Date: Wed, 6 Feb 2019 11:53:58 GMT From: pkg-fallout@FreeBSD.org To: pkg-fallout@FreeBSD.org Subject: [package - 120arm64-quarterly][biology/gatk] Failed for gatk-4.0.11.0 in build Message-ID: <201902061153.x16BrwEB052667@thunderx1.nyi.freebsd.org>
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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: branches/2019Q1/biology/gatk/Makefile 486619 2018-12-04 17:53:46Z yuri $ Log URL: http://thunderx1.nyi.freebsd.org/data/120arm64-quarterly/491975/logs/gatk-4.0.11.0.log Build URL: http://thunderx1.nyi.freebsd.org/build.html?mastername=120arm64-quarterly&build=491975 Log: =>> Building biology/gatk build started at Wed Feb 6 11:52:30 UTC 2019 port directory: /usr/ports/biology/gatk package name: gatk-4.0.11.0 building for: FreeBSD 120arm64-quarterly-job-15 12.0-RELEASE-p2 FreeBSD 12.0-RELEASE-p2 1200086 arm64 maintained by: yuri@FreeBSD.org Makefile ident: $FreeBSD: branches/2019Q1/biology/gatk/Makefile 486619 2018-12-04 17:53:46Z yuri $ Poudriere version: 3.2.8 Host OSVERSION: 1300002 Jail OSVERSION: 1200086 Job Id: 15 ---Begin Environment--- SHELL=/bin/csh OSVERSION=1200086 UNAME_v=FreeBSD 12.0-RELEASE-p2 1200086 UNAME_r=12.0-RELEASE-p2 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 LIBEXECPREFIX=/usr/local/libexec/poudriere POUDRIERE_VERSION=3.2.8 MASTERMNT=/usr/local/poudriere/data/.m/120arm64-quarterly/ref POUDRIERE_BUILD_TYPE=bulk PACKAGE_BUILDING=yes SAVED_TERM= PWD=/usr/local/poudriere/data/.m/120arm64-quarterly/ref/.p/pool P_PORTS_FEATURES=FLAVORS SELECTED_OPTIONS MASTERNAME=120arm64-quarterly SCRIPTPREFIX=/usr/local/share/poudriere OLDPWD=/usr/local/poudriere/data/.m/120arm64-quarterly/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 -fno-strict-aliasing " CPP="cpp" CPPFLAGS="" LDFLAGS=" " LIBS="" CXX="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=12.0 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--- USE_PACKAGE_DEPENDS=yes BATCH=yes WRKDIRPREFIX=/wrkdirs PORTSDIR=/usr/ports PACKAGES=/packages DISTDIR=/distfiles PACKAGE_BUILDING=yes PACKAGE_BUILDING_FLAVORS=yes #### /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_921dbbb2=FreeBSD clang version 6.0.1 (tags/RELEASE_601/final 335540) (based on LLVM 6.0.1) Target: aarch64-unknown-freebsd12.0 Thread model: posix InstalledDir: /usr/bin _ALTCCVERSION_921dbbb2=none _CXXINTERNAL_acaad9ca=FreeBSD clang version 6.0.1 (tags/RELEASE_601/final 335540) (based on LLVM 6.0.1) Target: aarch64-unknown-freebsd12.0 Thread model: posix InstalledDir: /usr/bin "/usr/bin/ld" "--eh-frame-hdr" "-dynamic-linker" "/libexec/ld-elf.so.1" "--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_921dbbb2_58173849=yes CC_OUTPUT_921dbbb2_9bdba57c=yes CC_OUTPUT_921dbbb2_6a4fe7f5=yes CC_OUTPUT_921dbbb2_6bcac02b=yes CC_OUTPUT_921dbbb2_67d20829=yes CC_OUTPUT_921dbbb2_bfa62e83=yes CC_OUTPUT_921dbbb2_f0b4d593=yes CC_OUTPUT_921dbbb2_308abb44=yes CC_OUTPUT_921dbbb2_f00456e5=yes 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 6.0.1 (tags/RELEASE_601/final 335540) (based on LLVM 6.0.1) Target: aarch64-unknown-freebsd12.0 Thread model: posix InstalledDir: /usr/bin _OBJC_ALTCCVERSION_921dbbb2=none ARCH=aarch64 OPSYS=FreeBSD _OSRELEASE=12.0-RELEASE-p2 OSREL=12.0 OSVERSION=1200086 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--- --Resource limits-- cpu time (seconds, -t) unlimited file size (512-blocks, -f) unlimited data seg size (kbytes, -d) 1048576 stack size (kbytes, -s) 1048576 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) 2048 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-- =======================<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-1.10.5_5.txz [120arm64-quarterly-job-15] Installing pkg-1.10.5_5... [120arm64-quarterly-job-15] 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 =========================================================================== =======================<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 FreeBSD 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 [120arm64-quarterly-job-15] Installing gradle4-4.6... [120arm64-quarterly-job-15] `-- Installing openjdk8-8.192.26_3... [120arm64-quarterly-job-15] | `-- Installing alsa-lib-1.1.2_2... [120arm64-quarterly-job-15] | `-- Extracting alsa-lib-1.1.2_2: .......... done [120arm64-quarterly-job-15] | `-- Installing dejavu-2.37... [120arm64-quarterly-job-15] | | `-- Installing fontconfig-2.12.6,1... [120arm64-quarterly-job-15] | | `-- Installing expat-2.2.6_1... [120arm64-quarterly-job-15] | | `-- Extracting expat-2.2.6_1: .......... done [120arm64-quarterly-job-15] | | `-- Installing freetype2-2.9.1... [120arm64-quarterly-job-15] | | `-- Extracting freetype2-2.9.1: .......... done [120arm64-quarterly-job-15] | | `-- 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 [120arm64-quarterly-job-15] | | `-- Installing mkfontdir-1.0.7... [120arm64-quarterly-job-15] | | `-- Installing mkfontscale-1.1.3_2... [120arm64-quarterly-job-15] | | | `-- Installing libfontenc-1.1.3_3... [120arm64-quarterly-job-15] | | | `-- Extracting libfontenc-1.1.3_3: ......... done [120arm64-quarterly-job-15] | | `-- Extracting mkfontscale-1.1.3_2: ..... done [120arm64-quarterly-job-15] | | `-- Extracting mkfontdir-1.0.7: ..... done [120arm64-quarterly-job-15] | `-- Extracting dejavu-2.37: .......... done [120arm64-quarterly-job-15] | `-- Installing giflib-5.1.4... [120arm64-quarterly-job-15] | `-- Extracting giflib-5.1.4: .......... done [120arm64-quarterly-job-15] | `-- Installing java-zoneinfo-2018.g... [120arm64-quarterly-job-15] | `-- Extracting java-zoneinfo-2018.g: .......... done [120arm64-quarterly-job-15] | `-- Installing javavmwrapper-2.6... [120arm64-quarterly-job-15] | `-- Extracting javavmwrapper-2.6: .......... done [120arm64-quarterly-job-15] | `-- Installing libX11-1.6.7,1... [120arm64-quarterly-job-15] | | `-- Installing libXau-1.0.8_5... [120arm64-quarterly-job-15] | | `-- Extracting libXau-1.0.8_5: .......... done [120arm64-quarterly-job-15] | | `-- Installing libXdmcp-1.1.2_2... [120arm64-quarterly-job-15] | | `-- Installing xorgproto-2018.4... [120arm64-quarterly-job-15] | | `-- Extracting xorgproto-2018.4: .......... done [120arm64-quarterly-job-15] | | `-- Extracting libXdmcp-1.1.2_2: ......... done [120arm64-quarterly-job-15] | | `-- Installing libxcb-1.13.1... [120arm64-quarterly-job-15] | | `-- Installing libpthread-stubs-0.4... [120arm64-quarterly-job-15] | | `-- Extracting libpthread-stubs-0.4: .... done [120arm64-quarterly-job-15] | | `-- Installing libxml2-2.9.7... [120arm64-quarterly-job-15] | | `-- Extracting libxml2-2.9.7: .......... done [120arm64-quarterly-job-15] | | `-- Extracting libxcb-1.13.1: .......... done [120arm64-quarterly-job-15] | `-- Extracting libX11-1.6.7,1: .......... done [120arm64-quarterly-job-15] | `-- Installing libXext-1.3.3_3,1... [120arm64-quarterly-job-15] | `-- Extracting libXext-1.3.3_3,1: .......... done [120arm64-quarterly-job-15] | `-- Installing libXi-1.7.9_2,1... [120arm64-quarterly-job-15] | | `-- Installing libXfixes-5.0.3_2... [120arm64-quarterly-job-15] | | `-- Extracting libXfixes-5.0.3_2: .......... done [120arm64-quarterly-job-15] | `-- Extracting libXi-1.7.9_2,1: .......... done [120arm64-quarterly-job-15] | `-- Installing libXrender-0.9.10_2... [120arm64-quarterly-job-15] | `-- Extracting libXrender-0.9.10_2: .......... done [120arm64-quarterly-job-15] | `-- Installing libXt-1.1.5_2,1... [120arm64-quarterly-job-15] | | `-- Installing libICE-1.0.9_3,1... [120arm64-quarterly-job-15] | | `-- Extracting libICE-1.0.9_3,1: .......... done [120arm64-quarterly-job-15] | | `-- Installing libSM-1.2.3,1... [120arm64-quarterly-job-15] | | `-- Extracting libSM-1.2.3,1: .......... done [120arm64-quarterly-job-15] | `-- Extracting libXt-1.1.5_2,1: .......... done [120arm64-quarterly-job-15] | `-- Installing libXtst-1.2.3_2... [120arm64-quarterly-job-15] | `-- Extracting libXtst-1.2.3_2: .......... done [120arm64-quarterly-job-15] | `-- Installing libffi-3.2.1_3... [120arm64-quarterly-job-15] | | `-- Installing indexinfo-0.3.1... [120arm64-quarterly-job-15] | | `-- Extracting indexinfo-0.3.1: .... done [120arm64-quarterly-job-15] | `-- Extracting libffi-3.2.1_3: .......... done [120arm64-quarterly-job-15] | `-- Installing libinotify-20180201_1... [120arm64-quarterly-job-15] | `-- Extracting libinotify-20180201_1: .......... done [120arm64-quarterly-job-15] `-- Extracting openjdk8-8.192.26_3: .......... done [120arm64-quarterly-job-15] 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 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 openjdk8-8.192.26_3: ====================================================================== 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 =========================================================================== =======================<phase: lib-depends >============================ ===> 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 [120arm64-quarterly-job-15] Installing gettext-runtime-0.19.8.1_2... [120arm64-quarterly-job-15] 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 =========================================================================== =======================<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) FAILURE: Build failed with an exception. * What went wrong: String index out of range: 2147483646 * 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
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