=> Building biology/gatk Started : Sunday, 7 JUL 2019 at 04:11:04 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 -------------------------------------------------- XDG_DATA_HOME=/construction/biology/gatk XDG_CONFIG_HOME=/construction/biology/gatk HOME=/construction/biology/gatk TMPDIR="/tmp" PATH=/construction/biology/gatk/.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/gatk XDG_CONFIG_HOME=/construction/biology/gatk HOME=/construction/biology/gatk TMPDIR="/tmp" PATH=/construction/biology/gatk/.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/gatk/stage -------------------------------------------------- -- PLIST_SUB -------------------------------------------------- JAVASHAREDIR="share/java" JAVAJARDIR="share/java/classes" OSREL=5.4 PREFIX=%D LOCALBASE=/usr/local RESETPREFIX=/usr/local LIB32DIR=lib PROFILE="@comment " DOCSDIR="share/doc/gatk" EXAMPLESDIR="share/examples/gatk" DATADIR="share/gatk" WWWDIR="www/gatk" ETCDIR="etc/gatk" -------------------------------------------------- -- SUB_LIST -------------------------------------------------- PORTVERSION=4.0.11.0 JAVA=/usr/local/openjdk8/bin/java 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/gatk DOCSDIR=/usr/local/share/doc/gatk EXAMPLESDIR=/usr/local/share/examples/gatk WWWDIR=/usr/local/www/gatk ETCDIR=/usr/local/etc/gatk -------------------------------------------------- -- /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 BSD3CLAUSE accepted by the user -------------------------------------------------------------------------------- -- Phase: pkg-depends -------------------------------------------------------------------------------- ===> gatk-4.0.11.0 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 ===> gatk-4.0.11.0 depends on file: /usr/local/sbin/pkg - found ===> Returning to build of gatk-4.0.11.0 -------------------------------------------------------------------------------- -- Phase: fetch-depends -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- -- Phase: fetch -------------------------------------------------------------------------------- ===> License BSD3CLAUSE accepted by the user ===> Fetching all distfiles required by gatk-4.0.11.0 for building -------------------------------------------------------------------------------- -- Phase: checksum -------------------------------------------------------------------------------- ===> License BSD3CLAUSE accepted by the user ===> Fetching all distfiles required by gatk-4.0.11.0 for building => SHA256 Checksum OK for gatk-4.0.11.0-deps.tar.gz. => SHA256 Checksum OK for broadinstitute-gatk-4.0.11.0_GH0.tar.gz. -------------------------------------------------------------------------------- -- Phase: extract-depends -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- -- Phase: extract -------------------------------------------------------------------------------- ===> License BSD3CLAUSE accepted by the user ===> Fetching all distfiles required by gatk-4.0.11.0 for building ===> Extracting for gatk-4.0.11.0 => SHA256 Checksum OK for gatk-4.0.11.0-deps.tar.gz. => SHA256 Checksum OK for broadinstitute-gatk-4.0.11.0_GH0.tar.gz. -------------------------------------------------------------------------------- -- Phase: patch-depends -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- -- Phase: patch -------------------------------------------------------------------------------- ===> Patching for gatk-4.0.11.0 ===> Applying ports patches for gatk-4.0.11.0 -------------------------------------------------------------------------------- -- Phase: build-depends -------------------------------------------------------------------------------- ===> gatk-4.0.11.0 depends on executable: gradle4 - not found ===> Installing existing package /packages/All/gradle4-4.6.txz Installing gradle4-4.6... `-- Installing openjdk8-8.181.13_1... | `-- Installing alsa-lib-1.1.2_2... | `-- Extracting alsa-lib-1.1.2_2: .......... done | `-- Installing dejavu-2.37_1... | | `-- Installing fontconfig-2.12.6,1... | | `-- Installing expat-2.2.6_1... | | `-- Extracting expat-2.2.6_1: .......... done | | `-- 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 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 giflib-5.1.9... | `-- Extracting giflib-5.1.9: .......... done | `-- Installing java-zoneinfo-2019.a... | `-- Extracting java-zoneinfo-2019.a: .......... done | `-- Installing javavmwrapper-2.6... | `-- Extracting javavmwrapper-2.6: .......... done | `-- 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 | | `-- Installing libxml2-2.9.9... | | `-- Extracting libxml2-2.9.9: .......... 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 libXi-1.7.9_2,1... | | `-- Installing libXfixes-5.0.3_2... | | `-- Extracting libXfixes-5.0.3_2: .......... done | `-- Extracting libXi-1.7.9_2,1: .......... done | `-- Installing libXrender-0.9.10_2... | `-- Extracting libXrender-0.9.10_2: .......... done | `-- Installing libXt-1.1.5_2,1... | | `-- 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 | `-- 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 gradle4-4.6: .......... 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 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 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 ====================================================================== ===> gatk-4.0.11.0 depends on executable: gradle4 - found ===> Returning to build of gatk-4.0.11.0 ===> gatk-4.0.11.0 depends on file: /usr/local/openjdk8/bin/java - found -------------------------------------------------------------------------------- -- Phase: lib-depends -------------------------------------------------------------------------------- ===> gatk-4.0.11.0 depends on shared library: libintl.so - not found ===> Installing existing package /packages/All/gettext-runtime-0.20.1.txz Installing gettext-runtime-0.20.1... `-- Installing indexinfo-0.3.1... `-- Extracting indexinfo-0.3.1: .... done Extracting gettext-runtime-0.20.1: .......... done ===> gatk-4.0.11.0 depends on shared library: libintl.so - found (/usr/local/lib/libintl.so) ===> Returning to build of gatk-4.0.11.0 -------------------------------------------------------------------------------- -- Phase: configure -------------------------------------------------------------------------------- ===> Configuring for gatk-4.0.11.0 -------------------------------------------------------------------------------- -- Phase: build -------------------------------------------------------------------------------- ===> Building for gatk-4.0.11.0 Starting a Gradle Daemon (subsequent builds will be faster) :compileJava :processResources :classes :shadowJar :localJar Deprecated Gradle features were used in this build, making it incompatible with Gradle 5.0. See https://docs.gradle.org/4.6/userguide/command_line_interface.html#sec:command_line_warnings BUILD SUCCESSFUL in 3m 39s 3 actionable tasks: 3 executed -------------------------------------------------------------------------------- -- Phase: run-depends -------------------------------------------------------------------------------- ===> gatk-4.0.11.0 depends on file: /usr/local/openjdk8/bin/java - found -------------------------------------------------------------------------------- -- Phase: stage -------------------------------------------------------------------------------- ===> Staging for gatk-4.0.11.0 ===> Generating temporary packing list install -m 555 /construction/biology/gatk/gatk.sh /construction/biology/gatk/stage/usr/local/bin/gatk install -m 0644 /construction/biology/gatk/gatk-4.0.11.0/build/libs/gatk-package-1.0-SNAPSHOT-local.jar /construction/biology/gatk/stage/usr/local/share/java/classes/GenomeAnalysisTK-4.0.11.0.jar ====> Compressing man pages (compress-man) -------------------------------------------------------------------------------- -- Phase: package -------------------------------------------------------------------------------- ===> Building package for gatk-4.0.11.0 file sizes/checksums [5]: . done packing files [5]: . done packing directories [0]: . done -------------------------------------------------- -- Termination -------------------------------------------------- Finished: Sunday, 7 JUL 2019 at 04:20:11 UTC Duration: 00:09:06