From owner-freebsd-pkg-fallout@freebsd.org Wed Dec 19 02:46:24 2018 Return-Path: Delivered-To: freebsd-pkg-fallout@mailman.ysv.freebsd.org Received: from mx1.freebsd.org (mx1.freebsd.org [IPv6:2610:1c1:1:606c::19:1]) by mailman.ysv.freebsd.org (Postfix) with ESMTP id 3D2111348A76 for ; Wed, 19 Dec 2018 02:46:24 +0000 (UTC) (envelope-from pkg-fallout@FreeBSD.org) Received: from mailman.ysv.freebsd.org (mailman.ysv.freebsd.org [IPv6:2001:1900:2254:206a::50:5]) by mx1.freebsd.org (Postfix) with ESMTP id BD9A59453B for ; Wed, 19 Dec 2018 02:46:23 +0000 (UTC) (envelope-from pkg-fallout@FreeBSD.org) Received: by mailman.ysv.freebsd.org (Postfix) id 828671348A73; Wed, 19 Dec 2018 02:46:23 +0000 (UTC) Delivered-To: pkg-fallout@mailman.ysv.freebsd.org Received: from mx1.freebsd.org (mx1.freebsd.org [IPv6:2610:1c1:1:606c::19:1]) by mailman.ysv.freebsd.org (Postfix) with ESMTP id 4AE821348A72 for ; Wed, 19 Dec 2018 02:46:23 +0000 (UTC) (envelope-from pkg-fallout@FreeBSD.org) Received: from mxrelay.nyi.freebsd.org (mxrelay.nyi.freebsd.org [IPv6:2610:1c1:1:606c::19:3]) (using TLSv1.3 with cipher TLS_AES_256_GCM_SHA384 (256/256 bits) server-signature RSA-PSS (4096 bits) client-signature RSA-PSS (4096 bits) client-digest SHA256) (Client CN "mxrelay.nyi.freebsd.org", Issuer "Let's Encrypt Authority X3" (verified OK)) by mx1.freebsd.org (Postfix) with ESMTPS id EF2E494538 for ; Wed, 19 Dec 2018 02:46:22 +0000 (UTC) (envelope-from pkg-fallout@FreeBSD.org) Received: from beefy16.nyi.freebsd.org (beefy16.nyi.freebsd.org [IPv6:2610:1c1:1:6080::16:e3]) (using TLSv1.3 with cipher TLS_AES_256_GCM_SHA384 (256/256 bits) server-signature RSA-PSS (4096 bits)) (Client did not present a certificate) by mxrelay.nyi.freebsd.org (Postfix) with ESMTPS id E027F8110 for ; Wed, 19 Dec 2018 02:46:22 +0000 (UTC) (envelope-from pkg-fallout@FreeBSD.org) Received: from beefy16.nyi.freebsd.org (localhost [127.0.0.1]) by beefy16.nyi.freebsd.org (8.15.2/8.15.2) with ESMTP id wBJ2kMXF075091 for ; Wed, 19 Dec 2018 02:46:22 GMT (envelope-from pkg-fallout@FreeBSD.org) Received: (from root@localhost) by beefy16.nyi.freebsd.org (8.15.2/8.15.2/Submit) id wBJ2kMaR075089; Wed, 19 Dec 2018 02:46:22 GMT (envelope-from pkg-fallout@FreeBSD.org) Date: Wed, 19 Dec 2018 02:46:22 GMT From: pkg-fallout@FreeBSD.org Message-Id: <201812190246.wBJ2kMaR075089@beefy16.nyi.freebsd.org> To: pkg-fallout@FreeBSD.org Subject: [package - head-armv7-default][biology/gatk] Failed for gatk-4.0.11.0 in build X-Rspamd-Queue-Id: EF2E494538 X-Spamd-Bar: -- Authentication-Results: mx1.freebsd.org X-Spamd-Result: default: False [-2.98 / 15.00]; local_wl_from(0.00)[FreeBSD.org]; NEURAL_HAM_MEDIUM(-1.00)[-0.999,0]; NEURAL_HAM_SHORT(-0.98)[-0.982,0]; ASN(0.00)[asn:11403, ipnet:2610:1c1:1::/48, country:US]; NEURAL_HAM_LONG(-1.00)[-0.999,0] X-BeenThere: freebsd-pkg-fallout@freebsd.org X-Mailman-Version: 2.1.29 Precedence: list List-Id: Fallout logs from package building List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , X-List-Received-Date: Wed, 19 Dec 2018 02:46:24 -0000 You are receiving this mail as a port that you maintain is failing to build on the FreeBSD package build server. Please investigate the failure and submit a PR to fix build. Maintainer: yuri@FreeBSD.org Last committer: yuri@FreeBSD.org Ident: $FreeBSD: head/biology/gatk/Makefile 486619 2018-12-04 17:53:46Z yuri $ Log URL: http://beefy16.nyi.freebsd.org/data/head-armv7-default/p487477_s342105/logs/gatk-4.0.11.0.log Build URL: http://beefy16.nyi.freebsd.org/build.html?mastername=head-armv7-default&build=p487477_s342105 Log: =>> Building biology/gatk build started at Wed Dec 19 02:45:19 UTC 2018 port directory: /usr/ports/biology/gatk package name: gatk-4.0.11.0 building for: FreeBSD head-armv7-default-job-04 13.0-CURRENT FreeBSD 13.0-CURRENT 1300005 arm maintained by: yuri@FreeBSD.org Makefile ident: $FreeBSD: head/biology/gatk/Makefile 486619 2018-12-04 17:53:46Z yuri $ Poudriere version: 3.2.8 Host OSVERSION: 1300002 Jail OSVERSION: 1300005 Job Id: 04 !!! Jail is newer than host. (Jail: 1300005, Host: 1300002) !!! !!! This is not supported. !!! !!! Host kernel must be same or newer than jail. !!! !!! Expect build failures. !!! ---Begin Environment--- SHELL=/bin/csh UNAME_p=armv7 UNAME_m=arm ABI_FILE=/usr/lib/crt1.o OSVERSION=1300005 UNAME_v=FreeBSD 13.0-CURRENT 1300005 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 QEMU_EMULATING=1 USER=root LIBEXECPREFIX=/usr/local/libexec/poudriere POUDRIERE_VERSION=3.2.8 MASTERMNT=/usr/local/poudriere/data/.m/head-armv7-default/ref POUDRIERE_BUILD_TYPE=bulk PACKAGE_BUILDING=yes SAVED_TERM= PWD=/usr/local/poudriere/data/.m/head-armv7-default/ref/.p/pool P_PORTS_FEATURES=FLAVORS SELECTED_OPTIONS MASTERNAME=head-armv7-default SCRIPTPREFIX=/usr/local/share/poudriere OLDPWD=/usr/local/poudriere/data/.m/head-armv7-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="/nxb-bin/usr/bin/cc" CFLAGS="-O2 -pipe -fno-strict-aliasing " CPP="/nxb-bin/usr/bin/cpp" CPPFLAGS="" LDFLAGS=" " LIBS="" CXX="/nxb-bin/usr/bin/c++" CXXFLAGS="-O2 -pipe -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=4.0.11.0 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 --End SUB_LIST-- ---Begin make.conf--- .sinclude "/etc/make.nxb.conf" USE_PACKAGE_DEPENDS=yes BATCH=yes WRKDIRPREFIX=/wrkdirs PORTSDIR=/usr/ports PACKAGES=/packages DISTDIR=/distfiles PACKAGE_BUILDING=yes PACKAGE_BUILDING_FLAVORS=yes MACHINE=arm MACHINE_ARCH=armv7 ARCH=${MACHINE_ARCH} #### /usr/local/etc/poudriere.d/make.conf #### # XXX: We really need this but cannot use it while 'make checksum' does not # try the next mirror on checksum failure. It currently retries the same # failed mirror and then fails rather then trying another. It *does* # try the next if the size is mismatched though. #MASTER_SITE_FREEBSD=yes # Build ALLOW_MAKE_JOBS_PACKAGES with 2 jobs MAKE_JOBS_NUMBER=2 # stable/10 includes src.conf too late but make.conf is in sys.mk .if ${.CURDIR:M/poudriere/jails/10*/usr/src/usr.bin/xlint*} # Disable build of llib now that head no longer has lint(1) LINT= true .endif #### /usr/ports/Mk/Scripts/ports_env.sh #### _CCVERSION_9d218390=FreeBSD clang version 7.0.1 (branches/release_70 348686) (based on LLVM 7.0.1) Target: armv7-unknown-freebsd13.0-gnueabihf Thread model: posix InstalledDir: /nxb-bin/usr/bin _ALTCCVERSION_9d218390=none _CXXINTERNAL_9c45a5b1=FreeBSD clang version 7.0.1 (branches/release_70 348686) (based on LLVM 7.0.1) Target: armv7-unknown-freebsd13.0-gnueabihf Thread model: posix InstalledDir: /nxb-bin/usr/bin "/nxb-bin/usr/bin/ld" "--eh-frame-hdr" "-dynamic-linker" "/libexec/ld-elf.so.1" "--hash-style=both" "--enable-new-dtags" "-o" "a.out" "/usr/lib/crt1.o" "/usr/lib/crti.o" "/usr/lib/crtbegin.o" "-L/usr/lib" "/dev/null" "-lc++" "-lm" "-lgcc" "--as-needed" "-lgcc_s" "--no-as-needed" "-lc" "-lgcc" "--as-needed" "-lgcc_s" "--no-as-needed" "/usr/lib/crtend.o" "/usr/lib/crtn.o" CC_OUTPUT_9d218390_58173849=yes CC_OUTPUT_9d218390_9bdba57c=yes CC_OUTPUT_9d218390_6a4fe7f5=yes CC_OUTPUT_9d218390_6bcac02b=yes CC_OUTPUT_9d218390_67d20829=yes CC_OUTPUT_9d218390_bfa62e83=yes CC_OUTPUT_9d218390_f0b4d593=yes CC_OUTPUT_9d218390_308abb44=yes CC_OUTPUT_9d218390_f00456e5=yes CC_OUTPUT_9d218390_65ad290d=yes CC_OUTPUT_9d218390_f2776b26=yes CC_OUTPUT_9d218390_b2657cc3=yes CC_OUTPUT_9d218390_380987f7=yes CC_OUTPUT_9d218390_160933ec=yes CC_OUTPUT_9d218390_fb62803b=yes _OBJC_CCVERSION_9d218390=FreeBSD clang version 7.0.1 (branches/release_70 348686) (based on LLVM 7.0.1) Target: armv7-unknown-freebsd13.0-gnueabihf Thread model: posix InstalledDir: /nxb-bin/usr/bin _OBJC_ALTCCVERSION_9d218390=none ARCH=armv7 OPSYS=FreeBSD _OSRELEASE=13.0-CURRENT OSREL=13.0 OSVERSION=1300005 PYTHONBASE=/usr/local CONFIGURE_MAX_CMD_LEN=262144 HAVE_PORTS_ENV=1 #### Misc Poudriere #### GID=0 UID=0 DISABLE_MAKE_JOBS=poudriere ---End make.conf--- ---Begin make.nxb.conf--- CC=/nxb-bin/usr/bin/cc CPP=/nxb-bin/usr/bin/cpp CXX=/nxb-bin/usr/bin/c++ AS=/nxb-bin/usr/bin/as NM=/nxb-bin/usr/bin/nm LD=/nxb-bin/usr/bin/ld OBJCOPY=/nxb-bin/usr/bin/objcopy SIZE=/nxb-bin/usr/bin/size STRIPBIN=/nxb-bin/usr/bin/strip SED=/nxb-bin/usr/bin/sed RANLIB=/nxb-bin/usr/bin/ranlib YACC=/nxb-bin/usr/bin/yacc MAKE=/nxb-bin/usr/bin/make STRINGS=/nxb-bin/usr/bin/strings AWK=/nxb-bin/usr/bin/awk FLEX=/nxb-bin/usr/bin/flex ---End make.nxb.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-4.0.11.0 depends on file: /usr/local/sbin/pkg - not found ===> Installing existing package /packages/All/pkg-1.10.5_5.txz [head-armv7-default-job-04] Installing pkg-1.10.5_5... [head-armv7-default-job-04] Extracting pkg-1.10.5_5: .......... done ===> gatk-4.0.11.0 depends on file: /usr/local/sbin/pkg - found ===> Returning to build of gatk-4.0.11.0 =========================================================================== =================================================== =========================================================================== =================================================== ===> License BSD3CLAUSE accepted by the user ===> Fetching all distfiles required by gatk-4.0.11.0 for building =========================================================================== =================================================== ===> 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. =========================================================================== =================================================== =========================================================================== =================================================== ===> 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. =========================================================================== =================================================== =========================================================================== =================================================== ===> Patching for gatk-4.0.11.0 ===> Applying FreeBSD patches for gatk-4.0.11.0 =========================================================================== =================================================== ===> gatk-4.0.11.0 depends on executable: gradle4 - not found ===> Installing existing package /packages/All/gradle4-4.6.txz [head-armv7-default-job-04] Installing gradle4-4.6... [head-armv7-default-job-04] `-- Installing openjdk8-8.192.26_1... [head-armv7-default-job-04] | `-- Installing alsa-lib-1.1.2_2... [head-armv7-default-job-04] | `-- Extracting alsa-lib-1.1.2_2: .......... done [head-armv7-default-job-04] | `-- Installing dejavu-2.37... [head-armv7-default-job-04] | | `-- Installing fontconfig-2.12.6,1... [head-armv7-default-job-04] | | `-- Installing expat-2.2.6_1... [head-armv7-default-job-04] | | `-- Extracting expat-2.2.6_1: .......... done [head-armv7-default-job-04] | | `-- Installing freetype2-2.9.1... [head-armv7-default-job-04] | | `-- Extracting freetype2-2.9.1: .......... done [head-armv7-default-job-04] | | `-- 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 [head-armv7-default-job-04] | | `-- Installing mkfontdir-1.0.7... [head-armv7-default-job-04] | | `-- Installing mkfontscale-1.1.3_2... [head-armv7-default-job-04] | | | `-- Installing libfontenc-1.1.3_3... [head-armv7-default-job-04] | | | `-- Extracting libfontenc-1.1.3_3: ......... done [head-armv7-default-job-04] | | `-- Extracting mkfontscale-1.1.3_2: ..... done [head-armv7-default-job-04] | | `-- Extracting mkfontdir-1.0.7: ..... done [head-armv7-default-job-04] | `-- Extracting dejavu-2.37: .......... done [head-armv7-default-job-04] | `-- Installing giflib-5.1.4... [head-armv7-default-job-04] | `-- Extracting giflib-5.1.4: .......... done [head-armv7-default-job-04] | `-- Installing java-zoneinfo-2018.g... [head-armv7-default-job-04] | `-- Extracting java-zoneinfo-2018.g: .......... done [head-armv7-default-job-04] | `-- Installing javavmwrapper-2.6... [head-armv7-default-job-04] | `-- Extracting javavmwrapper-2.6: .......... done [head-armv7-default-job-04] | `-- Installing libX11-1.6.7,1... [head-armv7-default-job-04] | | `-- Installing libXau-1.0.8_5... [head-armv7-default-job-04] | | `-- Extracting libXau-1.0.8_5: .......... done [head-armv7-default-job-04] | | `-- Installing libXdmcp-1.1.2_2... [head-armv7-default-job-04] | | `-- Installing xorgproto-2018.4... [head-armv7-default-job-04] | | `-- Extracting xorgproto-2018.4: .......... done [head-armv7-default-job-04] | | `-- Extracting libXdmcp-1.1.2_2: ......... done [head-armv7-default-job-04] | | `-- Installing libxcb-1.13.1... [head-armv7-default-job-04] | | `-- Installing libpthread-stubs-0.4... [head-armv7-default-job-04] | | `-- Extracting libpthread-stubs-0.4: .... done [head-armv7-default-job-04] | | `-- Installing libxml2-2.9.7... [head-armv7-default-job-04] | | `-- Extracting libxml2-2.9.7: .......... done [head-armv7-default-job-04] | | `-- Extracting libxcb-1.13.1: .......... done [head-armv7-default-job-04] | `-- Extracting libX11-1.6.7,1: .......... done [head-armv7-default-job-04] | `-- Installing libXext-1.3.3_3,1... [head-armv7-default-job-04] | `-- Extracting libXext-1.3.3_3,1: .......... done [head-armv7-default-job-04] | `-- Installing libXi-1.7.9_2,1... [head-armv7-default-job-04] | | `-- Installing libXfixes-5.0.3_2... [head-armv7-default-job-04] | | `-- Extracting libXfixes-5.0.3_2: .......... done [head-armv7-default-job-04] | `-- Extracting libXi-1.7.9_2,1: .......... done [head-armv7-default-job-04] | `-- Installing libXrender-0.9.10_2... [head-armv7-default-job-04] | `-- Extracting libXrender-0.9.10_2: .......... done [head-armv7-default-job-04] | `-- Installing libXt-1.1.5_2,1... [head-armv7-default-job-04] | | `-- Installing libICE-1.0.9_3,1... [head-armv7-default-job-04] | | `-- Extracting libICE-1.0.9_3,1: .......... done [head-armv7-default-job-04] | | `-- Installing libSM-1.2.3,1... [head-armv7-default-job-04] | | `-- Extracting libSM-1.2.3,1: .......... done [head-armv7-default-job-04] | `-- Extracting libXt-1.1.5_2,1: .......... done [head-armv7-default-job-04] | `-- Installing libXtst-1.2.3_2... [head-armv7-default-job-04] | `-- Extracting libXtst-1.2.3_2: .......... done [head-armv7-default-job-04] | `-- Installing libffi-3.2.1_3... [head-armv7-default-job-04] | | `-- Installing indexinfo-0.3.1... [head-armv7-default-job-04] | | `-- Extracting indexinfo-0.3.1: .... done [head-armv7-default-job-04] | `-- Extracting libffi-3.2.1_3: .......... done [head-armv7-default-job-04] `-- Extracting openjdk8-8.192.26_1: .......... done [head-armv7-default-job-04] Extracting gradle4-4.6: .......... done Message from freetype2-2.9.1: The 2.7.x series now uses the new subpixel hinting mode (V40 port's option) as the default, emulating a modern version of ClearType. This change inevitably leads to different rendering results, and you might change port's options to adapt it to your taste (or use the new "FREETYPE_PROPERTIES" environment variable). The environment variable "FREETYPE_PROPERTIES" can be used to control the driver properties. Example: FREETYPE_PROPERTIES=truetype:interpreter-version=35 \ cff:no-stem-darkening=1 \ autofitter:warping=1 This allows to select, say, the subpixel hinting mode at runtime for a given application. The controllable properties are listed in the section "Controlling FreeType Modules" in the reference's table of contents (/usr/local/share/doc/freetype2/reference/ft2-toc.html, if documentation was installed). Message from dejavu-2.37: Make sure that the freetype module is loaded. If it is not, add the following line to the "Modules" section of your X Windows configuration file: Load "freetype" Add the following line to the "Files" section of X Windows configuration file: FontPath "/usr/local/share/fonts/dejavu/" Note: your X Windows configuration file is typically /etc/X11/XF86Config if you are using XFree86, and /etc/X11/xorg.conf if you are using X.Org. Message from openjdk8-8.192.26_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-4.0.11.0 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 =========================================================================== =================================================== ===> gatk-4.0.11.0 depends on shared library: libintl.so - not found ===> Installing existing package /packages/All/gettext-runtime-0.19.8.1_2.txz [head-armv7-default-job-04] Installing gettext-runtime-0.19.8.1_2... [head-armv7-default-job-04] Extracting gettext-runtime-0.19.8.1_2: .......... 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 =========================================================================== =================================================== ===> Configuring for gatk-4.0.11.0 =========================================================================== =================================================== ===> Building for gatk-4.0.11.0 Starting a Gradle Daemon (subsequent builds will be faster) Could not write standard input to Gradle build daemon. java.io.IOException: Stream closed at java.lang.ProcessBuilder$NullOutputStream.write(ProcessBuilder.java:433) at java.io.OutputStream.write(OutputStream.java:116) at java.io.BufferedOutputStream.flushBuffer(BufferedOutputStream.java:82) at java.io.BufferedOutputStream.flush(BufferedOutputStream.java:140) at org.gradle.process.internal.streams.ExecOutputHandleRunner.forwardContent(ExecOutputHandleRunner.java:66) at org.gradle.process.internal.streams.ExecOutputHandleRunner.run(ExecOutputHandleRunner.java:51) at org.gradle.internal.concurrent.ExecutorPolicy$CatchAndRecordFailures.onExecute(ExecutorPolicy.java:63) at org.gradle.internal.concurrent.ManagedExecutorImpl$1.run(ManagedExecutorImpl.java:46) at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149) at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624) at org.gradle.internal.concurrent.ThreadFactoryImpl$ManagedThreadRunnable.run(ThreadFactoryImpl.java:55) at java.lang.Thread.run(Thread.java:748) FAILURE: Build failed with an exception. * What went wrong: Unable to start the daemon process. This problem might be caused by incorrect configuration of the daemon. For example, an unrecognized jvm option is used. Please refer to the user guide chapter on the daemon at https://docs.gradle.org/4.6/userguide/gradle_daemon.html Please read the following process output to find out more: ----------------------- * 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 *** Error code 1 Stop. make: stopped in /usr/ports/biology/gatk