=>> Building biology/jalview build started at Thu Mar 19 03:46:29 EDT 2026 port directory: /usr/ports/biology/jalview package name: jalview-2.11.2.5_1 building for: FreeBSD pkg.DaveG.ca 15.0-RELEASE-p3 FreeBSD 15.0-RELEASE-p3 1500068 amd64 maintained by: yuri@FreeBSD.org Makefile datestamp: -rw-r--r-- 1 root wheel 2032 Mar 6 20:23 /usr/ports/biology/jalview/Makefile Ports top last git commit: 8c988f802ea2 Ports top unclean checkout: no Port dir last git commit: 2baaf1637579 Port dir unclean checkout: no Poudriere version: poudriere-git-3.4.2 Host OSVERSION: 1500068 Jail OSVERSION: 1500068 Job Id: 03 ---Begin Environment--- SHELL=/bin/sh OSVERSION=1500068 UNAME_v=FreeBSD 15.0-RELEASE-p3 1500068 UNAME_r=15.0-RELEASE-p3 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_0_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_0_x64-HEAD-ALL/03/.p OUTPUT_REDIRECTED_STDOUT=3 P_PORTS_FEATURES=FLAVORS SUBPACKAGES SELECTED_OPTIONS MASTERNAME=freebsd_15_0_x64-HEAD-ALL SCRIPTPREFIX=/usr/local/share/poudriere SCRIPTNAME=bulk.sh OLDPWD=/usr/local/poudriere/data/.m/freebsd_15_0_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_1 depends on file: /usr/local/sbin/pkg - not found ===> Installing existing package /packages/All/pkg-2.6.2.pkg [pkg.DaveG.ca] Installing pkg-2.6.2... [pkg.DaveG.ca] Extracting pkg-2.6.2: .......... done ===> jalview-2.11.2.5_1 depends on file: /usr/local/sbin/pkg - found ===> Returning to build of jalview-2.11.2.5_1 =========================================================================== =================================================== ===== 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_1 for building =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Fetching all distfiles required by jalview-2.11.2.5_1 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_1 for building ===> Extracting for jalview-2.11.2.5_1 => 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_1 =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 ===> jalview-2.11.2.5_1 depends on executable: gradle761 - not found ===> Installing existing package /packages/All/gradle761-7.6.1_1.pkg [pkg.DaveG.ca] Installing gradle761-7.6.1_1... [pkg.DaveG.ca] `-- Installing openjdk21-21.0.10+7.1_1... [pkg.DaveG.ca] | `-- Installing alsa-lib-1.2.15.3... [pkg.DaveG.ca] | `-- Extracting alsa-lib-1.2.15.3: .......... done [pkg.DaveG.ca] | `-- Installing fontconfig-2.17.1,1... [pkg.DaveG.ca] | | `-- Installing expat-2.7.4... [pkg.DaveG.ca] | | `-- Extracting expat-2.7.4: .......... done [pkg.DaveG.ca] | | `-- Installing freetype2-2.14.1... [pkg.DaveG.ca] | | `-- Installing brotli-1.2.0,1... [pkg.DaveG.ca] | | `-- Extracting brotli-1.2.0,1: .......... done [pkg.DaveG.ca] | | `-- Installing png-1.6.55... [pkg.DaveG.ca] | | `-- Extracting png-1.6.55: .......... done [pkg.DaveG.ca] | | `-- Extracting freetype2-2.14.1: .......... done [pkg.DaveG.ca] | | `-- Installing gettext-runtime-0.26... [pkg.DaveG.ca] | | `-- Installing indexinfo-0.3.1_1... [pkg.DaveG.ca] | | `-- Extracting indexinfo-0.3.1_1: . done [pkg.DaveG.ca] | | `-- Extracting gettext-runtime-0.26: .......... done [pkg.DaveG.ca] | `-- Extracting fontconfig-2.17.1,1: .......... done [pkg.DaveG.ca] | `-- Installing giflib-5.2.2... [pkg.DaveG.ca] | `-- Extracting giflib-5.2.2: .......... done [pkg.DaveG.ca] | `-- Installing harfbuzz-12.3.2... [pkg.DaveG.ca] | | `-- Installing glib-2.84.4,2... [pkg.DaveG.ca] | | `-- Installing libffi-3.5.1... [pkg.DaveG.ca] | | `-- Extracting libffi-3.5.1: .......... done [pkg.DaveG.ca] | | `-- Installing libiconv-1.18_1... [pkg.DaveG.ca] | | `-- Extracting libiconv-1.18_1: .......... done [pkg.DaveG.ca] | | `-- Installing pcre2-10.47_1... [pkg.DaveG.ca] | | `-- Extracting pcre2-10.47_1: .......... done [pkg.DaveG.ca] | | `-- Installing py311-packaging-26.0... [pkg.DaveG.ca] | | | `-- Installing python311-3.11.15... [pkg.DaveG.ca] | | | `-- Installing mpdecimal-4.0.1... [pkg.DaveG.ca] | | | `-- Extracting mpdecimal-4.0.1: .......... done [pkg.DaveG.ca] | | | `-- Installing readline-8.3.3... [pkg.DaveG.ca] | | | `-- Extracting readline-8.3.3: .......... done [pkg.DaveG.ca] | | | `-- Extracting python311-3.11.15: .......... done [pkg.DaveG.ca] | | `-- Extracting py311-packaging-26.0: .......... done [pkg.DaveG.ca] | | `-- Extracting glib-2.84.4,2: .......... done [pkg.DaveG.ca] | | `-- Installing graphite2-1.3.14... [pkg.DaveG.ca] | | `-- Extracting graphite2-1.3.14: .......... done [pkg.DaveG.ca] | `-- Extracting harfbuzz-12.3.2: .......... done [pkg.DaveG.ca] | `-- Installing javavmwrapper-2.7.10_1... [pkg.DaveG.ca] | `-- Extracting javavmwrapper-2.7.10_1: .......... done [pkg.DaveG.ca] | `-- Installing jpeg-turbo-3.1.3... [pkg.DaveG.ca] | `-- Extracting jpeg-turbo-3.1.3: .......... done [pkg.DaveG.ca] | `-- Installing lcms2-2.18... [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-1.25... [pkg.DaveG.ca] | | `-- Extracting libdeflate-1.25: .......... done [pkg.DaveG.ca] | | `-- Installing zstd-1.5.7_1... [pkg.DaveG.ca] | | `-- Extracting zstd-1.5.7_1: .......... done [pkg.DaveG.ca] | | `-- Extracting tiff-4.7.1: .......... done [pkg.DaveG.ca] | `-- Extracting lcms2-2.18: .......... done [pkg.DaveG.ca] | `-- Installing libX11-1.8.13,1... [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 libX11-1.8.13,1: .......... 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 libXrandr-1.5.4... [pkg.DaveG.ca] | | `-- Installing libXrender-0.9.12... [pkg.DaveG.ca] | | `-- Extracting libXrender-0.9.12: ....... done [pkg.DaveG.ca] | `-- Extracting libXrandr-1.5.4: .......... 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 xorg-fonts-truetype-7.7_1... [pkg.DaveG.ca] | | `-- Installing dejavu-2.37_4... [pkg.DaveG.ca] | | `-- Installing mkfontscale-1.2.3... [pkg.DaveG.ca] | | | `-- Installing libfontenc-1.1.9... [pkg.DaveG.ca] | | | `-- Extracting libfontenc-1.1.9: ...... done [pkg.DaveG.ca] | | `-- Extracting mkfontscale-1.2.3: .... done [pkg.DaveG.ca] | | `-- Extracting dejavu-2.37_4: .......... done [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 openjdk21-21.0.10+7.1_1: .......... done [pkg.DaveG.ca] Extracting gradle761-7.6.1_1: .......... done ==> Running trigger: fontconfig.ucl Running fc-cache to build fontconfig cache... ==> Running trigger: gio-modules.ucl Generating GIO modules cache ==> Running trigger: glib-schemas.ucl Compiling glib schemas No schema files found: doing nothing. ===== 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 python311-3.11.15: -- Note that some standard Python modules are provided as separate ports as they require additional dependencies. They are available as: py311-gdbm databases/py-gdbm@py311 py311-sqlite3 databases/py-sqlite3@py311 py311-tkinter x11-toolkits/py-tkinter@py311 ===== Message from openjdk21-21.0.10+7.1_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_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_1 depends on executable: gradle761 - found ===> Returning to build of jalview-2.11.2.5_1 ===> jalview-2.11.2.5_1 depends on file: /usr/local/openjdk11/bin/java - not found ===> Installing existing package /packages/All/openjdk11-11.0.30+7.1.pkg [pkg.DaveG.ca] Installing openjdk11-11.0.30+7.1... [pkg.DaveG.ca] Extracting openjdk11-11.0.30+7.1: .......... done ===== Message from openjdk11-11.0.30+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_1 depends on file: /usr/local/openjdk11/bin/java - found ===> Returning to build of jalview-2.11.2.5_1 ===> jalview-2.11.2.5_1 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_1 depends on file: /usr/local/bin/ccache - found ===> Returning to build of jalview-2.11.2.5_1 =========================================================================== =================================================== ===== 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_1 =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Building for jalview-2.11.2.5_1 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 2m 32s 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_1 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_1 ===> 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=2026-03-19T07:46:29+0000' 'PKG_NOTE_ports_top_git_hash=8c988f802ea2' 'PKG_NOTE_ports_top_checkout_unclean=no' 'PKG_NOTE_port_git_hash=2baaf1637579' '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_1 ===> Building jalview-2.11.2.5_1 =========================================================================== =>> Cleaning up wrkdir ===> Cleaning for jalview-2.11.2.5_1 build of biology/jalview | jalview-2.11.2.5_1 ended at Thu Mar 19 03:49:38 EDT 2026 build time: 00:03:09