg/include/db4 -I/usr/pkg/include -I/usr/pkg/include/ncurses -O3 -pipe -fstack-protector -Wno-format -fno-builtin -I/usr/include -I/usr/pkg/include -I/usr/include -I/usr/pkg/include -fPIC
compile options: '-DNDEBUG=1 -DHAVE_BZ2_LIB=1 -Iblosc -I/usr/pkg/lib/python2.5/site-packages/numpy/core/include -I/usr/pkg/include -I/usr/pkg/include/python2.5 -c'
extra options: '-O3 -pipe -fstack-protector -Wno-format -fno-builtin -I/usr/include -I/usr/pkg/include -Isrc -DH5_USE_16_API'
gcc: src/H5TB-opt.c
In file included from /tmp/pkgsrc/math/py-pytables/work/.buildlink/include/python2.5/Python.h:8:0,
from src/utils.h:1,
from src/H5TB-opt.c:36:
/tmp/pkgsrc/math/py-pytables/work/.buildlink/include/python2.5/pyconfig.h:939:0: warning: "_POSIX_C_SOURCE" redefined
/usr/include/features.h:214:0: note: this is the location of the previous definition
src/H5TB-opt.c: In function 'H5TBOread_elements':
src/H5TB-opt.c:308:2: warning: passing argument 4 of 'H5Sselect_elements' from incompatible pointer type
/tmp/pkgsrc/math/py-pytables/work/.buildlink/include/H5Spublic.h:128:15: note: expected 'const hsize_t *' but argument is of type 'const hsize_t **'
src/H5TB-opt.c: In function 'H5TBOwrite_elements':
src/H5TB-opt.c:517:2: warning: passing argument 4 of 'H5Sselect_elements' from incompatible pointer type
/tmp/pkgsrc/math/py-pytables/work/.buildlink/include/H5Spublic.h:128:15: note: expected 'const hsize_t *' but argument is of type 'const hsize_t **'
gcc: tables/tableExtension.c
gcc -pthread -shared -L/tmp/pkgsrc/lang/python25/work/Python-2.5.6 -L/usr/lib -Wl,-R/usr/lib -L/usr/pkg/lib -Wl,-R/usr/pkg/lib -L/usr/lib -Wl,-R/usr/lib -L/usr/pkg/lib -Wl,-R/usr/pkg/lib -O3 -pipe -fstack-protector -Wno-format -fno-builtin -I/usr/include -I/usr/pkg/include -I/usr/include -I/usr/pkg/include build/temp.linux-x86_64-2.5/tables/tableExtension.o build/temp.linux-x86_64-2.5/src/utils.o build/temp.linux-x86_64-2.5/src/typeconv.o build/temp.linux-x86_64-2.5/src/H5TB-opt.o build/temp.linux-x86_64-2.5/src/H5ATTR.o build/temp.linux-x86_64-2.5/blosc/blosc.o build/temp.linux-x86_64-2.5/blosc/blosclz.o build/temp.linux-x86_64-2.5/blosc/shuffle.o build/temp.linux-x86_64-2.5/blosc/blosc_filter.o -L/usr/pkg/lib -L/usr/pkg/lib -lhdf5 -lpython2.5 -o build/lib.linux-x86_64-2.5/tables/tableExtension.so -L/usr/lib -Wl,-R/usr/lib -L/usr/pkg/lib -Wl,-R/usr/pkg/lib
building 'tables._comp_lzo' extension
C compiler: gcc -DNDEBUG -O3 -pipe -fstack-protector -Wno-format -fno-builtin -I/usr/include -I/usr/pkg/include/db4 -I/usr/pkg/include -I/usr/pkg/include/ncurses -O3 -pipe -fstack-protector -Wno-format -fno-builtin -I/usr/include -I/usr/pkg/include -I/usr/include -I/usr/pkg/include -fPIC
compile options: '-DNDEBUG=1 -DHAVE_BZ2_LIB=1 -Iblosc -I/usr/pkg/lib/python2.5/site-packages/numpy/core/include -I/usr/pkg/include -I/usr/pkg/include/python2.5 -c'
extra options: '-O3 -pipe -fstack-protector -Wno-format -fno-builtin -I/usr/include -I/usr/pkg/include -Isrc -DH5_USE_16_API'
gcc: tables/_comp_lzo.c
gcc: src/H5Zlzo.c
gcc -pthread -shared -L/tmp/pkgsrc/lang/python25/work/Python-2.5.6 -L/usr/lib -Wl,-R/usr/lib -L/usr/pkg/lib -Wl,-R/usr/pkg/lib -L/usr/lib -Wl,-R/usr/lib -L/usr/pkg/lib -Wl,-R/usr/pkg/lib -O3 -pipe -fstack-protector -Wno-format -fno-builtin -I/usr/include -I/usr/pkg/include -I/usr/include -I/usr/pkg/include build/temp.linux-x86_64-2.5/tables/_comp_lzo.o build/temp.linux-x86_64-2.5/src/H5Zlzo.o -L/usr/pkg/lib -L/usr/pkg/lib -lpython2.5 -o build/lib.linux-x86_64-2.5/tables/_comp_lzo.so -L/usr/lib -Wl,-R/usr/lib -L/usr/pkg/lib -Wl,-R/usr/pkg/lib
building 'tables._comp_bzip2' extension
C compiler: gcc -DNDEBUG -O3 -pipe -fstack-protector -Wno-format -fno-builtin -I/usr/include -I/usr/pkg/include/db4 -I/usr/pkg/include -I/usr/pkg/include/ncurses -O3 -pipe -fstack-protector -Wno-format -fno-builtin -I/usr/include -I/usr/pkg/include -I/usr/include -I/usr/pkg/include -fPIC
compile options: '-DNDEBUG=1 -DHAVE_BZ2_LIB=1 -Iblosc -I/usr/pkg/lib/python2.5/site-packages/numpy/core/include -I/usr/pkg/include -I/usr/pkg/include/python2.5 -c'
extra options: '-O3 -pipe -fstack-protector -Wno-format -fno-builtin -I/usr/include -I/usr/pkg/include -Isrc -DH5_USE_16_API'
gcc: src/H5Zbzip2.c
gcc: tables/_comp_bzip2.c
gcc -pthread -shared -L/tmp/pkgsrc/lang/python25/work/Python-2.5.6 -L/usr/lib -Wl,-R/usr/lib -L/usr/pkg/lib -Wl,-R/usr/pkg/lib -L/usr/lib -Wl,-R/usr/lib -L/usr/pkg/lib -Wl,-R/usr/pkg/lib -O3 -pipe -fstack-protector -Wno-format -fno-builtin -I/usr/include -I/usr/pkg/include -I/usr/include -I/usr/pkg/include build/temp.linux-x86_64-2.5/tables/_comp_bzip2.o build/temp.linux-x86_64-2.5/src/H5Zbzip2.o -L/usr/pkg/lib -L/usr/pkg/lib -lhdf5 -lbz2 -lpython2.5 -o build/lib.linux-x86_64-2.5/tables/_comp_bzip2.so -L/usr/lib -Wl,-R/usr/lib -L/usr/pkg/lib -Wl,-R/usr/pkg/lib
cythoning tables/linkExtension.pyx to tables/linkExtension.c
Traceback (most recent call last):
File "setup.py", line 710, in <module>
**setuptools_kwargs
File "/usr/pkg/lib/python2.5/distutils/core.py", line 151, in setup
dist.run_commands()
File "/usr/pkg/lib/python2.5/distutils/dist.py", line 974, in run_commands
self.run_command(cmd)
File "/usr/pkg/lib/python2.5/distutils/dist.py", line 994, in run_command
cmd_obj.run()
File "/usr/pkg/lib/python2.5/distutils/command/build.py", line 112, in run
self.run_command(cmd_name)
File "/usr/pkg/lib/python2.5/distutils/cmd.py", line 333, in run_command
self.distribution.run_command(command)
File "/usr/pkg/lib/python2.5/distutils/dist.py", line 994, in run_command
cmd_obj.run()
File "/usr/pkg/lib/python2.5/distutils/command/build_ext.py", line 290, in run
self.build_extensions()
File "/usr/pkg/lib/python2.5/site-packages/Cython/Distutils/build_ext.py", line 80, in build_extensions
ext.sources = self.cython_sources(ext.sources, ext)
File "/usr/pkg/lib/python2.5/site-packages/Cython/Distutils/build_ext.py", line 211, in cython_sources
full_module_name=module_name)
File "/usr/pkg/lib/python2.5/site-packages/Cython/Compiler/Main.py", line 749, in compile
return compile_single(source, options, full_module_name)
File "/usr/pkg/lib/python2.5/site-packages/Cython/Compiler/Main.py", line 696, in compile_single
return run_pipeline(source, options, full_module_name)
File "/usr/pkg/lib/python2.5/site-packages/Cython/Compiler/Main.py", line 590, in run_pipeline
pipeline = context.create_pyx_pipeline(options, result)
File "/usr/pkg/lib/python2.5/site-packages/Cython/Compiler/Main.py", line 191, in create_pyx_pipeline
] + self.create_pipeline(pxd=False, py=py) + test_support + [
File "/usr/pkg/lib/python2.5/site-packages/Cython/Compiler/Main.py", line 97, in create_pipeline
from ParseTreeTransforms import WithTransform, NormalizeTree, PostParse, PxdPostParse
File "/usr/pkg/lib/python2.5/site-packages/Cython/Compiler/ParseTreeTransforms.py", line 837, in <module>
class WithTransform(CythonTransform, SkipDeclarations):
File "/usr/pkg/lib/python2.5/site-packages/Cython/Compiler/ParseTreeTransforms.py", line 859, in WithTransform
pipeline=[NormalizeTree(None)])
File "/usr/pkg/lib/python2.5/site-packages/Cython/Compiler/TreeFragment.py", line 204, in __init__
t = transform(t)
File "Visitor.py", line 276, in Cython.Compiler.Visitor.CythonTransform.__call__ (/tmp/pkgsrc/devel/py-cython/work/Cython-0.13/Cython/Compiler/Visitor.c:4924)
File "Visitor.py", line 259, in Cython.Compiler.Visitor.VisitorTransform.__call__ (/tmp/pkgsrc/devel/py-cython/work/Cython-0.13/Cython/Compiler/Visitor.c:4684)
File "Visitor.py", line 28, in Cython.Compiler.Visitor.BasicVisitor.visit (/tmp/pkgsrc/devel/py-cython/work/Cython-0.13/Cython/Compiler/Visitor.c:1178)
File "/usr/pkg/lib/python2.5/site-packages/Cython/Compiler/ParseTreeTransforms.py", line 103, in visit_StatListNode
self.visitchildren(node)
File "Visitor.py", line 237, in Cython.Compiler.Visitor.VisitorTransform.visitchildren (/tmp/pkgsrc/devel/py-cython/work/Cython-0.13/Cython/Compiler/Visitor.c:4503)
File "Visitor.py", line 238, in Cython.Compiler.Visitor.VisitorTransform.visitchildren (/tmp/pkgsrc/devel/py-cython/work/Cython-0.13/Cython/Compiler/Visitor.c:4248)
File "Visitor.py", line 209, in Cython.Compiler.Visitor.TreeVisitor._visitchildren (/tmp/pkgsrc/devel/py-cython/work/Cython-0.13/Cython/Compiler/Visitor.c:3995)
File "Visitor.py", line 181, in Cython.Compiler.Visitor.TreeVisitor.visitchild (/tmp/pkgsrc/devel/py-cython/work/Cython-0.13/Cython/Compiler/Visitor.c:3455)
File "Visitor.py", line 179, in Cython.Compiler.Visitor.TreeVisitor.visitchild (/tmp/pkgsrc/devel/py-cython/work/Cython-0.13/Cython/Compiler/Visitor.c:3407)
File "Visitor.py", line 28, in Cython.Compiler.Visitor.BasicVisitor.visit (/tmp/pkgsrc/devel/py-cython/work/Cython-0.13/Cython/Compiler/Visitor.c:1178)
File "/usr/pkg/lib/python2.5/site-packages/Cython/Compiler/ParseTreeTransforms.py", line 94, in visit_StatNode
self.visitchildren(node)
File "Visitor.py", line 237, in Cython.Compiler.Visitor.VisitorTransform.visitchildren (/tmp/pkgsrc/devel/py-cython/work/Cython-0.13/Cython/Compiler/Visitor.c:4503)
File "Visitor.py", line 238, in Cython.Compiler.Visitor.VisitorTransform.visitchildren (/tmp/pkgsrc/devel/py-cython/work/Cython-0.13/Cython/Compiler/Visitor.c:4248)
File "Visitor.py", line 211, in Cython.Compiler.Visitor.TreeVisitor._visitchildren (/tmp/pkgsrc/devel/py-cython/work/Cython-0.13/Cython/Compiler/Visitor.c:4017)
File "Visitor.py", line 181, in Cython.Compiler.Visitor.TreeVisitor.visitchild (/tmp/pkgsrc/devel/py-cython/work/Cython-0.13/Cython/Compiler/Visitor.c:3455)
File "Visitor.py", line 179, in Cython.Compiler.Visitor.TreeVisitor.visitchild (/tmp/pkgsrc/devel/py-cython/work/Cython-0.13/Cython/Compiler/Visitor.c:3407)
File "Visitor.py", line 28, in Cython.Compiler.Visitor.BasicVisitor.visit (/tmp/pkgsrc/devel/py-cython/work/Cython-0.13/Cython/Compiler/Visitor.c:1178)
File "/usr/pkg/lib/python2.5/site-packages/Cython/Compiler/ParseTreeTransforms.py", line 94, in visit_StatNode
self.visitchildren(node)
File "Visitor.py", line 237, in Cython.Compiler.Visitor.VisitorTransform.visitchildren (/tmp/pkgsrc/devel/py-cython/work/Cython-0.13/Cython/Compiler/Visitor.c:4503)
File "Visitor.py", line 238, in Cython.Compiler.Visitor.VisitorTransform.visitchildren (/tmp/pkgsrc/devel/py-cython/work/Cython-0.13/Cython/Compiler/Visitor.c:4248)
File "Visitor.py", line 211, in Cython.Compiler.Visitor.TreeVisitor._visitchildren (/tmp/pkgsrc/devel/py-cython/work/Cython-0.13/Cython/Compiler/Visitor.c:4017)
File "Visitor.py", line 181, in Cython.Compiler.Visitor.TreeVisitor.visitchild (/tmp/pkgsrc/devel/py-cython/work/Cython-0.13/Cython/Compiler/Visitor.c:3455)
File "Visitor.py", line 179, in Cython.Compiler.Visitor.TreeVisitor.visitchild (/tmp/pkgsrc/devel/py-cython/work/Cython-0.13/Cython/Compiler/Visitor.c:3407)
File "Visitor.py", line 28, in Cython.Compiler.Visitor.BasicVisitor.visit (/tmp/pkgsrc/devel/py-cython/work/Cython-0.13/Cython/Compiler/Visitor.c:1178)
File "/usr/pkg/lib/python2.5/site-packages/Cython/Compiler/ParseTreeTransforms.py", line 103, in visit_StatListNode
self.visitchildren(node)
File "Visitor.py", line 237, in Cython.Compiler.Visitor.VisitorTransform.visitchildren (/tmp/pkgsrc/devel/py-cython/work/Cython-0.13/Cython/Compiler/Visitor.c:4503)
File "Visitor.py", line 238, in Cython.Compiler.Visitor.VisitorTransform.visitchildren (/tmp/pkgsrc/devel/py-cython/work/Cython-0.13/Cython/Compiler/Visitor.c:4248)
File "Visitor.py", line 209, in Cython.Compiler.Visitor.TreeVisitor._visitchildren (/tmp/pkgsrc/devel/py-cython/work/Cython-0.13/Cython/Compiler/Visitor.c:3995)
File "Visitor.py", line 185, in Cython.Compiler.Visitor.TreeVisitor.visitchild (/tmp/pkgsrc/devel/py-cython/work/Cython-0.13/Cython/Compiler/Visitor.c:3530)
File "Visitor.py", line 172, in Cython.Compiler.Visitor.TreeVisitor._raise_compiler_error (/tmp/pkgsrc/devel/py-cython/work/Cython-0.13/Cython/Compiler/Visitor.c:3274)
Cython.Compiler.Errors.CompilerCrash:
Error converting Pyrex file to C:
------------------------------------------------------------
...
EXIT = MGR.__exit__
MGR.__enter__()
EXC = True
try:
try:
EXCINFO = None
^
------------------------------------------------------------
(tree fragment):7:18: Compiler crash in NormalizeTree
StatListNode.stats[4] = TryFinallyStatNode((tree fragment):5:0,
preserve_exception = 1)
TryFinallyStatNode.body = TryExceptStatNode((tree fragment):6:4)
TryExceptStatNode.body = StatListNode((tree fragment):7:8)
StatListNode.stats[0] = SingleAssignmentNode((tree fragment):7:18)
Compiler crash traceback from this point on:
File "Visitor.py", line 179, in Cython.Compiler.Visitor.TreeVisitor.visitchild (/tmp/pkgsrc/devel/py-cython/work/Cython-0.13/Cython/Compiler/Visitor.c:3407)
File "Visitor.py", line 28, in Cython.Compiler.Visitor.BasicVisitor.visit (/tmp/pkgsrc/devel/py-cython/work/Cython-0.13/Cython/Compiler/Visitor.c:1178)
File "/usr/pkg/lib/python2.5/site-packages/Cython/Compiler/ParseTreeTransforms.py", line 94, in visit_StatNode
self.visitchildren(node)
SystemError: error return without exception set
/bin/sh: line 1: 17990 Segmentation fault /usr/bin/env USETOOLS=no PTHREAD_CFLAGS=\ -pthread\ PTHREAD_LDFLAGS=\ -pthread PTHREAD_LIBS=-lpthread\ -lrt PTHREADBASE=/usr DL_CFLAGS= DL_LDFLAGS= DL_LIBS= PYTHON=/usr/pkg/bin/python2.5 CC=gcc CFLAGS=-O3\ -pipe\ -fstack-protector\ -Wno-format\ -fno-builtin\ -I/usr/include\ -I/usr/pkg/include CPPFLAGS=-I/usr/include\ -I/usr/pkg/include CXX=g++ CXXFLAGS=-O3\ -pipe\ -fstack-protector\ -Wno-format\ -fno-builtin\ -I/usr/include\ -I/usr/pkg/include COMPILER_RPATH_FLAG=-Wl,-R F77=f77 FC=f77 FFLAGS=-O LANG=C LC_COLLATE=C LC_CTYPE=C LC_MESSAGES=C LC_MONETARY=C LC_NUMERIC=C LC_TIME=C LDFLAGS=-L/usr/lib\ -Wl,-R/usr/lib\ -L/usr/pkg/lib\ -Wl,-R/usr/pkg/lib LINKER_RPATH_FLAG=-R PATH=/tmp/pkgsrc/math/py-pytables/work/.wrapper/bin:/tmp/pkgsrc/math/py-pytables/work/.buildlink/bin:/tmp/pkgsrc/math/py-pytables/work/.gcc/bin:/tmp/pkgsrc/math/py-pytables/work/.tools/bin:/usr/pkg/bin:/bin:/usr/bin:/usr/pkg/bin:/usr/pkg/bin PREFIX=/usr/pkg PKG_SYSCONFDIR=/usr/pkg/etc CXXCPP=cpp HOME=/tmp/pkgsrc/math/py-pytables/work/.home CPP=cpp LINK_ALL_LIBGCC_HACK= LOCALBASE=/usr/pkg NO_WHOLE_ARCHIVE_FLAG=-Wl,--no-whole-archive WHOLE_ARCHIVE_FLAG=-Wl,--whole-archive X11BASE=/usr/pkg X11PREFIX=/usr/pkg PKGMANDIR=share/man PKGINFODIR=share/info MAKECONF=/dev/null OBJECT_FMT=ELF USETOOLS=no BSD_INSTALL_PROGRAM=/usr/bin/install\ -c\ -s\ -o\ pbulk\ -g\ pbulk\ -m\ 755 BSD_INSTALL_SCRIPT=/usr/bin/install\ -c\ -o\ pbulk\ -g\ pbulk\ -m\ 755 BSD_INSTALL_LIB=/usr/bin/install\ -c\ -o\ pbulk\ -g\ pbulk\ -m\ 755 BSD_INSTALL_DATA=/usr/bin/install\ -c\ -o\ pbulk\ -g\ pbulk\ -m\ 644 BSD_INSTALL_MAN=/usr/bin/install\ -c\ -o\ pbulk\ -g\ pbulk\ -m\ 644 BSD_INSTALL=/usr/bin/install BSD_INSTALL_PROGRAM_DIR=/usr/bin/install\ -d\ -o\ pbulk\ -g\ pbulk\ -m\ 755 BSD_INSTALL_SCRIPT_DIR=/usr/bin/install\ -d\ -o\ pbulk\ -g\ pbulk\ -m\ 755 BSD_INSTALL_LIB_DIR=/usr/bin/install\ -d\ -o\ pbulk\ -g\ pbulk\ -m\ 755 BSD_INSTALL_DATA_DIR=/usr/bin/install\ -d\ -o\ pbulk\ -g\ pbulk\ -m\ 755 BSD_INSTALL_MAN_DIR=/usr/bin/install\ -d\ -o\ pbulk\ -g\ pbulk\ -m\ 755 BSD_INSTALL_GAME=/usr/bin/install\ -c\ -s\ -o\ pbulk\ -g\ pbulk\ -m\ 2555 BSD_INSTALL_GAME_DATA=/usr/bin/install\ -c\ -o\ pbulk\ -g\ pbulk\ -m\ 664 BSD_INSTALL_GAME_DIR=/usr/bin/install\ -d\ -o\ pbulk\ -g\ pbulk\ -m\ 775 INSTALL_INFO= MAKEINFO=/tmp/pkgsrc/math/py-pytables/work/.tools/bin/makeinfo PKG_CONFIG= PKG_CONFIG_LIBDIR=/tmp/pkgsrc/math/py-pytables/work/.buildlink/lib/pkgconfig:/tmp/pkgsrc/math/py-pytables/work/.buildlink/share/pkgconfig PKG_CONFIG_LOG=/tmp/pkgsrc/math/py-pytables/work/.pkg-config.log PKG_CONFIG_PATH= WRAPPER_DEBUG=no WRAPPER_UPDATE_CACHE=yes VIEWBASE=/usr/pkg /usr/pkg/bin/python2.5 setup.py build --hdf5=/usr/pkg
*** Error code 139
Stop.
bmake: stopped in /usr/pkgsrc/math/py-pytables
*** Error code 1
Stop.
bmake: stopped in /usr/pkgsrc/math/py-pytables