=>> Building biology/jalview build started at Mon Nov 10 15:32:14 EST 2025 port directory: /usr/ports/biology/jalview package name: jalview-2.11.2.5 building for: FreeBSD pkg.DaveG.ca 15.0-ALPHA3 FreeBSD 15.0-ALPHA3 1500064 amd64 maintained by: yuri@FreeBSD.org Makefile datestamp: -rw-r--r-- 1 root wheel 2016 Jan 14 2025 /usr/ports/biology/jalview/Makefile Ports top last git commit: ec159283c191 Ports top unclean checkout: no Port dir last git commit: 0835676e361b Port dir unclean checkout: no Poudriere version: poudriere-git-3.4.2 Host OSVERSION: 1500068 Jail OSVERSION: 1500064 Job Id: 12 ---Begin Environment--- SHELL=/bin/sh OSVERSION=1500064 UNAME_v=FreeBSD 15.0-ALPHA3 1500064 UNAME_r=15.0-ALPHA3 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 MAKE_OBJDIR_CHECK_WRITABLE=0 LOCALBASE=/usr/local USER=root POUDRIERE_NAME=poudriere-git LIBEXECPREFIX=/usr/local/libexec/poudriere POUDRIERE_VERSION=3.4.2 MASTERMNT=/usr/local/poudriere/data/.m/freebsd_15_c_x64-HEAD-ALL/ref LC_COLLATE=C POUDRIERE_BUILD_TYPE=bulk PACKAGE_BUILDING=yes SAVED_TERM=tmux-256color OUTPUT_REDIRECTED_STDERR=4 OUTPUT_REDIRECTED=1 PWD=/usr/local/poudriere/data/.m/freebsd_15_c_x64-HEAD-ALL/12/.p OUTPUT_REDIRECTED_STDOUT=3 P_PORTS_FEATURES=FLAVORS SUBPACKAGES SELECTED_OPTIONS MASTERNAME=freebsd_15_c_x64-HEAD-ALL SCRIPTPREFIX=/usr/local/share/poudriere SCRIPTNAME=bulk.sh OLDPWD=/usr/local/poudriere/data/.m/freebsd_15_c_x64-HEAD-ALL/ref/.p/pool POUDRIERE_PKGNAME=poudriere-git-3.4.2 SCRIPTPATH=/usr/local/share/poudriere/bulk.sh POUDRIEREPATH=/usr/local/bin/poudriere ---End Environment--- ---Begin Poudriere Port Flags/Env--- PORT_FLAGS= PKGENV= FLAVOR= 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 --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 PREFIX=/usr/local LOCALBASE=/usr/local CC="cc" CFLAGS="-O2 -pipe -fstack-protector-strong -fno-strict-aliasing " CPP="cpp" CPPFLAGS="" LDFLAGS=" " LIBS="" CXX="c++" CXXFLAGS="-O2 -pipe -fstack-protector-strong -fno-strict-aliasing " 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=15.0 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--- DEFAULT_VERSIONS+=pgsql=15 DEFAULT_VERSIONS+=php=82 DISABLE_LICENSES=yes SELECTED_OPTIONS+=OPENBLAS ARCHDEF=AMD64K10h64SSE3 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 #### #### DEFAULT_VERSIONS+=pgsql=15 DEFAULT_VERSIONS+=php=82 DISABLE_LICENSES=yes SELECTED_OPTIONS+=OPENBLAS ARCHDEF=AMD64K10h64SSE3 WITH_CCACHE_BUILD=yes CCACHE_DIR=/root/.ccache #### Misc Poudriere #### .include "/etc/make.conf.ports_env" 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) 8192 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 pipebuf (-y) unlimited --End resource limits-- =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 ===> jalview-2.11.2.5 depends on file: /usr/local/sbin/pkg - not found ===> Installing existing package /packages/All/pkg-2.4.2_1.pkg [pkg.DaveG.ca] Installing pkg-2.4.2_1... [pkg.DaveG.ca] Extracting pkg-2.4.2_1: .......... done ===> jalview-2.11.2.5 depends on file: /usr/local/sbin/pkg - found ===> Returning to build of jalview-2.11.2.5 =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Fetching all distfiles required by jalview-2.11.2.5 for building =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> 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. =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> 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. =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Patching for jalview-2.11.2.5 =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 ===> jalview-2.11.2.5 depends on executable: gradle761 - not found ===> Installing existing package /packages/All/gradle761-7.6.1.pkg [pkg.DaveG.ca] Installing gradle761-7.6.1... [pkg.DaveG.ca] `-- Installing openjdk8-8.472.08.1... [pkg.DaveG.ca] | `-- Installing alsa-lib-1.2.14... [pkg.DaveG.ca] | `-- Extracting alsa-lib-1.2.14: .......... done [pkg.DaveG.ca] | `-- Installing dejavu-2.37_3... [pkg.DaveG.ca] | | `-- Installing fontconfig-2.15.0_3,1... [pkg.DaveG.ca] | | `-- Installing expat-2.7.3... [pkg.DaveG.ca] | | `-- Extracting expat-2.7.3: .......... done [pkg.DaveG.ca] | | `-- Installing freetype2-2.14.1... [pkg.DaveG.ca] | | | `-- Installing brotli-1.1.0,1... [pkg.DaveG.ca] | | | `-- Extracting brotli-1.1.0,1: .......... done [pkg.DaveG.ca] | | | `-- Installing png-1.6.50... [pkg.DaveG.ca] | | | `-- Extracting png-1.6.50: .......... done [pkg.DaveG.ca] | | `-- Extracting freetype2-2.14.1: .......... done [pkg.DaveG.ca] | | `-- Extracting fontconfig-2.15.0_3,1: .......... done [pkg.DaveG.ca] | | `-- Installing mkfontscale-1.2.3... [pkg.DaveG.ca] | | `-- Installing libfontenc-1.1.8... [pkg.DaveG.ca] | | `-- Extracting libfontenc-1.1.8: ...... done [pkg.DaveG.ca] | | `-- Extracting mkfontscale-1.2.3: .... done [pkg.DaveG.ca] | `-- Extracting dejavu-2.37_3: .......... done [pkg.DaveG.ca] | `-- Installing giflib-5.2.2... [pkg.DaveG.ca] | `-- Extracting giflib-5.2.2: .......... done [pkg.DaveG.ca] | `-- Installing java-zoneinfo-2021.e... [pkg.DaveG.ca] | `-- Extracting java-zoneinfo-2021.e: .......... done [pkg.DaveG.ca] | `-- Installing javavmwrapper-2.7.10... [pkg.DaveG.ca] | `-- Extracting javavmwrapper-2.7.10: .......... done [pkg.DaveG.ca] | `-- Installing libX11-1.8.12,1... [pkg.DaveG.ca] | | `-- Installing libxcb-1.17.0... [pkg.DaveG.ca] | | `-- Installing libXau-1.0.12... [pkg.DaveG.ca] | | `-- Extracting libXau-1.0.12: .......... done [pkg.DaveG.ca] | | `-- Installing libXdmcp-1.1.5... [pkg.DaveG.ca] | | | `-- Installing xorgproto-2024.1... [pkg.DaveG.ca] | | | `-- Extracting xorgproto-2024.1: .......... done [pkg.DaveG.ca] | | `-- Extracting libXdmcp-1.1.5: ...... done [pkg.DaveG.ca] | | `-- Extracting libxcb-1.17.0: .......... done [pkg.DaveG.ca] | `-- Extracting libX11-1.8.12,1: .......... done [pkg.DaveG.ca] | `-- Installing libXext-1.3.6,1... [pkg.DaveG.ca] | `-- Extracting libXext-1.3.6,1: .......... done [pkg.DaveG.ca] | `-- Installing libXi-1.8.2,1... [pkg.DaveG.ca] | | `-- Installing libXfixes-6.0.1... [pkg.DaveG.ca] | | `-- Extracting libXfixes-6.0.1: ....... done [pkg.DaveG.ca] | `-- Extracting libXi-1.8.2,1: .......... done [pkg.DaveG.ca] | `-- Installing libXrender-0.9.12... [pkg.DaveG.ca] | `-- Extracting libXrender-0.9.12: ....... done [pkg.DaveG.ca] | `-- Installing libXt-1.3.0,1... [pkg.DaveG.ca] | | `-- Installing libICE-1.1.2,1... [pkg.DaveG.ca] | | `-- Extracting libICE-1.1.2,1: .......... done [pkg.DaveG.ca] | | `-- Installing libSM-1.2.6,1... [pkg.DaveG.ca] | | `-- Extracting libSM-1.2.6,1: ........ done [pkg.DaveG.ca] | `-- Extracting libXt-1.3.0,1: .......... done [pkg.DaveG.ca] | `-- Installing libXtst-1.2.5... [pkg.DaveG.ca] | `-- Extracting libXtst-1.2.5: .......... done [pkg.DaveG.ca] | `-- Installing libinotify-20240724_3... [pkg.DaveG.ca] | `-- Extracting libinotify-20240724_3: .......... done [pkg.DaveG.ca] `-- Extracting openjdk8-8.472.08.1: .......... done [pkg.DaveG.ca] Extracting gradle761-7.6.1: .......... done ==> Running trigger: fontconfig.ucl Running fc-cache to build fontconfig cache... ===== Message from freetype2-2.14.1: -- 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/index.html, if documentation was installed). ===== Message from dejavu-2.37_3: -- 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-20240724_3: -- 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 openjdk8-8.472.08.1: -- This OpenJDK implementation may require procfs(5) mounted on /proc for some applications. If you have not done it yet, please do the following: mount -t procfs proc /proc To make it permanent, you need the following lines in /etc/fstab: proc /proc procfs rw 0 0 ===== Message from gradle761-7.6.1: -- ===> NOTICE: The gradle761 port currently does not have a maintainer. As a result, it is more likely to have unresolved issues, not be up-to-date, or even be removed in the future. To volunteer to maintain this port, please create an issue at: https://bugs.freebsd.org/bugzilla More information about port maintainership is available at: https://docs.freebsd.org/en/articles/contributing/#ports-contributing ===> jalview-2.11.2.5 depends on executable: gradle761 - 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/openjdk11-11.0.29+7.1.pkg [pkg.DaveG.ca] Installing openjdk11-11.0.29+7.1... [pkg.DaveG.ca] `-- Installing jpeg-turbo-3.1.2... [pkg.DaveG.ca] `-- Extracting jpeg-turbo-3.1.2: .......... done [pkg.DaveG.ca] `-- Installing lcms2-2.17... [pkg.DaveG.ca] | `-- Installing tiff-4.7.1... [pkg.DaveG.ca] | | `-- Installing jbigkit-2.1_3... [pkg.DaveG.ca] | | `-- Extracting jbigkit-2.1_3: .......... done [pkg.DaveG.ca] | | `-- Installing lerc-4.0.0... [pkg.DaveG.ca] | | `-- Extracting lerc-4.0.0: ..... done [pkg.DaveG.ca] | | `-- Installing libdeflate-1.24... [pkg.DaveG.ca] | | `-- Extracting libdeflate-1.24: .......... done [pkg.DaveG.ca] | | `-- Installing zstd-1.5.7... [pkg.DaveG.ca] | | `-- Installing liblz4-1.10.0_2,1... [pkg.DaveG.ca] | | `-- Extracting liblz4-1.10.0_2,1: .......... done [pkg.DaveG.ca] | | `-- Extracting zstd-1.5.7: .......... done [pkg.DaveG.ca] | `-- Extracting tiff-4.7.1: .......... done [pkg.DaveG.ca] `-- Extracting lcms2-2.17: .......... done [pkg.DaveG.ca] `-- Installing libXrandr-1.5.4... [pkg.DaveG.ca] `-- Extracting libXrandr-1.5.4: .......... done [pkg.DaveG.ca] `-- Installing xorg-fonts-truetype-7.7_1... [pkg.DaveG.ca] | `-- Installing encodings-1.1.0,1... [pkg.DaveG.ca] | `-- Extracting encodings-1.1.0,1: .......... done [pkg.DaveG.ca] | `-- Installing font-bh-ttf-1.0.3_5... [pkg.DaveG.ca] | `-- Extracting font-bh-ttf-1.0.3_5: .......... done [pkg.DaveG.ca] | `-- Installing font-misc-ethiopic-1.0.4... [pkg.DaveG.ca] | `-- Extracting font-misc-ethiopic-1.0.4: ... done [pkg.DaveG.ca] | `-- Installing font-misc-meltho-1.0.3_5... [pkg.DaveG.ca] | `-- Extracting font-misc-meltho-1.0.3_5: .......... done [pkg.DaveG.ca] Extracting openjdk11-11.0.29+7.1: .......... done ==> Running trigger: fontconfig.ucl Running fc-cache to build fontconfig cache... ===== Message from openjdk11-11.0.29+7.1: -- This OpenJDK implementation may require procfs(5) mounted on /proc for some applications. If you have not done it yet, please do the following: mount -t procfs proc /proc To make it permanent, you need the following lines in /etc/fstab: 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 ===> jalview-2.11.2.5 depends on file: /usr/local/bin/ccache - not found ===> Installing existing package /packages/All/ccache-3.7.12_8.pkg [pkg.DaveG.ca] Installing ccache-3.7.12_8... [pkg.DaveG.ca] Extracting ccache-3.7.12_8: ......... 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-3.7.12_8: -- NOTE: Please read /usr/local/share/doc/ccache/ccache-howto-freebsd.txt for information on using ccache with FreeBSD ports and src. ===> jalview-2.11.2.5 depends on file: /usr/local/bin/ccache - found ===> Returning to build of jalview-2.11.2.5 =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Configuring for jalview-2.11.2.5 =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Building for jalview-2.11.2.5 Welcome to Gradle 7.6.1! 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/7.6.1/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/7.6.1/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/7.6.1/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/7.6.1/userguide/validation_problems.html#implicit_dependency for more details about this problem. > Task :prepare > Task :compileJava Setting target compatibility to 11 Note: Some input files use or override a deprecated API. Note: Recompile with -Xlint:deprecation for details. Note: Some input files use unchecked or unsafe operations. Note: Recompile with -Xlint:unchecked for details. > Task :processResources Execution optimizations have been disabled for task ':processResources' 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 ':processResources' 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/7.6.1/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/resources_build'. Reason: Task ':processResources' uses this output of task ':copyResources' 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/7.6.1/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/resources_build'. Reason: Task ':processResources' uses this output of task ':createBuildProperties' 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/7.6.1/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/doc_build'. Reason: Task ':processResources' uses this output of task ':copyDocs' 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/7.6.1/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'. Reason: Task ':processResources' uses this output of task ':copyHelp' 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/7.6.1/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'. Reason: Task ':processResources' 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/7.6.1/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'. Reason: Task ':processResources' uses this output of task ':buildIndices' 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/7.6.1/userguide/validation_problems.html#implicit_dependency for more details about this problem. > Task :classes > Task :cleanPackageDir UP-TO-DATE > Task :compileLinkCheck Execution optimizations have been disabled for task ':compileLinkCheck' to ensure correctness due to the following reasons: - Gradle detected a problem with the following location: '/wrkdirs/usr/ports/biology/jalview/work/jalview/utils'. Reason: Task ':copyChannelResources' uses this output of task ':compileLinkCheck' 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/7.6.1/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/utils'. Reason: Task ':convertMdFiles' uses this output of task ':compileLinkCheck' 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/7.6.1/userguide/validation_problems.html#implicit_dependency for more details about this problem. > Task :linkCheck Checking help file links Results: 147 distinct help targets 147 help mappings 0 invalid targets 26 unused targets uniprotfetcher: html/features/uniprotsequencefetcher.html overviewprefs: html/features/preferences.html#overview cdnafeatures: html/features/codingfeatures.html ensemblfetch: html/features/ensemblsequencefetcher.html io.modellerpir: html/io/modellerpir.html pdbmcviewer: html/features/pdbviewer.html groovy.colours: html/features/groovy.html#groovyColours seqmappings: html/features/seqmappings.html uniprotfts: html/features/uniprotsequencefetcher.html#uniprotfts splitframe.mirrorfonts: html/features/splitView.html#mirror subtMatrices.pam250: html/calculations/scorematrices.html#pam250 search: html/features/search.html viewingpdbs.reps: html/features/viewingpdbs.html#viewreps alformats: html/io/fileformats.html strucprefs: html/features/preferences.html#structure siftsmapping: html/features/siftsmapping.html chimera.annotxfer: html/features/chimera.html#annotxfer pdbfts: html/features/pdbsequencefetcher.html#pdbfts newkeys: html/features/newkeystrokes.html importvcf.attribs: html/features/importvcf.html#attribs seqfeatures.settings.selcols: html/features/featuresettings.html#selectbyfeature jalarchive: html/features/jalarchive.html newsreader: html/webServices/newsreader.html popMenuAddref: html/menus/popupMenu.html#addrefannot splitframe.virtualfeats: html/features/splitView.html#virtualfeats overview: html/features/overview.html 0 invalid map urls 0 invalid image attributes 403 internal href links (79 with anchors) 0 invalid internal href links 0 invalid internal anchor links 105 external href links External links not verified as internet not available *** Success *** > Task :jar > Task :syncJars > Task :makeDist > Task :shadowJar 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/7.6.1/userguide/command_line_interface.html#sec:command_line_warnings Execution optimizations have been disabled for 4 invalid unit(s) of work during this build to ensure correctness. Please consult deprecation warnings for more details. BUILD SUCCESSFUL in 3m 58s 16 actionable tasks: 15 executed, 1 up-to-date =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 ===> jalview-2.11.2.5 depends on file: /usr/local/openjdk11/bin/java - found =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Staging for jalview-2.11.2.5 ===> Generating temporary packing list install -m 555 /wrkdirs/usr/ports/biology/jalview/work/jalview.sh /wrkdirs/usr/ports/biology/jalview/work/stage/usr/local/bin/jalview install -m 0644 /wrkdirs/usr/ports/biology/jalview/work/jalview/build/libs/jalview-all-TEST-j11.jar /wrkdirs/usr/ports/biology/jalview/work/stage/usr/local/share/java/jalview/jalview.jar ====> Compressing man pages (compress-man) =========================================================================== =================================================== ===== env: 'PKG_NOTES=build_timestamp ports_top_git_hash ports_top_checkout_unclean port_git_hash port_checkout_unclean built_by' 'PKG_NOTE_build_timestamp=2025-11-10T20:32:14+0000' 'PKG_NOTE_ports_top_git_hash=ec159283c191' 'PKG_NOTE_ports_top_checkout_unclean=no' 'PKG_NOTE_port_git_hash=0835676e361b' 'PKG_NOTE_port_checkout_unclean=no' 'PKG_NOTE_built_by=poudriere-git-3.4.2' NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Building packages for jalview-2.11.2.5 ===> Building jalview-2.11.2.5 =========================================================================== =>> Cleaning up wrkdir ===> Cleaning for jalview-2.11.2.5 build of biology/jalview | jalview-2.11.2.5 ended at Mon Nov 10 15:38:04 EST 2025 build time: 00:05:51