------------------------------------------------------------------------------- -- Phase: setup ------------------------------------------------------------------------------- Installing /packages/All/metis-5.1.0_8.tgz Message from metis-5.1.0_8: ===> NOTICE: The metis port currently does not have a maintainer. As a result, it is more likely to have unresolved issues, not be up-to-date, or even be removed in the future. To volunteer to maintain this port, please create an issue at: https://bugs.freebsd.org/bugzilla More information about port maintainership is available at: https://www.freebsd.org/doc/en/articles/contributing/ports-contributing.html#maintain-port Installing /packages/All/indexinfo-0.3.1.tgz Installing /packages/All/gmp-6.1.2_1.tgz Installing /packages/All/mpfr-4.0.2.tgz Installing /packages/All/mpc-1.1.0_2.tgz Installing /packages/All/gettext-runtime-0.20.1.tgz Installing /packages/All/binutils-2.32_1,1.tgz Installing /packages/All/gcc8-8.3.0_3.tgz Message from gcc8-8.3.0_3: 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/blas-3.5.0_6.tgz Installing /packages/All/lapack-3.5.0_8.tgz Installing /packages/All/openblas-0.2.20_10,1.tgz Installing /packages/All/suitesparse-5.2.0_4.tgz Installing /packages/All/expat-2.2.6_1.tgz Installing /packages/All/libffi-3.2.1_3.tgz Installing /packages/All/ncurses-6.1.20190525.tgz Installing /packages/All/readline-8.0.0.tgz Installing /packages/All/openssl-1.0.2s,1.tgz Message from openssl-1.0.2s,1: Edit /usr/local/openssl/openssl.cnf to fit your needs. Installing /packages/All/python27-2.7.16_1.tgz Message from python27-2.7.16_1: =========================================================================== Note that some standard Python modules are provided as separate ports as they require additional dependencies. They are available as: bsddb databases/py-bsddb gdbm databases/py-gdbm sqlite3 databases/py-sqlite3 tkinter x11-toolkits/py-tkinter =========================================================================== Installing /packages/All/py27-setuptools-41.0.1.tgz Message from py27-setuptools-41.0.1: ******************************************************************* Only /usr/local/bin/easy_install-2.7 script has been installed since Python 2.7 is not the default Python version. ******************************************************************* Installing /packages/All/py27-numpy-1.16.4_1,1.tgz Installing /packages/All/py27-cython-0.29_1.tgz Installing /packages/All/hdf-szip-2.1.1.tgz Installing /packages/All/hdf5-1.10.5_2.tgz Installing /packages/All/libnghttp2-1.39.1_1.tgz Installing /packages/All/ca_root_nss-3.45.tgz Message from ca_root_nss-3.45: ********************************* WARNING ********************************* FreeBSD does not, and can not warrant that the certification authorities whose certificates are included in this package have in any way been audited for trustworthiness or RFC 3647 compliance. Assessment and verification of trust is the complete responsibility of the system administrator. *********************************** NOTE ********************************** This package installs symlinks to support root certificates discovery by default for software that uses OpenSSL. This enables SSL Certificate Verification by client software without manual intervention. If you prefer to do this manually, replace the following symlinks with either an empty file or your site-local certificate bundle. * /etc/ssl/cert.pem * /usr/local/etc/ssl/cert.pem * /usr/local/openssl/cert.pem *************************************************************************** Installing /packages/All/curl-7.65.3.tgz Installing /packages/All/pkgconf-1.6.1,1.tgz Installing /packages/All/netcdf-4.7.0.tgz SUCCEEDED 00:00:13 ------------------------------------------------------------------------------- -- Phase: check-sanity ------------------------------------------------------------------------------- x SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: pkg-depends ------------------------------------------------------------------------------- x SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: fetch-depends ------------------------------------------------------------------------------- x SUCCEEDED 00:00:01 ------------------------------------------------------------------------------- -- Phase: fetch ------------------------------------------------------------------------------- x===> Fetching all distfiles required by py27-ScientificPython-2.9.4_4 for building SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: checksum ------------------------------------------------------------------------------- x===> Fetching all distfiles required by py27-ScientificPython-2.9.4_4 for building => SHA256 Checksum OK for ScientificPython-2.9.4.tar.gz. SUCCEEDED 00:00:02 ------------------------------------------------------------------------------- -- Phase: extract-depends ------------------------------------------------------------------------------- x SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: extract ------------------------------------------------------------------------------- x===> Fetching all distfiles required by py27-ScientificPython-2.9.4_4 for building ===> Extracting for py27-ScientificPython-2.9.4_4 => SHA256 Checksum OK for ScientificPython-2.9.4.tar.gz. Extracted Memory Use: 7.56M SUCCEEDED 00:00:01 ------------------------------------------------------------------------------- -- Phase: patch-depends ------------------------------------------------------------------------------- x SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: patch ------------------------------------------------------------------------------- x===> Patching for py27-ScientificPython-2.9.4_4 SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: build-depends ------------------------------------------------------------------------------- x SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: lib-depends ------------------------------------------------------------------------------- x SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: configure ------------------------------------------------------------------------------- x===> Configuring for py27-ScientificPython-2.9.4_4 Using netCDF installation in /usr/local Compiling Scientific/_vector.pyx because it depends on /usr/local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd. Compiling Scientific/_affinitypropagation.pyx because it depends on /usr/local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd. Compiling Scientific/_interpolation.pyx because it depends on /usr/local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd. [1/3] Cythonizing Scientific/_affinitypropagation.pyx /usr/local/lib/python2.7/site-packages/Cython/Compiler/Main.py:367: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /construction/science/py-ScientificPython/ScientificPython-2.9.4/Scientific/_affinitypropagation.pyx tree = Parsing.p_module(s, pxd, full_module_name) [2/3] Cythonizing Scientific/_interpolation.pyx /usr/local/lib/python2.7/site-packages/Cython/Compiler/Main.py:367: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /construction/science/py-ScientificPython/ScientificPython-2.9.4/Scientific/_interpolation.pyx tree = Parsing.p_module(s, pxd, full_module_name) warning: Scientific/_interpolation.pyx:13:16: Non-trivial type declarators in shared declaration (e.g. mix of pointers and values). Each pointer declaration should be on its own line. warning: Scientific/_interpolation.pyx:13:25: Non-trivial type declarators in shared declaration (e.g. mix of pointers and values). Each pointer declaration should be on its own line. [3/3] Cythonizing Scientific/_vector.pyx /usr/local/lib/python2.7/site-packages/Cython/Compiler/Main.py:367: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /construction/science/py-ScientificPython/ScientificPython-2.9.4/Scientific/_vector.pyx tree = Parsing.p_module(s, pxd, full_module_name) running config SUCCEEDED 00:00:04 ------------------------------------------------------------------------------- -- Phase: build ------------------------------------------------------------------------------- x===> Building for py27-ScientificPython-2.9.4_4 Using netCDF installation in /usr/local running build running build_py creating build creating build/lib.dragonfly-5.7-x86_64-2.7 creating build/lib.dragonfly-5.7-x86_64-2.7/Scientific copying Scientific/__init__.py -> build/lib.dragonfly-5.7-x86_64-2.7/Scientific copying Scientific/__pkginfo__.py -> build/lib.dragonfly-5.7-x86_64-2.7/Scientific copying Scientific/DictWithDefault.py -> build/lib.dragonfly-5.7-x86_64-2.7/Scientific copying Scientific/FFT.py -> build/lib.dragonfly-5.7-x86_64-2.7/Scientific copying Scientific/indexing.py -> build/lib.dragonfly-5.7-x86_64-2.7/Scientific copying Scientific/LA.py -> build/lib.dragonfly-5.7-x86_64-2.7/Scientific copying Scientific/Mathematica.py -> build/lib.dragonfly-5.7-x86_64-2.7/Scientific copying Scientific/N.py -> build/lib.dragonfly-5.7-x86_64-2.7/Scientific copying Scientific/NRNG.py -> build/lib.dragonfly-5.7-x86_64-2.7/Scientific copying Scientific/NumberDict.py -> build/lib.dragonfly-5.7-x86_64-2.7/Scientific creating build/lib.dragonfly-5.7-x86_64-2.7/Scientific/Clustering copying Scientific/Clustering/__init__.py -> build/lib.dragonfly-5.7-x86_64-2.7/Scientific/Clustering copying Scientific/Clustering/AffinityPropagation.py -> build/lib.dragonfly-5.7-x86_64-2.7/Scientific/Clustering creating build/lib.dragonfly-5.7-x86_64-2.7/Scientific/Functions copying Scientific/Functions/__init__.py -> build/lib.dragonfly-5.7-x86_64-2.7/Scientific/Functions copying Scientific/Functions/Derivatives.py -> build/lib.dragonfly-5.7-x86_64-2.7/Scientific/Functions copying Scientific/Functions/FindRoot.py -> build/lib.dragonfly-5.7-x86_64-2.7/Scientific/Functions copying Scientific/Functions/FirstDerivatives.py -> build/lib.dragonfly-5.7-x86_64-2.7/Scientific/Functions copying Scientific/Functions/Interpolation.py -> build/lib.dragonfly-5.7-x86_64-2.7/Scientific/Functions copying Scientific/Functions/LeastSquares.py -> build/lib.dragonfly-5.7-x86_64-2.7/Scientific/Functions copying Scientific/Functions/Polynomial.py -> build/lib.dragonfly-5.7-x86_64-2.7/Scientific/Functions copying Scientific/Functions/Rational.py -> build/lib.dragonfly-5.7-x86_64-2.7/Scientific/Functions copying Scientific/Functions/Romberg.py -> build/lib.dragonfly-5.7-x86_64-2.7/Scientific/Functions creating build/lib.dragonfly-5.7-x86_64-2.7/Scientific/Geometry copying Scientific/Geometry/__init__.py -> build/lib.dragonfly-5.7-x86_64-2.7/Scientific/Geometry copying Scientific/Geometry/Objects3D.py -> build/lib.dragonfly-5.7-x86_64-2.7/Scientific/Geometry copying Scientific/Geometry/Quaternion.py -> build/lib.dragonfly-5.7-x86_64-2.7/Scientific/Geometry copying Scientific/Geometry/TensorAnalysis.py -> build/lib.dragonfly-5.7-x86_64-2.7/Scientific/Geometry copying Scientific/Geometry/TensorModule.py -> build/lib.dragonfly-5.7-x86_64-2.7/Scientific/Geometry copying Scientific/Geometry/Transformation.py -> build/lib.dragonfly-5.7-x86_64-2.7/Scientific/Geometry copying Scientific/Geometry/VectorModule.py -> build/lib.dragonfly-5.7-x86_64-2.7/Scientific/Geometry creating build/lib.dragonfly-5.7-x86_64-2.7/Scientific/IO copying Scientific/IO/__init__.py -> build/lib.dragonfly-5.7-x86_64-2.7/Scientific/IO copying Scientific/IO/ArrayIO.py -> build/lib.dragonfly-5.7-x86_64-2.7/Scientific/IO copying Scientific/IO/FortranFormat.py -> build/lib.dragonfly-5.7-x86_64-2.7/Scientific/IO copying Scientific/IO/NetCDF.py -> build/lib.dragonfly-5.7-x86_64-2.7/Scientific/IO copying Scientific/IO/PDB.py -> build/lib.dragonfly-5.7-x86_64-2.7/Scientific/IO copying Scientific/IO/PDBExportFilters.py -> build/lib.dragonfly-5.7-x86_64-2.7/Scientific/IO copying Scientific/IO/PDBSpaceGroups.py -> build/lib.dragonfly-5.7-x86_64-2.7/Scientific/IO copying Scientific/IO/TextFile.py -> build/lib.dragonfly-5.7-x86_64-2.7/Scientific/IO creating build/lib.dragonfly-5.7-x86_64-2.7/Scientific/Physics copying Scientific/Physics/__init__.py -> build/lib.dragonfly-5.7-x86_64-2.7/Scientific/Physics copying Scientific/Physics/PhysicalQuantities.py -> build/lib.dragonfly-5.7-x86_64-2.7/Scientific/Physics copying Scientific/Physics/Potential.py -> build/lib.dragonfly-5.7-x86_64-2.7/Scientific/Physics creating build/lib.dragonfly-5.7-x86_64-2.7/Scientific/QtWidgets copying Scientific/QtWidgets/__init__.py -> build/lib.dragonfly-5.7-x86_64-2.7/Scientific/QtWidgets copying Scientific/QtWidgets/qt_fake.py -> build/lib.dragonfly-5.7-x86_64-2.7/Scientific/QtWidgets copying Scientific/QtWidgets/QtPlotCanvas.py -> build/lib.dragonfly-5.7-x86_64-2.7/Scientific/QtWidgets copying Scientific/QtWidgets/QtVisualizationCanvas.py -> build/lib.dragonfly-5.7-x86_64-2.7/Scientific/QtWidgets creating build/lib.dragonfly-5.7-x86_64-2.7/Scientific/Statistics copying Scientific/Statistics/__init__.py -> build/lib.dragonfly-5.7-x86_64-2.7/Scientific/Statistics copying Scientific/Statistics/Histogram.py -> build/lib.dragonfly-5.7-x86_64-2.7/Scientific/Statistics creating build/lib.dragonfly-5.7-x86_64-2.7/Scientific/Signals copying Scientific/Signals/__init__.py -> build/lib.dragonfly-5.7-x86_64-2.7/Scientific/Signals copying Scientific/Signals/Models.py -> build/lib.dragonfly-5.7-x86_64-2.7/Scientific/Signals creating build/lib.dragonfly-5.7-x86_64-2.7/Scientific/Threading copying Scientific/Threading/__init__.py -> build/lib.dragonfly-5.7-x86_64-2.7/Scientific/Threading copying Scientific/Threading/TaskManager.py -> build/lib.dragonfly-5.7-x86_64-2.7/Scientific/Threading creating build/lib.dragonfly-5.7-x86_64-2.7/Scientific/TkWidgets copying Scientific/TkWidgets/__init__.py -> build/lib.dragonfly-5.7-x86_64-2.7/Scientific/TkWidgets copying Scientific/TkWidgets/TkPlotCanvas.py -> build/lib.dragonfly-5.7-x86_64-2.7/Scientific/TkWidgets copying Scientific/TkWidgets/TkVisualizationCanvas.py -> build/lib.dragonfly-5.7-x86_64-2.7/Scientific/TkWidgets copying Scientific/TkWidgets/Utility.py -> build/lib.dragonfly-5.7-x86_64-2.7/Scientific/TkWidgets creating build/lib.dragonfly-5.7-x86_64-2.7/Scientific/Visualization copying Scientific/Visualization/__init__.py -> build/lib.dragonfly-5.7-x86_64-2.7/Scientific/Visualization copying Scientific/Visualization/Chimera.py -> build/lib.dragonfly-5.7-x86_64-2.7/Scientific/Visualization copying Scientific/Visualization/Color.py -> build/lib.dragonfly-5.7-x86_64-2.7/Scientific/Visualization copying Scientific/Visualization/PyMOL.py -> build/lib.dragonfly-5.7-x86_64-2.7/Scientific/Visualization copying Scientific/Visualization/VMD.py -> build/lib.dragonfly-5.7-x86_64-2.7/Scientific/Visualization copying Scientific/Visualization/VPython.py -> build/lib.dragonfly-5.7-x86_64-2.7/Scientific/Visualization copying Scientific/Visualization/VRML.py -> build/lib.dragonfly-5.7-x86_64-2.7/Scientific/Visualization copying Scientific/Visualization/VRML2.py -> build/lib.dragonfly-5.7-x86_64-2.7/Scientific/Visualization creating build/lib.dragonfly-5.7-x86_64-2.7/Scientific/MPI copying Scientific/MPI/__init__.py -> build/lib.dragonfly-5.7-x86_64-2.7/Scientific/MPI copying Scientific/MPI/core.py -> build/lib.dragonfly-5.7-x86_64-2.7/Scientific/MPI copying Scientific/MPI/IO.py -> build/lib.dragonfly-5.7-x86_64-2.7/Scientific/MPI creating build/lib.dragonfly-5.7-x86_64-2.7/Scientific/DistributedComputing copying Scientific/DistributedComputing/__init__.py -> build/lib.dragonfly-5.7-x86_64-2.7/Scientific/DistributedComputing copying Scientific/DistributedComputing/MasterSlave.py -> build/lib.dragonfly-5.7-x86_64-2.7/Scientific/DistributedComputing copying Scientific/DistributedComputing/TaskManager.py -> build/lib.dragonfly-5.7-x86_64-2.7/Scientific/DistributedComputing creating build/lib.dragonfly-5.7-x86_64-2.7/Scientific/BSP copying Scientific/BSP/__init__.py -> build/lib.dragonfly-5.7-x86_64-2.7/Scientific/BSP copying Scientific/BSP/Console.py -> build/lib.dragonfly-5.7-x86_64-2.7/Scientific/BSP copying Scientific/BSP/core.py -> build/lib.dragonfly-5.7-x86_64-2.7/Scientific/BSP copying Scientific/BSP/IO.py -> build/lib.dragonfly-5.7-x86_64-2.7/Scientific/BSP running build_ext building 'Scientific._netcdf' extension Warning: Can't read registry to find the necessary compiler setting Make sure that Python modules _winreg, win32api or win32con are installed. C compiler: cc -DNDEBUG -pipe -O2 -fno-strict-aliasing -fPIC creating build/temp.dragonfly-5.7-x86_64-2.7 creating build/temp.dragonfly-5.7-x86_64-2.7/Scientific compile options: '-IInclude -I/usr/local/include -I/usr/local/lib/python2.7/site-packages/numpy/core/include -I/usr/local/include/python2.7 -c' extra options: '-DNUMPY=1' cc: Scientific/_netcdf.c In file included from /usr/local/lib/python2.7/site-packages/numpy/core/include/numpy/ndarraytypes.h:1822, from /usr/local/lib/python2.7/site-packages/numpy/core/include/numpy/ndarrayobject.h:12, from /usr/local/lib/python2.7/site-packages/numpy/core/include/numpy/arrayobject.h:4, from Scientific/_netcdf.c:14: /usr/local/lib/python2.7/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 " \ ^~~~~~~ Scientific/_netcdf.c:189:7: warning: 'NPY_CHAR' is deprecated: Use NPY_STRING [-Wdeprecated-declarations] PyArray_CHAR, /* 8-bit character */ ^~~~~~~~~~~~ In file included from /usr/local/lib/python2.7/site-packages/numpy/core/include/numpy/ndarrayobject.h:12, from /usr/local/lib/python2.7/site-packages/numpy/core/include/numpy/arrayobject.h:4, from Scientific/_netcdf.c:14: /usr/local/lib/python2.7/site-packages/numpy/core/include/numpy/ndarraytypes.h:84:21: note: declared here NPY_CHAR NPY_ATTR_DEPRECATE("Use NPY_STRING"), ^~~~~~~~ Scientific/_netcdf.c: In function 'typecode': Scientific/_netcdf.c:325:3: warning: 'NPY_CHAR' is deprecated: Use NPY_STRING [-Wdeprecated-declarations] case PyArray_CHAR: ^~~~ In file included from /usr/local/lib/python2.7/site-packages/numpy/core/include/numpy/ndarrayobject.h:12, from /usr/local/lib/python2.7/site-packages/numpy/core/include/numpy/arrayobject.h:4, from Scientific/_netcdf.c:14: /usr/local/lib/python2.7/site-packages/numpy/core/include/numpy/ndarraytypes.h:84:21: note: declared here NPY_CHAR NPY_ATTR_DEPRECATE("Use NPY_STRING"), ^~~~~~~~ Scientific/_netcdf.c: In function 'netcdf_type_from_type': Scientific/_netcdf.c:422:3: warning: 'NPY_CHAR' is deprecated: Use NPY_STRING [-Wdeprecated-declarations] case PyArray_CHAR: ^~~~ In file included from /usr/local/lib/python2.7/site-packages/numpy/core/include/numpy/ndarrayobject.h:12, from /usr/local/lib/python2.7/site-packages/numpy/core/include/numpy/arrayobject.h:4, from Scientific/_netcdf.c:14: /usr/local/lib/python2.7/site-packages/numpy/core/include/numpy/ndarraytypes.h:84:21: note: declared here NPY_CHAR NPY_ATTR_DEPRECATE("Use NPY_STRING"), ^~~~~~~~ Scientific/_netcdf.c: In function 'collect_attributes': Scientific/_netcdf.c:477:5: warning: 'NPY_CHAR' is deprecated: Use NPY_STRING [-Wdeprecated-declarations] if (py_type == PyArray_CHAR) { ^~ In file included from /usr/local/lib/python2.7/site-packages/numpy/core/include/numpy/ndarrayobject.h:12, from /usr/local/lib/python2.7/site-packages/numpy/core/include/numpy/arrayobject.h:4, from Scientific/_netcdf.c:14: /usr/local/lib/python2.7/site-packages/numpy/core/include/numpy/ndarraytypes.h:84:21: note: declared here NPY_CHAR NPY_ATTR_DEPRECATE("Use NPY_STRING"), ^~~~~~~~ Scientific/_netcdf.c: In function 'PyNetCDFVariable_ReadAsString': Scientific/_netcdf.c:1659:3: warning: 'NPY_CHAR' is deprecated: Use NPY_STRING [-Wdeprecated-declarations] if (self->type != PyArray_CHAR || self->nd != 1) { ^~ In file included from /usr/local/lib/python2.7/site-packages/numpy/core/include/numpy/ndarrayobject.h:12, from /usr/local/lib/python2.7/site-packages/numpy/core/include/numpy/arrayobject.h:4, from Scientific/_netcdf.c:14: /usr/local/lib/python2.7/site-packages/numpy/core/include/numpy/ndarraytypes.h:84:21: note: declared here NPY_CHAR NPY_ATTR_DEPRECATE("Use NPY_STRING"), ^~~~~~~~ Scientific/_netcdf.c: In function 'PyNetCDFVariable_WriteString': Scientific/_netcdf.c:1891:3: warning: 'NPY_CHAR' is deprecated: Use NPY_STRING [-Wdeprecated-declarations] if (self->type != PyArray_CHAR || self->nd != 1) { ^~ In file included from /usr/local/lib/python2.7/site-packages/numpy/core/include/numpy/ndarrayobject.h:12, from /usr/local/lib/python2.7/site-packages/numpy/core/include/numpy/arrayobject.h:4, from Scientific/_netcdf.c:14: /usr/local/lib/python2.7/site-packages/numpy/core/include/numpy/ndarraytypes.h:84:21: note: declared here NPY_CHAR NPY_ATTR_DEPRECATE("Use NPY_STRING"), ^~~~~~~~ cc -shared -pipe -O2 -fno-strict-aliasing build/temp.dragonfly-5.7-x86_64-2.7/Scientific/_netcdf.o -L/usr/local/lib -L/usr/local/lib -lnetcdf -lpython2.7 -o build/lib.dragonfly-5.7-x86_64-2.7/Scientific/_netcdf.so building 'Scientific._vector' extension C compiler: cc -DNDEBUG -pipe -O2 -fno-strict-aliasing -fPIC compile options: '-IInclude -I/usr/local/lib/python2.7/site-packages/numpy/core/include -I/usr/local/include/python2.7 -c' extra options: '-DNUMPY=1' cc: Scientific/_vector.c In file included from /usr/local/lib/python2.7/site-packages/numpy/core/include/numpy/ndarraytypes.h:1822, from /usr/local/lib/python2.7/site-packages/numpy/core/include/numpy/ndarrayobject.h:12, from /usr/local/lib/python2.7/site-packages/numpy/core/include/numpy/arrayobject.h:4, from Scientific/_vector.c:637: /usr/local/lib/python2.7/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 -shared -pipe -O2 -fno-strict-aliasing build/temp.dragonfly-5.7-x86_64-2.7/Scientific/_vector.o -L/usr/local/lib -lm -lpython2.7 -o build/lib.dragonfly-5.7-x86_64-2.7/Scientific/_vector.so building 'Scientific._affinitypropagation' extension C compiler: cc -DNDEBUG -pipe -O2 -fno-strict-aliasing -fPIC compile options: '-IInclude -I/usr/local/lib/python2.7/site-packages/numpy/core/include -I/usr/local/include/python2.7 -c' extra options: '-DNUMPY=1' cc: Scientific/_affinitypropagation.c In file included from /usr/local/lib/python2.7/site-packages/numpy/core/include/numpy/ndarraytypes.h:1822, from /usr/local/lib/python2.7/site-packages/numpy/core/include/numpy/ndarrayobject.h:12, from /usr/local/lib/python2.7/site-packages/numpy/core/include/numpy/arrayobject.h:4, from Scientific/_affinitypropagation.c:636: /usr/local/lib/python2.7/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 -shared -pipe -O2 -fno-strict-aliasing build/temp.dragonfly-5.7-x86_64-2.7/Scientific/_affinitypropagation.o -L/usr/local/lib -lm -lpython2.7 -o build/lib.dragonfly-5.7-x86_64-2.7/Scientific/_affinitypropagation.so building 'Scientific._interpolation' extension C compiler: cc -DNDEBUG -pipe -O2 -fno-strict-aliasing -fPIC compile options: '-IInclude -I/usr/local/lib/python2.7/site-packages/numpy/core/include -I/usr/local/include/python2.7 -c' extra options: '-DNUMPY=1' cc: Scientific/_interpolation.c In file included from /usr/local/lib/python2.7/site-packages/numpy/core/include/numpy/ndarraytypes.h:1822, from /usr/local/lib/python2.7/site-packages/numpy/core/include/numpy/ndarrayobject.h:12, from /usr/local/lib/python2.7/site-packages/numpy/core/include/numpy/arrayobject.h:4, from Scientific/_interpolation.c:636: /usr/local/lib/python2.7/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 -shared -pipe -O2 -fno-strict-aliasing build/temp.dragonfly-5.7-x86_64-2.7/Scientific/_interpolation.o -L/usr/local/lib -lm -lpython2.7 -o build/lib.dragonfly-5.7-x86_64-2.7/Scientific/_interpolation.so running build_scripts creating build/scripts-2.7 copying and adjusting task_manager -> build/scripts-2.7 copying and adjusting bsp_virtual -> build/scripts-2.7 changing mode of build/scripts-2.7/task_manager from 644 to 755 changing mode of build/scripts-2.7/bsp_virtual from 644 to 755 SUCCEEDED 00:00:08 ------------------------------------------------------------------------------- -- Phase: run-depends ------------------------------------------------------------------------------- x SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: stage ------------------------------------------------------------------------------- x===> Staging for py27-ScientificPython-2.9.4_4 ===> Generating temporary packing list Using netCDF installation in /usr/local running install running build running build_py running build_ext running build_scripts running install_lib creating /construction/science/py-ScientificPython/stage/usr/local/lib/python2.7 creating /construction/science/py-ScientificPython/stage/usr/local/lib/python2.7/site-packages creating /construction/science/py-ScientificPython/stage/usr/local/lib/python2.7/site-packages/Scientific copying build/lib.dragonfly-5.7-x86_64-2.7/Scientific/LA.py -> /construction/science/py-ScientificPython/stage/usr/local/lib/python2.7/site-packages/Scientific copying build/lib.dragonfly-5.7-x86_64-2.7/Scientific/Mathematica.py -> /construction/science/py-ScientificPython/stage/usr/local/lib/python2.7/site-packages/Scientific creating /construction/science/py-ScientificPython/stage/usr/local/lib/python2.7/site-packages/Scientific/DistributedComputing copying build/lib.dragonfly-5.7-x86_64-2.7/Scientific/DistributedComputing/TaskManager.py -> /construction/science/py-ScientificPython/stage/usr/local/lib/python2.7/site-packages/Scientific/DistributedComputing copying build/lib.dragonfly-5.7-x86_64-2.7/Scientific/DistributedComputing/__init__.py -> /construction/science/py-ScientificPython/stage/usr/local/lib/python2.7/site-packages/Scientific/DistributedComputing copying build/lib.dragonfly-5.7-x86_64-2.7/Scientific/DistributedComputing/MasterSlave.py -> /construction/science/py-ScientificPython/stage/usr/local/lib/python2.7/site-packages/Scientific/DistributedComputing creating /construction/science/py-ScientificPython/stage/usr/local/lib/python2.7/site-packages/Scientific/MPI copying build/lib.dragonfly-5.7-x86_64-2.7/Scientific/MPI/IO.py -> /construction/science/py-ScientificPython/stage/usr/local/lib/python2.7/site-packages/Scientific/MPI copying build/lib.dragonfly-5.7-x86_64-2.7/Scientific/MPI/core.py -> /construction/science/py-ScientificPython/stage/usr/local/lib/python2.7/site-packages/Scientific/MPI copying build/lib.dragonfly-5.7-x86_64-2.7/Scientific/MPI/__init__.py -> /construction/science/py-ScientificPython/stage/usr/local/lib/python2.7/site-packages/Scientific/MPI copying build/lib.dragonfly-5.7-x86_64-2.7/Scientific/NRNG.py -> /construction/science/py-ScientificPython/stage/usr/local/lib/python2.7/site-packages/Scientific creating /construction/science/py-ScientificPython/stage/usr/local/lib/python2.7/site-packages/Scientific/Geometry copying build/lib.dragonfly-5.7-x86_64-2.7/Scientific/Geometry/__init__.py -> /construction/science/py-ScientificPython/stage/usr/local/lib/python2.7/site-packages/Scientific/Geometry copying build/lib.dragonfly-5.7-x86_64-2.7/Scientific/Geometry/TensorModule.py -> /construction/science/py-ScientificPython/stage/usr/local/lib/python2.7/site-packages/Scientific/Geometry copying build/lib.dragonfly-5.7-x86_64-2.7/Scientific/Geometry/VectorModule.py -> /construction/science/py-ScientificPython/stage/usr/local/lib/python2.7/site-packages/Scientific/Geometry copying build/lib.dragonfly-5.7-x86_64-2.7/Scientific/Geometry/TensorAnalysis.py -> /construction/science/py-ScientificPython/stage/usr/local/lib/python2.7/site-packages/Scientific/Geometry copying build/lib.dragonfly-5.7-x86_64-2.7/Scientific/Geometry/Transformation.py -> /construction/science/py-ScientificPython/stage/usr/local/lib/python2.7/site-packages/Scientific/Geometry copying build/lib.dragonfly-5.7-x86_64-2.7/Scientific/Geometry/Quaternion.py -> /construction/science/py-ScientificPython/stage/usr/local/lib/python2.7/site-packages/Scientific/Geometry copying build/lib.dragonfly-5.7-x86_64-2.7/Scientific/Geometry/Objects3D.py -> /construction/science/py-ScientificPython/stage/usr/local/lib/python2.7/site-packages/Scientific/Geometry copying build/lib.dragonfly-5.7-x86_64-2.7/Scientific/FFT.py -> /construction/science/py-ScientificPython/stage/usr/local/lib/python2.7/site-packages/Scientific copying build/lib.dragonfly-5.7-x86_64-2.7/Scientific/DictWithDefault.py -> /construction/science/py-ScientificPython/stage/usr/local/lib/python2.7/site-packages/Scientific copying build/lib.dragonfly-5.7-x86_64-2.7/Scientific/__pkginfo__.py -> /construction/science/py-ScientificPython/stage/usr/local/lib/python2.7/site-packages/Scientific copying build/lib.dragonfly-5.7-x86_64-2.7/Scientific/N.py -> /construction/science/py-ScientificPython/stage/usr/local/lib/python2.7/site-packages/Scientific creating /construction/science/py-ScientificPython/stage/usr/local/lib/python2.7/site-packages/Scientific/Clustering copying build/lib.dragonfly-5.7-x86_64-2.7/Scientific/Clustering/AffinityPropagation.py -> /construction/science/py-ScientificPython/stage/usr/local/lib/python2.7/site-packages/Scientific/Clustering copying build/lib.dragonfly-5.7-x86_64-2.7/Scientific/Clustering/__init__.py -> /construction/science/py-ScientificPython/stage/usr/local/lib/python2.7/site-packages/Scientific/Clustering copying build/lib.dragonfly-5.7-x86_64-2.7/Scientific/__init__.py -> /construction/science/py-ScientificPython/stage/usr/local/lib/python2.7/site-packages/Scientific creating /construction/science/py-ScientificPython/stage/usr/local/lib/python2.7/site-packages/Scientific/Visualization copying build/lib.dragonfly-5.7-x86_64-2.7/Scientific/Visualization/Chimera.py -> /construction/science/py-ScientificPython/stage/usr/local/lib/python2.7/site-packages/Scientific/Visualization copying build/lib.dragonfly-5.7-x86_64-2.7/Scientific/Visualization/VMD.py -> /construction/science/py-ScientificPython/stage/usr/local/lib/python2.7/site-packages/Scientific/Visualization copying build/lib.dragonfly-5.7-x86_64-2.7/Scientific/Visualization/VPython.py -> /construction/science/py-ScientificPython/stage/usr/local/lib/python2.7/site-packages/Scientific/Visualization copying build/lib.dragonfly-5.7-x86_64-2.7/Scientific/Visualization/__init__.py -> /construction/science/py-ScientificPython/stage/usr/local/lib/python2.7/site-packages/Scientific/Visualization copying build/lib.dragonfly-5.7-x86_64-2.7/Scientific/Visualization/Color.py -> /construction/science/py-ScientificPython/stage/usr/local/lib/python2.7/site-packages/Scientific/Visualization copying build/lib.dragonfly-5.7-x86_64-2.7/Scientific/Visualization/VRML2.py -> /construction/science/py-ScientificPython/stage/usr/local/lib/python2.7/site-packages/Scientific/Visualization copying build/lib.dragonfly-5.7-x86_64-2.7/Scientific/Visualization/VRML.py -> /construction/science/py-ScientificPython/stage/usr/local/lib/python2.7/site-packages/Scientific/Visualization copying build/lib.dragonfly-5.7-x86_64-2.7/Scientific/Visualization/PyMOL.py -> /construction/science/py-ScientificPython/stage/usr/local/lib/python2.7/site-packages/Scientific/Visualization creating /construction/science/py-ScientificPython/stage/usr/local/lib/python2.7/site-packages/Scientific/IO copying build/lib.dragonfly-5.7-x86_64-2.7/Scientific/IO/FortranFormat.py -> /construction/science/py-ScientificPython/stage/usr/local/lib/python2.7/site-packages/Scientific/IO copying build/lib.dragonfly-5.7-x86_64-2.7/Scientific/IO/PDBSpaceGroups.py -> /construction/science/py-ScientificPython/stage/usr/local/lib/python2.7/site-packages/Scientific/IO copying build/lib.dragonfly-5.7-x86_64-2.7/Scientific/IO/PDB.py -> /construction/science/py-ScientificPython/stage/usr/local/lib/python2.7/site-packages/Scientific/IO copying build/lib.dragonfly-5.7-x86_64-2.7/Scientific/IO/NetCDF.py -> /construction/science/py-ScientificPython/stage/usr/local/lib/python2.7/site-packages/Scientific/IO copying build/lib.dragonfly-5.7-x86_64-2.7/Scientific/IO/ArrayIO.py -> /construction/science/py-ScientificPython/stage/usr/local/lib/python2.7/site-packages/Scientific/IO copying build/lib.dragonfly-5.7-x86_64-2.7/Scientific/IO/TextFile.py -> /construction/science/py-ScientificPython/stage/usr/local/lib/python2.7/site-packages/Scientific/IO copying build/lib.dragonfly-5.7-x86_64-2.7/Scientific/IO/PDBExportFilters.py -> /construction/science/py-ScientificPython/stage/usr/local/lib/python2.7/site-packages/Scientific/IO copying build/lib.dragonfly-5.7-x86_64-2.7/Scientific/IO/__init__.py -> /construction/science/py-ScientificPython/stage/usr/local/lib/python2.7/site-packages/Scientific/IO creating /construction/science/py-ScientificPython/stage/usr/local/lib/python2.7/site-packages/Scientific/TkWidgets copying build/lib.dragonfly-5.7-x86_64-2.7/Scientific/TkWidgets/TkVisualizationCanvas.py -> /construction/science/py-ScientificPython/stage/usr/local/lib/python2.7/site-packages/Scientific/TkWidgets copying build/lib.dragonfly-5.7-x86_64-2.7/Scientific/TkWidgets/TkPlotCanvas.py -> /construction/science/py-ScientificPython/stage/usr/local/lib/python2.7/site-packages/Scientific/TkWidgets copying build/lib.dragonfly-5.7-x86_64-2.7/Scientific/TkWidgets/__init__.py -> /construction/science/py-ScientificPython/stage/usr/local/lib/python2.7/site-packages/Scientific/TkWidgets copying build/lib.dragonfly-5.7-x86_64-2.7/Scientific/TkWidgets/Utility.py -> /construction/science/py-ScientificPython/stage/usr/local/lib/python2.7/site-packages/Scientific/TkWidgets creating /construction/science/py-ScientificPython/stage/usr/local/lib/python2.7/site-packages/Scientific/Threading copying build/lib.dragonfly-5.7-x86_64-2.7/Scientific/Threading/TaskManager.py -> /construction/science/py-ScientificPython/stage/usr/local/lib/python2.7/site-packages/Scientific/Threading copying build/lib.dragonfly-5.7-x86_64-2.7/Scientific/Threading/__init__.py -> /construction/science/py-ScientificPython/stage/usr/local/lib/python2.7/site-packages/Scientific/Threading creating /construction/science/py-ScientificPython/stage/usr/local/lib/python2.7/site-packages/Scientific/Statistics copying build/lib.dragonfly-5.7-x86_64-2.7/Scientific/Statistics/Histogram.py -> /construction/science/py-ScientificPython/stage/usr/local/lib/python2.7/site-packages/Scientific/Statistics copying build/lib.dragonfly-5.7-x86_64-2.7/Scientific/Statistics/__init__.py -> /construction/science/py-ScientificPython/stage/usr/local/lib/python2.7/site-packages/Scientific/Statistics copying build/lib.dragonfly-5.7-x86_64-2.7/Scientific/indexing.py -> /construction/science/py-ScientificPython/stage/usr/local/lib/python2.7/site-packages/Scientific creating /construction/science/py-ScientificPython/stage/usr/local/lib/python2.7/site-packages/Scientific/QtWidgets copying build/lib.dragonfly-5.7-x86_64-2.7/Scientific/QtWidgets/qt_fake.py -> /construction/science/py-ScientificPython/stage/usr/local/lib/python2.7/site-packages/Scientific/QtWidgets copying build/lib.dragonfly-5.7-x86_64-2.7/Scientific/QtWidgets/__init__.py -> /construction/science/py-ScientificPython/stage/usr/local/lib/python2.7/site-packages/Scientific/QtWidgets copying build/lib.dragonfly-5.7-x86_64-2.7/Scientific/QtWidgets/QtPlotCanvas.py -> /construction/science/py-ScientificPython/stage/usr/local/lib/python2.7/site-packages/Scientific/QtWidgets copying build/lib.dragonfly-5.7-x86_64-2.7/Scientific/QtWidgets/QtVisualizationCanvas.py -> /construction/science/py-ScientificPython/stage/usr/local/lib/python2.7/site-packages/Scientific/QtWidgets creating /construction/science/py-ScientificPython/stage/usr/local/lib/python2.7/site-packages/Scientific/Functions copying build/lib.dragonfly-5.7-x86_64-2.7/Scientific/Functions/LeastSquares.py -> /construction/science/py-ScientificPython/stage/usr/local/lib/python2.7/site-packages/Scientific/Functions copying build/lib.dragonfly-5.7-x86_64-2.7/Scientific/Functions/FirstDerivatives.py -> /construction/science/py-ScientificPython/stage/usr/local/lib/python2.7/site-packages/Scientific/Functions copying build/lib.dragonfly-5.7-x86_64-2.7/Scientific/Functions/Polynomial.py -> /construction/science/py-ScientificPython/stage/usr/local/lib/python2.7/site-packages/Scientific/Functions copying build/lib.dragonfly-5.7-x86_64-2.7/Scientific/Functions/Derivatives.py -> /construction/science/py-ScientificPython/stage/usr/local/lib/python2.7/site-packages/Scientific/Functions copying build/lib.dragonfly-5.7-x86_64-2.7/Scientific/Functions/Romberg.py -> /construction/science/py-ScientificPython/stage/usr/local/lib/python2.7/site-packages/Scientific/Functions copying build/lib.dragonfly-5.7-x86_64-2.7/Scientific/Functions/Rational.py -> /construction/science/py-ScientificPython/stage/usr/local/lib/python2.7/site-packages/Scientific/Functions copying build/lib.dragonfly-5.7-x86_64-2.7/Scientific/Functions/__init__.py -> /construction/science/py-ScientificPython/stage/usr/local/lib/python2.7/site-packages/Scientific/Functions copying build/lib.dragonfly-5.7-x86_64-2.7/Scientific/Functions/FindRoot.py -> /construction/science/py-ScientificPython/stage/usr/local/lib/python2.7/site-packages/Scientific/Functions copying build/lib.dragonfly-5.7-x86_64-2.7/Scientific/Functions/Interpolation.py -> /construction/science/py-ScientificPython/stage/usr/local/lib/python2.7/site-packages/Scientific/Functions copying build/lib.dragonfly-5.7-x86_64-2.7/Scientific/NumberDict.py -> /construction/science/py-ScientificPython/stage/usr/local/lib/python2.7/site-packages/Scientific creating /construction/science/py-ScientificPython/stage/usr/local/lib/python2.7/site-packages/Scientific/BSP copying build/lib.dragonfly-5.7-x86_64-2.7/Scientific/BSP/IO.py -> /construction/science/py-ScientificPython/stage/usr/local/lib/python2.7/site-packages/Scientific/BSP copying build/lib.dragonfly-5.7-x86_64-2.7/Scientific/BSP/__init__.py -> /construction/science/py-ScientificPython/stage/usr/local/lib/python2.7/site-packages/Scientific/BSP copying build/lib.dragonfly-5.7-x86_64-2.7/Scientific/BSP/Console.py -> /construction/science/py-ScientificPython/stage/usr/local/lib/python2.7/site-packages/Scientific/BSP copying build/lib.dragonfly-5.7-x86_64-2.7/Scientific/BSP/core.py -> /construction/science/py-ScientificPython/stage/usr/local/lib/python2.7/site-packages/Scientific/BSP creating /construction/science/py-ScientificPython/stage/usr/local/lib/python2.7/site-packages/Scientific/Signals copying build/lib.dragonfly-5.7-x86_64-2.7/Scientific/Signals/__init__.py -> /construction/science/py-ScientificPython/stage/usr/local/lib/python2.7/site-packages/Scientific/Signals copying build/lib.dragonfly-5.7-x86_64-2.7/Scientific/Signals/Models.py -> /construction/science/py-ScientificPython/stage/usr/local/lib/python2.7/site-packages/Scientific/Signals creating /construction/science/py-ScientificPython/stage/usr/local/lib/python2.7/site-packages/Scientific/Physics copying build/lib.dragonfly-5.7-x86_64-2.7/Scientific/Physics/__init__.py -> /construction/science/py-ScientificPython/stage/usr/local/lib/python2.7/site-packages/Scientific/Physics copying build/lib.dragonfly-5.7-x86_64-2.7/Scientific/Physics/PhysicalQuantities.py -> /construction/science/py-ScientificPython/stage/usr/local/lib/python2.7/site-packages/Scientific/Physics copying build/lib.dragonfly-5.7-x86_64-2.7/Scientific/Physics/Potential.py -> /construction/science/py-ScientificPython/stage/usr/local/lib/python2.7/site-packages/Scientific/Physics copying build/lib.dragonfly-5.7-x86_64-2.7/Scientific/_vector.so -> /construction/science/py-ScientificPython/stage/usr/local/lib/python2.7/site-packages/Scientific copying build/lib.dragonfly-5.7-x86_64-2.7/Scientific/_netcdf.so -> /construction/science/py-ScientificPython/stage/usr/local/lib/python2.7/site-packages/Scientific copying build/lib.dragonfly-5.7-x86_64-2.7/Scientific/_interpolation.so -> /construction/science/py-ScientificPython/stage/usr/local/lib/python2.7/site-packages/Scientific copying build/lib.dragonfly-5.7-x86_64-2.7/Scientific/_affinitypropagation.so -> /construction/science/py-ScientificPython/stage/usr/local/lib/python2.7/site-packages/Scientific byte-compiling /construction/science/py-ScientificPython/stage/usr/local/lib/python2.7/site-packages/Scientific/LA.py to LA.pyc byte-compiling /construction/science/py-ScientificPython/stage/usr/local/lib/python2.7/site-packages/Scientific/Mathematica.py to Mathematica.pyc byte-compiling /construction/science/py-ScientificPython/stage/usr/local/lib/python2.7/site-packages/Scientific/DistributedComputing/TaskManager.py to TaskManager.pyc byte-compiling /construction/science/py-ScientificPython/stage/usr/local/lib/python2.7/site-packages/Scientific/DistributedComputing/__init__.py to __init__.pyc byte-compiling /construction/science/py-ScientificPython/stage/usr/local/lib/python2.7/site-packages/Scientific/DistributedComputing/MasterSlave.py to MasterSlave.pyc byte-compiling /construction/science/py-ScientificPython/stage/usr/local/lib/python2.7/site-packages/Scientific/MPI/IO.py to IO.pyc byte-compiling /construction/science/py-ScientificPython/stage/usr/local/lib/python2.7/site-packages/Scientific/MPI/core.py to core.pyc byte-compiling /construction/science/py-ScientificPython/stage/usr/local/lib/python2.7/site-packages/Scientific/MPI/__init__.py to __init__.pyc byte-compiling /construction/science/py-ScientificPython/stage/usr/local/lib/python2.7/site-packages/Scientific/NRNG.py to NRNG.pyc byte-compiling /construction/science/py-ScientificPython/stage/usr/local/lib/python2.7/site-packages/Scientific/Geometry/__init__.py to __init__.pyc byte-compiling /construction/science/py-ScientificPython/stage/usr/local/lib/python2.7/site-packages/Scientific/Geometry/TensorModule.py to TensorModule.pyc byte-compiling /construction/science/py-ScientificPython/stage/usr/local/lib/python2.7/site-packages/Scientific/Geometry/VectorModule.py to VectorModule.pyc byte-compiling /construction/science/py-ScientificPython/stage/usr/local/lib/python2.7/site-packages/Scientific/Geometry/TensorAnalysis.py to TensorAnalysis.pyc byte-compiling /construction/science/py-ScientificPython/stage/usr/local/lib/python2.7/site-packages/Scientific/Geometry/Transformation.py to Transformation.pyc byte-compiling /construction/science/py-ScientificPython/stage/usr/local/lib/python2.7/site-packages/Scientific/Geometry/Quaternion.py to Quaternion.pyc byte-compiling /construction/science/py-ScientificPython/stage/usr/local/lib/python2.7/site-packages/Scientific/Geometry/Objects3D.py to Objects3D.pyc byte-compiling /construction/science/py-ScientificPython/stage/usr/local/lib/python2.7/site-packages/Scientific/FFT.py to FFT.pyc byte-compiling /construction/science/py-ScientificPython/stage/usr/local/lib/python2.7/site-packages/Scientific/DictWithDefault.py to DictWithDefault.pyc byte-compiling /construction/science/py-ScientificPython/stage/usr/local/lib/python2.7/site-packages/Scientific/__pkginfo__.py to __pkginfo__.pyc byte-compiling /construction/science/py-ScientificPython/stage/usr/local/lib/python2.7/site-packages/Scientific/N.py to N.pyc byte-compiling /construction/science/py-ScientificPython/stage/usr/local/lib/python2.7/site-packages/Scientific/Clustering/AffinityPropagation.py to AffinityPropagation.pyc byte-compiling /construction/science/py-ScientificPython/stage/usr/local/lib/python2.7/site-packages/Scientific/Clustering/__init__.py to __init__.pyc byte-compiling /construction/science/py-ScientificPython/stage/usr/local/lib/python2.7/site-packages/Scientific/__init__.py to __init__.pyc byte-compiling /construction/science/py-ScientificPython/stage/usr/local/lib/python2.7/site-packages/Scientific/Visualization/Chimera.py to Chimera.pyc byte-compiling /construction/science/py-ScientificPython/stage/usr/local/lib/python2.7/site-packages/Scientific/Visualization/VMD.py to VMD.pyc byte-compiling /construction/science/py-ScientificPython/stage/usr/local/lib/python2.7/site-packages/Scientific/Visualization/VPython.py to VPython.pyc byte-compiling /construction/science/py-ScientificPython/stage/usr/local/lib/python2.7/site-packages/Scientific/Visualization/__init__.py to __init__.pyc byte-compiling /construction/science/py-ScientificPython/stage/usr/local/lib/python2.7/site-packages/Scientific/Visualization/Color.py to Color.pyc byte-compiling /construction/science/py-ScientificPython/stage/usr/local/lib/python2.7/site-packages/Scientific/Visualization/VRML2.py to VRML2.pyc byte-compiling /construction/science/py-ScientificPython/stage/usr/local/lib/python2.7/site-packages/Scientific/Visualization/VRML.py to VRML.pyc byte-compiling /construction/science/py-ScientificPython/stage/usr/local/lib/python2.7/site-packages/Scientific/Visualization/PyMOL.py to PyMOL.pyc byte-compiling /construction/science/py-ScientificPython/stage/usr/local/lib/python2.7/site-packages/Scientific/IO/FortranFormat.py to FortranFormat.pyc byte-compiling /construction/science/py-ScientificPython/stage/usr/local/lib/python2.7/site-packages/Scientific/IO/PDBSpaceGroups.py to PDBSpaceGroups.pyc byte-compiling /construction/science/py-ScientificPython/stage/usr/local/lib/python2.7/site-packages/Scientific/IO/PDB.py to PDB.pyc byte-compiling /construction/science/py-ScientificPython/stage/usr/local/lib/python2.7/site-packages/Scientific/IO/NetCDF.py to NetCDF.pyc byte-compiling /construction/science/py-ScientificPython/stage/usr/local/lib/python2.7/site-packages/Scientific/IO/ArrayIO.py to ArrayIO.pyc byte-compiling /construction/science/py-ScientificPython/stage/usr/local/lib/python2.7/site-packages/Scientific/IO/TextFile.py to TextFile.pyc byte-compiling /construction/science/py-ScientificPython/stage/usr/local/lib/python2.7/site-packages/Scientific/IO/PDBExportFilters.py to PDBExportFilters.pyc byte-compiling /construction/science/py-ScientificPython/stage/usr/local/lib/python2.7/site-packages/Scientific/IO/__init__.py to __init__.pyc byte-compiling /construction/science/py-ScientificPython/stage/usr/local/lib/python2.7/site-packages/Scientific/TkWidgets/TkVisualizationCanvas.py to TkVisualizationCanvas.pyc byte-compiling /construction/science/py-ScientificPython/stage/usr/local/lib/python2.7/site-packages/Scientific/TkWidgets/TkPlotCanvas.py to TkPlotCanvas.pyc byte-compiling /construction/science/py-ScientificPython/stage/usr/local/lib/python2.7/site-packages/Scientific/TkWidgets/__init__.py to __init__.pyc byte-compiling /construction/science/py-ScientificPython/stage/usr/local/lib/python2.7/site-packages/Scientific/TkWidgets/Utility.py to Utility.pyc byte-compiling /construction/science/py-ScientificPython/stage/usr/local/lib/python2.7/site-packages/Scientific/Threading/TaskManager.py to TaskManager.pyc byte-compiling /construction/science/py-ScientificPython/stage/usr/local/lib/python2.7/site-packages/Scientific/Threading/__init__.py to __init__.pyc byte-compiling /construction/science/py-ScientificPython/stage/usr/local/lib/python2.7/site-packages/Scientific/Statistics/Histogram.py to Histogram.pyc byte-compiling /construction/science/py-ScientificPython/stage/usr/local/lib/python2.7/site-packages/Scientific/Statistics/__init__.py to __init__.pyc byte-compiling /construction/science/py-ScientificPython/stage/usr/local/lib/python2.7/site-packages/Scientific/indexing.py to indexing.pyc byte-compiling /construction/science/py-ScientificPython/stage/usr/local/lib/python2.7/site-packages/Scientific/QtWidgets/qt_fake.py to qt_fake.pyc byte-compiling /construction/science/py-ScientificPython/stage/usr/local/lib/python2.7/site-packages/Scientific/QtWidgets/__init__.py to __init__.pyc byte-compiling /construction/science/py-ScientificPython/stage/usr/local/lib/python2.7/site-packages/Scientific/QtWidgets/QtPlotCanvas.py to QtPlotCanvas.pyc byte-compiling /construction/science/py-ScientificPython/stage/usr/local/lib/python2.7/site-packages/Scientific/QtWidgets/QtVisualizationCanvas.py to QtVisualizationCanvas.pyc byte-compiling /construction/science/py-ScientificPython/stage/usr/local/lib/python2.7/site-packages/Scientific/Functions/LeastSquares.py to LeastSquares.pyc byte-compiling /construction/science/py-ScientificPython/stage/usr/local/lib/python2.7/site-packages/Scientific/Functions/FirstDerivatives.py to FirstDerivatives.pyc byte-compiling /construction/science/py-ScientificPython/stage/usr/local/lib/python2.7/site-packages/Scientific/Functions/Polynomial.py to Polynomial.pyc byte-compiling /construction/science/py-ScientificPython/stage/usr/local/lib/python2.7/site-packages/Scientific/Functions/Derivatives.py to Derivatives.pyc byte-compiling /construction/science/py-ScientificPython/stage/usr/local/lib/python2.7/site-packages/Scientific/Functions/Romberg.py to Romberg.pyc byte-compiling /construction/science/py-ScientificPython/stage/usr/local/lib/python2.7/site-packages/Scientific/Functions/Rational.py to Rational.pyc byte-compiling /construction/science/py-ScientificPython/stage/usr/local/lib/python2.7/site-packages/Scientific/Functions/__init__.py to __init__.pyc byte-compiling /construction/science/py-ScientificPython/stage/usr/local/lib/python2.7/site-packages/Scientific/Functions/FindRoot.py to FindRoot.pyc byte-compiling /construction/science/py-ScientificPython/stage/usr/local/lib/python2.7/site-packages/Scientific/Functions/Interpolation.py to Interpolation.pyc byte-compiling /construction/science/py-ScientificPython/stage/usr/local/lib/python2.7/site-packages/Scientific/NumberDict.py to NumberDict.pyc byte-compiling /construction/science/py-ScientificPython/stage/usr/local/lib/python2.7/site-packages/Scientific/BSP/IO.py to IO.pyc byte-compiling /construction/science/py-ScientificPython/stage/usr/local/lib/python2.7/site-packages/Scientific/BSP/__init__.py to __init__.pyc byte-compiling /construction/science/py-ScientificPython/stage/usr/local/lib/python2.7/site-packages/Scientific/BSP/Console.py to Console.pyc byte-compiling /construction/science/py-ScientificPython/stage/usr/local/lib/python2.7/site-packages/Scientific/BSP/core.py to core.pyc byte-compiling /construction/science/py-ScientificPython/stage/usr/local/lib/python2.7/site-packages/Scientific/Signals/__init__.py to __init__.pyc byte-compiling /construction/science/py-ScientificPython/stage/usr/local/lib/python2.7/site-packages/Scientific/Signals/Models.py to Models.pyc byte-compiling /construction/science/py-ScientificPython/stage/usr/local/lib/python2.7/site-packages/Scientific/Physics/__init__.py to __init__.pyc byte-compiling /construction/science/py-ScientificPython/stage/usr/local/lib/python2.7/site-packages/Scientific/Physics/PhysicalQuantities.py to PhysicalQuantities.pyc byte-compiling /construction/science/py-ScientificPython/stage/usr/local/lib/python2.7/site-packages/Scientific/Physics/Potential.py to Potential.pyc writing byte-compilation script '/tmp/tmp2uIzpA.py' /usr/local/bin/python2.7 -O /tmp/tmp2uIzpA.py removing /tmp/tmp2uIzpA.py running install_headers creating /construction/science/py-ScientificPython/stage/usr/local/include/python2.7 creating /construction/science/py-ScientificPython/stage/usr/local/include/python2.7/Scientific copying Include/Scientific/arrayobject.h -> /construction/science/py-ScientificPython/stage/usr/local/include/python2.7/Scientific copying Include/Scientific/bspmodule.h -> /construction/science/py-ScientificPython/stage/usr/local/include/python2.7/Scientific copying Include/Scientific/mpimodule.h -> /construction/science/py-ScientificPython/stage/usr/local/include/python2.7/Scientific copying Include/Scientific/netcdfmodule.h -> /construction/science/py-ScientificPython/stage/usr/local/include/python2.7/Scientific copying Include/Scientific/PyBSP_API.h -> /construction/science/py-ScientificPython/stage/usr/local/include/python2.7/Scientific copying Include/Scientific/PyMPI_API.h -> /construction/science/py-ScientificPython/stage/usr/local/include/python2.7/Scientific copying /usr/local/include/netcdf.h -> /construction/science/py-ScientificPython/stage/usr/local/include/python2.7/Scientific running install_egg_info running egg_info creating ScientificPython.egg-info writing ScientificPython.egg-info/PKG-INFO writing top-level names to ScientificPython.egg-info/top_level.txt writing dependency_links to ScientificPython.egg-info/dependency_links.txt writing manifest file 'ScientificPython.egg-info/SOURCES.txt' reading manifest file 'ScientificPython.egg-info/SOURCES.txt' reading manifest template 'MANIFEST.in' warning: no previously-included files found matching 'Scientific/BSP/Tasks.py' writing manifest file 'ScientificPython.egg-info/SOURCES.txt' Copying ScientificPython.egg-info to /construction/science/py-ScientificPython/stage/usr/local/lib/python2.7/site-packages/ScientificPython-2.9.4-py2.7.egg-info running install_scripts copying build/scripts-2.7/task_manager -> /construction/science/py-ScientificPython/stage/usr/local/bin copying build/scripts-2.7/bsp_virtual -> /construction/science/py-ScientificPython/stage/usr/local/bin changing mode of /construction/science/py-ScientificPython/stage/usr/local/bin/task_manager to 755 changing mode of /construction/science/py-ScientificPython/stage/usr/local/bin/bsp_virtual to 755 writing list of installed files to '/construction/science/py-ScientificPython/.PLIST.pymodtmp' ===> Creating unique files: Move MAN files needing SUFFIX ===> Creating unique files: Move files needing SUFFIX Move: bin/task_manager --> bin/task_manager-2.7 Link: @bin/task_manager --> bin/task_manager-2.7 Move: bin/bsp_virtual --> bin/bsp_virtual-2.7 Link: @bin/bsp_virtual --> bin/bsp_virtual-2.7 ====> Compressing man pages (compress-man) ====> Running Q/A tests (stage-qa) Error: /usr/local/lib/python2.7/site-packages/Scientific/_affinitypropagation.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 Error: /usr/local/lib/python2.7/site-packages/Scientific/_netcdf.so is linked to /usr/local/lib/libhdf5_hl.so.100 from science/hdf5 but it is not declared as a dependency Warning: you need LIB_DEPENDS+=libhdf5_hl.so:science/hdf5 Error: /usr/local/lib/python2.7/site-packages/Scientific/_netcdf.so is linked to /usr/local/lib/libhdf5.so.103 from science/hdf5 but it is not declared as a dependency Warning: you need LIB_DEPENDS+=libhdf5.so:science/hdf5 Error: /usr/local/lib/python2.7/site-packages/Scientific/_netcdf.so is linked to /usr/local/lib/libcurl.so.4 from ftp/curl but it is not declared as a dependency Warning: you need LIB_DEPENDS+=libcurl.so:ftp/curl Error: /usr/local/lib/python2.7/site-packages/Scientific/_netcdf.so is linked to /usr/local/lib/libsz.so.2 from science/szip but it is not declared as a dependency Warning: you need LIB_DEPENDS+=libsz.so:science/szip Error: /usr/local/lib/python2.7/site-packages/Scientific/_netcdf.so is linked to /usr/local/lib/libnghttp2.so.14 from www/libnghttp2 but it is not declared as a dependency Warning: you need LIB_DEPENDS+=libnghttp2.so:www/libnghttp2 Error: /usr/local/lib/python2.7/site-packages/Scientific/_netcdf.so is linked to /usr/local/lib/libssl.so.9 from security/openssl but it is not declared as a dependency Warning: you need USES=ssl Error: /usr/local/lib/python2.7/site-packages/Scientific/_netcdf.so is linked to /usr/local/lib/libcrypto.so.9 from security/openssl but it is not declared as a dependency Warning: you need USES=ssl Warning: You have disabled the licenses framework with DISABLE_LICENSES, unable to run checks SUCCEEDED 00:00:03 ------------------------------------------------------------------------------- -- Phase: check-plist ------------------------------------------------------------------------------- x====> Checking for pkg-plist issues (check-plist) ===> Parsing plist ===> Checking for items in STAGEDIR missing from pkg-plist ===> Checking for items in pkg-plist which are not in STAGEDIR ===> No pkg-plist issues found (check-plist) SUCCEEDED 00:00:01 ------------------------------------------------------------------------------- -- Phase: package ------------------------------------------------------------------------------- x===> Building package for py27-ScientificPython-2.9.4_4 file sizes/checksums [232]: 0% file sizes/checksums [232]: 43% file sizes/checksums [232]: 86% file sizes/checksums [232]: 100% packing files [232]: 0% packing files [232]: 43% packing files [232]: 86% packing files [232]: 100% packing directories [0]: 0% packing directories [0]: 100% SUCCEEDED 00:00:00 TOTAL TIME 00:00:33