=>> Building biology/gatk build started at Thu Aug 15 21:14:17 CEST 2019 port directory: /usr/ports/biology/gatk package name: gatk-4.1.2.0.43 building for: FreeBSD cur-default-job-01 13.0-CURRENT FreeBSD 13.0-CURRENT 1300030 amd64 maintained by: yuri@FreeBSD.org Makefile ident: $FreeBSD: head/biology/gatk/Makefile 507364 2019-07-26 18:03:08Z yuri $ Poudriere version: 3.3.99.20190311 Host OSVERSION: 1300030 Jail OSVERSION: 1300030 Job Id: 01 ---Begin Environment--- SHELL=/bin/csh OSVERSION=1300030 UNAME_v=FreeBSD 13.0-CURRENT 1300030 UNAME_r=13.0-CURRENT BLOCKSIZE=K MAIL=/var/mail/root STATUS=1 HOME=/root PATH=/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin LOCALBASE=/usr/local USER=root TRYBROKEN=yes LIBEXECPREFIX=/usr/local/libexec/poudriere POUDRIERE_VERSION=3.3.99.20190311 MASTERMNT=/pou/data/.m/cur-default/ref POUDRIERE_BUILD_TYPE=bulk PACKAGE_BUILDING=yes SAVED_TERM=screen PWD=/pou/data/.m/cur-default/ref/.p/pool P_PORTS_FEATURES=FLAVORS SELECTED_OPTIONS MASTERNAME=cur-default SCRIPTPREFIX=/usr/local/share/poudriere OLDPWD=/pou/data/.m/cur-default/ref/.p SCRIPTPATH=/usr/local/share/poudriere/bulk.sh POUDRIEREPATH=/usr/local/bin/poudriere ---End Environment--- ---Begin Poudriere Port Flags/Env--- PORT_FLAGS= PKGENV= FLAVOR= DEPENDS_ARGS= MAKE_ARGS= ---End Poudriere Port Flags/Env--- ---Begin OPTIONS List--- ---End OPTIONS List--- --MAINTAINER-- yuri@FreeBSD.org --End MAINTAINER-- --CONFIGURE_ARGS-- --End CONFIGURE_ARGS-- --CONFIGURE_ENV-- XDG_DATA_HOME=/wrkdirs/usr/ports/biology/gatk/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/gatk/work HOME=/wrkdirs/usr/ports/biology/gatk/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/gatk/work/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin SHELL=/bin/sh CONFIG_SHELL=/bin/sh --End CONFIGURE_ENV-- --MAKE_ENV-- XDG_DATA_HOME=/wrkdirs/usr/ports/biology/gatk/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/gatk/work HOME=/wrkdirs/usr/ports/biology/gatk/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/gatk/work/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin NO_PIE=yes MK_DEBUG_FILES=no MK_KERNEL_SYMBOLS=no SHELL=/bin/sh NO_LINT=YES PREFIX=/usr/local LOCALBASE=/usr/local CC="cc" CFLAGS="-O2 -pipe -fstack-protector-strong -fno-strict-aliasing " CPP="cpp" CPPFLAGS="" LDFLAGS=" -fstack-protector-strong " LIBS="" CXX="c++" CXXFLAGS="-O2 -pipe -fstack-protector-strong -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" --End MAKE_ENV-- --PLIST_SUB-- JAVASHAREDIR="share/java" JAVAJARDIR="share/java/classes" OSREL=13.0 PREFIX=%D LOCALBASE=/usr/local RESETPREFIX=/usr/local LIB32DIR=lib DOCSDIR="share/doc/gatk" EXAMPLESDIR="share/examples/gatk" DATADIR="share/gatk" WWWDIR="www/gatk" ETCDIR="etc/gatk" --End PLIST_SUB-- --SUB_LIST-- PORTVERSION=4.1.2.0.43 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 --End SUB_LIST-- ---Begin make.conf--- USE_PACKAGE_DEPENDS=yes BATCH=yes WRKDIRPREFIX=/wrkdirs PORTSDIR=/usr/ports PACKAGES=/packages DISTDIR=/distfiles FORCE_PACKAGE=yes PACKAGE_BUILDING=yes PACKAGE_BUILDING_FLAVORS=yes #### /usr/local/etc/poudriere.d/make.conf #### WARNING_WAIT=0 #DISABLE_LICENSES=yes #### /usr/local/etc/poudriere.d/cur-default-make.conf #### WITH_CCACHE_BUILD=yes WARNING_WAIT=0 DEFAULT_VERSIONS= perl5=5.30 python=3.6 python3=3.6 ruby=2.5 pgsql=11 php=7.3 mysql=10.4m gcc=9 samba=4.10 WITH_CCACHE_BUILD=yes CCACHE_DIR=/root/.ccache #### /usr/ports/Mk/Scripts/ports_env.sh #### _CCVERSION_921dbbb2=FreeBSD clang version 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CC_OUTPUT_921dbbb2_65ad290d=yes CC_OUTPUT_921dbbb2_f2776b26=yes CC_OUTPUT_921dbbb2_b2657cc3=yes CC_OUTPUT_921dbbb2_380987f7=yes CC_OUTPUT_921dbbb2_160933ec=yes CC_OUTPUT_921dbbb2_fb62803b=yes _OBJC_CCVERSION_921dbbb2=FreeBSD clang version 8.0.0 (tags/RELEASE_800/final 356365) (based on LLVM 8.0.0) Target: x86_64-unknown-freebsd13.0 Thread model: posix InstalledDir: /usr/bin _OBJC_ALTCCVERSION_921dbbb2=none ARCH=amd64 OPSYS=FreeBSD _OSRELEASE=13.0-CURRENT OSREL=13.0 OSVERSION=1300030 PYTHONBASE=/usr/local HAVE_COMPAT_IA32_KERN=YES _SMP_CPUS=32 CONFIGURE_MAX_CMD_LEN=262144 HAVE_PORTS_ENV=1 #### Misc Poudriere #### GID=0 UID=0 ---End make.conf--- --Resource limits-- cpu time (seconds, -t) unlimited file size (512-blocks, -f) unlimited data seg size (kbytes, -d) 33554432 stack size (kbytes, -s) 524288 core file size (512-blocks, -c) unlimited max memory size (kbytes, -m) unlimited locked memory (kbytes, -l) unlimited max user processes (-u) 89999 open files (-n) 1024 virtual mem size (kbytes, -v) unlimited swap limit (kbytes, -w) unlimited socket buffer size (bytes, -b) unlimited pseudo-terminals (-p) unlimited kqueues (-k) unlimited umtx shared locks (-o) unlimited --End resource limits-- =================================================== ===> License BSD3CLAUSE accepted by the user =========================================================================== =================================================== ===> gatk-4.1.2.0.43 depends on file: /usr/local/sbin/pkg - not found ===> Installing existing package /packages/All/pkg-1.11.1.txz [cur-default-job-01] Installing pkg-1.11.1... [cur-default-job-01] Extracting pkg-1.11.1: .......... done ===> gatk-4.1.2.0.43 depends on file: /usr/local/sbin/pkg - found ===> Returning to build of gatk-4.1.2.0.43 =========================================================================== =================================================== =========================================================================== =================================================== ===> License BSD3CLAUSE accepted by the user ===> Fetching all distfiles required by gatk-4.1.2.0.43 for building =========================================================================== =================================================== ===> License BSD3CLAUSE accepted by the user ===> Fetching all distfiles required by gatk-4.1.2.0.43 for building => SHA256 Checksum OK for gatk-4.1.2.0-43-deps.tar.gz. => SHA256 Checksum OK for broadinstitute-gatk-4.1.2.0-43-g1f31a805b_GH0.tar.gz. =========================================================================== =================================================== =========================================================================== =================================================== ===> License BSD3CLAUSE accepted by the user ===> Fetching all distfiles required by gatk-4.1.2.0.43 for building ===> Extracting for gatk-4.1.2.0.43 => SHA256 Checksum OK for gatk-4.1.2.0-43-deps.tar.gz. => SHA256 Checksum OK for broadinstitute-gatk-4.1.2.0-43-g1f31a805b_GH0.tar.gz. =========================================================================== =================================================== =========================================================================== =================================================== ===> Patching for gatk-4.1.2.0.43 ===> Applying FreeBSD patches for gatk-4.1.2.0.43 =========================================================================== =================================================== ===> gatk-4.1.2.0.43 depends on executable: gradle - not found ===> Installing existing package /packages/All/gradle-5.6.txz [cur-default-job-01] Installing gradle-5.6... [cur-default-job-01] `-- Installing openjdk8-8.222.10.1_1... [cur-default-job-01] | `-- Installing dejavu-2.37_1... [cur-default-job-01] | | `-- Installing fontconfig-2.12.6,1... [cur-default-job-01] | | `-- Installing expat-2.2.7... [cur-default-job-01] | | `-- Extracting expat-2.2.7: .......... done [cur-default-job-01] | | `-- Installing freetype2-2.10.1... [cur-default-job-01] | | | `-- Installing png-1.6.37... [cur-default-job-01] | | | `-- Extracting png-1.6.37: .......... done [cur-default-job-01] | | `-- Extracting freetype2-2.10.1: .......... done [cur-default-job-01] | | `-- 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 [cur-default-job-01] | | `-- Installing mkfontscale-1.2.1... [cur-default-job-01] | | `-- Installing libfontenc-1.1.4... [cur-default-job-01] | | `-- Extracting libfontenc-1.1.4: ......... done [cur-default-job-01] | | `-- Extracting mkfontscale-1.2.1: ....... done [cur-default-job-01] | `-- Extracting dejavu-2.37_1: .......... done [cur-default-job-01] | `-- Installing giflib-5.1.9... [cur-default-job-01] | `-- Extracting giflib-5.1.9: .......... done [cur-default-job-01] | `-- Installing java-zoneinfo-2019.b... [cur-default-job-01] | `-- Extracting java-zoneinfo-2019.b: .......... done [cur-default-job-01] | `-- Installing javavmwrapper-2.7.3... [cur-default-job-01] | `-- Extracting javavmwrapper-2.7.3: .......... done [cur-default-job-01] | `-- Installing libX11-1.6.8,1... [cur-default-job-01] | | `-- Installing libXau-1.0.9... [cur-default-job-01] | | `-- Extracting libXau-1.0.9: .......... done [cur-default-job-01] | | `-- Installing libXdmcp-1.1.3... [cur-default-job-01] | | `-- Installing xorgproto-2019.1... [cur-default-job-01] | | `-- Extracting xorgproto-2019.1: .......... done [cur-default-job-01] | | `-- Extracting libXdmcp-1.1.3: ......... done [cur-default-job-01] | | `-- Installing libxcb-1.13.1... [cur-default-job-01] | | `-- Installing libpthread-stubs-0.4... [cur-default-job-01] | | `-- Extracting libpthread-stubs-0.4: .... done [cur-default-job-01] | | `-- Installing libxml2-2.9.9... [cur-default-job-01] | | `-- Extracting libxml2-2.9.9: .......... done [cur-default-job-01] | | `-- Extracting libxcb-1.13.1: .......... done [cur-default-job-01] | `-- Extracting libX11-1.6.8,1: .......... done [cur-default-job-01] | `-- Installing libXext-1.3.4,1... [cur-default-job-01] | `-- Extracting libXext-1.3.4,1: .......... done [cur-default-job-01] | `-- Installing libXi-1.7.10,1... [cur-default-job-01] | | `-- Installing libXfixes-5.0.3_2... [cur-default-job-01] | | `-- Extracting libXfixes-5.0.3_2: .......... done [cur-default-job-01] | `-- Extracting libXi-1.7.10,1: .......... done [cur-default-job-01] | `-- Installing libXrender-0.9.10_2... [cur-default-job-01] | `-- Extracting libXrender-0.9.10_2: .......... done [cur-default-job-01] | `-- Installing libXt-1.2.0,1... [cur-default-job-01] | | `-- Installing libICE-1.0.9_3,1... [cur-default-job-01] | | `-- Extracting libICE-1.0.9_3,1: .......... done [cur-default-job-01] | | `-- Installing libSM-1.2.3,1... [cur-default-job-01] | | `-- Extracting libSM-1.2.3,1: .......... done [cur-default-job-01] | `-- Extracting libXt-1.2.0,1: .......... done [cur-default-job-01] | `-- Installing libXtst-1.2.3_2... [cur-default-job-01] | `-- Extracting libXtst-1.2.3_2: .......... done [cur-default-job-01] | `-- Installing libinotify-20180201_1... [cur-default-job-01] | `-- Extracting libinotify-20180201_1: .......... done [cur-default-job-01] `-- Extracting openjdk8-8.222.10.1_1: .......... done [cur-default-job-01] Extracting gradle-5.6: .......... done Message from freetype2-2.10.1: The 2.7.x series now uses the new subpixel hinting mode (V40 port's option) as the default, emulating a modern version of ClearType. This change inevitably leads to different rendering results, and you might change port's options to adapt it to your taste (or use the new "FREETYPE_PROPERTIES" environment variable). The environment variable "FREETYPE_PROPERTIES" can be used to control the driver properties. Example: FREETYPE_PROPERTIES=truetype:interpreter-version=35 \ cff:no-stem-darkening=1 \ autofitter:warping=1 This allows to select, say, the subpixel hinting mode at runtime for a given application. If LONG_PCF_NAMES port's option was enabled, the PCF family names may include the foundry and information whether they contain wide characters. For example, "Sony Fixed" or "Misc Fixed Wide", instead of "Fixed". This can be disabled at run time with using pcf:no-long-family-names property, if needed. Example: FREETYPE_PROPERTIES=pcf:no-long-family-names=1 How to recreate fontconfig cache with using such environment variable, if needed: # env FREETYPE_PROPERTIES=pcf:no-long-family-names=1 fc-cache -fsv The controllable properties are listed in the section "Controlling FreeType Modules" in the reference's table of contents (/usr/local/share/doc/freetype2/reference/site/index.html, if documentation was installed). 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 libinotify-20180201_1: ============================================================================ Libinotify functionality on FreeBSD is missing support for - detecting a file being moved into or out of a directory within the same filesystem - certain modifications to a symbolic link (rather than the file it points to.) in addition to the known limitations on all platforms using kqueue(2) where various open and close notifications are unimplemented. This means the following regression tests will fail: Directory notifications: IN_MOVED_FROM IN_MOVED_TO Open/close notifications: IN_OPEN IN_CLOSE_NOWRITE IN_CLOSE_WRITE Symbolic Link notifications: IN_DONT_FOLLOW IN_ATTRIB IN_MOVE_SELF IN_DELETE_SELF Kernel patches to address the missing directory and symbolic link notifications are available from: https://github.com/libinotify-kqueue/libinotify-kqueue/tree/master/patches ============================================================================= You might want to consider increasing the kern.maxfiles tunable if you plan to use this library for applications that need to monitor activity of a lot of files. ============================================================================= Message from openjdk8-8.222.10.1_1: This OpenJDK implementation requires fdescfs(5) mounted on /dev/fd and procfs(5) mounted on /proc. If you have not done it yet, please do the following: mount -t fdescfs fdesc /dev/fd mount -t procfs proc /proc To make it permanent, you need the following lines in /etc/fstab: fdesc /dev/fd fdescfs rw 0 0 proc /proc procfs rw 0 0 ===> gatk-4.1.2.0.43 depends on executable: gradle - found ===> Returning to build of gatk-4.1.2.0.43 ===> gatk-4.1.2.0.43 depends on file: /usr/local/openjdk8/bin/java - found ===> gatk-4.1.2.0.43 depends on file: /usr/local/bin/ccache - not found ===> Installing existing package /packages/All/ccache-3.7.1.txz [cur-default-job-01] Installing ccache-3.7.1... [cur-default-job-01] Extracting ccache-3.7.1: .......... done Create compiler links... create symlink for cc create symlink for cc (world) create symlink for c++ create symlink for c++ (world) create symlink for CC create symlink for CC (world) create symlink for clang create symlink for clang (world) create symlink for clang++ create symlink for clang++ (world) Message from ccache-3.7.1: NOTE: Please read /usr/local/share/doc/ccache/ccache-howto-freebsd.txt for information on using ccache with FreeBSD ports and src. ===> gatk-4.1.2.0.43 depends on file: /usr/local/bin/ccache - found ===> Returning to build of gatk-4.1.2.0.43 =========================================================================== =================================================== ===> gatk-4.1.2.0.43 depends on shared library: libintl.so - not found ===> Installing existing package /packages/All/gettext-runtime-0.20.1.txz [cur-default-job-01] Installing gettext-runtime-0.20.1... [cur-default-job-01] `-- Installing indexinfo-0.3.1... [cur-default-job-01] `-- Extracting indexinfo-0.3.1: .... done [cur-default-job-01] Extracting gettext-runtime-0.20.1: .......... done ===> gatk-4.1.2.0.43 depends on shared library: libintl.so - found (/usr/local/lib/libintl.so) ===> Returning to build of gatk-4.1.2.0.43 =========================================================================== =================================================== ===> Configuring for gatk-4.1.2.0.43 =========================================================================== =================================================== ===> Building for gatk-4.1.2.0.43 Welcome to Gradle 5.6! Here are the highlights of this release: - Incremental Groovy compilation - Groovy compile avoidance - Test fixtures for Java projects - Manage plugin versions via settings script For more details see https://docs.gradle.org/5.6/release-notes.html Starting a Gradle Daemon (subsequent builds will be faster) FAILURE: Build failed with an exception. * Where: Build file '/wrkdirs/usr/ports/biology/gatk/work/gatk-4.1.2.0-43-g1f31a805b/build.gradle' line: 16 * What went wrong: Plugin [id: 'de.undercouch.download', version: '2.1.0'] was not found in any of the following sources: - Gradle Core Plugins (plugin is not in 'org.gradle' namespace) - Plugin Repositories (could not resolve plugin artifact 'de.undercouch.download:de.undercouch.download.gradle.plugin:2.1.0') Searched in the following repositories: Gradle Central Plugin Repository * Try: Run with --stacktrace option to get the stack trace. Run with --info or --debug option to get more log output. Run with --scan to get full insights. * Get more help at https://help.gradle.org BUILD FAILED in 2s *** Error code 1 Stop. make: stopped in /usr/ports/biology/gatk =>> Cleaning up wrkdir ===> Cleaning for gatk-4.1.2.0.43 build of biology/gatk | gatk-4.1.2.0.43 ended at Thu Aug 15 21:14:42 CEST 2019 build time: 00:00:25 !!! build failure encountered !!!