------------------------------------------------------------------------------- -- Phase: setup ------------------------------------------------------------------------------- Installing /packages/All/metis-5.1.0_8.txz Installing /packages/All/tbb-2020.2.txz Installing /packages/All/indexinfo-0.3.1.txz Installing /packages/All/gmp-6.2.0.txz Installing /packages/All/mpfr-4.0.2.txz Installing /packages/All/mpc-1.1.0_2.txz UNFLAVORED devel/binutils -> use devel/binutils@native Installing /packages/All/gettext-runtime-0.20.2.txz Installing /packages/All/binutils-2.33.1_2,1.txz Installing /packages/All/gcc8-8.4.0.txz ===== Message from gcc8-8.4.0: -- To ensure binaries built with this toolchain find appropriate versions of the necessary run-time libraries, you may want to link using -Wl,-rpath=/usr/local/lib/gcc8 For ports leveraging USE_GCC, USES=compiler, or USES=fortran this happens transparently. Installing /packages/All/openblas-0.3.9_2,1.txz Installing /packages/All/suitesparse-5.7.2_1.txz Installing /packages/All/libffi-3.2.1_3.txz Installing /packages/All/expat-2.2.8.txz Installing /packages/All/ncurses-6.1.20190525.txz Installing /packages/All/readline-8.0.4.txz Installing /packages/All/openssl-1.1.1g,1.txz Installing /packages/All/python37-3.7.7.txz ===== Message from python37-3.7.7: -- Note that some standard Python modules are provided as separate ports as they require additional dependencies. They are available as: py37-gdbm databases/py-gdbm@py37 py37-sqlite3 databases/py-sqlite3@py37 py37-tkinter x11-toolkits/py-tkinter@py37 Installing /packages/All/py37-setuptools-44.0.0.txz Installing /packages/All/py37-numpy-1.16.5_5,1.txz UNFLAVORED devel/binutils -> use devel/binutils@native SUCCEEDED 00:00:30 ------------------------------------------------------------------------------- -- Phase: check-sanity ------------------------------------------------------------------------------- SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: pkg-depends ------------------------------------------------------------------------------- ===> py37-spglib-1.14.1 depends on file: /usr/local/sbin/pkg - found SUCCEEDED 00:00:01 ------------------------------------------------------------------------------- -- Phase: fetch-depends ------------------------------------------------------------------------------- SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: fetch ------------------------------------------------------------------------------- ===> py37-spglib-1.14.1 depends on file: /usr/local/sbin/pkg - found ===> Fetching all distfiles required by py37-spglib-1.14.1 for building SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: checksum ------------------------------------------------------------------------------- ===> py37-spglib-1.14.1 depends on file: /usr/local/sbin/pkg - found ===> Fetching all distfiles required by py37-spglib-1.14.1 for building => SHA256 Checksum OK for spglib-1.14.1.post0.tar.gz. SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: extract-depends ------------------------------------------------------------------------------- SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: extract ------------------------------------------------------------------------------- ===> py37-spglib-1.14.1 depends on file: /usr/local/sbin/pkg - found ===> Fetching all distfiles required by py37-spglib-1.14.1 for building ===> Extracting for py37-spglib-1.14.1 => SHA256 Checksum OK for spglib-1.14.1.post0.tar.gz. Extracted Memory Use: 10.44M SUCCEEDED 00:00:01 ------------------------------------------------------------------------------- -- Phase: patch-depends ------------------------------------------------------------------------------- SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: patch ------------------------------------------------------------------------------- ===> Patching for py37-spglib-1.14.1 SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: build-depends ------------------------------------------------------------------------------- ===> py37-spglib-1.14.1 depends on package: py37-numpy>=1.16,1<1.19,1 - found ===> py37-spglib-1.14.1 depends on package: py37-setuptools>0 - found ===> py37-spglib-1.14.1 depends on file: /usr/local/bin/python3.7 - found SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: lib-depends ------------------------------------------------------------------------------- SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: configure ------------------------------------------------------------------------------- ===> py37-spglib-1.14.1 depends on package: py37-numpy>=1.16,1<1.19,1 - found ===> py37-spglib-1.14.1 depends on package: py37-setuptools>0 - found ===> py37-spglib-1.14.1 depends on file: /usr/local/bin/python3.7 - found ===> Configuring for py37-spglib-1.14.1 setuptools is used. /usr/local/lib/python3.7/site-packages/setuptools/dist.py:476: UserWarning: Normalizing '1.14.1-0' to '1.14.1.post0' normalized_version, running config SUCCEEDED 00:00:02 ------------------------------------------------------------------------------- -- Phase: build ------------------------------------------------------------------------------- ===> Building for py37-spglib-1.14.1 setuptools is used. /usr/local/lib/python3.7/site-packages/setuptools/dist.py:476: UserWarning: Normalizing '1.14.1-0' to '1.14.1.post0' normalized_version, running build running build_py creating build creating build/lib.dragonfly-5.9-x86_64-3.7 creating build/lib.dragonfly-5.9-x86_64-3.7/spglib copying spglib/__init__.py -> build/lib.dragonfly-5.9-x86_64-3.7/spglib copying spglib/spglib.py -> build/lib.dragonfly-5.9-x86_64-3.7/spglib running build_ext building 'spglib._spglib' extension creating build/temp.dragonfly-5.9-x86_64-3.7 creating build/temp.dragonfly-5.9-x86_64-3.7/src cc -Wno-unused-result -Wsign-compare -DNDEBUG -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -fPIC -Isrc -I/usr/local/include/python3.7m -I/usr/local/lib/python3.7/site-packages/numpy/core/include -c _spglib.c -o build/temp.dragonfly-5.9-x86_64-3.7/_spglib.o In file included from /usr/local/lib/python3.7/site-packages/numpy/core/include/numpy/ndarraytypes.h:1822, from /usr/local/lib/python3.7/site-packages/numpy/core/include/numpy/ndarrayobject.h:12, from /usr/local/lib/python3.7/site-packages/numpy/core/include/numpy/arrayobject.h:4, from _spglib.c:38: /usr/local/lib/python3.7/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp] #warning "Using deprecated NumPy API, disable it with " \ ^~~~~~~ cc -Wno-unused-result -Wsign-compare -DNDEBUG -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -fPIC -Isrc -I/usr/local/include/python3.7m -I/usr/local/lib/python3.7/site-packages/numpy/core/include -c src/arithmetic.c -o build/temp.dragonfly-5.9-x86_64-3.7/src/arithmetic.o cc -Wno-unused-result -Wsign-compare -DNDEBUG -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -fPIC -Isrc -I/usr/local/include/python3.7m -I/usr/local/lib/python3.7/site-packages/numpy/core/include -c src/cell.c -o build/temp.dragonfly-5.9-x86_64-3.7/src/cell.o cc -Wno-unused-result -Wsign-compare -DNDEBUG -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -fPIC -Isrc -I/usr/local/include/python3.7m -I/usr/local/lib/python3.7/site-packages/numpy/core/include -c src/delaunay.c -o build/temp.dragonfly-5.9-x86_64-3.7/src/delaunay.o cc -Wno-unused-result -Wsign-compare -DNDEBUG -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -fPIC -Isrc -I/usr/local/include/python3.7m -I/usr/local/lib/python3.7/site-packages/numpy/core/include -c src/debug.c -o build/temp.dragonfly-5.9-x86_64-3.7/src/debug.o cc -Wno-unused-result -Wsign-compare -DNDEBUG -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -fPIC -Isrc -I/usr/local/include/python3.7m -I/usr/local/lib/python3.7/site-packages/numpy/core/include -c src/determination.c -o build/temp.dragonfly-5.9-x86_64-3.7/src/determination.o cc -Wno-unused-result -Wsign-compare -DNDEBUG -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -fPIC -Isrc -I/usr/local/include/python3.7m -I/usr/local/lib/python3.7/site-packages/numpy/core/include -c src/hall_symbol.c -o build/temp.dragonfly-5.9-x86_64-3.7/src/hall_symbol.o cc -Wno-unused-result -Wsign-compare -DNDEBUG -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -fPIC -Isrc -I/usr/local/include/python3.7m -I/usr/local/lib/python3.7/site-packages/numpy/core/include -c src/kgrid.c -o build/temp.dragonfly-5.9-x86_64-3.7/src/kgrid.o cc -Wno-unused-result -Wsign-compare -DNDEBUG -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -fPIC -Isrc -I/usr/local/include/python3.7m -I/usr/local/lib/python3.7/site-packages/numpy/core/include -c src/kpoint.c -o build/temp.dragonfly-5.9-x86_64-3.7/src/kpoint.o src/kpoint.c: In function 'kpt_get_irreducible_reciprocal_mesh': src/kpoint.c:247:17: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long unsigned int'} and 'int' [-Wsign-compare] for (i = 0; i < mesh[0] * mesh[1] * mesh[2]; i++) { ^ src/kpoint.c: In function 'kpt_get_stabilized_reciprocal_mesh': src/kpoint.c:302:17: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long unsigned int'} and 'int' [-Wsign-compare] for (i = 0; i < mesh[0] * mesh[1] * mesh[2]; i++) { ^ src/kpoint.c: In function 'kpt_relocate_BZ_grid_address': src/kpoint.c:421:25: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long unsigned int'} and 'int' [-Wsign-compare] if (dense_bz_map[i] == num_bz_map) { ^~ src/kpoint.c: In function 'get_point_group_reciprocal_with_q': src/kpoint.c:567:19: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'const long unsigned int'} [-Wsign-compare] for (j = 0; j < num_q; j++) { ^ src/kpoint.c:573:21: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'const long unsigned int'} [-Wsign-compare] for (k = 0; k < num_q; k++) { ^ cc -Wno-unused-result -Wsign-compare -DNDEBUG -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -fPIC -Isrc -I/usr/local/include/python3.7m -I/usr/local/lib/python3.7/site-packages/numpy/core/include -c src/mathfunc.c -o build/temp.dragonfly-5.9-x86_64-3.7/src/mathfunc.o cc -Wno-unused-result -Wsign-compare -DNDEBUG -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -fPIC -Isrc -I/usr/local/include/python3.7m -I/usr/local/lib/python3.7/site-packages/numpy/core/include -c src/niggli.c -o build/temp.dragonfly-5.9-x86_64-3.7/src/niggli.o cc -Wno-unused-result -Wsign-compare -DNDEBUG -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -fPIC -Isrc -I/usr/local/include/python3.7m -I/usr/local/lib/python3.7/site-packages/numpy/core/include -c src/overlap.c -o build/temp.dragonfly-5.9-x86_64-3.7/src/overlap.o cc -Wno-unused-result -Wsign-compare -DNDEBUG -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -fPIC -Isrc -I/usr/local/include/python3.7m -I/usr/local/lib/python3.7/site-packages/numpy/core/include -c src/pointgroup.c -o build/temp.dragonfly-5.9-x86_64-3.7/src/pointgroup.o cc -Wno-unused-result -Wsign-compare -DNDEBUG -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -fPIC -Isrc -I/usr/local/include/python3.7m -I/usr/local/lib/python3.7/site-packages/numpy/core/include -c src/primitive.c -o build/temp.dragonfly-5.9-x86_64-3.7/src/primitive.o cc -Wno-unused-result -Wsign-compare -DNDEBUG -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -fPIC -Isrc -I/usr/local/include/python3.7m -I/usr/local/lib/python3.7/site-packages/numpy/core/include -c src/refinement.c -o build/temp.dragonfly-5.9-x86_64-3.7/src/refinement.o cc -Wno-unused-result -Wsign-compare -DNDEBUG -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -fPIC -Isrc -I/usr/local/include/python3.7m -I/usr/local/lib/python3.7/site-packages/numpy/core/include -c src/sitesym_database.c -o build/temp.dragonfly-5.9-x86_64-3.7/src/sitesym_database.o cc -Wno-unused-result -Wsign-compare -DNDEBUG -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -fPIC -Isrc -I/usr/local/include/python3.7m -I/usr/local/lib/python3.7/site-packages/numpy/core/include -c src/site_symmetry.c -o build/temp.dragonfly-5.9-x86_64-3.7/src/site_symmetry.o cc -Wno-unused-result -Wsign-compare -DNDEBUG -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -fPIC -Isrc -I/usr/local/include/python3.7m -I/usr/local/lib/python3.7/site-packages/numpy/core/include -c src/spacegroup.c -o build/temp.dragonfly-5.9-x86_64-3.7/src/spacegroup.o cc -Wno-unused-result -Wsign-compare -DNDEBUG -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -fPIC -Isrc -I/usr/local/include/python3.7m -I/usr/local/lib/python3.7/site-packages/numpy/core/include -c src/spin.c -o build/temp.dragonfly-5.9-x86_64-3.7/src/spin.o cc -Wno-unused-result -Wsign-compare -DNDEBUG -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -fPIC -Isrc -I/usr/local/include/python3.7m -I/usr/local/lib/python3.7/site-packages/numpy/core/include -c src/spg_database.c -o build/temp.dragonfly-5.9-x86_64-3.7/src/spg_database.o cc -Wno-unused-result -Wsign-compare -DNDEBUG -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -fPIC -Isrc -I/usr/local/include/python3.7m -I/usr/local/lib/python3.7/site-packages/numpy/core/include -c src/spglib.c -o build/temp.dragonfly-5.9-x86_64-3.7/src/spglib.o cc -Wno-unused-result -Wsign-compare -DNDEBUG -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -fPIC -Isrc -I/usr/local/include/python3.7m -I/usr/local/lib/python3.7/site-packages/numpy/core/include -c src/symmetry.c -o build/temp.dragonfly-5.9-x86_64-3.7/src/symmetry.o cc -shared -pipe -O2 -fno-strict-aliasing build/temp.dragonfly-5.9-x86_64-3.7/_spglib.o build/temp.dragonfly-5.9-x86_64-3.7/src/arithmetic.o build/temp.dragonfly-5.9-x86_64-3.7/src/cell.o build/temp.dragonfly-5.9-x86_64-3.7/src/delaunay.o build/temp.dragonfly-5.9-x86_64-3.7/src/debug.o build/temp.dragonfly-5.9-x86_64-3.7/src/determination.o build/temp.dragonfly-5.9-x86_64-3.7/src/hall_symbol.o build/temp.dragonfly-5.9-x86_64-3.7/src/kgrid.o build/temp.dragonfly-5.9-x86_64-3.7/src/kpoint.o build/temp.dragonfly-5.9-x86_64-3.7/src/mathfunc.o build/temp.dragonfly-5.9-x86_64-3.7/src/niggli.o build/temp.dragonfly-5.9-x86_64-3.7/src/overlap.o build/temp.dragonfly-5.9-x86_64-3.7/src/pointgroup.o build/temp.dragonfly-5.9-x86_64-3.7/src/primitive.o build/temp.dragonfly-5.9-x86_64-3.7/src/refinement.o build/temp.dragonfly-5.9-x86_64-3.7/src/sitesym_database.o build/temp.dragonfly-5.9-x86_64-3.7/src/site_symmetry.o build/temp.dragonfly-5.9-x86_64-3.7/src/spacegroup.o build/temp.dragonfly-5.9-x86_64-3.7/src/spin.o build/temp.dragonfly-5.9-x86_64-3.7/src/spg_database.o build/temp.dragonfly-5.9-x86_64-3.7/src/spglib.o build/temp.dragonfly-5.9-x86_64-3.7/src/symmetry.o -L/usr/local/lib -lpython3.7m -o build/lib.dragonfly-5.9-x86_64-3.7/spglib/_spglib.so SUCCEEDED 00:00:09 ------------------------------------------------------------------------------- -- Phase: run-depends ------------------------------------------------------------------------------- ===> py37-spglib-1.14.1 depends on package: py37-numpy>=1.16,1<1.19,1 - found ===> py37-spglib-1.14.1 depends on package: py37-setuptools>0 - found ===> py37-spglib-1.14.1 depends on file: /usr/local/bin/python3.7 - found SUCCEEDED 00:00:01 ------------------------------------------------------------------------------- -- Phase: stage ------------------------------------------------------------------------------- ===> Staging for py37-spglib-1.14.1 ===> py37-spglib-1.14.1 depends on package: py37-numpy>=1.16,1<1.19,1 - found ===> py37-spglib-1.14.1 depends on package: py37-setuptools>0 - found ===> py37-spglib-1.14.1 depends on file: /usr/local/bin/python3.7 - found ===> Generating temporary packing list setuptools is used. /usr/local/lib/python3.7/site-packages/setuptools/dist.py:476: UserWarning: Normalizing '1.14.1-0' to '1.14.1.post0' normalized_version, running install running build running build_py running build_ext running install_lib creating /construction/science/py-spglib/stage/usr/local/lib/python3.7 creating /construction/science/py-spglib/stage/usr/local/lib/python3.7/site-packages creating /construction/science/py-spglib/stage/usr/local/lib/python3.7/site-packages/spglib copying build/lib.dragonfly-5.9-x86_64-3.7/spglib/__init__.py -> /construction/science/py-spglib/stage/usr/local/lib/python3.7/site-packages/spglib copying build/lib.dragonfly-5.9-x86_64-3.7/spglib/spglib.py -> /construction/science/py-spglib/stage/usr/local/lib/python3.7/site-packages/spglib copying build/lib.dragonfly-5.9-x86_64-3.7/spglib/_spglib.so -> /construction/science/py-spglib/stage/usr/local/lib/python3.7/site-packages/spglib byte-compiling /construction/science/py-spglib/stage/usr/local/lib/python3.7/site-packages/spglib/__init__.py to __init__.cpython-37.pyc byte-compiling /construction/science/py-spglib/stage/usr/local/lib/python3.7/site-packages/spglib/spglib.py to spglib.cpython-37.pyc writing byte-compilation script '/tmp/tmp6rigsfs3.py' /usr/local/bin/python3.7 /tmp/tmp6rigsfs3.py removing /tmp/tmp6rigsfs3.py running install_egg_info running egg_info writing spglib.egg-info/PKG-INFO writing dependency_links to spglib.egg-info/dependency_links.txt writing requirements to spglib.egg-info/requires.txt writing top-level names to spglib.egg-info/top_level.txt reading manifest file 'spglib.egg-info/SOURCES.txt' reading manifest template 'MANIFEST.in' warning: no previously-included files matching '*.pyc' found under directory 'test' writing manifest file 'spglib.egg-info/SOURCES.txt' Copying spglib.egg-info to /construction/science/py-spglib/stage/usr/local/lib/python3.7/site-packages/spglib-1.14.1.post0-py3.7.egg-info running install_scripts writing list of installed files to '/construction/science/py-spglib/.PLIST.pymodtmp' ====> Compressing man pages (compress-man) ====> Running Q/A tests (stage-qa) Error: /usr/local/lib/python3.7/site-packages/spglib/_spglib.so is linked to /usr/local/lib/libintl.so.8 from devel/gettext-runtime but it is not declared as a dependency Warning: you need USES+=gettext-runtime Warning: You have disabled the licenses framework with DISABLE_LICENSES, unable to run checks SUCCEEDED 00:00:03 ------------------------------------------------------------------------------- -- Phase: package ------------------------------------------------------------------------------- ===> Building package for py37-spglib-1.14.1 file sizes/checksums [12]: 0% file sizes/checksums [12]: 100% packing files [12]: 0% packing files [12]: 100% packing directories [0]: 0% packing directories [0]: 100% SUCCEEDED 00:00:00 TOTAL TIME 00:00:47