=> Building math/rpy Started : Wednesday, 22 NOV 2017 at 03:44:01 UTC Platform: 5.1-DEVELOPMENT DragonFly v5.1.0.211.g5913f-DEVELOPMENT #23: Mon Nov 6 09:10:01 PST 2017 root@pkgbox64.dragonflybsd.org:/usr/obj/usr/src/sys/X86_64_GENERIC x86_64 -------------------------------------------------- -- Environment -------------------------------------------------- UNAME_r=5.0-SYNTH UNAME_m=x86_64 UNAME_p=x86_64 UNAME_v=DragonFly 5.0-SYNTH UNAME_s=DragonFly PATH=/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin SSL_NO_VERIFY_PEER=1 TERM=dumb PKG_CACHEDIR=/var/cache/pkg8 PKG_DBDIR=/var/db/pkg8 PORTSDIR=/xports LANG=C HOME=/root USER=root -------------------------------------------------- -- Options -------------------------------------------------- -------------------------------------------------- -- CONFIGURE_ENV -------------------------------------------------- PYTHON="/usr/local/bin/python2.7" XDG_DATA_HOME=/construction/math/rpy XDG_CONFIG_HOME=/construction/math/rpy HOME=/construction/math/rpy TMPDIR="/tmp" PATH=/construction/math/rpy/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin SHELL=/bin/sh CONFIG_SHELL=/bin/sh CCVER=gcc50 -------------------------------------------------- -- CONFIGURE_ARGS -------------------------------------------------- -------------------------------------------------- -- MAKE_ENV -------------------------------------------------- XDG_DATA_HOME=/construction/math/rpy XDG_CONFIG_HOME=/construction/math/rpy HOME=/construction/math/rpy TMPDIR="/tmp" PATH=/construction/math/rpy/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin NO_PIE=yes MK_DEBUG_FILES=no MK_KERNEL_SYMBOLS=no SHELL=/bin/sh NO_LINT=YES CCVER=gcc50 LDSHARED="cc -shared" PYTHONDONTWRITEBYTECODE= PYTHONOPTIMIZE= PREFIX=/usr/local LOCALBASE=/usr/local LIBDIR="/usr/lib" NOPROFILE=1 CC="cc" CFLAGS="-pipe -O2 -fno-strict-aliasing" CPP="cpp" CPPFLAGS="" LDFLAGS=" -L/usr/local/lib/R/modules -L/usr/local/lib/R/lib" LIBS="" CXX="c++" CXXFLAGS=" -pipe -O2 -fno-strict-aliasing" MANPREFIX="/usr/local" BSD_INSTALL_PROGRAM="install -s -m 555" BSD_INSTALL_LIB="install -s -m 0644" BSD_INSTALL_SCRIPT="install -m 555" BSD_INSTALL_DATA="install -m 0644" BSD_INSTALL_MAN="install -m 444" -------------------------------------------------- -- MAKE_ARGS -------------------------------------------------- DESTDIR=/construction/math/rpy/stage -------------------------------------------------- -- PLIST_SUB -------------------------------------------------- PYTHON_INCLUDEDIR=include/python2.7 PYTHON_LIBDIR=lib/python2.7 PYTHON_PLATFORM=dragonfly5 PYTHON_PYOEXTENSION=pyo PYTHON_SITELIBDIR=lib/python2.7/site-packages PYTHON_SUFFIX=27 PYTHON_VER=2.7 PYTHON_VERSION=python2.7 PYTHON2="" PYTHON3="@comment " OSREL=5.0 PREFIX=%D LOCALBASE=/usr/local RESETPREFIX=/usr/local PORTDOCS="" PORTEXAMPLES="" LIB32DIR=lib PROFILE="@comment " DOCSDIR="share/doc/rpy" EXAMPLESDIR="share/examples/rpy" DATADIR="share/rpy" WWWDIR="www/rpy" ETCDIR="etc/rpy" -------------------------------------------------- -- SUB_LIST -------------------------------------------------- PREFIX=/usr/local LOCALBASE=/usr/local DATADIR=/usr/local/share/rpy DOCSDIR=/usr/local/share/doc/rpy EXAMPLESDIR=/usr/local/share/examples/rpy WWWDIR=/usr/local/www/rpy ETCDIR=/usr/local/etc/rpy -------------------------------------------------- -- /etc/make.conf -------------------------------------------------- SYNTHPROFILE=Release-5.0 USE_PACKAGE_DEPENDS_ONLY=yes PACKAGE_BUILDING=yes BATCH=yes PKG_CREATE_VERBOSE=yes PORTSDIR=/xports DISTDIR=/distfiles WRKDIRPREFIX=/construction PORT_DBDIR=/options PACKAGES=/packages MAKE_JOBS_NUMBER_LIMIT=5 HAVE_COMPAT_IA32_KERN= CONFIGURE_MAX_CMD_LEN=262144 _SMP_CPUS=8 UID=0 ARCH=x86_64 OPSYS=DragonFly DFLYVERSION=500000 OSVERSION=9999999 OSREL=5.0 _OSRELEASE=5.0-SYNTH -------------------------------------------------------------------------------- -- Phase: check-sanity -------------------------------------------------------------------------------- ===> 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 ===> License GPLv2 LGPL21 MPL11 accepted by the user -------------------------------------------------------------------------------- -- Phase: pkg-depends -------------------------------------------------------------------------------- ===> rpy-1.0.3_36 depends on file: /usr/local/sbin/pkg - not found ===> Installing existing package /packages/All/pkg-1.10.2.txz Installing pkg-1.10.2... Extracting pkg-1.10.2: .......... done ===> rpy-1.0.3_36 depends on file: /usr/local/sbin/pkg - found ===> Returning to build of rpy-1.0.3_36 -------------------------------------------------------------------------------- -- Phase: fetch-depends -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- -- Phase: fetch -------------------------------------------------------------------------------- ===> 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 ===> License GPLv2 LGPL21 MPL11 accepted by the user ===> Fetching all distfiles required by rpy-1.0.3_36 for building -------------------------------------------------------------------------------- -- Phase: checksum -------------------------------------------------------------------------------- ===> 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 ===> License GPLv2 LGPL21 MPL11 accepted by the user ===> Fetching all distfiles required by rpy-1.0.3_36 for building => SHA256 Checksum OK for rpy-1.0.3.tar.gz. -------------------------------------------------------------------------------- -- Phase: extract-depends -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- -- Phase: extract -------------------------------------------------------------------------------- ===> 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 ===> License GPLv2 LGPL21 MPL11 accepted by the user ===> Fetching all distfiles required by rpy-1.0.3_36 for building ===> Extracting for rpy-1.0.3_36 => SHA256 Checksum OK for rpy-1.0.3.tar.gz. -------------------------------------------------------------------------------- -- Phase: patch-depends -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- -- Phase: patch -------------------------------------------------------------------------------- ===> Patching for rpy-1.0.3_36 ===> Applying ports patches for rpy-1.0.3_36 -------------------------------------------------------------------------------- -- Phase: build-depends -------------------------------------------------------------------------------- ===> rpy-1.0.3_36 depends on file: /usr/local/lib/python2.7/site-packages/numpy/core/numeric.py - not found ===> Installing existing package /packages/All/py27-numpy-1.13.3,1.txz Installing py27-numpy-1.13.3,1... `-- Installing blas-3.5.0_3... | `-- Installing gcc5-5.5.0... | | `-- Installing binutils-2.28,1... | | `-- Installing gettext-runtime-0.19.8.1_1... | | | `-- Installing indexinfo-0.3.1... | | | `-- Extracting indexinfo-0.3.1: .... done | | `-- Extracting gettext-runtime-0.19.8.1_1: .......... done | | `-- Extracting binutils-2.28,1: .......... done | | `-- Installing gmp-6.1.2... | | `-- Extracting gmp-6.1.2: .......... done | | `-- Installing mpc-1.0.3... | | `-- Installing mpfr-3.1.6... | | `-- Extracting mpfr-3.1.6: .......... done | | `-- Extracting mpc-1.0.3: ...... done | `-- Extracting gcc5-5.5.0: .......... done `-- Extracting blas-3.5.0_3: ....... done `-- Installing cblas-1.0_7... `-- Extracting cblas-1.0_7: ......... done `-- Installing lapack-3.5.0_3... `-- Extracting lapack-3.5.0_3: .......... done `-- Installing py27-setuptools-36.5.0... | `-- Installing python27-2.7.14_1... | | `-- Installing expat-2.2.1... | | `-- Extracting expat-2.2.1: .......... done | | `-- Installing libffi-3.2.1_1... | | `-- Extracting libffi-3.2.1_1: .......... done | | `-- Installing libressl-2.6.3... | | `-- Extracting libressl-2.6.3: .......... done | | `-- Installing ncurses-6.0.0s20171007_1... | | `-- Extracting ncurses-6.0.0s20171007_1: .......... done | | `-- Installing readline-7.0.3_1... | | `-- Extracting readline-7.0.3_1: .......... done | `-- Extracting python27-2.7.14_1: .......... done `-- Extracting py27-setuptools-36.5.0: .......... done `-- Installing suitesparse-4.0.2_7... | `-- Installing openblas-0.2.20_1,1... | `-- Extracting openblas-0.2.20_1,1: ......... done `-- Extracting suitesparse-4.0.2_7: .......... done Extracting py27-numpy-1.13.3,1: .......... done Message from gcc5-5.5.0: 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/gcc5 For ports leveraging USE_GCC, USES=compiler, or USES=fortran this happens transparently. Message from cblas-1.0_7: ===> NOTICE: The cblas 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 Message from python27-2.7.14_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 =========================================================================== ===> rpy-1.0.3_36 depends on file: /usr/local/lib/python2.7/site-packages/numpy/core/numeric.py - found ===> Returning to build of rpy-1.0.3_36 ===> rpy-1.0.3_36 depends on package: py27-setuptools>0 - found ===> rpy-1.0.3_36 depends on file: /usr/local/bin/python2.7 - found -------------------------------------------------------------------------------- -- Phase: lib-depends -------------------------------------------------------------------------------- ===> rpy-1.0.3_36 depends on shared library: libR.so - not found ===> Installing existing package /packages/All/R-3.4.2_2.txz Installing R-3.4.2_2... `-- Installing cairo-1.14.8_1,2... | `-- Installing dri2proto-2.8... | `-- Extracting dri2proto-2.8: .... done | `-- Installing fontconfig-2.12.1,1... | | `-- Installing freetype2-2.8_1... | | `-- Extracting freetype2-2.8_1: .......... done | `-- Extracting fontconfig-2.12.1,1: .......... done 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 glib-2.50.2_7,1... | | `-- Installing libiconv-1.14_11... | | `-- Extracting libiconv-1.14_11: .......... done | | `-- Installing pcre-8.40_1... | | `-- Extracting pcre-8.40_1: .......... done | | `-- Installing perl5-5.24.3... | | `-- Extracting perl5-5.24.3: .......... done | `-- Extracting glib-2.50.2_7,1: .......... done No schema files found: doing nothing. | `-- Installing glproto-1.4.17... | `-- Extracting glproto-1.4.17: ...... done | `-- Installing libX11-1.6.5,1... | | `-- Installing kbproto-1.0.7... | | `-- Extracting kbproto-1.0.7: .......... done | | `-- Installing libXau-1.0.8_3... | | `-- Installing xproto-7.0.31... | | `-- Extracting xproto-7.0.31: .......... done | | `-- Extracting libXau-1.0.8_3: .......... done | | `-- Installing libXdmcp-1.1.2... | | `-- Extracting libXdmcp-1.1.2: ......... done | | `-- Installing libxcb-1.12_2... | | `-- Installing libpthread-stubs-0.4... | | `-- Extracting libpthread-stubs-0.4: . done | | `-- Installing libxml2-2.9.4... | | `-- Extracting libxml2-2.9.4: .......... done | | `-- Extracting libxcb-1.12_2: .......... done | `-- Extracting libX11-1.6.5,1: .......... done | `-- Installing libXext-1.3.3_1,1... | | `-- Installing xextproto-7.3.0... | | `-- Extracting xextproto-7.3.0: .......... done | `-- Extracting libXext-1.3.3_1,1: .......... done | `-- Installing libXrender-0.9.10... | | `-- Installing renderproto-0.11.1... | | `-- Extracting renderproto-0.11.1: .... done | `-- Extracting libXrender-0.9.10: .......... done | `-- Installing mesa-libs-17.2.4... | | `-- Installing libXdamage-1.1.4_3... | | `-- Installing damageproto-1.2.1... | | `-- Extracting 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Installing dbus-glib-0.108... | | | `-- Installing dbus-1.10.16_1... | | | `-- Installing libICE-1.0.9_1,1... | | | `-- Extracting libICE-1.0.9_1,1: .......... done | | | `-- Installing libSM-1.2.2_3,1... | | | `-- Extracting libSM-1.2.2_3,1: .......... done ===> Creating groups. 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Creating group 'avahi' with gid '558'. ===> Creating users Creating user 'avahi' with uid '558'. | | `-- Extracting avahi-app-0.6.31_5: .......... done | | `-- Installing gnutls-3.5.16... | | `-- Installing libidn2-2.0.4... | | | `-- Installing libunistring-0.9.7... | | | `-- Extracting libunistring-0.9.7: .......... done | | `-- Extracting libidn2-2.0.4: .......... done | | `-- Installing libtasn1-4.12... | | `-- Extracting libtasn1-4.12: .......... done | | `-- Installing nettle-3.3... | | `-- Extracting nettle-3.3: .......... done | | `-- Installing p11-kit-0.23.9... | | `-- Extracting p11-kit-0.23.9: .......... done | | `-- Installing trousers-0.3.14_1... | | | `-- Installing tpm-emulator-0.7.4_2... ===> Creating groups. Using existing group '_tss'. ===> Creating users Using existing user '_tss'. | | | `-- Extracting tpm-emulator-0.7.4_2: ......... done ===> Creating groups. Using existing group '_tss'. ===> Creating users Using existing user '_tss'. | | `-- Extracting trousers-0.3.14_1: .......... done | | `-- Extracting gnutls-3.5.16: .......... done | | `-- Installing libpaper-1.1.24.4... | | `-- Extracting libpaper-1.1.24.4: .......... done ===> Creating groups. Creating group 'cups' with gid '193'. ===> Creating users Creating user 'cups' with uid '193'. | `-- Extracting cups-2.2.6: .......... done | `-- Installing gsfonts-8.11_8... | `-- Extracting gsfonts-8.11_8: .......... done | `-- Installing jbig2dec-0.14... | `-- Extracting jbig2dec-0.14: .......... done | `-- Installing jpeg-turbo-1.5.2... | `-- Extracting jpeg-turbo-1.5.2: .......... done | `-- Installing lcms2-2.8... | | `-- Installing tiff-4.0.8... | | `-- Installing jbigkit-2.1_1... | | `-- Extracting jbigkit-2.1_1: .......... done | | `-- Extracting tiff-4.0.8: .......... done | `-- Extracting lcms2-2.8: .......... done | `-- Installing libidn-1.33_1... | `-- Extracting libidn-1.33_1: .......... done `-- Extracting ghostscript9-agpl-base-9.16_5: .......... done `-- Installing gmake-4.2.1_1... `-- Extracting gmake-4.2.1_1: .......... done `-- Installing icu-60.1,1... `-- Extracting icu-60.1,1: .......... done `-- Installing libXScrnSaver-1.2.2_3... | `-- Installing scrnsaverproto-1.2.2... | `-- Extracting scrnsaverproto-1.2.2: ... done `-- Extracting libXScrnSaver-1.2.2_3: .......... done `-- Installing libXmu-1.1.2_3,1... | `-- Installing libXt-1.1.5,1... | `-- Extracting libXt-1.1.5,1: .......... done `-- Extracting libXmu-1.1.2_3,1: .......... done `-- Installing pango-1.40.6... | `-- Installing encodings-1.0.4_3,1... | | `-- Installing font-util-1.3.1... | | `-- Extracting font-util-1.3.1: .......... done | `-- Extracting encodings-1.0.4_3,1: .......... done | `-- Installing harfbuzz-1.5.1_1... | | `-- Installing graphite2-1.3.10... | | `-- Extracting graphite2-1.3.10: .......... done | `-- Extracting harfbuzz-1.5.1_1: .......... done | `-- Installing libXft-2.3.2_1... | `-- Extracting libXft-2.3.2_1: ......... done | `-- Installing xorg-fonts-truetype-7.7_1... | | `-- Installing dejavu-2.37... | | `-- Installing mkfontdir-1.0.7... | | | `-- Installing mkfontscale-1.1.2... | | | `-- Installing libfontenc-1.1.3_1... | | | `-- Extracting libfontenc-1.1.3_1: ......... done | | | `-- Extracting mkfontscale-1.1.2: .. done | | `-- Extracting mkfontdir-1.0.7: .. done | | `-- Extracting dejavu-2.37: .......... done | | `-- Installing font-bh-ttf-1.0.3_3... | | `-- Extracting font-bh-ttf-1.0.3_3: .......... done | | `-- Installing font-misc-ethiopic-1.0.3_3... | | `-- Extracting font-misc-ethiopic-1.0.3_3: ... done | | `-- Installing font-misc-meltho-1.0.3_3... | | `-- Extracting font-misc-meltho-1.0.3_3: .......... done `-- Extracting pango-1.40.6: .......... done `-- Installing tcl86-8.6.7... `-- Extracting tcl86-8.6.7: .......... done `-- Installing tk86-8.6.7... `-- Extracting tk86-8.6.7: .......... done `-- Installing wget-1.19.2... `-- Extracting wget-1.19.2: .......... done Extracting R-3.4.2_2: .......... done Message from freetype2-2.8_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. The controllable properties are listed in the section "Controlling FreeType Modules" in the reference's table of contents (/usr/local/share/doc/freetype2/reference/ft2-toc.html, if documentation was installed). Message from perl5-5.24.3: The /usr/bin/perl symlink has been removed starting with Perl 5.20. For shebangs, you should either use: #!/usr/local/bin/perl or #!/usr/bin/env perl The first one will only work if you have a /usr/local/bin/perl, the second will work as long as perl is in PATH. Message from ca_root_nss-3.34: ********************************* 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 *************************************************************************** Message from gcc6-6.4.0_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/gcc6 For ports leveraging USE_GCC, USES=compiler, or USES=fortran this happens transparently. Message from trousers-0.3.14_1: 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 Message from ghostscript9-agpl-base-9.16_5: Note: in order to use the script "dvipdf", dvips must be installed. This program is provided by another package print/tex-dvipsk. FAPIfontmap and FAPIcidfmap in /usr/local/share/ghostscript/9.16/Resource/Init have to be configured if you want to use FAPI feature. Message from dejavu-2.37: 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. Message from R-3.4.2_2: ======================================================================== On 11.1 and later, there is a problem downloading R packages when R is built with gfortran. Use either of these workarounds until a permanent solution is found. 1. If you are on an amd64 system, use flang to build R. R is now built by default using flang on amd64. 2. If you use gfortran to build R, add options(download.file.method="wget") to ~/.Rprofile followed by a newline. Details: https://bugs.freebsd.org/bugzilla/show_bug.cgi?id=221127 ======================================================================== ===> rpy-1.0.3_36 depends on shared library: libR.so - found (/usr/local/lib/R/lib/libR.so) ===> Returning to build of rpy-1.0.3_36 -------------------------------------------------------------------------------- -- Phase: configure -------------------------------------------------------------------------------- ===> Configuring for rpy-1.0.3_36 RHOMES= [] DEBUG= False Setting RHOMES to ['/usr/local/lib/R'] ### Using R verion 3.4.2 installed at /usr/local/lib/R ### RHOME= /usr/local/lib/R copying src/rpymodule.c -> src/rpymodule3042.c copying src/R_eval.c -> src/R_eval3042.c copying src/io.c -> src/io3042.c running config -------------------------------------------------------------------------------- -- Phase: build -------------------------------------------------------------------------------- ===> Building for rpy-1.0.3_36 RHOMES= [] DEBUG= False Setting RHOMES to ['/usr/local/lib/R'] ### Using R verion 3.4.2 installed at /usr/local/lib/R ### RHOME= /usr/local/lib/R copying src/rpymodule.c -> src/rpymodule3042.c copying src/R_eval.c -> src/R_eval3042.c copying src/io.c -> src/io3042.c running build running build_py creating build creating build/lib.dragonfly-5.0-SYNTH-x86_64-2.7 copying rpy.py -> build/lib.dragonfly-5.0-SYNTH-x86_64-2.7 copying rpy_io.py -> build/lib.dragonfly-5.0-SYNTH-x86_64-2.7 copying rpy_version.py -> build/lib.dragonfly-5.0-SYNTH-x86_64-2.7 copying rpy_tools.py -> build/lib.dragonfly-5.0-SYNTH-x86_64-2.7 copying rpy_options.py -> build/lib.dragonfly-5.0-SYNTH-x86_64-2.7 copying rpy_wintools.py -> build/lib.dragonfly-5.0-SYNTH-x86_64-2.7 running build_ext building '_rpy3042' extension creating build/temp.dragonfly-5.0-SYNTH-x86_64-2.7 creating build/temp.dragonfly-5.0-SYNTH-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=_rpy3042 -DINIT_RPY=init_rpy3042 -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/rpymodule3042.c -o build/temp.dragonfly-5.0-SYNTH-x86_64-2.7/src/rpymodule3042.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:1809:0, from /usr/local/lib/python2.7/site-packages/numpy/core/include/numpy/ndarrayobject.h:18, from /usr/local/lib/python2.7/site-packages/numpy/core/include/numpy/arrayobject.h:4, from src/RPy.h:99, from src/rpymodule3042.c:51: /usr/local/lib/python2.7/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:15:2: warning: #warning "Using deprecated NumPy API, disable it by " "#defining NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp] #warning "Using deprecated NumPy API, disable it by " \ ^ src/rpymodule3042.c:1565:3: warning: initialization from incompatible pointer type [-Wincompatible-pointer-types] (inquiry)Robj_len, /* sq_length */ ^ src/rpymodule3042.c:1565:3: note: (near initialization for 'Robj_as_sequence.sq_length') src/rpymodule3042.c:1568:3: warning: 'intargfunc' is deprecated [-Wdeprecated-declarations] (intargfunc)Robj_item, /* sq_item */ ^ src/rpymodule3042.c:1568:3: warning: initialization from incompatible pointer type [-Wincompatible-pointer-types] src/rpymodule3042.c:1568:3: note: (near initialization for 'Robj_as_sequence.sq_item') src/rpymodule3042.c:1569:3: warning: 'intintargfunc' is deprecated [-Wdeprecated-declarations] (intintargfunc)Robj_slice, /* sq_slice */ ^ src/rpymodule3042.c:1569:3: warning: initialization from incompatible pointer type [-Wincompatible-pointer-types] src/rpymodule3042.c:1569:3: note: (near initialization for 'Robj_as_sequence.sq_slice') src/rpymodule3042.c:1570:3: warning: initialization from incompatible pointer type [-Wincompatible-pointer-types] (intobjargproc)Robj_ass_item, /* sq_ass_item */ ^ src/rpymodule3042.c:1570:3: note: (near initialization for 'Robj_as_sequence.sq_ass_item') cc -DNDEBUG -O3 -Wall -pipe -O2 -fno-strict-aliasing -fPIC -DWITH_NUMERIC=3 -DPY_ARRAY_TYPES_PREFIX=PyArray_ -DRPY_SHNAME=_rpy3042 -DINIT_RPY=init_rpy3042 -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_eval3042.c -o build/temp.dragonfly-5.0-SYNTH-x86_64-2.7/src/R_eval3042.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:1809:0, from /usr/local/lib/python2.7/site-packages/numpy/core/include/numpy/ndarrayobject.h:18, from /usr/local/lib/python2.7/site-packages/numpy/core/include/numpy/arrayobject.h:4, from src/RPy.h:99, from src/R_eval3042.c:63: /usr/local/lib/python2.7/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:15:2: warning: #warning "Using deprecated NumPy API, disable it by " "#defining NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp] #warning "Using deprecated NumPy API, disable it by " \ ^ In file included from /usr/local/lib/python2.7/site-packages/numpy/core/include/numpy/ndarrayobject.h:27:0, from /usr/local/lib/python2.7/site-packages/numpy/core/include/numpy/arrayobject.h:4, from src/RPy.h:99, from src/R_eval3042.c:63: /usr/local/lib/python2.7/site-packages/numpy/core/include/numpy/__multiarray_api.h:1453:1: 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=_rpy3042 -DINIT_RPY=init_rpy3042 -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/io3042.c -o build/temp.dragonfly-5.0-SYNTH-x86_64-2.7/src/io3042.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:1809:0, from /usr/local/lib/python2.7/site-packages/numpy/core/include/numpy/ndarrayobject.h:18, from /usr/local/lib/python2.7/site-packages/numpy/core/include/numpy/arrayobject.h:4, from src/RPy.h:99, from src/io3042.c:43: /usr/local/lib/python2.7/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:15:2: warning: #warning "Using deprecated NumPy API, disable it by " "#defining NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp] #warning "Using deprecated NumPy API, disable it by " \ ^ In file included from /usr/local/lib/python2.7/site-packages/numpy/core/include/numpy/ndarrayobject.h:27:0, from /usr/local/lib/python2.7/site-packages/numpy/core/include/numpy/arrayobject.h:4, from src/RPy.h:99, from src/io3042.c:43: /usr/local/lib/python2.7/site-packages/numpy/core/include/numpy/__multiarray_api.h:1453:1: 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=_rpy3042 -DINIT_RPY=init_rpy3042 -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-5.0-SYNTH-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-5.0-SYNTH-x86_64-2.7/src/rpymodule3042.o build/temp.dragonfly-5.0-SYNTH-x86_64-2.7/src/R_eval3042.o build/temp.dragonfly-5.0-SYNTH-x86_64-2.7/src/io3042.o build/temp.dragonfly-5.0-SYNTH-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-5.0-SYNTH-x86_64-2.7/_rpy3042.so -------------------------------------------------------------------------------- -- Phase: run-depends -------------------------------------------------------------------------------- ===> rpy-1.0.3_36 depends on file: /usr/local/lib/python2.7/site-packages/numpy/core/numeric.py - found ===> rpy-1.0.3_36 depends on package: py27-setuptools>0 - found ===> rpy-1.0.3_36 depends on file: /usr/local/bin/python2.7 - found -------------------------------------------------------------------------------- -- Phase: stage -------------------------------------------------------------------------------- ===> Staging for rpy-1.0.3_36 ===> Generating temporary packing list RHOMES= [] DEBUG= False Setting RHOMES to ['/usr/local/lib/R'] ### Using R verion 3.4.2 installed at /usr/local/lib/R ### RHOME= /usr/local/lib/R copying src/rpymodule.c -> src/rpymodule3042.c copying src/R_eval.c -> src/R_eval3042.c copying src/io.c -> src/io3042.c running install running build running build_py running build_ext running install_lib creating /construction/math/rpy/stage/usr/local/lib/python2.7 creating /construction/math/rpy/stage/usr/local/lib/python2.7/site-packages copying build/lib.dragonfly-5.0-SYNTH-x86_64-2.7/_rpy3042.so -> /construction/math/rpy/stage/usr/local/lib/python2.7/site-packages copying build/lib.dragonfly-5.0-SYNTH-x86_64-2.7/rpy_io.py -> /construction/math/rpy/stage/usr/local/lib/python2.7/site-packages copying build/lib.dragonfly-5.0-SYNTH-x86_64-2.7/rpy_options.py -> /construction/math/rpy/stage/usr/local/lib/python2.7/site-packages copying build/lib.dragonfly-5.0-SYNTH-x86_64-2.7/rpy_version.py -> /construction/math/rpy/stage/usr/local/lib/python2.7/site-packages copying build/lib.dragonfly-5.0-SYNTH-x86_64-2.7/rpy.py -> /construction/math/rpy/stage/usr/local/lib/python2.7/site-packages copying build/lib.dragonfly-5.0-SYNTH-x86_64-2.7/rpy_wintools.py -> /construction/math/rpy/stage/usr/local/lib/python2.7/site-packages copying build/lib.dragonfly-5.0-SYNTH-x86_64-2.7/rpy_tools.py -> /construction/math/rpy/stage/usr/local/lib/python2.7/site-packages byte-compiling /construction/math/rpy/stage/usr/local/lib/python2.7/site-packages/rpy_io.py to rpy_io.pyc byte-compiling /construction/math/rpy/stage/usr/local/lib/python2.7/site-packages/rpy_options.py to rpy_options.pyc byte-compiling /construction/math/rpy/stage/usr/local/lib/python2.7/site-packages/rpy_version.py to rpy_version.pyc byte-compiling /construction/math/rpy/stage/usr/local/lib/python2.7/site-packages/rpy.py to rpy.pyc byte-compiling /construction/math/rpy/stage/usr/local/lib/python2.7/site-packages/rpy_wintools.py to rpy_wintools.pyc byte-compiling /construction/math/rpy/stage/usr/local/lib/python2.7/site-packages/rpy_tools.py to rpy_tools.pyc writing byte-compilation script '/tmp/tmpdAS22R.py' /usr/local/bin/python2.7 -O /tmp/tmpdAS22R.py removing /tmp/tmpdAS22R.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/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/rpy/.PLIST.pymodtmp' ====> Compressing man pages (compress-man) -------------------------------------------------------------------------------- -- Phase: package -------------------------------------------------------------------------------- ===> Building package for rpy-1.0.3_36 file sizes/checksums [28]: . done packing files [28]: . done packing directories [0]: . done -------------------------------------------------- -- Termination -------------------------------------------------- Finished: Wednesday, 22 NOV 2017 at 03:45:22 UTC Duration: 00:01:21