=> Building biology/ddocent Started : Sunday, 7 JUL 2019 at 04:06:42 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 -------------------------------------------------- ac_cv_path_PERL=/usr/local/bin/perl ac_cv_path_PERL_PATH=/usr/local/bin/perl PERL_USE_UNSAFE_INC=1 PYTHON="/usr/local/bin/python3.6" XDG_DATA_HOME=/construction/biology/ddocent XDG_CONFIG_HOME=/construction/biology/ddocent HOME=/construction/biology/ddocent TMPDIR="/tmp" PATH=/construction/biology/ddocent/.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 -------------------------------------------------- PERL_USE_UNSAFE_INC=1 XDG_DATA_HOME=/construction/biology/ddocent XDG_CONFIG_HOME=/construction/biology/ddocent HOME=/construction/biology/ddocent TMPDIR="/tmp" PATH=/construction/biology/ddocent/.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 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/ddocent/stage -------------------------------------------------- -- PLIST_SUB -------------------------------------------------- JAVASHAREDIR="share/java" JAVAJARDIR="share/java/classes" PYTHON_INCLUDEDIR=include/python3.6m PYTHON_LIBDIR=lib/python3.6 PYTHON_PLATFORM=dragonfly5 PYTHON_SITELIBDIR=lib/python3.6/site-packages PYTHON_SUFFIX=36 PYTHON_VER=3.6 PYTHON_VERSION=python3.6 PYTHON2="@comment " PYTHON3="" OSREL=5.4 PREFIX=%D LOCALBASE=/usr/local RESETPREFIX=/usr/local LIB32DIR=lib PERL_VERSION=5.28.2 PERL_VER=5.28 PERL5_MAN1=lib/perl5/site_perl/man/man1 PERL5_MAN3=lib/perl5/site_perl/man/man3 SITE_PERL=lib/perl5/site_perl SITE_ARCH=lib/perl5/site_perl/mach/5.28 PROFILE="@comment " DOCSDIR="share/doc/dDocent" EXAMPLESDIR="share/examples/dDocent" DATADIR="share/dDocent" WWWDIR="www/dDocent" ETCDIR="etc/dDocent" -------------------------------------------------- -- SUB_LIST -------------------------------------------------- JAVASHAREDIR="/usr/local/share/java" JAVAJARDIR="/usr/local/share/java/classes" JAVALIBDIR="/usr/local/share/java/classes" PREFIX=/usr/local LOCALBASE=/usr/local DATADIR=/usr/local/share/dDocent DOCSDIR=/usr/local/share/doc/dDocent EXAMPLESDIR=/usr/local/share/examples/dDocent WWWDIR=/usr/local/www/dDocent ETCDIR=/usr/local/etc/dDocent -------------------------------------------------- -- /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 MIT accepted by the user -------------------------------------------------------------------------------- -- Phase: pkg-depends -------------------------------------------------------------------------------- ===> dDocent-2.7.8 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 ===> dDocent-2.7.8 depends on file: /usr/local/sbin/pkg - found ===> Returning to build of dDocent-2.7.8 -------------------------------------------------------------------------------- -- Phase: fetch-depends -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- -- Phase: fetch -------------------------------------------------------------------------------- ===> License MIT accepted by the user ===> Fetching all distfiles required by dDocent-2.7.8 for building -------------------------------------------------------------------------------- -- Phase: checksum -------------------------------------------------------------------------------- ===> License MIT accepted by the user ===> Fetching all distfiles required by dDocent-2.7.8 for building => SHA256 Checksum OK for jpuritz-dDocent-v2.7.8_GH0.tar.gz. -------------------------------------------------------------------------------- -- Phase: extract-depends -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- -- Phase: extract -------------------------------------------------------------------------------- ===> License MIT accepted by the user ===> Fetching all distfiles required by dDocent-2.7.8 for building ===> Extracting for dDocent-2.7.8 => SHA256 Checksum OK for jpuritz-dDocent-v2.7.8_GH0.tar.gz. -------------------------------------------------------------------------------- -- Phase: patch-depends -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- -- Phase: patch -------------------------------------------------------------------------------- ===> Patching for dDocent-2.7.8 ===> Applying ports patches for dDocent-2.7.8 -------------------------------------------------------------------------------- -- Phase: build-depends -------------------------------------------------------------------------------- ===> dDocent-2.7.8 depends on file: /usr/local/bin/python3.6 - not found ===> Installing existing package /packages/All/python36-3.6.8_2.txz Installing python36-3.6.8_2... `-- 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 python36-3.6.8_2: .......... 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 =========================================================================== ===> dDocent-2.7.8 depends on file: /usr/local/bin/python3.6 - found ===> Returning to build of dDocent-2.7.8 ===> dDocent-2.7.8 depends on package: perl5>=5.28.r1<5.29 - not found ===> Installing existing package /packages/All/perl5-5.28.2.txz Installing perl5-5.28.2... Extracting perl5-5.28.2: .......... done Message from perl5-5.28.2: 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. ===> dDocent-2.7.8 depends on package: perl5>=5.28.r1<5.29 - found ===> Returning to build of dDocent-2.7.8 -------------------------------------------------------------------------------- -- Phase: lib-depends -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- -- Phase: configure -------------------------------------------------------------------------------- ===> Configuring for dDocent-2.7.8 -------------------------------------------------------------------------------- -- Phase: build -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- -- Phase: run-depends -------------------------------------------------------------------------------- ===> dDocent-2.7.8 depends on package: unzip>=0 - not found ===> Installing existing package /packages/All/unzip-6.0_8.txz Installing unzip-6.0_8... Extracting unzip-6.0_8: .......... done ===> dDocent-2.7.8 depends on package: unzip>=0 - found ===> Returning to build of dDocent-2.7.8 ===> dDocent-2.7.8 depends on package: mawk>=0 - not found ===> Installing existing package /packages/All/mawk-1.3.4.20161120.txz Installing mawk-1.3.4.20161120... Extracting mawk-1.3.4.20161120: ..... done ===> dDocent-2.7.8 depends on package: mawk>=0 - found ===> Returning to build of dDocent-2.7.8 ===> dDocent-2.7.8 depends on package: gawk>=0 - not found ===> Installing existing package /packages/All/gawk-5.0.0.txz Installing gawk-5.0.0... `-- Installing libsigsegv-2.12... `-- Extracting libsigsegv-2.12: ........ done Extracting gawk-5.0.0: .......... done Message from libsigsegv-2.12: ==== Note that the stackoverflow handling functions of this library need procfs mounted on /proc. ==== ===> dDocent-2.7.8 depends on package: gawk>=0 - found ===> Returning to build of dDocent-2.7.8 ===> dDocent-2.7.8 depends on package: coreutils>=0 - not found ===> Installing existing package /packages/All/coreutils-8.31.txz Installing coreutils-8.31... Extracting coreutils-8.31: .......... done ===> dDocent-2.7.8 depends on package: coreutils>=0 - found ===> Returning to build of dDocent-2.7.8 ===> dDocent-2.7.8 depends on package: gnuplot>=0 - not found ===> Installing existing package /packages/All/gnuplot-5.2.7.txz Installing gnuplot-5.2.7... `-- 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 | `-- 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 gmp-6.1.2_1... | | `-- Extracting gmp-6.1.2_1: .......... 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 libgd-2.2.5_1,1... | `-- Installing webp-1.0.2... | | `-- Installing giflib-5.1.9... | | `-- Extracting giflib-5.1.9: .......... done | `-- Extracting webp-1.0.2: .......... done `-- Extracting libgd-2.2.5_1,1: .......... done `-- Installing lua53-5.3.5_3... | `-- Installing libedit-3.1.20190324,1... | `-- Extracting libedit-3.1.20190324,1: .......... done `-- Extracting lua53-5.3.5_3: .......... done `-- Installing tex-kpathsea-6.2.1_2... `-- Extracting tex-kpathsea-6.2.1_2: .......... done `-- Installing wx28-gtk2-2.8.12_7... | `-- Installing ORBit2-2.14.19_2... | | `-- Installing libIDL-0.8.14_4... | | `-- Extracting libIDL-0.8.14_4: ......... done | `-- Extracting ORBit2-2.14.19_2: .......... done | `-- Installing gconf2-3.2.6_5... | | `-- Installing dconf-0.28.0... | | `-- Extracting dconf-0.28.0: .......... done | | `-- Installing polkit-0.114_2... | | `-- Installing spidermonkey52-52.9.0_3... | | | `-- Installing icu-64.2,1... | | | `-- Extracting icu-64.2,1: .......... done | | | `-- Installing nspr-4.21... | | | `-- Extracting nspr-4.21: .......... done | | `-- Extracting spidermonkey52-52.9.0_3: .......... done ===> Creating groups. Creating group 'polkitd' with gid '565'. ===> Creating users Creating user 'polkitd' with uid '565'. | | `-- Extracting polkit-0.114_2: ......... done | `-- Extracting gconf2-3.2.6_5: .......... done | `-- Installing gstreamer-0.10.36_6... | `-- Extracting gstreamer-0.10.36_6: .......... done | `-- Installing gstreamer-plugins-0.10.36_12,3... | | `-- Installing libXv-1.0.11_2,1... | | `-- Extracting libXv-1.0.11_2,1: .......... done | | `-- Installing orc-0.4.28... | | `-- Extracting orc-0.4.28: .......... done | `-- Extracting gstreamer-plugins-0.10.36_12,3: .......... done | `-- Installing libGLU-9.0.0_3... | `-- Extracting libGLU-9.0.0_3: ...... done | `-- Installing libmspack-0.9.1... | `-- Extracting libmspack-0.9.1: ......... done | `-- Installing pangox-compat-0.0.2_2... | `-- Extracting pangox-compat-0.0.2_2: ....... done | `-- Installing wx28-gtk2-common-2.8.12_7... | `-- Extracting wx28-gtk2-common-2.8.12_7: .......... done `-- Extracting wx28-gtk2-2.8.12_7: .......... done Extracting gnuplot-5.2.7: .......... done 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. ===> dDocent-2.7.8 depends on package: gnuplot>=0 - found ===> Returning to build of dDocent-2.7.8 ===> dDocent-2.7.8 depends on package: parallel>=0 - not found ===> Installing existing package /packages/All/parallel-20180922.txz Installing parallel-20180922... Extracting parallel-20180922: .......... done ===> dDocent-2.7.8 depends on package: parallel>=0 - found ===> Returning to build of dDocent-2.7.8 ===> dDocent-2.7.8 depends on executable: bash - not found ===> Installing existing package /packages/All/bash-5.0.7.txz Installing bash-5.0.7... Extracting bash-5.0.7: .......... done ===> dDocent-2.7.8 depends on executable: bash - found ===> Returning to build of dDocent-2.7.8 ===> dDocent-2.7.8 depends on package: bwa>=0.7.13 - not found ===> Installing existing package /packages/All/bwa-0.7.17.txz Installing bwa-0.7.17... Extracting bwa-0.7.17: ....... done ===> dDocent-2.7.8 depends on package: bwa>=0.7.13 - found ===> Returning to build of dDocent-2.7.8 ===> dDocent-2.7.8 depends on package: cd-hit>=0 - not found ===> Installing existing package /packages/All/cd-hit-4.8.1.txz Installing cd-hit-4.8.1... Extracting cd-hit-4.8.1: .......... done ===> dDocent-2.7.8 depends on package: cd-hit>=0 - found ===> Returning to build of dDocent-2.7.8 ===> dDocent-2.7.8 depends on package: samtools>=1.3 - not found ===> Installing existing package /packages/All/samtools-1.9.txz Installing samtools-1.9... `-- Installing htslib-1.9... | `-- Installing curl-7.65.1... | | `-- Installing libnghttp2-1.39.1... | | `-- Extracting libnghttp2-1.39.1: .......... done | `-- Extracting curl-7.65.1: .......... done `-- Extracting htslib-1.9: .......... done Extracting samtools-1.9: .......... done Message from samtools-1.9: The miscellaneous tools included with Samtools have been installed to /usr/local/bin/samtools_misc Add that directory to your path if you want to use these tools. Some of these tools depend on Perl5/Python, and it will need to be installed to use them. ===> dDocent-2.7.8 depends on package: samtools>=1.3 - found ===> Returning to build of dDocent-2.7.8 ===> dDocent-2.7.8 depends on package: vcftools>=0.1.15 - not found ===> Installing existing package /packages/All/vcftools-0.1.16.txz Installing vcftools-0.1.16... Extracting vcftools-0.1.16: .......... done ===> dDocent-2.7.8 depends on package: vcftools>=0.1.15 - found ===> Returning to build of dDocent-2.7.8 ===> dDocent-2.7.8 depends on package: trimmomatic>=0 - not found ===> Installing existing package /packages/All/trimmomatic-0.35.txz Installing trimmomatic-0.35... `-- Installing openjdk8-8.181.13_1... | `-- Installing alsa-lib-1.1.2_2... | `-- Extracting alsa-lib-1.1.2_2: .......... done | `-- Installing java-zoneinfo-2019.a... | `-- Extracting java-zoneinfo-2019.a: .......... done | `-- Installing javavmwrapper-2.6... | `-- Extracting javavmwrapper-2.6: .......... done | `-- Installing libXt-1.1.5_2,1... | `-- Extracting libXt-1.1.5_2,1: .......... done | `-- Installing libXtst-1.2.3_2... | `-- Extracting libXtst-1.2.3_2: .......... done `-- Extracting openjdk8-8.181.13_1: .......... done Extracting trimmomatic-0.35: .......... done Message from openjdk8-8.181.13_1: ====================================================================== This OpenJDK implementation requires procfs(5) mounted on /proc. If you have not done it yet, please do the following: mount -t procfs proc /proc To make it permanent, you need the following line in /etc/fstab: proc /proc procfs rw 0 0 ====================================================================== ===> dDocent-2.7.8 depends on package: trimmomatic>=0 - found ===> Returning to build of dDocent-2.7.8 ===> dDocent-2.7.8 depends on package: bamtools>=0 - not found ===> Installing existing package /packages/All/bamtools-2.5.1.txz Installing bamtools-2.5.1... `-- Installing jsoncpp-1.8.1_6... `-- Extracting jsoncpp-1.8.1_6: .......... done Extracting bamtools-2.5.1: .......... done ===> dDocent-2.7.8 depends on package: bamtools>=0 - found ===> Returning to build of dDocent-2.7.8 ===> dDocent-2.7.8 depends on package: stacks>=0 - not found ===> Installing existing package /packages/All/stacks-2.4.txz Installing stacks-2.4... Extracting stacks-2.4: .......... done ===> dDocent-2.7.8 depends on package: stacks>=0 - found ===> Returning to build of dDocent-2.7.8 ===> dDocent-2.7.8 depends on package: rainbow>=0 - not found ===> Installing existing package /packages/All/rainbow-2.0.4.txz Installing rainbow-2.0.4... Extracting rainbow-2.0.4: ...... done ===> dDocent-2.7.8 depends on package: rainbow>=0 - found ===> Returning to build of dDocent-2.7.8 ===> dDocent-2.7.8 depends on package: trimadap>=0 - not found ===> Installing existing package /packages/All/trimadap-0.1.3.txz Installing trimadap-0.1.3... Extracting trimadap-0.1.3: .... done ===> dDocent-2.7.8 depends on package: trimadap>=0 - found ===> Returning to build of dDocent-2.7.8 ===> dDocent-2.7.8 depends on package: seqtk>=0 - not found ===> Installing existing package /packages/All/seqtk-1.2.8.txz Installing seqtk-1.2.8... Extracting seqtk-1.2.8: .... done ===> dDocent-2.7.8 depends on package: seqtk>=0 - found ===> Returning to build of dDocent-2.7.8 ===> dDocent-2.7.8 depends on package: bedtools>=2.26.0 - not found ===> Installing existing package /packages/All/bedtools-2.27.1_2.txz Installing bedtools-2.27.1_2... Extracting bedtools-2.27.1_2: .......... done ===> dDocent-2.7.8 depends on package: bedtools>=2.26.0 - found ===> Returning to build of dDocent-2.7.8 ===> dDocent-2.7.8 depends on package: pear-merger>=0 - not found ===> Installing existing package /packages/All/pear-merger-0.9.6.txz Installing pear-merger-0.9.6... Extracting pear-merger-0.9.6: ..... done ===> dDocent-2.7.8 depends on package: pear-merger>=0 - found ===> Returning to build of dDocent-2.7.8 ===> dDocent-2.7.8 depends on package: vcflib>=0 - not found ===> Installing existing package /packages/All/vcflib-1.0.0.r1.130.txz Installing vcflib-1.0.0.r1.130... `-- Installing fastahack-g20160702... `-- Extracting fastahack-g20160702: .......... done `-- Installing filevercmp-g20151117... `-- Extracting filevercmp-g20151117: ...... done `-- Installing fsom-g20151117_1... `-- Extracting fsom-g20151117_1: ........ done `-- Installing intervaltree-g20151213_1... `-- Extracting intervaltree-g20151213_1: ..... done `-- Installing multichoose-1.0.3.2... `-- Extracting multichoose-1.0.3.2: .......... done `-- Installing smithwaterman-g20160702... `-- Extracting smithwaterman-g20160702: .......... done `-- Installing tabixpp-1.0.0.10... `-- Extracting tabixpp-1.0.0.10: ........ done Extracting vcflib-1.0.0.r1.130: .......... done ===> dDocent-2.7.8 depends on package: vcflib>=0 - found ===> Returning to build of dDocent-2.7.8 ===> dDocent-2.7.8 depends on executable: freebayes - not found ===> Installing existing package /packages/All/freebayes-1.2.0_1.txz Installing freebayes-1.2.0_1... Extracting freebayes-1.2.0_1: ..... done ===> dDocent-2.7.8 depends on executable: freebayes - found ===> Returning to build of dDocent-2.7.8 ===> dDocent-2.7.8 depends on executable: fastp - not found ===> Installing existing package /packages/All/fastp-0.20.0.txz Installing fastp-0.20.0... Extracting fastp-0.20.0: .... done ===> dDocent-2.7.8 depends on executable: fastp - found ===> Returning to build of dDocent-2.7.8 ===> dDocent-2.7.8 depends on file: /usr/local/openjdk8/bin/java - found ===> dDocent-2.7.8 depends on file: /usr/local/bin/python3.6 - found ===> dDocent-2.7.8 depends on package: perl5>=5.28.r1<5.29 - found -------------------------------------------------------------------------------- -- Phase: stage -------------------------------------------------------------------------------- ===> Staging for dDocent-2.7.8 ===> Generating temporary packing list install -m 555 /construction/biology/ddocent/dDocent-2.7.8/dDocent /construction/biology/ddocent/dDocent-2.7.8/*.sh /xports/biology/ddocent/files/ddocent-assembly-test /xports/biology/ddocent/files/ddocent-assembly-test-cleanup /construction/biology/ddocent/dDocent-2.7.8/scripts/*.sh /construction/biology/ddocent/dDocent-2.7.8/scripts/*.pl /construction/biology/ddocent/dDocent-2.7.8/scripts/dDocent_filters /construction/biology/ddocent/stage/usr/local/bin ====> Compressing man pages (compress-man) -------------------------------------------------------------------------------- -- Phase: package -------------------------------------------------------------------------------- ===> Building package for dDocent-2.7.8 file sizes/checksums [19]: . done packing files [19]: . done packing directories [0]: . done -------------------------------------------------- -- Termination -------------------------------------------------- Finished: Sunday, 7 JUL 2019 at 04:08:12 UTC Duration: 00:01:30