=> Building biology/groopm Started : Sunday, 7 JUL 2019 at 04:13:01 UTC Platform: 5.7-DEVELOPMENT DragonFly v5.7.0.83.g49866-DEVELOPMENT #40: Sun Jun 30 03:00:04 PDT 2019 root@pkgbox64.dragonflybsd.org:/usr/obj/usr/src/sys/X86_64_GENERIC x86_64 -------------------------------------------------- -- Environment -------------------------------------------------- UNAME_r=5.4-SYNTH UNAME_m=x86_64 UNAME_p=x86_64 UNAME_v=DragonFly 5.4-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/biology/groopm XDG_CONFIG_HOME=/construction/biology/groopm HOME=/construction/biology/groopm TMPDIR="/tmp" PATH=/construction/biology/groopm/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin SHELL=/bin/sh CONFIG_SHELL=/bin/sh CCVER=gcc80 -------------------------------------------------- -- CONFIGURE_ARGS -------------------------------------------------- -------------------------------------------------- -- MAKE_ENV -------------------------------------------------- XDG_DATA_HOME=/construction/biology/groopm XDG_CONFIG_HOME=/construction/biology/groopm HOME=/construction/biology/groopm TMPDIR="/tmp" PATH=/construction/biology/groopm/.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=gcc80 LDSHARED="cc -shared" PYTHONDONTWRITEBYTECODE= PYTHONOPTIMIZE= PREFIX=/usr/local LOCALBASE=/usr/local NOPROFILE=1 CC="cc" CFLAGS="-pipe -O2 -fno-strict-aliasing " CPP="cpp" CPPFLAGS="" LDFLAGS=" " 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/biology/groopm/stage -------------------------------------------------- -- PLIST_SUB -------------------------------------------------- PYTHON_INCLUDEDIR=include/python2.7 PYTHON_LIBDIR=lib/python2.7 PYTHON_PLATFORM=dragonfly5 PYTHON_SITELIBDIR=lib/python2.7/site-packages PYTHON_SUFFIX=27 PYTHON_VER=2.7 PYTHON_VERSION=python2.7 PYTHON2="" PYTHON3="@comment " OSREL=5.4 PREFIX=%D LOCALBASE=/usr/local RESETPREFIX=/usr/local LIB32DIR=lib PROFILE="@comment " DOCSDIR="share/doc/GroopM" EXAMPLESDIR="share/examples/GroopM" DATADIR="share/GroopM" WWWDIR="www/GroopM" ETCDIR="etc/GroopM" -------------------------------------------------- -- SUB_LIST -------------------------------------------------- PREFIX=/usr/local LOCALBASE=/usr/local DATADIR=/usr/local/share/GroopM DOCSDIR=/usr/local/share/doc/GroopM EXAMPLESDIR=/usr/local/share/examples/GroopM WWWDIR=/usr/local/www/GroopM ETCDIR=/usr/local/etc/GroopM -------------------------------------------------- -- /etc/make.conf -------------------------------------------------- SYNTHPROFILE=Release-5.4 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 _PERL5_FROM_BIN=5.28.1 _ALTCCVERSION_921dbbb2=none _OBJC_ALTCCVERSION_921dbbb2=none _SMP_CPUS=8 UID=0 ARCH=x86_64 OPSYS=DragonFly DFLYVERSION=500400 OSVERSION=9999999 OSREL=5.4 _OSRELEASE=5.4-SYNTH PYTHONBASE=/usr/local _PKG_CHECKED=1 -------------------------------------------------------------------------------- -- Phase: check-sanity -------------------------------------------------------------------------------- ===> License GPLv3 accepted by the user -------------------------------------------------------------------------------- -- Phase: pkg-depends -------------------------------------------------------------------------------- ===> GroopM-0.3.4_1 depends on file: /usr/local/sbin/pkg - not found ===> Installing existing package /packages/All/pkg-1.11.1.txz Installing pkg-1.11.1... Extracting pkg-1.11.1: .......... done ===> GroopM-0.3.4_1 depends on file: /usr/local/sbin/pkg - found ===> Returning to build of GroopM-0.3.4_1 -------------------------------------------------------------------------------- -- Phase: fetch-depends -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- -- Phase: fetch -------------------------------------------------------------------------------- ===> License GPLv3 accepted by the user ===> Fetching all distfiles required by GroopM-0.3.4_1 for building -------------------------------------------------------------------------------- -- Phase: checksum -------------------------------------------------------------------------------- ===> License GPLv3 accepted by the user ===> Fetching all distfiles required by GroopM-0.3.4_1 for building => SHA256 Checksum OK for GroopM-0.3.4.tar.gz. -------------------------------------------------------------------------------- -- Phase: extract-depends -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- -- Phase: extract -------------------------------------------------------------------------------- ===> License GPLv3 accepted by the user ===> Fetching all distfiles required by GroopM-0.3.4_1 for building ===> Extracting for GroopM-0.3.4_1 => SHA256 Checksum OK for GroopM-0.3.4.tar.gz. -------------------------------------------------------------------------------- -- Phase: patch-depends -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- -- Phase: patch -------------------------------------------------------------------------------- ===> Patching for GroopM-0.3.4_1 -------------------------------------------------------------------------------- -- Phase: build-depends -------------------------------------------------------------------------------- ===> GroopM-0.3.4_1 depends on package: py27-setuptools>0 - not found ===> Installing existing package /packages/All/py27-setuptools-41.0.0.txz Installing py27-setuptools-41.0.0... `-- Installing python27-2.7.16_1... | `-- Installing expat-2.2.6_1... | `-- Extracting expat-2.2.6_1: .......... done | `-- Installing gettext-runtime-0.20.1... | | `-- Installing indexinfo-0.3.1... | | `-- Extracting indexinfo-0.3.1: .... done | `-- Extracting gettext-runtime-0.20.1: .......... done | `-- Installing libffi-3.2.1_3... | `-- Extracting libffi-3.2.1_3: .......... done | `-- Installing libressl-2.9.2... | `-- Extracting libressl-2.9.2: .......... done | `-- Installing ncurses-6.1.20190525... | `-- Extracting ncurses-6.1.20190525: .......... done | `-- Installing readline-8.0.0... | `-- Extracting readline-8.0.0: .......... done `-- Extracting python27-2.7.16_1: .......... done Extracting py27-setuptools-41.0.0: .......... done 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 =========================================================================== Message from py27-setuptools-41.0.0: ******************************************************************* Only /usr/local/bin/easy_install-2.7 script has been installed since Python 2.7 is not the default Python version. ******************************************************************* ===> GroopM-0.3.4_1 depends on package: py27-setuptools>0 - found ===> Returning to build of GroopM-0.3.4_1 ===> GroopM-0.3.4_1 depends on file: /usr/local/bin/python2.7 - found -------------------------------------------------------------------------------- -- Phase: lib-depends -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- -- Phase: configure -------------------------------------------------------------------------------- ===> Configuring for GroopM-0.3.4_1 running config -------------------------------------------------------------------------------- -- Phase: build -------------------------------------------------------------------------------- ===> Building for GroopM-0.3.4_1 running build running build_py creating build creating build/lib creating build/lib/groopm copying groopm/groopmUtils.py -> build/lib/groopm copying groopm/ellipsoid.py -> build/lib/groopm copying groopm/som.py -> build/lib/groopm copying groopm/groopmExceptions.py -> build/lib/groopm copying groopm/groopmTimekeeper.py -> build/lib/groopm copying groopm/profileManager.py -> build/lib/groopm copying groopm/bin.py -> build/lib/groopm copying groopm/torusMesh.py -> build/lib/groopm copying groopm/PCA.py -> build/lib/groopm copying groopm/refine.py -> build/lib/groopm copying groopm/rainbow.py -> build/lib/groopm copying groopm/cluster.py -> build/lib/groopm copying groopm/binManager.py -> build/lib/groopm copying groopm/groopm.py -> build/lib/groopm copying groopm/mstore.py -> build/lib/groopm copying groopm/__init__.py -> build/lib/groopm running build_scripts creating build/scripts-2.7 copying and adjusting bin/groopm -> build/scripts-2.7 changing mode of build/scripts-2.7/groopm from 644 to 755 -------------------------------------------------------------------------------- -- Phase: run-depends -------------------------------------------------------------------------------- ===> GroopM-0.3.4_1 depends on package: py27-numpy>0 - not found ===> Installing existing package /packages/All/py27-numpy-1.16.1_2,1.txz Installing py27-numpy-1.16.1_2,1... `-- Installing gcc8-8.3.0_2... | `-- Installing binutils-2.32_1,1... | `-- Extracting binutils-2.32_1,1: .......... done | `-- Installing gmp-6.1.2_1... | `-- Extracting gmp-6.1.2_1: .......... done | `-- Installing mpc-1.1.0_2... | | `-- Installing mpfr-4.0.2... | | `-- Extracting mpfr-4.0.2: .......... done | `-- Extracting mpc-1.1.0_2: ......... done `-- Extracting gcc8-8.3.0_2: .......... done `-- Installing openblas-0.2.20_8,1... `-- Extracting openblas-0.2.20_8,1: ......... done `-- Installing suitesparse-5.2.0_3... | `-- Installing lapack-3.5.0_7... | | `-- Installing blas-3.5.0_5... | | `-- Extracting blas-3.5.0_5: ....... done | `-- Extracting lapack-3.5.0_7: .......... done | `-- Installing metis-5.1.0_7... | `-- Extracting metis-5.1.0_7: .......... done `-- Extracting suitesparse-5.2.0_3: .......... done Extracting py27-numpy-1.16.1_2,1: .......... done Message from gcc8-8.3.0_2: 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. Message from metis-5.1.0_7: ===> 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 ===> GroopM-0.3.4_1 depends on package: py27-numpy>0 - found ===> Returning to build of GroopM-0.3.4_1 ===> GroopM-0.3.4_1 depends on package: py27-matplotlib>=1.1.0 - not found ===> Installing existing package /packages/All/py27-matplotlib-2.2.4.txz Installing py27-matplotlib-2.2.4... `-- Installing atk-2.28.1... | `-- Installing glib-2.56.3_5,1... | | `-- Installing libiconv-1.14_11... | | `-- Extracting libiconv-1.14_11: .......... done | | `-- Installing libxml2-2.9.9... | | `-- Extracting libxml2-2.9.9: .......... done | | `-- Installing pcre-8.43_1... | | `-- Extracting pcre-8.43_1: .......... done | | `-- Installing python36-3.6.8_2... | | `-- Extracting python36-3.6.8_2: .......... done | `-- Extracting glib-2.56.3_5,1: .......... done No schema files found: doing nothing. `-- Extracting atk-2.28.1: .......... done `-- Installing cairo-1.16.0,2... | `-- Installing fontconfig-2.12.6,1... | | `-- Installing freetype2-2.10.0... | | `-- Extracting freetype2-2.10.0: .......... done | `-- Extracting fontconfig-2.12.6,1: .......... 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 libX11-1.6.7,1... | | `-- Installing libXau-1.0.9... | | `-- Extracting libXau-1.0.9: .......... done | | `-- Installing libXdmcp-1.1.3... | | `-- Installing xorgproto-2018.4... | | `-- Extracting xorgproto-2018.4: .......... done | | `-- Extracting libXdmcp-1.1.3: ......... done | | `-- Installing libxcb-1.13.1... | | `-- Installing libpthread-stubs-0.4... | | `-- Extracting libpthread-stubs-0.4: .... done | | `-- Extracting libxcb-1.13.1: .......... done | `-- Extracting libX11-1.6.7,1: .......... done | `-- Installing libXext-1.3.4,1... | `-- Extracting libXext-1.3.4,1: .......... done | `-- Installing libXrender-0.9.10_2... | `-- Extracting libXrender-0.9.10_2: .......... done | `-- Installing mesa-libs-18.3.2... | | `-- Installing libXdamage-1.1.5... | | `-- Installing libXfixes-5.0.3_2... | | `-- Extracting libXfixes-5.0.3_2: .......... done | | `-- Extracting libXdamage-1.1.5: ......... done | | `-- Installing libXrandr-1.5.2... | | `-- Extracting libXrandr-1.5.2: .......... done | | `-- Installing libXxf86vm-1.1.4_3... | | `-- Extracting libXxf86vm-1.1.4_3: .......... done | | `-- Installing libdrm-2.4.98... | | `-- Installing libpciaccess-0.13.5... | | | `-- Installing pciids-20190418... | | | `-- Extracting pciids-20190418: ..... done | | `-- Extracting libpciaccess-0.13.5: ......... done | | `-- Extracting libdrm-2.4.98: .......... done | | `-- Installing libelf-0.8.13_3... | | `-- Extracting libelf-0.8.13_3: .......... done | | `-- Installing libxshmfence-1.3... | | `-- Extracting libxshmfence-1.3: ......... done | | `-- Installing wayland-1.16.0... | | `-- Extracting wayland-1.16.0: .......... done | `-- Extracting mesa-libs-18.3.2: .......... done | `-- Installing pixman-0.34.0_1... | `-- Extracting pixman-0.34.0_1: .......... done | `-- Installing png-1.6.37... | `-- Extracting png-1.6.37: .......... done `-- Extracting cairo-1.16.0,2: .......... done `-- Installing gdk-pixbuf2-2.36.12... | `-- Installing jpeg-turbo-2.0.2... | `-- Extracting jpeg-turbo-2.0.2: .......... done | `-- Installing shared-mime-info-1.10_1... | `-- Extracting shared-mime-info-1.10_1: .......... done | `-- Installing tiff-4.0.10_1... | | `-- Installing jbigkit-2.1_1... | | `-- Extracting jbigkit-2.1_1: .......... done | `-- Extracting tiff-4.0.10_1: .......... done `-- Extracting gdk-pixbuf2-2.36.12: .......... done `-- Installing gtk2-2.24.32... | `-- Installing cups-2.2.11... | | `-- Installing avahi-app-0.7_2... | | `-- Installing dbus-1.12.12... | | | `-- Installing libICE-1.0.9_3,1... | | | `-- Extracting libICE-1.0.9_3,1: .......... done | | | `-- Installing libSM-1.2.3,1... | | | `-- Extracting libSM-1.2.3,1: .......... done ===> Creating groups. Creating group 'messagebus' with gid '556'. ===> Creating users Creating user 'messagebus' with uid '556'. | | `-- Extracting dbus-1.12.12: ......... done | | `-- Installing dbus-glib-0.110... | | `-- Extracting dbus-glib-0.110: .......... done | | `-- Installing gdbm-1.18.1_1... | | `-- Extracting gdbm-1.18.1_1: .......... done | | `-- Installing gnome_subr-1.0... | | `-- Extracting gnome_subr-1.0: .... done | | `-- Installing gobject-introspection-1.56.1,1... | | `-- Extracting gobject-introspection-1.56.1,1: .......... done | | `-- Installing libdaemon-0.14_1... | | `-- Extracting libdaemon-0.14_1: .......... done ===> Creating groups. Creating group 'avahi' with gid '558'. ===> Creating users Creating user 'avahi' with uid '558'. | | `-- Extracting avahi-app-0.7_2: .......... done | | `-- Installing gnutls-3.6.8... | | `-- Installing ca_root_nss-3.44... | | `-- Extracting ca_root_nss-3.44: ........ done | | `-- Installing libidn2-2.2.0... | | | `-- Installing libunistring-0.9.10_1... | | | `-- Extracting libunistring-0.9.10_1: .......... done | | `-- Extracting libidn2-2.2.0: .......... done | | `-- Installing libtasn1-4.13_1... | | `-- Extracting libtasn1-4.13_1: .......... done | | `-- Installing nettle-3.4.1_1... | | `-- Extracting nettle-3.4.1_1: .......... done | | `-- Installing p11-kit-0.23.15... | | `-- Extracting p11-kit-0.23.15: .......... done | | `-- Installing trousers-0.3.14_2... | | | `-- 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_2: .......... done | | `-- Extracting gnutls-3.6.8: .......... 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-2.2.11: .......... done | `-- Installing gtk-update-icon-cache-2.24.32... | | `-- Installing hicolor-icon-theme-0.17... | | `-- Extracting hicolor-icon-theme-0.17: . done | | `-- Installing libXcomposite-0.4.5,1... | | `-- Extracting libXcomposite-0.4.5,1: .......... done | | `-- Installing libXcursor-1.2.0... | | `-- Extracting libXcursor-1.2.0: .......... done | | `-- Installing libXi-1.7.9_2,1... | | `-- Extracting libXi-1.7.9_2,1: .......... done | | `-- Installing libXinerama-1.1.4_2,1... | | `-- Extracting libXinerama-1.1.4_2,1: .......... done | | `-- Installing pango-1.42.4_2... | | `-- Installing encodings-1.0.5,1... | | | `-- Installing font-util-1.3.1... | | | `-- Extracting font-util-1.3.1: .......... done | | `-- Extracting encodings-1.0.5,1: .......... done | | `-- Installing fribidi-0.19.7... | | `-- Extracting fribidi-0.19.7: .......... done | | `-- Installing harfbuzz-2.5.1... | | | `-- Installing graphite2-1.3.13... | | | `-- Extracting graphite2-1.3.13: .......... done | | `-- Extracting harfbuzz-2.5.1: .......... done | | `-- Installing libXft-2.3.2_3... | | `-- Extracting libXft-2.3.2_3: .......... done | | `-- Installing xorg-fonts-truetype-7.7_1... | | | `-- Installing dejavu-2.37_1... | | | `-- Installing mkfontscale-1.2.1... | | | | `-- Installing libfontenc-1.1.4... | | | | `-- Extracting libfontenc-1.1.4: ......... done | | | `-- Extracting mkfontscale-1.2.1: ....... done | | | `-- Extracting dejavu-2.37_1: .......... done | | | `-- Installing font-bh-ttf-1.0.3_4... | | | `-- Extracting font-bh-ttf-1.0.3_4: .......... done | | | `-- Installing font-misc-ethiopic-1.0.3_4... | | | `-- Extracting font-misc-ethiopic-1.0.3_4: ... done | | | `-- Installing font-misc-meltho-1.0.3_4... | | | `-- Extracting font-misc-meltho-1.0.3_4: .......... done | | `-- Extracting pango-1.42.4_2: .......... done | `-- Extracting gtk-update-icon-cache-2.24.32: .... done `-- Extracting gtk2-2.24.32: .......... done `-- Installing libglade2-2.6.4_9... | `-- Installing xmlcatmgr-2.2_2... | `-- Extracting xmlcatmgr-2.2_2: ......... done + Creating /usr/local/share/sgml/catalog + Registering CATALOG catalog.ports (SGML) + Creating /usr/local/share/sgml/catalog.ports + Creating /usr/local/share/xml/catalog + Registering nextCatalog catalog.ports (XML) + Creating /usr/local/share/xml/catalog.ports `-- Extracting libglade2-2.6.4_9: .......... done `-- Installing py27-backports.functools_lru_cache-1.5... | `-- Installing py27-backports-1... | `-- Extracting py27-backports-1: ...... done `-- Extracting py27-backports.functools_lru_cache-1.5: .......... done `-- Installing py27-cycler-0.10.0... | `-- Installing py27-six-1.12.0... | `-- Extracting py27-six-1.12.0: .......... done `-- Extracting py27-cycler-0.10.0: .......... done `-- Installing py27-dateutil-2.8.0... `-- Extracting py27-dateutil-2.8.0: .......... done `-- Installing py27-gobject-2.28.6_8... | `-- Installing py27-cairo-1.14.1... | `-- Extracting py27-cairo-1.14.1: .......... done `-- Extracting py27-gobject-2.28.6_8: .......... done `-- Installing py27-gtk2-2.24.0_5... `-- Extracting py27-gtk2-2.24.0_5: .......... done `-- Installing py27-kiwisolver-1.1.0... `-- Extracting py27-kiwisolver-1.1.0: ......... done `-- Installing py27-pyparsing-2.4.0... `-- Extracting py27-pyparsing-2.4.0: .......... done `-- Installing py27-pytz-2019.1,1... `-- Extracting py27-pytz-2019.1,1: .......... done `-- Installing py27-tkinter-2.7.16_6... | `-- Installing tcl86-8.6.9_1... | `-- Extracting tcl86-8.6.9_1: .......... done | `-- Installing tk86-8.6.9_1... | | `-- Installing libXScrnSaver-1.2.3_2... | | `-- Extracting libXScrnSaver-1.2.3_2: .......... done | `-- Extracting tk86-8.6.9_1: .......... done `-- Extracting py27-tkinter-2.7.16_6: ........ done `-- Installing py27-tornado-5.1.1... | `-- Installing py27-backports_abc-0.5... | `-- Extracting py27-backports_abc-0.5: .......... done | `-- Installing py27-futures-3.2.0... | `-- Extracting py27-futures-3.2.0: .......... done | `-- Installing py27-singledispatch-3.4.0.3_1... | `-- Extracting py27-singledispatch-3.4.0.3_1: .......... done `-- Extracting py27-tornado-5.1.1: .......... done Extracting py27-matplotlib-2.2.4: .......... done Message from python36-3.6.8_2: =========================================================================== 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 =========================================================================== Message from freetype2-2.10.0: 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/site/index.html, if documentation was installed). Message from ca_root_nss-3.44: ********************************* 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 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 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. Message from xmlcatmgr-2.2_2: The following catalogs are installed: 1) /usr/local/share/sgml/catalog The top level catalog for SGML stuff. It is not changed by any ports/packages except textproc/xmlcatmgr. 2) /usr/local/share/sgml/catalog.ports This catalog is for handling SGML stuff installed under /usr/local/share/sgml. It is changed by ports/packages. 3) /usr/local/share/xml/catalog The top level catalog for XML stuff. It is not changed by any ports/packages except textproc/xmlcatmgr. 4) /usr/local/share/xml/catalog.ports This catalog is for handling XML stuff installed under /usr/local/share/xml. It is changed by ports/packages. ===> GroopM-0.3.4_1 depends on package: py27-matplotlib>=1.1.0 - found ===> Returning to build of GroopM-0.3.4_1 ===> GroopM-0.3.4_1 depends on package: py27-scipy>=0.10.1 - not found ===> Installing existing package /packages/All/py27-scipy-1.2.0_1.txz Installing py27-scipy-1.2.0_1... Extracting py27-scipy-1.2.0_1: .......... done ===> GroopM-0.3.4_1 depends on package: py27-scipy>=0.10.1 - found ===> Returning to build of GroopM-0.3.4_1 ===> GroopM-0.3.4_1 depends on package: py27-tables>=2.3 - not found ===> Installing existing package /packages/All/py27-tables-3.5.2.txz Installing py27-tables-3.5.2... `-- Installing hdf5-1.10.5_1... | `-- Installing hdf-szip-2.1.1... | `-- Extracting hdf-szip-2.1.1: .......... done `-- Extracting hdf5-1.10.5_1: .......... done `-- Installing lzo2-2.10_1... `-- Extracting lzo2-2.10_1: .......... done `-- Installing py27-numexpr-2.6.9... `-- Extracting py27-numexpr-2.6.9: .......... done `-- Installing ucl-1.03_5... `-- Extracting ucl-1.03_5: .......... done Extracting py27-tables-3.5.2: .......... done Message from ucl-1.03_5: ===> NOTICE: The ucl 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 ===> GroopM-0.3.4_1 depends on package: py27-tables>=2.3 - found ===> Returning to build of GroopM-0.3.4_1 ===> GroopM-0.3.4_1 depends on package: py27-setuptools>0 - found ===> GroopM-0.3.4_1 depends on file: /usr/local/bin/python2.7 - found -------------------------------------------------------------------------------- -- Phase: stage -------------------------------------------------------------------------------- ===> Staging for GroopM-0.3.4_1 ===> Generating temporary packing list running install running build running build_py running build_scripts running install_lib creating /construction/biology/groopm/stage/usr/local/lib/python2.7 creating /construction/biology/groopm/stage/usr/local/lib/python2.7/site-packages creating /construction/biology/groopm/stage/usr/local/lib/python2.7/site-packages/groopm copying build/lib/groopm/PCA.py -> /construction/biology/groopm/stage/usr/local/lib/python2.7/site-packages/groopm copying build/lib/groopm/groopmTimekeeper.py -> /construction/biology/groopm/stage/usr/local/lib/python2.7/site-packages/groopm copying build/lib/groopm/mstore.py -> /construction/biology/groopm/stage/usr/local/lib/python2.7/site-packages/groopm copying build/lib/groopm/bin.py -> /construction/biology/groopm/stage/usr/local/lib/python2.7/site-packages/groopm copying build/lib/groopm/som.py -> /construction/biology/groopm/stage/usr/local/lib/python2.7/site-packages/groopm copying build/lib/groopm/groopmUtils.py -> /construction/biology/groopm/stage/usr/local/lib/python2.7/site-packages/groopm copying build/lib/groopm/refine.py -> /construction/biology/groopm/stage/usr/local/lib/python2.7/site-packages/groopm copying build/lib/groopm/ellipsoid.py -> /construction/biology/groopm/stage/usr/local/lib/python2.7/site-packages/groopm copying build/lib/groopm/__init__.py -> /construction/biology/groopm/stage/usr/local/lib/python2.7/site-packages/groopm copying build/lib/groopm/profileManager.py -> /construction/biology/groopm/stage/usr/local/lib/python2.7/site-packages/groopm copying build/lib/groopm/cluster.py -> /construction/biology/groopm/stage/usr/local/lib/python2.7/site-packages/groopm copying build/lib/groopm/groopmExceptions.py -> /construction/biology/groopm/stage/usr/local/lib/python2.7/site-packages/groopm copying build/lib/groopm/torusMesh.py -> /construction/biology/groopm/stage/usr/local/lib/python2.7/site-packages/groopm copying build/lib/groopm/groopm.py -> /construction/biology/groopm/stage/usr/local/lib/python2.7/site-packages/groopm copying build/lib/groopm/rainbow.py -> /construction/biology/groopm/stage/usr/local/lib/python2.7/site-packages/groopm copying build/lib/groopm/binManager.py -> /construction/biology/groopm/stage/usr/local/lib/python2.7/site-packages/groopm byte-compiling /construction/biology/groopm/stage/usr/local/lib/python2.7/site-packages/groopm/PCA.py to PCA.pyc byte-compiling /construction/biology/groopm/stage/usr/local/lib/python2.7/site-packages/groopm/groopmTimekeeper.py to groopmTimekeeper.pyc byte-compiling /construction/biology/groopm/stage/usr/local/lib/python2.7/site-packages/groopm/mstore.py to mstore.pyc byte-compiling /construction/biology/groopm/stage/usr/local/lib/python2.7/site-packages/groopm/bin.py to bin.pyc byte-compiling /construction/biology/groopm/stage/usr/local/lib/python2.7/site-packages/groopm/som.py to som.pyc byte-compiling /construction/biology/groopm/stage/usr/local/lib/python2.7/site-packages/groopm/groopmUtils.py to groopmUtils.pyc byte-compiling /construction/biology/groopm/stage/usr/local/lib/python2.7/site-packages/groopm/refine.py to refine.pyc byte-compiling /construction/biology/groopm/stage/usr/local/lib/python2.7/site-packages/groopm/ellipsoid.py to ellipsoid.pyc byte-compiling /construction/biology/groopm/stage/usr/local/lib/python2.7/site-packages/groopm/__init__.py to __init__.pyc byte-compiling /construction/biology/groopm/stage/usr/local/lib/python2.7/site-packages/groopm/profileManager.py to profileManager.pyc byte-compiling /construction/biology/groopm/stage/usr/local/lib/python2.7/site-packages/groopm/cluster.py to cluster.pyc byte-compiling /construction/biology/groopm/stage/usr/local/lib/python2.7/site-packages/groopm/groopmExceptions.py to groopmExceptions.pyc byte-compiling /construction/biology/groopm/stage/usr/local/lib/python2.7/site-packages/groopm/torusMesh.py to torusMesh.pyc byte-compiling /construction/biology/groopm/stage/usr/local/lib/python2.7/site-packages/groopm/groopm.py to groopm.pyc byte-compiling /construction/biology/groopm/stage/usr/local/lib/python2.7/site-packages/groopm/rainbow.py to rainbow.pyc byte-compiling /construction/biology/groopm/stage/usr/local/lib/python2.7/site-packages/groopm/binManager.py to binManager.pyc writing byte-compilation script '/tmp/tmpcoTpJ7.py' /usr/local/bin/python2.7 -O /tmp/tmpcoTpJ7.py removing /tmp/tmpcoTpJ7.py running install_egg_info running egg_info creating GroopM.egg-info writing requirements to GroopM.egg-info/requires.txt writing GroopM.egg-info/PKG-INFO writing top-level names to GroopM.egg-info/top_level.txt writing dependency_links to GroopM.egg-info/dependency_links.txt writing manifest file 'GroopM.egg-info/SOURCES.txt' reading manifest file 'GroopM.egg-info/SOURCES.txt' writing manifest file 'GroopM.egg-info/SOURCES.txt' Copying GroopM.egg-info to /construction/biology/groopm/stage/usr/local/lib/python2.7/site-packages/GroopM-0.3.4-py2.7.egg-info running install_scripts copying build/scripts-2.7/groopm -> /construction/biology/groopm/stage/usr/local/bin changing mode of /construction/biology/groopm/stage/usr/local/bin/groopm to 755 writing list of installed files to '/construction/biology/groopm/.PLIST.pymodtmp' ====> Compressing man pages (compress-man) -------------------------------------------------------------------------------- -- Phase: package -------------------------------------------------------------------------------- ===> Building package for GroopM-0.3.4_1 file sizes/checksums [57]: . done packing files [57]: . done packing directories [0]: . done -------------------------------------------------- -- Termination -------------------------------------------------- Finished: Sunday, 7 JUL 2019 at 04:14:32 UTC Duration: 00:01:30