------------------------------------------------------------------------------- -- 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/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/pcre-8.43_2.tgz Installing /packages/All/icu-64.2,1.tgz Installing /packages/All/png-1.6.37.tgz Installing /packages/All/jbigkit-2.1_1.tgz Installing /packages/All/jpeg-turbo-2.0.2.tgz Installing /packages/All/tiff-4.0.10_1.tgz Installing /packages/All/freetype2-2.10.1.tgz Message from freetype2-2.10.1: The 2.7.x series now uses the new subpixel hinting mode (V40 port's option) as the default, emulating a modern version of ClearType. This change inevitably leads to different rendering results, and you might change port's options to adapt it to your taste (or use the new "FREETYPE_PROPERTIES" environment variable). The environment variable "FREETYPE_PROPERTIES" can be used to control the driver properties. Example: FREETYPE_PROPERTIES=truetype:interpreter-version=35 \ cff:no-stem-darkening=1 \ autofitter:warping=1 This allows to select, say, the subpixel hinting mode at runtime for a given application. If LONG_PCF_NAMES port's option was enabled, the PCF family names may include the foundry and information whether they contain wide characters. For example, "Sony Fixed" or "Misc Fixed Wide", instead of "Fixed". This can be disabled at run time with using pcf:no-long-family-names property, if needed. Example: FREETYPE_PROPERTIES=pcf:no-long-family-names=1 How to recreate fontconfig cache with using such environment variable, if needed: # env FREETYPE_PROPERTIES=pcf:no-long-family-names=1 fc-cache -fsv The controllable properties are listed in the section "Controlling FreeType Modules" in the reference's table of contents (/usr/local/share/doc/freetype2/reference/site/index.html, if documentation was installed). Installing /packages/All/fontconfig-2.12.6,1.tgz Running fc-cache to build fontconfig cache... /usr/local/share/fonts: skipping, no such directory /usr/local/lib/X11/fonts: skipping, no such directory /var/db/fontconfig: cleaning cache directory fc-cache: succeeded Installing /packages/All/libxml2-2.9.9.tgz Installing /packages/All/libiconv-1.14_11.tgz Installing /packages/All/python36-3.6.9.tgz Message from python36-3.6.9: =========================================================================== Note that some standard Python modules are provided as separate ports as they require additional dependencies. They are available as: py36-gdbm databases/py-gdbm@py36 py36-sqlite3 databases/py-sqlite3@py36 py36-tkinter x11-toolkits/py-tkinter@py36 =========================================================================== Installing /packages/All/glib-2.56.3_6,1.tgz No schema files found: doing nothing. Installing /packages/All/wayland-1.16.0.tgz Installing /packages/All/pciids-20190725.tgz Installing /packages/All/libpciaccess-0.16.tgz Installing /packages/All/libdrm-2.4.99.tgz Installing /packages/All/libelf-0.8.13_3.tgz Installing /packages/All/libXau-1.0.9.tgz Installing /packages/All/xorgproto-2019.1.tgz Installing /packages/All/libXdmcp-1.1.3.tgz Installing /packages/All/libpthread-stubs-0.4.tgz Installing /packages/All/libxcb-1.13.1.tgz Installing /packages/All/libX11-1.6.8,1.tgz Installing /packages/All/libXfixes-5.0.3_2.tgz Installing /packages/All/libXdamage-1.1.5.tgz Installing /packages/All/libXext-1.3.4,1.tgz Installing /packages/All/libXrender-0.9.10_2.tgz Installing /packages/All/libXrandr-1.5.2.tgz Installing /packages/All/libxshmfence-1.3.tgz Installing /packages/All/libXxf86vm-1.1.4_3.tgz Installing /packages/All/mesa-libs-18.3.2_1.tgz Installing /packages/All/pixman-0.38.4.tgz Installing /packages/All/cairo-1.16.0,2.tgz Installing /packages/All/graphite2-1.3.13_1.tgz Installing /packages/All/harfbuzz-2.5.3_1.tgz Installing /packages/All/fribidi-0.19.7.tgz Installing /packages/All/libfontenc-1.1.4.tgz Installing /packages/All/mkfontscale-1.2.1.tgz Installing /packages/All/font-bh-ttf-1.0.3_4.tgz Installing /packages/All/font-misc-meltho-1.0.3_4.tgz Installing /packages/All/font-misc-ethiopic-1.0.3_4.tgz Installing /packages/All/font-util-1.3.1.tgz Installing /packages/All/encodings-1.0.5,1.tgz Installing /packages/All/dejavu-2.37_1.tgz Message from dejavu-2.37_1: Make sure that the freetype module is loaded. If it is not, add the following line to the "Modules" section of your X Windows configuration file: Load "freetype" Add the following line to the "Files" section of X Windows configuration file: FontPath "/usr/local/share/fonts/dejavu/" Note: your X Windows configuration file is typically /etc/X11/XF86Config if you are using XFree86, and /etc/X11/xorg.conf if you are using X.Org. Installing /packages/All/xorg-fonts-truetype-7.7_1.tgz Installing /packages/All/libXft-2.3.2_3.tgz Installing /packages/All/pango-1.42.4_3.tgz Installing /packages/All/tcl86-8.6.9_1.tgz Installing /packages/All/libXScrnSaver-1.2.3_2.tgz Installing /packages/All/tk86-8.6.9_1.tgz Installing /packages/All/gmake-4.2.1_3.tgz Installing /packages/All/libidn-1.35.tgz Installing /packages/All/jbig2dec-0.16.tgz Installing /packages/All/libpaper-1.1.24.4.tgz Installing /packages/All/libdaemon-0.14_1.tgz Installing /packages/All/libICE-1.0.9_3,1.tgz Installing /packages/All/libSM-1.2.3,1.tgz Installing /packages/All/dbus-1.12.12.tgz ===> Creating groups. Creating group 'messagebus' with gid '556'. ===> Creating users Creating user 'messagebus' with uid '556'. Installing /packages/All/dbus-glib-0.110.tgz Installing /packages/All/gdbm-1.18.1_1.tgz Installing /packages/All/gobject-introspection-1.56.1,1.tgz Installing /packages/All/gnome_subr-1.0.tgz Installing /packages/All/avahi-app-0.7_2.tgz ===> Creating groups. Creating group 'avahi' with gid '558'. ===> Creating users Creating user 'avahi' with uid '558'. Installing /packages/All/nettle-3.5.1_1.tgz Installing /packages/All/libtasn1-4.14.tgz Installing /packages/All/libunistring-0.9.10_1.tgz Installing /packages/All/libidn2-2.2.0.tgz Installing /packages/All/p11-kit-0.23.16.1.tgz Installing /packages/All/tpm-emulator-0.7.4_2.tgz ===> Creating groups. Creating group '_tss' with gid '601'. ===> Creating users Creating user '_tss' with uid '601'. Installing /packages/All/trousers-0.3.14_2.tgz ===> Creating groups. Using existing group '_tss'. ===> Creating users Using existing user '_tss'. Message from trousers-0.3.14_2: To run tcsd automatically, add the following line to /etc/rc.conf: tcsd_enable="YES" You might want to edit /usr/local/etc/tcsd.conf to reflect your setup. If you want to use tcsd with software TPM emulator, use the following configuration in /etc/rc.conf: tcsd_enable="YES" tcsd_mode="emulator" tpmd_enable="YES" To use TPM, add your_account to '_tss' group like following: # pw groupmod _tss -m your_account Installing /packages/All/gnutls-3.6.9.tgz Installing /packages/All/cups-2.2.11.tgz ===> Creating groups. Creating group 'cups' with gid '193'. ===> Creating users Creating user 'cups' with uid '193'. Installing /packages/All/poppler-data-0.4.9.tgz Installing /packages/All/ghostscript9-agpl-base-9.27_2.tgz Message from ghostscript9-agpl-base-9.27_2: This package installs a script named dvipdf that depends on dvips. If you want to use this script you need to install print/tex-dvipsk. Installing /packages/All/libXt-1.2.0,1.tgz Installing /packages/All/libXmu-1.1.3,1.tgz Installing /packages/All/R-3.6.1_1.tgz SUCCEEDED 00:00:36 ------------------------------------------------------------------------------- -- Phase: check-sanity ------------------------------------------------------------------------------- x===> NOTICE: The rpy 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 SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: pkg-depends ------------------------------------------------------------------------------- x SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: fetch-depends ------------------------------------------------------------------------------- x SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: fetch ------------------------------------------------------------------------------- x===> NOTICE: The rpy 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 ===> Fetching all distfiles required by py27-rpy-1.0.3_40 for building SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: checksum ------------------------------------------------------------------------------- x===> NOTICE: The rpy 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 ===> Fetching all distfiles required by py27-rpy-1.0.3_40 for building => SHA256 Checksum OK for rpy-1.0.3.tar.gz. SUCCEEDED 00:00:01 ------------------------------------------------------------------------------- -- Phase: extract-depends ------------------------------------------------------------------------------- x SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: extract ------------------------------------------------------------------------------- x===> NOTICE: The rpy 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 ===> Fetching all distfiles required by py27-rpy-1.0.3_40 for building ===> Extracting for py27-rpy-1.0.3_40 => SHA256 Checksum OK for rpy-1.0.3.tar.gz. Extracted Memory Use: 0.47M SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: patch-depends ------------------------------------------------------------------------------- x SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: patch ------------------------------------------------------------------------------- x===> Patching for py27-rpy-1.0.3_40 ===> Applying ports patches for py27-rpy-1.0.3_40 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-rpy-1.0.3_40 RHOMES= [] DEBUG= False Setting RHOMES to ['/usr/local/lib/R'] ### Using R verion 3.6.1 installed at /usr/local/lib/R ### RHOME= /usr/local/lib/R copying src/rpymodule.c -> src/rpymodule3061.c copying src/R_eval.c -> src/R_eval3061.c copying src/io.c -> src/io3061.c running config SUCCEEDED 00:00:01 ------------------------------------------------------------------------------- -- Phase: build ------------------------------------------------------------------------------- x===> Building for py27-rpy-1.0.3_40 RHOMES= [] DEBUG= False Setting RHOMES to ['/usr/local/lib/R'] ### Using R verion 3.6.1 installed at /usr/local/lib/R ### RHOME= /usr/local/lib/R copying src/rpymodule.c -> src/rpymodule3061.c copying src/R_eval.c -> src/R_eval3061.c copying src/io.c -> src/io3061.c running build running build_py creating build creating build/lib.dragonfly-5.7-x86_64-2.7 copying rpy.py -> build/lib.dragonfly-5.7-x86_64-2.7 copying rpy_io.py -> build/lib.dragonfly-5.7-x86_64-2.7 copying rpy_version.py -> build/lib.dragonfly-5.7-x86_64-2.7 copying rpy_tools.py -> build/lib.dragonfly-5.7-x86_64-2.7 copying rpy_options.py -> build/lib.dragonfly-5.7-x86_64-2.7 copying rpy_wintools.py -> build/lib.dragonfly-5.7-x86_64-2.7 running build_ext building '_rpy3061' extension creating build/temp.dragonfly-5.7-x86_64-2.7 creating build/temp.dragonfly-5.7-x86_64-2.7/src cc -DNDEBUG -O3 -Wall -pipe -O2 -fno-strict-aliasing -fPIC -DWITH_NUMERIC=3 -DPY_ARRAY_TYPES_PREFIX=PyArray_ -DRPY_SHNAME=_rpy3061 -DINIT_RPY=init_rpy3061 -UPRE_2_2 -I/usr/local/lib/R/include -Isrc -I/usr/local/lib/R/include -I/usr/local/lib/python2.7/site-packages/numpy/core/include -I/usr/local/include/python2.7 -c src/rpymodule3061.c -o build/temp.dragonfly-5.7-x86_64-2.7/src/rpymodule3061.o -shared -L/usr/local/lib/R/lib -lRlapack 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 src/RPy.h:99, from src/rpymodule3061.c:51: /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 " \ ^~~~~~~ src/rpymodule3061.c:1565:3: warning: initialization of 'Py_ssize_t (*)(PyObject *)' {aka 'long int (*)(struct _object *)'} from incompatible pointer type 'int (*)(PyObject *)' {aka 'int (*)(struct _object *)'} [-Wincompatible-pointer-types] (inquiry)Robj_len, /* sq_length */ ^ src/rpymodule3061.c:1565:3: note: (near initialization for 'Robj_as_sequence.sq_length') src/rpymodule3061.c:1568:3: warning: 'intargfunc' is deprecated [-Wdeprecated-declarations] (intargfunc)Robj_item, /* sq_item */ ^ src/rpymodule3061.c:1568:3: warning: initialization of 'PyObject * (*)(PyObject *, Py_ssize_t)' {aka 'struct _object * (*)(struct _object *, long int)'} from incompatible pointer type 'PyObject * (*)(PyObject *, int)' {aka 'struct _object * (*)(struct _object *, int)'} [-Wincompatible-pointer-types] src/rpymodule3061.c:1568:3: note: (near initialization for 'Robj_as_sequence.sq_item') src/rpymodule3061.c:1569:3: warning: 'intintargfunc' is deprecated [-Wdeprecated-declarations] (intintargfunc)Robj_slice, /* sq_slice */ ^ src/rpymodule3061.c:1569:3: warning: initialization of 'PyObject * (*)(PyObject *, Py_ssize_t, Py_ssize_t)' {aka 'struct _object * (*)(struct _object *, long int, long int)'} from incompatible pointer type 'PyObject * (*)(PyObject *, int, int)' {aka 'struct _object * (*)(struct _object *, int, int)'} [-Wincompatible-pointer-types] src/rpymodule3061.c:1569:3: note: (near initialization for 'Robj_as_sequence.sq_slice') src/rpymodule3061.c:1570:3: warning: initialization of 'int (*)(PyObject *, Py_ssize_t, PyObject *)' {aka 'int (*)(struct _object *, long int, struct _object *)'} from incompatible pointer type 'int (*)(PyObject *, int, PyObject *)' {aka 'int (*)(struct _object *, int, struct _object *)'} [-Wincompatible-pointer-types] (intobjargproc)Robj_ass_item, /* sq_ass_item */ ^ src/rpymodule3061.c:1570:3: note: (near initialization for 'Robj_as_sequence.sq_ass_item') src/rpymodule3061.c: In function 'init_rpy3061': src/rpymodule3061.c:1985:3: warning: 'strncpy' specified bound 1024 equals destination size [-Wstringop-truncation] strncpy(RHOME, getenv("RPY_RHOME"), BUFSIZ); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/rpymodule3061.c:1986:3: warning: 'strncpy' specified bound 1024 equals destination size [-Wstringop-truncation] strncpy(RVERSION, getenv("RPY_RVERSION"), BUFSIZ); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/rpymodule3061.c:1987:3: warning: 'strncpy' specified bound 1024 equals destination size [-Wstringop-truncation] strncpy(RVER, getenv("RPY_RVER"), BUFSIZ); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/rpymodule3061.c:1988:3: warning: 'strncpy' specified bound 1024 equals destination size [-Wstringop-truncation] strncpy(RUSER, getenv("RPY_RUSER"), BUFSIZ); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ cc -DNDEBUG -O3 -Wall -pipe -O2 -fno-strict-aliasing -fPIC -DWITH_NUMERIC=3 -DPY_ARRAY_TYPES_PREFIX=PyArray_ -DRPY_SHNAME=_rpy3061 -DINIT_RPY=init_rpy3061 -UPRE_2_2 -I/usr/local/lib/R/include -Isrc -I/usr/local/lib/R/include -I/usr/local/lib/python2.7/site-packages/numpy/core/include -I/usr/local/include/python2.7 -c src/R_eval3061.c -o build/temp.dragonfly-5.7-x86_64-2.7/src/R_eval3061.o -shared -L/usr/local/lib/R/lib -lRlapack 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 src/RPy.h:99, from src/R_eval3061.c:63: /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 " \ ^~~~~~~ In file included from /usr/local/lib/python2.7/site-packages/numpy/core/include/numpy/ndarrayobject.h:21, from /usr/local/lib/python2.7/site-packages/numpy/core/include/numpy/arrayobject.h:4, from src/RPy.h:99, from src/R_eval3061.c:63: /usr/local/lib/python2.7/site-packages/numpy/core/include/numpy/__multiarray_api.h:1463:1: warning: '_import_array' defined but not used [-Wunused-function] _import_array(void) ^~~~~~~~~~~~~ cc -DNDEBUG -O3 -Wall -pipe -O2 -fno-strict-aliasing -fPIC -DWITH_NUMERIC=3 -DPY_ARRAY_TYPES_PREFIX=PyArray_ -DRPY_SHNAME=_rpy3061 -DINIT_RPY=init_rpy3061 -UPRE_2_2 -I/usr/local/lib/R/include -Isrc -I/usr/local/lib/R/include -I/usr/local/lib/python2.7/site-packages/numpy/core/include -I/usr/local/include/python2.7 -c src/io3061.c -o build/temp.dragonfly-5.7-x86_64-2.7/src/io3061.o -shared -L/usr/local/lib/R/lib -lRlapack 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 src/RPy.h:99, from src/io3061.c:43: /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 " \ ^~~~~~~ In file included from /usr/local/lib/python2.7/site-packages/numpy/core/include/numpy/ndarrayobject.h:21, from /usr/local/lib/python2.7/site-packages/numpy/core/include/numpy/arrayobject.h:4, from src/RPy.h:99, from src/io3061.c:43: /usr/local/lib/python2.7/site-packages/numpy/core/include/numpy/__multiarray_api.h:1463:1: warning: '_import_array' defined but not used [-Wunused-function] _import_array(void) ^~~~~~~~~~~~~ cc -DNDEBUG -O3 -Wall -pipe -O2 -fno-strict-aliasing -fPIC -DWITH_NUMERIC=3 -DPY_ARRAY_TYPES_PREFIX=PyArray_ -DRPY_SHNAME=_rpy3061 -DINIT_RPY=init_rpy3061 -UPRE_2_2 -I/usr/local/lib/R/include -Isrc -I/usr/local/lib/R/include -I/usr/local/lib/python2.7/site-packages/numpy/core/include -I/usr/local/include/python2.7 -c src/setenv.c -o build/temp.dragonfly-5.7-x86_64-2.7/src/setenv.o -shared -L/usr/local/lib/R/lib -lRlapack cc -shared -L/usr/local/lib/R/modules -L/usr/local/lib/R/lib -pipe -O2 -fno-strict-aliasing build/temp.dragonfly-5.7-x86_64-2.7/src/rpymodule3061.o build/temp.dragonfly-5.7-x86_64-2.7/src/R_eval3061.o build/temp.dragonfly-5.7-x86_64-2.7/src/io3061.o build/temp.dragonfly-5.7-x86_64-2.7/src/setenv.o -L/usr/local/lib/R/bin -L/usr/local/lib/R/lib -L/usr/local/lib -R/usr/local/lib/R/bin -R/usr/local/lib/R/lib -lR -lpython2.7 -o build/lib.dragonfly-5.7-x86_64-2.7/_rpy3061.so SUCCEEDED 00:00:01 ------------------------------------------------------------------------------- -- Phase: run-depends ------------------------------------------------------------------------------- x SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: stage ------------------------------------------------------------------------------- x===> Staging for py27-rpy-1.0.3_40 ===> Generating temporary packing list RHOMES= [] DEBUG= False Setting RHOMES to ['/usr/local/lib/R'] ### Using R verion 3.6.1 installed at /usr/local/lib/R ### RHOME= /usr/local/lib/R copying src/rpymodule.c -> src/rpymodule3061.c copying src/R_eval.c -> src/R_eval3061.c copying src/io.c -> src/io3061.c running install running build running build_py running build_ext running install_lib creating /construction/math/py-rpy/stage/usr/local/lib/python2.7 creating /construction/math/py-rpy/stage/usr/local/lib/python2.7/site-packages copying build/lib.dragonfly-5.7-x86_64-2.7/rpy_version.py -> /construction/math/py-rpy/stage/usr/local/lib/python2.7/site-packages copying build/lib.dragonfly-5.7-x86_64-2.7/rpy_wintools.py -> /construction/math/py-rpy/stage/usr/local/lib/python2.7/site-packages copying build/lib.dragonfly-5.7-x86_64-2.7/rpy_tools.py -> /construction/math/py-rpy/stage/usr/local/lib/python2.7/site-packages copying build/lib.dragonfly-5.7-x86_64-2.7/rpy_options.py -> /construction/math/py-rpy/stage/usr/local/lib/python2.7/site-packages copying build/lib.dragonfly-5.7-x86_64-2.7/rpy.py -> /construction/math/py-rpy/stage/usr/local/lib/python2.7/site-packages copying build/lib.dragonfly-5.7-x86_64-2.7/rpy_io.py -> /construction/math/py-rpy/stage/usr/local/lib/python2.7/site-packages copying build/lib.dragonfly-5.7-x86_64-2.7/_rpy3061.so -> /construction/math/py-rpy/stage/usr/local/lib/python2.7/site-packages byte-compiling /construction/math/py-rpy/stage/usr/local/lib/python2.7/site-packages/rpy_version.py to rpy_version.pyc byte-compiling /construction/math/py-rpy/stage/usr/local/lib/python2.7/site-packages/rpy_wintools.py to rpy_wintools.pyc byte-compiling /construction/math/py-rpy/stage/usr/local/lib/python2.7/site-packages/rpy_tools.py to rpy_tools.pyc byte-compiling /construction/math/py-rpy/stage/usr/local/lib/python2.7/site-packages/rpy_options.py to rpy_options.pyc byte-compiling /construction/math/py-rpy/stage/usr/local/lib/python2.7/site-packages/rpy.py to rpy.pyc byte-compiling /construction/math/py-rpy/stage/usr/local/lib/python2.7/site-packages/rpy_io.py to rpy_io.pyc writing byte-compilation script '/tmp/tmpyZoyQM.py' /usr/local/bin/python2.7 -O /tmp/tmpyZoyQM.py removing /tmp/tmpyZoyQM.py running install_egg_info running egg_info creating rpy.egg-info writing rpy.egg-info/PKG-INFO writing top-level names to rpy.egg-info/top_level.txt writing dependency_links to rpy.egg-info/dependency_links.txt writing manifest file 'rpy.egg-info/SOURCES.txt' reading manifest file 'rpy.egg-info/SOURCES.txt' reading manifest template 'MANIFEST.in' warning: no files found matching 'debian*' anywhere in distribution warning: no previously-included files matching '*[0-9].[ch]' found anywhere in distribution warning: no files found matching 'COPYING' warning: no previously-included files matching '.cvsignore' found anywhere in distribution warning: no previously-included files matching '*.pyc' found anywhere in distribution warning: no previously-included files matching '*.bak' found anywhere in distribution warning: no previously-included files matching '.tnatr*' found anywhere in distribution warning: no previously-included files matching '*.tgz' found anywhere in distribution warning: no previously-included files matching '*.tar.gz' found anywhere in distribution warning: no previously-included files matching '*~' found anywhere in distribution warning: no previously-included files matching 'core*' found anywhere in distribution warning: no previously-included files matching '*patch*' found anywhere in distribution warning: no previously-included files matching '*diff*' found anywhere in distribution warning: no previously-included files matching '.svn' found anywhere in distribution no previously-included directories found matching 'debian/.svn' no previously-included directories found matching 'CVS' no previously-included directories found matching 'dist' no previously-included directories found matching 'doc/manual_html' writing manifest file 'rpy.egg-info/SOURCES.txt' Copying rpy.egg-info to /construction/math/py-rpy/stage/usr/local/lib/python2.7/site-packages/rpy-1.0.3-py2.7.egg-info running install_scripts writing list of installed files to '/construction/math/py-rpy/.PLIST.pymodtmp' ====> Compressing man pages (compress-man) ====> Running Q/A tests (stage-qa) Error: /usr/local/lib/python2.7/site-packages/_rpy3061.so is linked to /usr/local/lib/gcc8/libgfortran.so.5 from lang/gcc8 but it is not declared as a dependency Error: /usr/local/lib/python2.7/site-packages/_rpy3061.so is linked to /usr/local/lib/gcc8/libquadmath.so.0 from lang/gcc8 but it is not declared as a dependency Error: /usr/local/lib/python2.7/site-packages/_rpy3061.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/_rpy3061.so is linked to /usr/local/lib/libreadline.so.8 from devel/readline but it is not declared as a dependency Warning: you need USES+=readline Error: /usr/local/lib/python2.7/site-packages/_rpy3061.so is linked to /usr/local/lib/libpcre.so.1 from devel/pcre but it is not declared as a dependency Warning: you need LIB_DEPENDS+=libpcre.so:devel/pcre Error: /usr/local/lib/python2.7/site-packages/_rpy3061.so is linked to /usr/local/lib/libicuuc.so.64 from devel/icu but it is not declared as a dependency Warning: you need LIB_DEPENDS+=libicuuc.so:devel/icu Error: /usr/local/lib/python2.7/site-packages/_rpy3061.so is linked to /usr/local/lib/libicui18n.so.64 from devel/icu but it is not declared as a dependency Warning: you need LIB_DEPENDS+=libicui18n.so:devel/icu Error: /usr/local/lib/python2.7/site-packages/_rpy3061.so is linked to /usr/local/lib/gcc8/libgcc_s.so.1 from lang/gcc8 but it is not declared as a dependency Error: /usr/local/lib/python2.7/site-packages/_rpy3061.so is linked to /usr/local/lib/libncurses.so.6 from devel/ncurses but it is not declared as a dependency Warning: you need USES+=ncurses Error: /usr/local/lib/python2.7/site-packages/_rpy3061.so is linked to /usr/local/lib/libtinfo.so.6 from devel/ncurses but it is not declared as a dependency Warning: you need USES+=ncurses Error: /usr/local/lib/python2.7/site-packages/_rpy3061.so is linked to /usr/local/lib/libicudata.so.64 from devel/icu but it is not declared as a dependency Warning: you need LIB_DEPENDS+=libicudata.so:devel/icu Warning: You have disabled the licenses framework with DISABLE_LICENSES, unable to run checks SUCCEEDED 00:00:02 ------------------------------------------------------------------------------- -- 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-rpy-1.0.3_40 file sizes/checksums [23]: 0% file sizes/checksums [23]: 100% packing files [23]: 0% packing files [23]: 100% packing directories [0]: 0% packing directories [0]: 100% SUCCEEDED 00:00:00 TOTAL TIME 00:00:44