[package - 131releng-armv7-quarterly][biology/jalview] Failed for jalview-2.11.2.5 in build
- Go to: [ bottom of page ] [ top of archives ] [ this month ]
Date: Sat, 10 Jun 2023 22:00:21 UTC
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 Log URL: https://pkg-status.freebsd.org/ampere1/data/131releng-armv7-quarterly/56083eef528f/logs/jalview-2.11.2.5.log Build URL: https://pkg-status.freebsd.org/ampere1/build.html?mastername=131releng-armv7-quarterly&build=56083eef528f Log: =>> Building biology/jalview build started at Sat Jun 10 21:57:53 UTC 2023 port directory: /usr/ports/biology/jalview package name: jalview-2.11.2.5 building for: FreeBSD 131releng-armv7-quarterly-job-13 13.1-RELEASE-p7 FreeBSD 13.1-RELEASE-p7 1301000 arm maintained by: yuri@FreeBSD.org Makefile ident: Poudriere version: 3.2.8-23-ga7f8d188 Host OSVERSION: 1400073 Jail OSVERSION: 1301000 Job Id: 13 ---Begin Environment--- SHELL=/bin/csh OSVERSION=1301000 UNAME_v=FreeBSD 13.1-RELEASE-p7 1301000 UNAME_r=13.1-RELEASE-p7 BLOCKSIZE=K MAIL=/var/mail/root MM_CHARSET=UTF-8 LANG=C.UTF-8 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=3.2.8-23-ga7f8d188 MASTERMNT=/usr/local/poudriere/data/.m/131releng-armv7-quarterly/ref POUDRIERE_BUILD_TYPE=bulk PACKAGE_BUILDING=yes SAVED_TERM= PWD=/usr/local/poudriere/data/.m/131releng-armv7-quarterly/ref/.p/pool P_PORTS_FEATURES=FLAVORS SELECTED_OPTIONS MASTERNAME=131releng-armv7-quarterly SCRIPTPREFIX=/usr/local/share/poudriere OLDPWD=/usr/local/poudriere/data/.m/131releng-armv7-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/jalview/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/jalview/work XDG_CACHE_HOME=/wrkdirs/usr/ports/biology/jalview/work/.cache HOME=/wrkdirs/usr/ports/biology/jalview/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/jalview/work/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin PKG_CONFIG_LIBDIR=/wrkdirs/usr/ports/biology/jalview/work/.pkgconfig:/usr/local/libdata/pkgconfig:/usr/local/share/pkgconfig:/usr/libdata/pkgconfig SHELL=/bin/sh CONFIG_SHELL=/bin/sh LANG=en_US.UTF-8 LC_ALL=en_US.UTF-8 --End CONFIGURE_ENV-- --MAKE_ENV-- XDG_DATA_HOME=/wrkdirs/usr/ports/biology/jalview/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/jalview/work XDG_CACHE_HOME=/wrkdirs/usr/ports/biology/jalview/work/.cache HOME=/wrkdirs/usr/ports/biology/jalview/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/jalview/work/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin PKG_CONFIG_LIBDIR=/wrkdirs/usr/ports/biology/jalview/work/.pkgconfig:/usr/local/libdata/pkgconfig:/usr/local/share/pkgconfig:/usr/libdata/pkgconfig MK_DEBUG_FILES=no MK_KERNEL_SYMBOLS=no SHELL=/bin/sh NO_LINT=YES LANG=en_US.UTF-8 LC_ALL=en_US.UTF-8 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="inst all -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=13.1 PREFIX=%D LOCALBASE=/usr/local RESETPREFIX=/usr/local LIB32DIR=lib DOCSDIR="share/doc/jalview" EXAMPLESDIR="share/examples/jalview" DATADIR="share/java/jalview" WWWDIR="www/jalview" ETCDIR="etc/jalview" --End PLIST_SUB-- --SUB_LIST-- JAVA=/usr/local/openjdk11/bin/java JAVASHAREDIR="/usr/local/share/java" JAVAJARDIR="/usr/local/share/java/classes" JAVALIBDIR="/usr/local/share/java/classes" JAVA_VERSION="11" PREFIX=/usr/local LOCALBASE=/usr/local DATADIR=/usr/local/share/java/jalview DOCSDIR=/usr/local/share/doc/jalview EXAMPLESDIR=/usr/local/share/examples/jalview WWWDIR=/usr/local/www/jalview ETCDIR=/usr/local/etc/jalview --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 #### /usr/ports/Mk/Scripts/ports_env.sh #### _CCVERSION_921dbbb2=FreeBSD clang version 13.0.0 (git@github.com:llvm/llvm-project.git llvmorg-13.0.0-0-gd7b669b3a303) Target: armv7-unknown-freebsd13.1-gnueabihf Thread model: posix InstalledDir: /usr/bin _ALTCCVERSION_921dbbb2=none _CXXINTERNAL_acaad9ca=FreeBSD clang version 13.0.0 (git@github.com:llvm/llvm-project.git llvmorg-13.0.0-0-gd7b669b3a303) Target: armv7-unknown-freebsd13.1-gnueabihf Thread model: posix InstalledDir: /usr/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_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_53255a77=yes CC_OUTPUT_921dbbb2_911cfe02=yes CC_OUTPUT_921dbbb2_b2657cc3=yes CC_OUTPUT_921dbbb2_380987f7=yes CC_OUTPUT_921dbbb2_160933ec=yes CC_OUTPUT_921dbbb2_fb62803b=yes CC_OUTPUT_921dbbb2_af59ad06=yes CC_OUTPUT_921dbbb2_a15f3fcf=yes _OBJC_CCVERSION_921dbbb2=FreeBSD clang version 13.0.0 (git@github.com:llvm/llvm-project.git llvmorg-13.0.0-0-gd7b669b3a303) Target: armv7-unknown-freebsd13.1-gnueabihf Thread model: posix InstalledDir: /usr/bin _OBJC_ALTCCVERSION_921dbbb2=none ARCH=armv7 OPSYS=FreeBSD _OSRELEASE=13.1-RELEASE-p7 OSREL=13.1 OSVERSION=1301000 PYTHONBASE=/usr/local CONFIGURE_MAX_CMD_LEN=524288 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) 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) 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-- =======================<phase: check-sanity >============================ ===> License GPLv3 accepted by the user =========================================================================== =======================<phase: pkg-depends >============================ ===> jalview-2.11.2.5 depends on file: /usr/local/sbin/pkg - not found ===> Installing existing package /packages/All/pkg-1.19.1_1.pkg [131releng-armv7-quarterly-job-13] Installing pkg-1.19.1_1... [131releng-armv7-quarterly-job-13] Extracting pkg-1.19.1_1: .......... done ===> jalview-2.11.2.5 depends on file: /usr/local/sbin/pkg - found ===> Returning to build of jalview-2.11.2.5 =========================================================================== =======================<phase: fetch-depends >============================ =========================================================================== =======================<phase: fetch >============================ ===> License GPLv3 accepted by the user ===> Fetching all distfiles required by jalview-2.11.2.5 for building =========================================================================== =======================<phase: checksum >============================ ===> License GPLv3 accepted by the user ===> Fetching all distfiles required by jalview-2.11.2.5 for building => SHA256 Checksum OK for jalview_2_11_2_5.tar.gz. => SHA256 Checksum OK for jalview-2.11.2.5-deps.tar.gz. =========================================================================== =======================<phase: extract-depends>============================ =========================================================================== =======================<phase: extract >============================ ===> License GPLv3 accepted by the user ===> Fetching all distfiles required by jalview-2.11.2.5 for building ===> Extracting for jalview-2.11.2.5 => SHA256 Checksum OK for jalview_2_11_2_5.tar.gz. => SHA256 Checksum OK for jalview-2.11.2.5-deps.tar.gz. =========================================================================== =======================<phase: patch-depends >============================ =========================================================================== =======================<phase: patch >============================ ===> Patching for jalview-2.11.2.5 =========================================================================== =======================<phase: build-depends >============================ ===> jalview-2.11.2.5 depends on executable: gradle - not found ===> Installing existing package /packages/All/gradle-7.6.pkg [131releng-armv7-quarterly-job-13] Installing gradle-7.6... [131releng-armv7-quarterly-job-13] `-- Installing openjdk8-8.362.09.1_1... [131releng-armv7-quarterly-job-13] | `-- Installing alsa-lib-1.2.2_1... [131releng-armv7-quarterly-job-13] | `-- Extracting alsa-lib-1.2.2_1: .......... done [131releng-armv7-quarterly-job-13] | `-- Installing dejavu-2.37_1... [131releng-armv7-quarterly-job-13] | | `-- Installing fontconfig-2.14.2,1... [131releng-armv7-quarterly-job-13] | | `-- Installing expat-2.5.0... [131releng-armv7-quarterly-job-13] | | `-- Extracting expat-2.5.0: .......... done [131releng-armv7-quarterly-job-13] | | `-- Installing freetype2-2.12.1_2... [131releng-armv7-quarterly-job-13] | | | `-- Installing brotli-1.0.9,1... [131releng-armv7-quarterly-job-13] | | | `-- Extracting brotli-1.0.9,1: .......... done [131releng-armv7-quarterly-job-13] | | | `-- Installing png-1.6.39... <snip> 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/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-20211018: -- 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 openjdk8-8.362.09.1_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 ===> jalview-2.11.2.5 depends on executable: gradle - found ===> Returning to build of jalview-2.11.2.5 ===> jalview-2.11.2.5 depends on file: /usr/local/openjdk11/bin/java - not found ===> Installing existing package /packages/All/openjdk11-11.0.18+10.1.pkg [131releng-armv7-quarterly-job-13] Installing openjdk11-11.0.18+10.1... [131releng-armv7-quarterly-job-13] `-- Installing jpeg-turbo-2.1.5.1... [131releng-armv7-quarterly-job-13] `-- Extracting jpeg-turbo-2.1.5.1: .......... done [131releng-armv7-quarterly-job-13] `-- Installing lcms2-2.13.1... [131releng-armv7-quarterly-job-13] | `-- Installing tiff-4.4.0_1... [131releng-armv7-quarterly-job-13] | | `-- Installing jbigkit-2.1_1... [131releng-armv7-quarterly-job-13] | | `-- Extracting jbigkit-2.1_1: .......... done [131releng-armv7-quarterly-job-13] | | `-- Installing libdeflate-1.18... [131releng-armv7-quarterly-job-13] | | `-- Extracting libdeflate-1.18: .......... done [131releng-armv7-quarterly-job-13] | | `-- Installing zstd-1.5.4... [131releng-armv7-quarterly-job-13] | | `-- Installing liblz4-1.9.4,1... [131releng-armv7-quarterly-job-13] | | `-- Extracting liblz4-1.9.4,1: .......... done [131releng-armv7-quarterly-job-13] | | `-- Extracting zstd-1.5.4: .......... done [131releng-armv7-quarterly-job-13] | `-- Extracting tiff-4.4.0_1: .......... done [131releng-armv7-quarterly-job-13] `-- Extracting lcms2-2.13.1: .......... done [131releng-armv7-quarterly-job-13] `-- Installing libXrandr-1.5.2... [131releng-armv7-quarterly-job-13] `-- Extracting libXrandr-1.5.2: .......... done [131releng-armv7-quarterly-job-13] `-- Installing xorg-fonts-truetype-7.7_1... [131releng-armv7-quarterly-job-13] | `-- Installing encodings-1.0.5,1... [131releng-armv7-quarterly-job-13] | `-- Extracting encodings-1.0.5,1: .......... done [131releng-armv7-quarterly-job-13] | `-- Installing font-bh-ttf-1.0.3_4... [131releng-armv7-quarterly-job-13] | `-- Extracting font-bh-ttf-1.0.3_4: .......... done [131releng-armv7-quarterly-job-13] | `-- Installing font-misc-ethiopic-1.0.4... [131releng-armv7-quarterly-job-13] | `-- Extracting font-misc-ethiopic-1.0.4: ...... done [131releng-armv7-quarterly-job-13] | `-- Installing font-misc-meltho-1.0.3_4... [131releng-armv7-quarterly-job-13] | `-- Extracting font-misc-meltho-1.0.3_4: .......... done [131releng-armv7-quarterly-job-13] `-- Extracting xorg-fonts-truetype-7.7_1: ... done [131releng-armv7-quarterly-job-13] Extracting openjdk11-11.0.18+10.1: .......... done Running fc-cache to build fontconfig cache... ===== Message from openjdk11-11.0.18+10.1: -- 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 ===> jalview-2.11.2.5 depends on file: /usr/local/openjdk11/bin/java - found ===> Returning to build of jalview-2.11.2.5 =========================================================================== =======================<phase: lib-depends >============================ =========================================================================== =======================<phase: configure >============================ ===> Configuring for jalview-2.11.2.5 =========================================================================== =======================<phase: build >============================ ===> Building for jalview-2.11.2.5 Welcome to Gradle 7.6! Here are the highlights of this release: - Added support for Java 19. - Introduced `--rerun` flag for individual task rerun. - Improved dependency block for test suites to be strongly typed. - Added a pluggable system for Java toolchains provisioning. For more details see https://docs.gradle.org/7.6/release-notes.html Starting a Gradle Daemon (subsequent builds will be faster) > Configure project : Using properties from file './utils/channels/default/channel_gradle.properties' JALVIEW_VERSION is set to '2.11.2.5' HEADLESS BUILD J2S ENABLED Not in a git repository. Using git values from RELEASE properties file. Using a LOCAL profile. > Task :copyHelp > Task :buildIndices > Task :copyResources > Task :copyChannelResources > Task :createBuildProperties Execution optimizations have been disabled for task ':createBuildProperties' to ensure correctness due to the following reasons: - Gradle detected a problem with the following location: '/wrkdirs/usr/ports/biology/jalview/work/jalview/build/resources/resources_build'. Reason: Task ':createBuildProperties' uses this output of task ':copyChannelResources' without declaring an explicit or implicit dependency. This can lead to incorrect results being produced, depending on what order the tasks are executed. Please refer to https://docs.gradle.org/7.6/userguide/validation_problems.html#implicit_dependency for more details about this problem. > Task :buildResources > Task :copyDocs > Task :convertMdFiles Creating /wrkdirs/usr/ports/biology/jalview/work/jalview/build/resources/doc_build/doc/README-DMG_creation.html Creating /wrkdirs/usr/ports/biology/jalview/work/jalview/build/resources/doc_build/doc/README-DMG_background_image_creation.html Creating /wrkdirs/usr/ports/biology/jalview/work/jalview/build/resources/doc_build/doc/building.html Creating /wrkdirs/usr/ports/biology/jalview/work/jalview/build/resources/doc_build/doc/releaseprocess.html > Task :releasesTemplates Execution optimizations have been disabled for task ':releasesTemplates' to ensure correctness due to the following reasons: - Gradle detected a problem with the following location: '/wrkdirs/usr/ports/biology/jalview/work/jalview/build/resources/help_build/help/html/releases.html'. Reason: Task ':buildIndices' uses this output of task ':releasesTemplates' without declaring an explicit or implicit dependency. This can lead to incorrect results being produced, depending on what order the tasks are executed. Please refer to https://docs.gradle.org/7.6/userguide/validation_problems.html#implicit_dependency for more details about this problem. - Gradle detected a problem with the following location: '/wrkdirs/usr/ports/biology/jalview/work/jalview/build/resources/help_build/help/html/whatsNew.html'. Reason: Task ':buildIndices' uses this output of task ':releasesTemplates' without declaring an explicit or implicit dependency. This can lead to incorrect results being produced, depending on what order the tasks are executed. Please refer to https://docs.gradle.org/7.6/userguide/validation_problems.html#implicit_dependency for more details about this problem. > Task :prepare > Task :compileJava FAILED FAILURE: Build failed with an exception. * Where: Build file '/wrkdirs/usr/ports/biology/jalview/work/jalview/build.gradle' line: 1036 * What went wrong: Execution failed for task ':compileJava'. > java.lang.NullPointerException (no error message) * 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 Deprecated Gradle features were used in this build, making it incompatible with Gradle 8.0. You can use '--warning-mode all' to show the individual deprecation warnings and determine if they come from your own scripts or plugins. See https://docs.gradle.org/7.6/userguide/command_line_interface.html#sec:command_line_warnings Execution optimizations have been disabled for 2 invalid unit(s) of work during this build to ensure correctness. Please consult deprecation warnings for more details. BUILD FAILED in 1m 34s 9 actionable tasks: 9 executed *** Error code 1 Stop. make: stopped in /usr/ports/biology/jalview