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Maintainer: [email protected] Log URL: https://pkg-status.freebsd.org/beefy23/data/150releng-amd64-default/60cacedb31ba/logs/artemis-17.0.1.11.log Build URL: https://pkg-status.freebsd.org/beefy23/build.html?mastername=150releng-amd64-default&build=60cacedb31ba Log: =>> Building biology/artemis build started at Sat Oct 25 19:32:47 -00 2025 port directory: /usr/ports/biology/artemis package name: artemis-17.0.1.11 building for: FreeBSD 150releng-amd64-default-job-06 15.0-BETA3 FreeBSD 15.0-BETA3 1500068 amd64 maintained by: [email protected] Makefile datestamp: -rw-r--r-- 1 root wheel 1415 Sep 30 01:01 /usr/ports/biology/artemis/Makefile Ports top last git commit: 60cacedb3 Ports top unclean checkout: no Port dir last git commit: b64b73fd9 Port dir unclean checkout: no Poudriere version: poudriere-git-3.4.4 Host OSVERSION: 1600000 Jail OSVERSION: 1500068 Job Id: 06 ---Begin Environment--- SHELL=/bin/sh OSVERSION=1500068 UNAME_v=FreeBSD 15.0-BETA3 1500068 UNAME_r=15.0-BETA3 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=3.4.4 MASTERMNT=/usr/local/poudriere/data/.m/150releng-amd64-default/ref LC_COLLATE=C POUDRIERE_BUILD_TYPE=bulk PACKAGE_BUILDING=yes SAVED_TERM= OUTPUT_REDIRECTED_STDERR=4 OUTPUT_REDIRECTED=1 PWD=/usr/local/poudriere/data/.m/150releng-amd64-default/06/.p OUTPUT_REDIRECTED_STDOUT=3 P_PORTS_FEATURES=FLAVORS SUBPACKAGES SELECTED_OPTIONS MASTERNAME=150releng-amd64-default SCRIPTPREFIX=/usr/local/share/poudriere SCRIPTNAME=bulk.sh OLDPWD=/usr/local/poudriere/data/.m/150releng-amd64-default/ref/.p/pool POUDRIERE_PKGNAME=poudriere-git-3.4.4 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-- [email protected] --End MAINTAINER-- --CONFIGURE_ARGS-- --End CONFIGURE_ARGS-- --CONFIGURE_ENV-- MAKE=/usr/local/bin/gmake XDG_DATA_HOME=/wrkdirs/usr/ports/biology/artemis/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/artemis/work XDG_CACHE_HOME=/wrkdirs/usr/ports/biology/artemis/work/.cache HOME=/wrkdirs/usr/ports/biology/artemis/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/artemis/work/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin PKG_CONFIG_LIBDIR=/wrkdirs/usr/ports/biology/artemis/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/artemis/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/artemis/work XDG_CACHE_HOME=/wrkdirs/usr/ports/biology/artemis/work/.cache HOME=/wrkdirs/usr/ports/biology/artemis/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/artemis/work/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin PKG_CONFIG_LIBDIR=/wrkdirs/usr/ports/biology/artemis/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-- PORTVERSION="17.0.1.11" JAVASHAREDIR="share/java" JAVAJARDIR="share/java/classes" OSREL=15.0 PREFIX=%D LOCALBASE=/usr/local RESETPREFIX=/usr/local LIB32DIR=lib DOCSDIR="share/doc/artemis" EXAMPLESDIR="share/examples/artemis" DATADIR="share/artemis" WWWDIR="www/artemis" ETCDIR="etc/artemis" --End PLIST_SUB-- --SUB_LIST-- 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/artemis DOCSDIR=/usr/local/share/doc/artemis EXAMPLESDIR=/usr/local/share/examples/artemis WWWDIR=/usr/local/www/artemis ETCDIR=/usr/local/etc/artemis --End SUB_LIST-- ---Begin 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 3 jobs MAKE_JOBS_NUMBER=3 USE_PACKAGE_DEPENDS=yes BATCH=yes WRKDIRPREFIX=/wrkdirs PORTSDIR=/usr/ports PACKAGES=/packages DISTDIR=/distfiles PACKAGE_BUILDING=yes PACKAGE_BUILDING_FLAVORS=yes #### #### # 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 3 jobs MAKE_JOBS_NUMBER=3 #### 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-- =======================<phase: check-sanity >============================ ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> License GPLv3 accepted by the user =========================================================================== =======================<phase: pkg-depends >============================ ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 ===> artemis-17.0.1.11 depends on file: /usr/local/sbin/pkg - not found ===> Installing existing package /packages/All/pkg-2.3.1_1.pkg [150releng-amd64-default-job-06] Installing pkg-2.3.1_1... [150releng-amd64-default-job-06] Extracting pkg-2.3.1_1: .......... done ===> artemis-17.0.1.11 depends on file: /usr/local/sbin/pkg - found ===> Returning to build of artemis-17.0.1.11 =========================================================================== =======================<phase: fetch-depends >============================ ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 =========================================================================== =======================<phase: fetch >============================ ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> License GPLv3 accepted by the user ===> Fetching all distfiles required by artemis-17.0.1.11 for building =========================================================================== =======================<phase: checksum >============================ ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> License GPLv3 accepted by the user ===> Fetching all distfiles required by artemis-17.0.1.11 for building => SHA256 Checksum OK for sanger-pathogens-artemis-v17.0.1-11-g3e43d27e_GH0.tar.gz. =========================================================================== =======================<phase: extract-depends>============================ ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 =========================================================================== =======================<phase: extract >============================ ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> License GPLv3 accepted by the user ===> Fetching all distfiles required by artemis-17.0.1.11 for building ===> Extracting for artemis-17.0.1.11 => SHA256 Checksum OK for sanger-pathogens-artemis-v17.0.1-11-g3e43d27e_GH0.tar.gz. =========================================================================== =======================<phase: patch-depends >============================ ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 =========================================================================== =======================<phase: patch >============================ ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Patching for artemis-17.0.1.11 =========================================================================== =======================<phase: build-depends >============================ ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 ===> artemis-17.0.1.11 depends on package: gmake>=4.4.1 - not found ===> Installing existing package /packages/All/gmake-4.4.1.pkg [150releng-amd64-default-job-06] Installing gmake-4.4.1... [150releng-amd64-default-job-06] `-- Installing gettext-runtime-0.23.1... [150releng-amd64-default-job-06] | `-- Installing indexinfo-0.3.1_1... [150releng-amd64-default-job-06] | `-- Extracting indexinfo-0.3.1_1: .... done [150releng-amd64-default-job-06] `-- Extracting gettext-runtime-0.23.1: .......... done [150releng-amd64-default-job-06] Extracting gmake-4.4.1: .......... done ===> artemis-17.0.1.11 depends on package: gmake>=4.4.1 - found ===> Returning to build of artemis-17.0.1.11 ===> artemis-17.0.1.11 depends on file: /usr/local/openjdk8/bin/java - not found ===> Installing existing package /packages/All/openjdk8-8.462.08.1.pkg [150releng-amd64-default-job-06] Installing openjdk8-8.462.08.1... [150releng-amd64-default-job-06] `-- Installing alsa-lib-1.2.14... [150releng-amd64-default-job-06] `-- Extracting alsa-lib-1.2.14: .......... done [150releng-amd64-default-job-06] `-- Installing dejavu-2.37_3... [150releng-amd64-default-job-06] | `-- Installing fontconfig-2.15.0_3,1... [150releng-amd64-default-job-06] | | `-- Installing expat-2.7.3... [150releng-amd64-default-job-06] | | `-- Extracting expat-2.7.3: .......... done [150releng-amd64-default-job-06] | | `-- Installing freetype2-2.14.1... [150releng-amd64-default-job-06] | | `-- Installing brotli-1.1.0,1... [150releng-amd64-default-job-06] | | `-- Extracting brotli-1.1.0,1: .......... done [150releng-amd64-default-job-06] | | `-- Installing png-1.6.50... [150releng-amd64-default-job-06] | | `-- Extracting png-1.6.50: .......... done [150releng-amd64-default-job-06] | | `-- Extracting freetype2-2.14.1: .......... done [150releng-amd64-default-job-06] | `-- Extracting fontconfig-2.15.0_3,1: .......... done [150releng-amd64-default-job-06] | `-- Installing mkfontscale-1.2.3... [150releng-amd64-default-job-06] | | `-- Installing libfontenc-1.1.8... [150releng-amd64-default-job-06] | | `-- Extracting libfontenc-1.1.8: ......... done [150releng-amd64-default-job-06] | `-- Extracting mkfontscale-1.2.3: ....... done [150releng-amd64-default-job-06] `-- Extracting dejavu-2.37_3: .......... done [150releng-amd64-default-job-06] `-- Installing giflib-5.2.2... [150releng-amd64-default-job-06] `-- Extracting giflib-5.2.2: .......... done [150releng-amd64-default-job-06] `-- Installing java-zoneinfo-2021.e... [150releng-amd64-default-job-06] `-- Extracting java-zoneinfo-2021.e: .......... done [150releng-amd64-default-job-06] `-- Installing javavmwrapper-2.7.10... [150releng-amd64-default-job-06] `-- Extracting javavmwrapper-2.7.10: .......... done [150releng-amd64-default-job-06] `-- Installing libX11-1.8.12,1... [150releng-amd64-default-job-06] | `-- Installing libxcb-1.17.0... [150releng-amd64-default-job-06] | | `-- Installing libXau-1.0.12... [150releng-amd64-default-job-06] | | `-- Extracting libXau-1.0.12: .......... done [150releng-amd64-default-job-06] | | `-- Installing libXdmcp-1.1.5... [150releng-amd64-default-job-06] | | `-- Installing xorgproto-2024.1... [150releng-amd64-default-job-06] | | `-- Extracting xorgproto-2024.1: .......... done [150releng-amd64-default-job-06] | | `-- Extracting libXdmcp-1.1.5: ......... done [150releng-amd64-default-job-06] | `-- Extracting libxcb-1.17.0: .......... done [150releng-amd64-default-job-06] `-- Extracting libX11-1.8.12,1: .......... done [150releng-amd64-default-job-06] `-- Installing libXext-1.3.6,1... [150releng-amd64-default-job-06] `-- Extracting libXext-1.3.6,1: .......... done [150releng-amd64-default-job-06] `-- Installing libXi-1.8.2,1... [150releng-amd64-default-job-06] | `-- Installing libXfixes-6.0.1... [150releng-amd64-default-job-06] | `-- Extracting libXfixes-6.0.1: .......... done [150releng-amd64-default-job-06] `-- Extracting libXi-1.8.2,1: .......... done [150releng-amd64-default-job-06] `-- Installing libXrender-0.9.12... [150releng-amd64-default-job-06] `-- Extracting libXrender-0.9.12: .......... done [150releng-amd64-default-job-06] `-- Installing libXt-1.3.0,1... [150releng-amd64-default-job-06] | `-- Installing libICE-1.1.2,1... [150releng-amd64-default-job-06] | `-- Extracting libICE-1.1.2,1: .......... done [150releng-amd64-default-job-06] | `-- Installing libSM-1.2.6,1... [150releng-amd64-default-job-06] | `-- Extracting libSM-1.2.6,1: .......... done [150releng-amd64-default-job-06] `-- Extracting libXt-1.3.0,1: .......... done [150releng-amd64-default-job-06] `-- Installing libXtst-1.2.5... [150releng-amd64-default-job-06] `-- Extracting libXtst-1.2.5: .......... done [150releng-amd64-default-job-06] `-- Installing libinotify-20240724_3... [150releng-amd64-default-job-06] `-- Extracting libinotify-20240724_3: .......... done [150releng-amd64-default-job-06] Extracting openjdk8-8.462.08.1: .......... 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 openjdk8-8.462.08.1: -- 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 ===> artemis-17.0.1.11 depends on file: /usr/local/openjdk8/bin/java - found ===> Returning to build of artemis-17.0.1.11 =========================================================================== =======================<phase: lib-depends >============================ ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 =========================================================================== =======================<phase: configure >============================ ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Configuring for artemis-17.0.1.11 =========================================================================== =======================<phase: build >============================ ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Building for artemis-17.0.1.11 CLASSPATH=lib/commons-lang-2.6.jar:lib/biojava.jar:lib/jemAlign.jar:lib/j2ssh/j2ssh-core.jar:lib/ibatis/ibatis-2.3.4.726.jar:lib/ibatis/log4j-1.2.14.jar:lib/postgresql-8.4-701.jdbc3.jar:lib/picard/picard.jar:lib/commons-net-3.6.jar:lib/batik/batik-awt-util.jar:lib/batik/batik-dom.jar:lib/batik/batik-ext.jar:lib/batik/batik-svggen.jar:lib/batik/batik-util.jar:lib/batik/batik-xml.jar:. javac -source 1.8 -target 1.8 uk/ac/sanger/artemis/Action.java CLASSPATH=lib/commons-lang-2.6.jar:lib/biojava.jar:lib/jemAlign.jar:lib/j2ssh/j2ssh-core.jar:lib/ibatis/ibatis-2.3.4.726.jar:lib/ibatis/log4j-1.2.14.jar:lib/postgresql-8.4-701.jdbc3.jar:lib/picard/picard.jar:lib/commons-net-3.6.jar:lib/batik/batik-awt-util.jar:lib/batik/batik-dom.jar:lib/batik/batik-ext.jar:lib/batik/batik-svggen.jar:lib/batik/batik-util.jar:lib/batik/batik-xml.jar:. javac -source 1.8 -target 1.8 uk/ac/sanger/artemis/ActionController.java CLASSPATH=lib/commons-lang-2.6.jar:lib/biojava.jar:lib/jemAlign.jar:lib/j2ssh/j2ssh-core.jar:lib/ibatis/ibatis-2.3.4.726.jar:lib/ibatis/log4j-1.2.14.jar:lib/postgresql-8.4-701.jdbc3.jar:lib/picard/picard.jar:lib/commons-net-3.6.jar:lib/batik/batik-awt-util.jar:lib/batik/batik-dom.jar:lib/batik/batik-ext.jar:lib/batik/batik-svggen.jar:lib/batik/batik-util.jar:lib/batik/batik-xml.jar:. javac -source 1.8 -target 1.8 uk/ac/sanger/artemis/ActionVector.java ./uk/ac/sanger/artemis/Feature.java:69: error: cannot access MarkerChangeListener MarkerChangeListener, OptionChangeListener ^ bad class file: ./uk/ac/sanger/artemis/sequence/MarkerChangeListener.class class file contains wrong class: uk.ac.sanger.artemis.sequence.SequenceChangeListener Please remove or make sure it appears in the correct subdirectory of the classpath. 1 error gmake: *** [Makefile:47: uk/ac/sanger/artemis/ActionVector.class] Error 1 gmake: *** Waiting for unfinished jobs.... warning: Implicitly compiled files were not subject to annotation processing. Use -proc:none to disable annotation processing or -implicit to specify a policy for implicit compilation. 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. 1 warning ===> Compilation failed unexpectedly. Try to set MAKE_JOBS_UNSAFE=yes and rebuild before reporting the failure to the maintainer. *** Error code 1 Stop. make: stopped making "build" in /usr/ports/biology/artemis
