------------------------------------------------------------------------------- -- 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 Installing /packages/All/py37-cython-0.29.15.txz UNFLAVORED devel/binutils -> use devel/binutils@native SUCCEEDED 00:00:38 ------------------------------------------------------------------------------- -- Phase: check-sanity ------------------------------------------------------------------------------- SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: pkg-depends ------------------------------------------------------------------------------- ===> py37-gsd-1.10.0 depends on file: /usr/local/sbin/pkg - found SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: fetch-depends ------------------------------------------------------------------------------- SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: fetch ------------------------------------------------------------------------------- ===> py37-gsd-1.10.0 depends on file: /usr/local/sbin/pkg - found ===> Fetching all distfiles required by py37-gsd-1.10.0 for building SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: checksum ------------------------------------------------------------------------------- ===> py37-gsd-1.10.0 depends on file: /usr/local/sbin/pkg - found ===> Fetching all distfiles required by py37-gsd-1.10.0 for building => SHA256 Checksum OK for gsd-v1.10.0.tar.gz. SUCCEEDED 00:00:01 ------------------------------------------------------------------------------- -- Phase: extract-depends ------------------------------------------------------------------------------- SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: extract ------------------------------------------------------------------------------- ===> py37-gsd-1.10.0 depends on file: /usr/local/sbin/pkg - found ===> Fetching all distfiles required by py37-gsd-1.10.0 for building ===> Extracting for py37-gsd-1.10.0 => SHA256 Checksum OK for gsd-v1.10.0.tar.gz. Extracted Memory Use: 0.54M SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: patch-depends ------------------------------------------------------------------------------- SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: patch ------------------------------------------------------------------------------- ===> Patching for py37-gsd-1.10.0 SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: build-depends ------------------------------------------------------------------------------- ===> py37-gsd-1.10.0 depends on package: py37-numpy>=1.16,1<1.19,1 - found ===> py37-gsd-1.10.0 depends on executable: cython-3.7 - found ===> py37-gsd-1.10.0 depends on package: py37-setuptools>0 - found ===> py37-gsd-1.10.0 depends on file: /usr/local/bin/python3.7 - found SUCCEEDED 00:00:01 ------------------------------------------------------------------------------- -- Phase: lib-depends ------------------------------------------------------------------------------- SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: configure ------------------------------------------------------------------------------- ===> py37-gsd-1.10.0 depends on package: py37-numpy>=1.16,1<1.19,1 - found ===> py37-gsd-1.10.0 depends on executable: cython-3.7 - found ===> py37-gsd-1.10.0 depends on package: py37-setuptools>0 - found ===> py37-gsd-1.10.0 depends on file: /usr/local/bin/python3.7 - found ===> Configuring for py37-gsd-1.10.0 Compiling gsd/fl.pyx because it changed. [1/1] Cythonizing gsd/fl.pyx running config SUCCEEDED 00:00:07 ------------------------------------------------------------------------------- -- Phase: build ------------------------------------------------------------------------------- ===> Building for py37-gsd-1.10.0 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/gsd copying gsd/__init__.py -> build/lib.dragonfly-5.9-x86_64-3.7/gsd copying gsd/hoomd.py -> build/lib.dragonfly-5.9-x86_64-3.7/gsd copying gsd/pygsd.py -> build/lib.dragonfly-5.9-x86_64-3.7/gsd running build_ext building 'gsd.fl' extension creating build/temp.dragonfly-5.9-x86_64-3.7 creating build/temp.dragonfly-5.9-x86_64-3.7/gsd 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 -I./gsd -I/usr/local/lib/python3.7/site-packages/numpy/core/include -I/usr/local/include/python3.7m -c gsd/fl.c -o build/temp.dragonfly-5.9-x86_64-3.7/gsd/fl.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 gsd/fl.c:623: /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 -I./gsd -I/usr/local/lib/python3.7/site-packages/numpy/core/include -I/usr/local/include/python3.7m -c gsd/gsd.c -o build/temp.dragonfly-5.9-x86_64-3.7/gsd/gsd.o gsd/gsd.c: In function '__gsd_expand_index': gsd/gsd.c:161:50: warning: comparison of integer expressions of different signedness: 'ssize_t' {aka 'long int'} and 'long unsigned int' [-Wsign-compare] if (bytes_written == -1 || bytes_written != sizeof(struct gsd_index_entry) * handle->header.index_allocated_entries) ^~ gsd/gsd.c:189:48: warning: comparison of integer expressions of different signedness: 'ssize_t' {aka 'long int'} and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] if (bytes_read == -1 || bytes_read != bytes_to_copy) ^~ gsd/gsd.c:197:54: warning: comparison of integer expressions of different signedness: 'ssize_t' {aka 'long int'} and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] if (bytes_written == -1 || bytes_written != bytes_to_copy) ^~ gsd/gsd.c:216:54: warning: comparison of integer expressions of different signedness: 'ssize_t' {aka 'long int'} and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] if (bytes_written == -1 || bytes_written != bytes_to_copy) ^~ gsd/gsd.c: In function '__is_entry_valid': gsd/gsd.c:375:33: warning: comparison of integer expressions of different signedness: 'long unsigned int' and 'int64_t' {aka 'long int'} [-Wsign-compare] if ((entry.location + size) > handle->file_size) ^ gsd/gsd.c: In function '__gsd_read_header': gsd/gsd.c:457:117: warning: comparison of integer expressions of different signedness: 'long unsigned int' and 'int64_t' {aka 'long int'} [-Wsign-compare] if (handle->header.index_location + sizeof(struct gsd_index_entry) * handle->header.index_allocated_entries > handle->file_size) ^ gsd/gsd.c:470:44: warning: comparison of integer expressions of different signedness: 'ssize_t' {aka 'long int'} and 'long unsigned int' [-Wsign-compare] if (bytes_read == -1 || bytes_read != sizeof(struct gsd_index_entry) * handle->header.index_allocated_entries) ^~ gsd/gsd.c:496:122: warning: comparison of integer expressions of different signedness: 'long unsigned int' and 'int64_t' {aka 'long int'} [-Wsign-compare] if (handle->header.namelist_location + sizeof(struct gsd_namelist_entry) * handle->header.namelist_allocated_entries > handle->file_size) ^ gsd/gsd.c:509:40: warning: comparison of integer expressions of different signedness: 'ssize_t' {aka 'long int'} and 'long unsigned int' [-Wsign-compare] if (bytes_read == -1 || bytes_read != sizeof(struct gsd_namelist_entry) * handle->header.namelist_allocated_entries) ^~ gsd/gsd.c: In function 'gsd_end_frame': gsd/gsd.c:915:50: warning: comparison of integer expressions of different signedness: 'ssize_t' {aka 'long int'} and 'long unsigned int' [-Wsign-compare] if (bytes_written == -1 || bytes_written != sizeof(struct gsd_index_entry)*entries_to_write) ^~ gsd/gsd.c: In function 'gsd_write_chunk': gsd/gsd.c:982:46: warning: comparison of integer expressions of different signedness: 'ssize_t' {aka 'long int'} and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] if (bytes_written == -1 || bytes_written != size) ^~ gsd/gsd.c: In function 'gsd_read_chunk': gsd/gsd.c:1115:34: warning: comparison of integer expressions of different signedness: 'long unsigned int' and 'int64_t' {aka 'long int'} [-Wsign-compare] if ((chunk->location + size) > handle->file_size) ^ gsd/gsd.c:1121:40: warning: comparison of integer expressions of different signedness: 'ssize_t' {aka 'long int'} and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] if (bytes_read == -1 || bytes_read != size) ^~ cc -shared -pipe -O2 -fno-strict-aliasing build/temp.dragonfly-5.9-x86_64-3.7/gsd/fl.o build/temp.dragonfly-5.9-x86_64-3.7/gsd/gsd.o -L/usr/local/lib -lpython3.7m -o build/lib.dragonfly-5.9-x86_64-3.7/gsd/fl.so SUCCEEDED 00:00:12 ------------------------------------------------------------------------------- -- Phase: run-depends ------------------------------------------------------------------------------- ===> py37-gsd-1.10.0 depends on package: py37-numpy>=1.16,1<1.19,1 - found ===> py37-gsd-1.10.0 depends on package: py37-setuptools>0 - found ===> py37-gsd-1.10.0 depends on file: /usr/local/bin/python3.7 - found SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: stage ------------------------------------------------------------------------------- ===> Staging for py37-gsd-1.10.0 ===> py37-gsd-1.10.0 depends on package: py37-numpy>=1.16,1<1.19,1 - found ===> py37-gsd-1.10.0 depends on package: py37-setuptools>0 - found ===> py37-gsd-1.10.0 depends on file: /usr/local/bin/python3.7 - found ===> Generating temporary packing list running install running build running build_py running build_ext running install_lib creating /construction/science/py-gsd/stage/usr/local/lib/python3.7 creating /construction/science/py-gsd/stage/usr/local/lib/python3.7/site-packages creating /construction/science/py-gsd/stage/usr/local/lib/python3.7/site-packages/gsd copying build/lib.dragonfly-5.9-x86_64-3.7/gsd/pygsd.py -> /construction/science/py-gsd/stage/usr/local/lib/python3.7/site-packages/gsd copying build/lib.dragonfly-5.9-x86_64-3.7/gsd/hoomd.py -> /construction/science/py-gsd/stage/usr/local/lib/python3.7/site-packages/gsd copying build/lib.dragonfly-5.9-x86_64-3.7/gsd/__init__.py -> /construction/science/py-gsd/stage/usr/local/lib/python3.7/site-packages/gsd copying build/lib.dragonfly-5.9-x86_64-3.7/gsd/fl.so -> /construction/science/py-gsd/stage/usr/local/lib/python3.7/site-packages/gsd byte-compiling /construction/science/py-gsd/stage/usr/local/lib/python3.7/site-packages/gsd/pygsd.py to pygsd.cpython-37.pyc byte-compiling /construction/science/py-gsd/stage/usr/local/lib/python3.7/site-packages/gsd/hoomd.py to hoomd.cpython-37.pyc byte-compiling /construction/science/py-gsd/stage/usr/local/lib/python3.7/site-packages/gsd/__init__.py to __init__.cpython-37.pyc writing byte-compilation script '/tmp/tmp2twj8ath.py' /usr/local/bin/python3.7 /tmp/tmp2twj8ath.py removing /tmp/tmp2twj8ath.py running install_egg_info running egg_info creating gsd.egg-info writing gsd.egg-info/PKG-INFO writing dependency_links to gsd.egg-info/dependency_links.txt writing requirements to gsd.egg-info/requires.txt writing top-level names to gsd.egg-info/top_level.txt writing manifest file 'gsd.egg-info/SOURCES.txt' reading manifest file 'gsd.egg-info/SOURCES.txt' reading manifest template 'MANIFEST.in' warning: no files found matching 'ChangeLog.md' writing manifest file 'gsd.egg-info/SOURCES.txt' Copying gsd.egg-info to /construction/science/py-gsd/stage/usr/local/lib/python3.7/site-packages/gsd-1.10.0-py3.7.egg-info running install_scripts writing list of installed files to '/construction/science/py-gsd/.PLIST.pymodtmp' ====> Compressing man pages (compress-man) ====> Running Q/A tests (stage-qa) Warning: 'lib/python3.7/site-packages/gsd/fl.so' is not stripped consider trying INSTALL_TARGET=install-strip or using ${STRIP_CMD} Error: /usr/local/lib/python3.7/site-packages/gsd/fl.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-gsd-1.10.0 file sizes/checksums [15]: 0% file sizes/checksums [15]: 100% packing files [15]: 0% packing files [15]: 100% packing directories [0]: 0% packing directories [0]: 100% SUCCEEDED 00:00:00 TOTAL TIME 00:01:03