Error building 9.0.beta6

[mmarco]

Hi,

I tried to update to the last beta an got an error when trying to compile numpy. The error persists on an installation from zero:

[numpy-1.16.1] gcc: build/src.linux-x86_64-3.7/numpy/core/src/multiarray/_multiarray_tests.c
[numpy-1.16.1] gcc: numpy/core/src/common/mem_overlap.c
[numpy-1.16.1] gcc -pthread -shared -L/home/mmarco/sagep3/local/lib -Wl,-rpath,/home/mmarco/sagep3/local/lib -L. -L/home/mmarco/sagep3/local/lib -Wl,-rpath,/home/mmarco/sagep3/local/lib -L/home/mmarco/sagep3/local/lib -Wl,-rpath,/home/mmarco/sagep3/local/lib -shared build/temp.linux-x86_64-3.7/build/src.linux-x86_64-3.7/numpy/core/src/multiarray/_multiarray_tests.o build/temp.linux-x86_64-3.7/numpy/core/src/common/mem_overlap.o -L/home/mmarco/sagep3/local/lib -Lbuild/temp.linux-x86_64-3.7 -lnpymath -lpython3.7m -o build/lib.linux-x86_64-3.7/numpy/core/_multiarray_tests.cpython-37m-x86_64-linux-gnu.so
[numpy-1.16.1] building 'numpy.core._multiarray_umath' extension
[numpy-1.16.1] compiling C sources
[numpy-1.16.1] C compiler: gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -Wno-unused -fPIC
[numpy-1.16.1]
[numpy-1.16.1] creating build/temp.linux-x86_64-3.7/numpy/core/src/multiarray
[numpy-1.16.1] creating build/temp.linux-x86_64-3.7/numpy/core/src/umath
[numpy-1.16.1] creating build/temp.linux-x86_64-3.7/build/src.linux-x86_64-3.7/numpy/core/src/umath
[numpy-1.16.1] compile options: '-DNPY_INTERNAL_BUILD=1 -DHAVE_NPY_CONFIG_H=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE=1 -D_LARGEFILE64_SOURCE=1 -DNO_ATLAS_INFO=1 -DHAVE_CBLAS -I/usr/include -I/home/mmarco/sagep3/local/include -Ibuild/src.linux-x86_64-3.7/numpy/core/src/umath -Ibuild/src.linux-x86_64-3.7/numpy/core/src/npymath -Ibuild/src.linux-x86_64-3.7/numpy/core/src/common -Inumpy/core/include -Ibuild/src.linux-x86_64-3.7/numpy/core/include/numpy -Inumpy/core/src/common -Inumpy/core/src -Inumpy/core -Inumpy/core/src/npymath -Inumpy/core/src/multiarray -Inumpy/core/src/umath -Inumpy/core/src/npysort -I/home/mmarco/sagep3/local/include/python3.7m -Ibuild/src.linux-x86_64-3.7/numpy/core/src/common -Ibuild/src.linux-x86_64-3.7/numpy/core/src/npymath -Ibuild/src.linux-x86_64-3.7/numpy/core/src/common -Ibuild/src.linux-x86_64-3.7/numpy/core/src/npymath -c'
[numpy-1.16.1] gcc: numpy/core/src/multiarray/alloc.c
[numpy-1.16.1] gcc: numpy/core/src/multiarray/array_assign_scalar.c
[numpy-1.16.1] gcc: numpy/core/src/multiarray/buffer.c
[numpy-1.16.1] gcc: numpy/core/src/multiarray/conversion_utils.c
[numpy-1.16.1] gcc: numpy/core/src/multiarray/common.c
[numpy-1.16.1] gcc: numpy/core/src/multiarray/datetime_strings.c
[numpy-1.16.1] gcc: numpy/core/src/multiarray/descriptor.c
[numpy-1.16.1] gcc: build/src.linux-x86_64-3.7/numpy/core/src/multiarray/einsum.c
[numpy-1.16.1] gcc: numpy/core/src/multiarray/arrayobject.c
[numpy-1.16.1] gcc: numpy/core/src/multiarray/array_assign_array.c
[numpy-1.16.1] gcc: numpy/core/src/multiarray/ctors.c
[numpy-1.16.1] gcc: numpy/core/src/multiarray/arrayfunction_override.c
[numpy-1.16.1] gcc: numpy/core/src/multiarray/datetime_busday.c
[numpy-1.16.1] gcc: numpy/core/src/multiarray/calculation.c
[numpy-1.16.1] gcc: numpy/core/src/multiarray/convert.c
[numpy-1.16.1] gcc: numpy/core/src/multiarray/hashdescr.c
[numpy-1.16.1] gcc: numpy/core/src/multiarray/item_selection.c
[numpy-1.16.1] gcc: numpy/core/src/multiarray/convert_datatype.c
[numpy-1.16.1] gcc: numpy/core/src/multiarray/datetime_busdaycal.c
[numpy-1.16.1] gcc: numpy/core/src/multiarray/compiled_base.c
[numpy-1.16.1] gcc: build/src.linux-x86_64-3.7/numpy/core/src/multiarray/arraytypes.c
[numpy-1.16.1] gcc: numpy/core/src/multiarray/dragon4.c
[numpy-1.16.1] gcc: build/src.linux-x86_64-3.7/numpy/core/src/multiarray/lowlevel_strided_loops.c
[numpy-1.16.1] gcc: numpy/core/src/multiarray/multiarraymodule.c
[numpy-1.16.1] gcc: numpy/core/src/multiarray/dtype_transfer.c
[numpy-1.16.1] gcc: numpy/core/src/multiarray/nditer_constr.c
[numpy-1.16.1] gcc: numpy/core/src/multiarray/datetime.c
[numpy-1.16.1] gcc: numpy/core/src/multiarray/iterators.c
[numpy-1.16.1] gcc: numpy/core/src/multiarray/refcount.c
[numpy-1.16.1] gcc: numpy/core/src/multiarray/scalarapi.c
[numpy-1.16.1] gcc: numpy/core/src/multiarray/nditer_pywrap.c
[numpy-1.16.1] gcc: numpy/core/src/multiarray/sequence.c
[numpy-1.16.1] gcc: numpy/core/src/multiarray/temp_elide.c
[numpy-1.16.1] gcc: numpy/core/src/multiarray/shape.c
[numpy-1.16.1] gcc: build/src.linux-x86_64-3.7/numpy/core/src/multiarray/scalartypes.c
[numpy-1.16.1] gcc: numpy/core/src/multiarray/typeinfo.c
[numpy-1.16.1] gcc: numpy/core/src/multiarray/usertypes.c
[numpy-1.16.1] gcc: numpy/core/src/multiarray/vdot.c
[numpy-1.16.1] gcc: build/src.linux-x86_64-3.7/numpy/core/src/umath/loops.c
[numpy-1.16.1] gcc: numpy/core/src/umath/umathmodule.c
[numpy-1.16.1] gcc: numpy/core/src/multiarray/number.c
[numpy-1.16.1] gcc: numpy/core/src/umath/reduction.c
[numpy-1.16.1] gcc: build/src.linux-x86_64-3.7/numpy/core/src/multiarray/nditer_templ.c
[numpy-1.16.1] gcc: numpy/core/src/umath/extobj.c
[numpy-1.16.1] gcc: numpy/core/src/umath/cpuid.c
[numpy-1.16.1] gcc: numpy/core/src/umath/ufunc_type_resolution.c
[numpy-1.16.1] gcc: build/src.linux-x86_64-3.7/numpy/core/src/umath/scalarmath.c
[numpy-1.16.1] gcc: numpy/core/src/multiarray/nditer_api.c
[numpy-1.16.1] gcc: numpy/core/src/umath/override.c
[numpy-1.16.1] gcc: numpy/core/src/multiarray/strfuncs.c
[numpy-1.16.1] gcc: numpy/core/src/multiarray/flagsobject.c
[numpy-1.16.1] gcc: numpy/core/src/npymath/npy_math.c
[numpy-1.16.1] gcc: build/src.linux-x86_64-3.7/numpy/core/src/npymath/ieee754.c
[numpy-1.16.1] gcc: build/src.linux-x86_64-3.7/numpy/core/src/npymath/npy_math_complex.c
[numpy-1.16.1] gcc: numpy/core/src/multiarray/getset.c
[numpy-1.16.1] gcc: numpy/core/src/common/array_assign.c
[numpy-1.16.1] gcc: numpy/core/src/common/mem_overlap.c
[numpy-1.16.1] gcc: numpy/core/src/npymath/halffloat.c
[numpy-1.16.1] gcc: numpy/core/src/common/ucsnarrow.c
[numpy-1.16.1] gcc: numpy/core/src/common/cblasfuncs.c
[numpy-1.16.1] gcc: numpy/core/src/common/ufunc_override.c
[numpy-1.16.1] gcc: numpy/core/src/common/numpyos.c
[numpy-1.16.1] gcc: numpy/core/src/common/python_xerbla.c
[numpy-1.16.1] gcc: numpy/core/src/common/npy_longdouble.c
[numpy-1.16.1] gcc: numpy/core/src/multiarray/mapping.c
[numpy-1.16.1] gcc: numpy/core/src/multiarray/methods.c
[numpy-1.16.1] gcc: build/src.linux-x86_64-3.7/numpy/core/src/umath/matmul.c
[numpy-1.16.1] gcc: numpy/core/src/umath/ufunc_object.c
[numpy-1.16.1] numpy/core/src/umath/ufunc_object.c: In function '_parse_signature':
[numpy-1.16.1] numpy/core/src/umath/ufunc_object.c:657:19: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare]
[numpy-1.16.1]   657 |     for (i = 0; i < len; i++) {
[numpy-1.16.1]       |                   ^
[numpy-1.16.1] gcc -pthread -shared -L/home/mmarco/sagep3/local/lib -Wl,-rpath,/home/mmarco/sagep3/local/lib -L. -L/home/mmarco/sagep3/local/lib -Wl,-rpath,/home/mmarco/sagep3/local/lib -L/home/mmarco/sagep3/local/lib -Wl,-rpath,/home/mmarco/sagep3/local/lib -shared build/temp.linux-x86_64-3.7/numpy/core/src/multiarray/alloc.o build/temp.linux-x86_64-3.7/numpy/core/src/multiarray/arrayobject.o build/temp.linux-x86_64-3.7/build/src.linux-x86_64-3.7/numpy/core/src/multiarray/arraytypes.o build/temp.linux-x86_64-3.7/numpy/core/src/multiarray/array_assign_scalar.o build/temp.linux-x86_64-3.7/numpy/core/src/multiarray/array_assign_array.o build/temp.linux-x86_64-3.7/numpy/core/src/multiarray/arrayfunction_override.o build/temp.linux-x86_64-3.7/numpy/core/src/multiarray/buffer.o build/temp.linux-x86_64-3.7/numpy/core/src/multiarray/calculation.o build/temp.linux-x86_64-3.7/numpy/core/src/multiarray/compiled_base.o build/temp.linux-x86_64-3.7/numpy/core/src/multiarray/common.o build/temp.linux-x86_64-3.7/numpy/core/src/multiarray/convert.o build/temp.linux-x86_64-3.7/numpy/core/src/multiarray/convert_datatype.o build/temp.linux-x86_64-3.7/numpy/core/src/multiarray/conversion_utils.o build/temp.linux-x86_64-3.7/numpy/core/src/multiarray/ctors.o build/temp.linux-x86_64-3.7/numpy/core/src/multiarray/datetime.o build/temp.linux-x86_64-3.7/numpy/core/src/multiarray/datetime_strings.o build/temp.linux-x86_64-3.7/numpy/core/src/multiarray/datetime_busday.o build/temp.linux-x86_64-3.7/numpy/core/src/multiarray/datetime_busdaycal.o build/temp.linux-x86_64-3.7/numpy/core/src/multiarray/descriptor.o build/temp.linux-x86_64-3.7/numpy/core/src/multiarray/dragon4.o build/temp.linux-x86_64-3.7/numpy/core/src/multiarray/dtype_transfer.o build/temp.linux-x86_64-3.7/build/src.linux-x86_64-3.7/numpy/core/src/multiarray/einsum.o build/temp.linux-x86_64-3.7/numpy/core/src/multiarray/flagsobject.o build/temp.linux-x86_64-3.7/numpy/core/src/multiarray/getset.o build/temp.linux-x86_64-3.7/numpy/core/src/multiarray/hashdescr.o build/temp.linux-x86_64-3.7/numpy/core/src/multiarray/item_selection.o build/temp.linux-x86_64-3.7/numpy/core/src/multiarray/iterators.o build/temp.linux-x86_64-3.7/build/src.linux-x86_64-3.7/numpy/core/src/multiarray/lowlevel_strided_loops.o build/temp.linux-x86_64-3.7/numpy/core/src/multiarray/mapping.o build/temp.linux-x86_64-3.7/numpy/core/src/multiarray/methods.o build/temp.linux-x86_64-3.7/numpy/core/src/multiarray/multiarraymodule.o build/temp.linux-x86_64-3.7/build/src.linux-x86_64-3.7/numpy/core/src/multiarray/nditer_templ.o build/temp.linux-x86_64-3.7/numpy/core/src/multiarray/nditer_api.o build/temp.linux-x86_64-3.7/numpy/core/src/multiarray/nditer_constr.o build/temp.linux-x86_64-3.7/numpy/core/src/multiarray/nditer_pywrap.o build/temp.linux-x86_64-3.7/numpy/core/src/multiarray/number.o build/temp.linux-x86_64-3.7/numpy/core/src/multiarray/refcount.o build/temp.linux-x86_64-3.7/numpy/core/src/multiarray/sequence.o build/temp.linux-x86_64-3.7/numpy/core/src/multiarray/shape.o build/temp.linux-x86_64-3.7/numpy/core/src/multiarray/scalarapi.o build/temp.linux-x86_64-3.7/build/src.linux-x86_64-3.7/numpy/core/src/multiarray/scalartypes.o build/temp.linux-x86_64-3.7/numpy/core/src/multiarray/strfuncs.o build/temp.linux-x86_64-3.7/numpy/core/src/multiarray/temp_elide.o build/temp.linux-x86_64-3.7/numpy/core/src/multiarray/typeinfo.o build/temp.linux-x86_64-3.7/numpy/core/src/multiarray/usertypes.o build/temp.linux-x86_64-3.7/numpy/core/src/multiarray/vdot.o build/temp.linux-x86_64-3.7/numpy/core/src/umath/umathmodule.o build/temp.linux-x86_64-3.7/numpy/core/src/umath/reduction.o build/temp.linux-x86_64-3.7/build/src.linux-x86_64-3.7/numpy/core/src/umath/loops.o build/temp.linux-x86_64-3.7/build/src.linux-x86_64-3.7/numpy/core/src/umath/matmul.o build/temp.linux-x86_64-3.7/numpy/core/src/umath/ufunc_object.o build/temp.linux-x86_64-3.7/numpy/core/src/umath/extobj.o build/temp.linux-x86_64-3.7/numpy/core/src/umath/cpuid.o build/temp.linux-x86_64-3.7/build/src.linux-x86_64-3.7/numpy/core/src/umath/scalarmath.o build/temp.linux-x86_64-3.7/numpy/core/src/umath/ufunc_type_resolution.o build/temp.linux-x86_64-3.7/numpy/core/src/umath/override.o build/temp.linux-x86_64-3.7/numpy/core/src/npymath/npy_math.o build/temp.linux-x86_64-3.7/build/src.linux-x86_64-3.7/numpy/core/src/npymath/ieee754.o build/temp.linux-x86_64-3.7/build/src.linux-x86_64-3.7/numpy/core/src/npymath/npy_math_complex.o build/temp.linux-x86_64-3.7/numpy/core/src/npymath/halffloat.o build/temp.linux-x86_64-3.7/numpy/core/src/common/array_assign.o build/temp.linux-x86_64-3.7/numpy/core/src/common/mem_overlap.o build/temp.linux-x86_64-3.7/numpy/core/src/common/npy_longdouble.o build/temp.linux-x86_64-3.7/numpy/core/src/common/ucsnarrow.o build/temp.linux-x86_64-3.7/numpy/core/src/common/ufunc_override.o build/temp.linux-x86_64-3.7/numpy/core/src/common/numpyos.o build/temp.linux-x86_64-3.7/numpy/core/src/common/cblasfuncs.o build/temp.linux-x86_64-3.7/numpy/core/src/common/python_xerbla.o -L/home/mmarco/sagep3/local/lib -L/usr/lib64 -L/home/mmarco/sagep3/local/lib -Lbuild/temp.linux-x86_64-3.7 -lnpymath -lnpysort -lopenblas -lblas -lm -lpython3.7m -o build/lib.linux-x86_64-3.7/numpy/core/_multiarray_umath.cpython-37m-x86_64-linux-gnu.so
[numpy-1.16.1] /usr/lib/gcc/x86_64-pc-linux-gnu/9.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: cannot find -lblas
[numpy-1.16.1] collect2: error: ld returned 1 exit status
[numpy-1.16.1] Running from numpy source directory.
[numpy-1.16.1] /home/mmarco/sagep3/local/var/tmp/sage/build/numpy-1.16.1/src/numpy/distutils/system_info.py:636: UserWarning:
[numpy-1.16.1]     Atlas (http://math-atlas.sourceforge.net/) libraries not found.
[numpy-1.16.1]     Directories to search for the libraries can be specified in the
[numpy-1.16.1]     numpy/distutils/site.cfg file (section [atlas]) or by setting
[numpy-1.16.1]     the ATLAS environment variable.
[numpy-1.16.1]   self.calc_info()
[numpy-1.16.1] /home/mmarco/sagep3/local/var/tmp/sage/build/numpy-1.16.1/src/numpy/distutils/system_info.py:636: UserWarning:
[numpy-1.16.1]     Atlas (http://math-atlas.sourceforge.net/) libraries not found.
[numpy-1.16.1]     Directories to search for the libraries can be specified in the
[numpy-1.16.1]     numpy/distutils/site.cfg file (section [atlas]) or by setting
[numpy-1.16.1]     the ATLAS environment variable.
[numpy-1.16.1]   self.calc_info()
[numpy-1.16.1] /home/mmarco/sagep3/local/lib/python3.7/distutils/dist.py:274: UserWarning: Unknown distribution option: 'define_macros'
[numpy-1.16.1]   warnings.warn(msg)
[numpy-1.16.1] /home/mmarco/sagep3/local/var/tmp/sage/build/numpy-1.16.1/src/numpy/distutils/fcompiler/__init__.py:517: UserWarning: FFLAGS is used as is, not appended to flags already defined by numpy.distutils! Use NPY_DISTUTILS_APPEND_FLAGS=1 to obtain appending behavior instead (this behavior will become default in a future release).
[numpy-1.16.1]   fflags = self.flag_vars.flags + dflags + oflags + aflags
[numpy-1.16.1] /home/mmarco/sagep3/local/var/tmp/sage/build/numpy-1.16.1/src/numpy/distutils/fcompiler/__init__.py:530: UserWarning: LDFLAGS is used as is, not appended to flags already defined by numpy.distutils! Use NPY_DISTUTILS_APPEND_FLAGS=1 to obtain appending behavior instead (this behavior will become default in a future release).
[numpy-1.16.1]   linker_so_flags = self.flag_vars.linker_so
[numpy-1.16.1] /home/mmarco/sagep3/local/var/tmp/sage/build/numpy-1.16.1/src/numpy/distutils/fcompiler/__init__.py:540: UserWarning: LDFLAGS is used as is, not appended to flags already defined by numpy.distutils! Use NPY_DISTUTILS_APPEND_FLAGS=1 to obtain appending behavior instead (this behavior will become default in a future release).
[numpy-1.16.1]   linker_exe_flags = self.flag_vars.linker_exe
[numpy-1.16.1] /home/mmarco/sagep3/local/var/tmp/sage/build/numpy-1.16.1/src/numpy/distutils/fcompiler/__init__.py:517: UserWarning: FFLAGS is used as is, not appended to flags already defined by numpy.distutils! Use NPY_DISTUTILS_APPEND_FLAGS=1 to obtain appending behavior instead (this behavior will become default in a future release).
[numpy-1.16.1]   fflags = self.flag_vars.flags + dflags + oflags + aflags
[numpy-1.16.1] /home/mmarco/sagep3/local/var/tmp/sage/build/numpy-1.16.1/src/numpy/distutils/fcompiler/__init__.py:530: UserWarning: LDFLAGS is used as is, not appended to flags already defined by numpy.distutils! Use NPY_DISTUTILS_APPEND_FLAGS=1 to obtain appending behavior instead (this behavior will become default in a future release).
[numpy-1.16.1]   linker_so_flags = self.flag_vars.linker_so
[numpy-1.16.1] /home/mmarco/sagep3/local/var/tmp/sage/build/numpy-1.16.1/src/numpy/distutils/fcompiler/__init__.py:540: UserWarning: LDFLAGS is used as is, not appended to flags already defined by numpy.distutils! Use NPY_DISTUTILS_APPEND_FLAGS=1 to obtain appending behavior instead (this behavior will become default in a future release).
[numpy-1.16.1]   linker_exe_flags = self.flag_vars.linker_exe
[numpy-1.16.1] error: Command "gcc -pthread -shared -L/home/mmarco/sagep3/local/lib -Wl,-rpath,/home/mmarco/sagep3/local/lib -L. -L/home/mmarco/sagep3/local/lib -Wl,-rpath,/home/mmarco/sagep3/local/lib -L/home/mmarco/sagep3/local/lib -Wl,-rpath,/home/mmarco/sagep3/local/lib -shared build/temp.linux-x86_64-3.7/numpy/core/src/multiarray/alloc.o build/temp.linux-x86_64-3.7/numpy/core/src/multiarray/arrayobject.o build/temp.linux-x86_64-3.7/build/src.linux-x86_64-3.7/numpy/core/src/multiarray/arraytypes.o build/temp.linux-x86_64-3.7/numpy/core/src/multiarray/array_assign_scalar.o build/temp.linux-x86_64-3.7/numpy/core/src/multiarray/array_assign_array.o build/temp.linux-x86_64-3.7/numpy/core/src/multiarray/arrayfunction_override.o build/temp.linux-x86_64-3.7/numpy/core/src/multiarray/buffer.o build/temp.linux-x86_64-3.7/numpy/core/src/multiarray/calculation.o build/temp.linux-x86_64-3.7/numpy/core/src/multiarray/compiled_base.o build/temp.linux-x86_64-3.7/numpy/core/src/multiarray/common.o build/temp.linux-x86_64-3.7/numpy/core/src/multiarray/convert.o build/temp.linux-x86_64-3.7/numpy/core/src/multiarray/convert_datatype.o build/temp.linux-x86_64-3.7/numpy/core/src/multiarray/conversion_utils.o build/temp.linux-x86_64-3.7/numpy/core/src/multiarray/ctors.o build/temp.linux-x86_64-3.7/numpy/core/src/multiarray/datetime.o build/temp.linux-x86_64-3.7/numpy/core/src/multiarray/datetime_strings.o build/temp.linux-x86_64-3.7/numpy/core/src/multiarray/datetime_busday.o build/temp.linux-x86_64-3.7/numpy/core/src/multiarray/datetime_busdaycal.o build/temp.linux-x86_64-3.7/numpy/core/src/multiarray/descriptor.o build/temp.linux-x86_64-3.7/numpy/core/src/multiarray/dragon4.o build/temp.linux-x86_64-3.7/numpy/core/src/multiarray/dtype_transfer.o build/temp.linux-x86_64-3.7/build/src.linux-x86_64-3.7/numpy/core/src/multiarray/einsum.o build/temp.linux-x86_64-3.7/numpy/core/src/multiarray/flagsobject.o build/temp.linux-x86_64-3.7/numpy/core/src/multiarray/getset.o build/temp.linux-x86_64-3.7/numpy/core/src/multiarray/hashdescr.o build/temp.linux-x86_64-3.7/numpy/core/src/multiarray/item_selection.o build/temp.linux-x86_64-3.7/numpy/core/src/multiarray/iterators.o build/temp.linux-x86_64-3.7/build/src.linux-x86_64-3.7/numpy/core/src/multiarray/lowlevel_strided_loops.o build/temp.linux-x86_64-3.7/numpy/core/src/multiarray/mapping.o build/temp.linux-x86_64-3.7/numpy/core/src/multiarray/methods.o build/temp.linux-x86_64-3.7/numpy/core/src/multiarray/multiarraymodule.o build/temp.linux-x86_64-3.7/build/src.linux-x86_64-3.7/numpy/core/src/multiarray/nditer_templ.o build/temp.linux-x86_64-3.7/numpy/core/src/multiarray/nditer_api.o build/temp.linux-x86_64-3.7/numpy/core/src/multiarray/nditer_constr.o build/temp.linux-x86_64-3.7/numpy/core/src/multiarray/nditer_pywrap.o build/temp.linux-x86_64-3.7/numpy/core/src/multiarray/number.o build/temp.linux-x86_64-3.7/numpy/core/src/multiarray/refcount.o build/temp.linux-x86_64-3.7/numpy/core/src/multiarray/sequence.o build/temp.linux-x86_64-3.7/numpy/core/src/multiarray/shape.o build/temp.linux-x86_64-3.7/numpy/core/src/multiarray/scalarapi.o build/temp.linux-x86_64-3.7/build/src.linux-x86_64-3.7/numpy/core/src/multiarray/scalartypes.o build/temp.linux-x86_64-3.7/numpy/core/src/multiarray/strfuncs.o build/temp.linux-x86_64-3.7/numpy/core/src/multiarray/temp_elide.o build/temp.linux-x86_64-3.7/numpy/core/src/multiarray/typeinfo.o build/temp.linux-x86_64-3.7/numpy/core/src/multiarray/usertypes.o build/temp.linux-x86_64-3.7/numpy/core/src/multiarray/vdot.o build/temp.linux-x86_64-3.7/numpy/core/src/umath/umathmodule.o build/temp.linux-x86_64-3.7/numpy/core/src/umath/reduction.o build/temp.linux-x86_64-3.7/build/src.linux-x86_64-3.7/numpy/core/src/umath/loops.o build/temp.linux-x86_64-3.7/build/src.linux-x86_64-3.7/numpy/core/src/umath/matmul.o build/temp.linux-x86_64-3.7/numpy/core/src/umath/ufunc_object.o build/temp.linux-x86_64-3.7/numpy/core/src/umath/extobj.o build/temp.linux-x86_64-3.7/numpy/core/src/umath/cpuid.o build/temp.linux-x86_64-3.7/build/src.linux-x86_64-3.7/numpy/core/src/umath/scalarmath.o build/temp.linux-x86_64-3.7/numpy/core/src/umath/ufunc_type_resolution.o build/temp.linux-x86_64-3.7/numpy/core/src/umath/override.o build/temp.linux-x86_64-3.7/numpy/core/src/npymath/npy_math.o build/temp.linux-x86_64-3.7/build/src.linux-x86_64-3.7/numpy/core/src/npymath/ieee754.o build/temp.linux-x86_64-3.7/build/src.linux-x86_64-3.7/numpy/core/src/npymath/npy_math_complex.o build/temp.linux-x86_64-3.7/numpy/core/src/npymath/halffloat.o build/temp.linux-x86_64-3.7/numpy/core/src/common/array_assign.o build/temp.linux-x86_64-3.7/numpy/core/src/common/mem_overlap.o build/temp.linux-x86_64-3.7/numpy/core/src/common/npy_longdouble.o build/temp.linux-x86_64-3.7/numpy/core/src/common/ucsnarrow.o build/temp.linux-x86_64-3.7/numpy/core/src/common/ufunc_override.o build/temp.linux-x86_64-3.7/numpy/core/src/common/numpyos.o build/temp.linux-x86_64-3.7/numpy/core/src/common/cblasfuncs.o build/temp.linux-x86_64-3.7/numpy/core/src/common/python_xerbla.o -L/home/mmarco/sagep3/local/lib -L/usr/lib64 -L/home/mmarco/sagep3/local/lib -Lbuild/temp.linux-x86_64-3.7 -lnpymath -lnpysort -lopenblas -lblas -lm -lpython3.7m -o build/lib.linux-x86_64-3.7/numpy/core/_multiarray_umath.cpython-37m-x86_64-linux-gnu.so" failed with exit status 1
[numpy-1.16.1] ************************************************************************************************************************************************************************************
[numpy-1.16.1] Error building / installing numpy
[numpy-1.16.1] ************************************************************************************************************************************************************************************
[numpy-1.16.1]
[numpy-1.16.1] real     1m9.458s
[numpy-1.16.1] user     2m31.554s
[numpy-1.16.1] sys      0m5.076s
[numpy-1.16.1] ************************************************************************
[numpy-1.16.1] Error installing package numpy-1.16.1
[numpy-1.16.1] ************************************************************************
[numpy-1.16.1] Please email sage-devel (http://groups.google.com/group/sage-devel)
[numpy-1.16.1] explaining the problem and including the log file
[numpy-1.16.1]   /home/mmarco/sagep3/logs/pkgs/numpy-1.16.1.log
[numpy-1.16.1] Describe your computer, operating system, etc.
[numpy-1.16.1] If you want to try to fix the problem yourself, *don't* just cd to
[numpy-1.16.1] /home/mmarco/sagep3/local/var/tmp/sage/build/numpy-1.16.1 and type 'make' or whatever is appropriate.
[numpy-1.16.1] Instead, the following commands setup all environment variables
[numpy-1.16.1] correctly and load a subshell for you to debug the error:
[numpy-1.16.1]   (cd '/home/mmarco/sagep3/local/var/tmp/sage/build/numpy-1.16.1' && '/home/mmarco/sagep3/sage' --sh)
[numpy-1.16.1] When you are done debugging, you can type "exit" to leave the subshell.
[numpy-1.16.1] ************************************************************************
make[3]: *** [Makefile:2151: /home/mmarco/sagep3/local/var/lib/sage/installed/numpy-1.16.1] Error 1
make[3]: se sale del directorio '/home/mmarco/sagep3/build/make'
make[2]: *** [Makefile:1829: all-start] Error 2
make[2]: se sale del directorio '/home/mmarco/sagep3/build/make'

real    79m33,742s
user    94m17,108s
sys     7m4,820s
***************************************************************
Error building Sage.

Somebody else has experienced something like this?

[Dima Pasechnik]

On Wed, Nov 20, 2019 at 8:26 AM mmarco <mma...@unizar.es> wrote:
>
> Hi,
>
> I tried to update to the last beta an got an error when trying to compile numpy. The error persists on an installation from zero:

are you trying to use external blas/lapack?

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[mmarco]

I didn't do anything specific to try to use external blas/lapack. How can I check if sage is trying to?

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[Dima Pasechnik]

On Wed, Nov 20, 2019 at 5:25 PM mmarco <mma...@unizar.es> wrote:
>
> I didn't do anything specific to try to use external blas/lapack. How can I check if sage is trying to?

I just though you might be doing something like this, based on a
bizarre error your log shows:

[numpy-1.16.1] /usr/lib/gcc/x86_64-pc-linux-gnu/9.2.0/../../../../x86_64-pc-linux-gnu/bin/ld:
cannot find -lblas

Normally speaking, if you use openblas from Sage, there is no -lblas
anywhere in the linking commands of Numpy, cause
Numpy configuration would try to look for blas, not find it, and do
not try to link against blas.so at all.

Have a look in logs/pkgs/numpy-1.16.1.log to see where it finds blas.
E.g. in the log on my machine I see there

Library blas was not found. Ignoring
FOUND:
libraries = ['openblas']
library_dirs = ['/home/dimpase/sage/local/lib']
language = c
define_macros = [('HAVE_CBLAS', None)]
include_dirs = ['/home/dimpase/sage/local/include']

HTH
Dima

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[mmarco]

The log shows this:

 FOUND:
    libraries = ['openblas', 'blas']
    library_dirs = ['/home/mmarco/sagep3/local/lib', '/usr/lib64']
    include_dirs = ['/usr/include', '/home/mmarco/sagep3/local/include']
    language = c
--

  FOUND:
    define_macros = [('NO_ATLAS_INFO', 1), ('HAVE_CBLAS', None)]
    libraries = ['openblas', 'blas']
    library_dirs = ['/home/mmarco/sagep3/local/lib', '/usr/lib64']
    include_dirs = ['/usr/include', '/home/mmarco/sagep3/local/include']
    language = c

  FOUND:
    libraries = ['openblas']
    library_dirs = ['/home/mmarco/sagep3/local/lib']
    language = f77

  FOUND:
    define_macros = [('NO_ATLAS_INFO', 1), ('HAVE_CBLAS', None)]
    libraries = ['openblas', 'openblas', 'blas']
    library_dirs = ['/home/mmarco/sagep3/local/lib', '/usr/lib64']
    language = c
    include_dirs = ['/usr/include', '/home/mmarco/sagep3/local/include']

> To view this discussion on the web visit https://groups.google.com/d/msgid/sage-devel/5218bcb7-a559-4236-af00-d8be40a0febb%40googlegroups.com.

[Dima Pasechnik]

On Wed, Nov 20, 2019 at 5:45 PM mmarco <mma...@unizar.es> wrote:
>
> The log shows this:
>
>
>
>
> FOUND:
> libraries = ['openblas', 'blas']
> library_dirs = ['/home/mmarco/sagep3/local/lib', '/usr/lib64']
> include_dirs = ['/usr/include', '/home/mmarco/sagep3/local/include']
> language = c
> --
>
> FOUND:
> define_macros = [('NO_ATLAS_INFO', 1), ('HAVE_CBLAS', None)]
> libraries = ['openblas', 'blas']
> library_dirs = ['/home/mmarco/sagep3/local/lib', '/usr/lib64']
> include_dirs = ['/usr/include', '/home/mmarco/sagep3/local/include']
> language = c
>
>
> FOUND:
> libraries = ['openblas']
> library_dirs = ['/home/mmarco/sagep3/local/lib']
> language = f77
>
> FOUND:
> define_macros = [('NO_ATLAS_INFO', 1), ('HAVE_CBLAS', None)]
> libraries = ['openblas', 'openblas', 'blas']
> library_dirs = ['/home/mmarco/sagep3/local/lib', '/usr/lib64']
> language = c
> include_dirs = ['/usr/include', '/home/mmarco/sagep3/local/include']

OK, so my diagnosis was correct. An immediate workaround would be to
get rid of blas.so in /usr/lib64
just temporarily, to enable Numpy to build, then you can put it back

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[Dima Pasechnik]

It might also be that in your case the patch we apply:
build/pkgs/numpy/patches/numpy-1.10.2-no-hardcode-blas.patch
does more harm than good.

[mmarco]

I see, thanks.

Is it a default behaviour?

[Dima Pasechnik]

On Wed, 20 Nov 2019 at 18:09, mmarco <mma...@unizar.es> wrote:

I see, thanks.

Is it a default behaviour?

no, it appears that you have a weird configuration, e.g. I have libblas installed systemwide, but things just work.

Perhaps it is a Numpy bug.

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[mmarco]

I might have found an explanation: I had some broken symlinks in /usr/lib64 named libblas.*

Aparently my package manager didn't remove them after uninstalling an old blas version

El miércoles, 20 de noviembre de 2019, 19:30:42 (UTC+1), Dima Pasechnik escribió:

On Wed, 20 Nov 2019 at 18:09, mmarco <mma...@unizar.es> wrote:

I see, thanks.

Is it a default behaviour?

no, it appears that you have a weird configuration, e.g. I have libblas installed systemwide, but things just work.

Perhaps it is a Numpy bug.

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