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Maintainer: [email protected] Log URL: https://pkg-status.freebsd.org/beefy12/data/140amd64-default/43e3af5f5763/logs/igv-2.16.0_1.log Build URL: https://pkg-status.freebsd.org/beefy12/build.html?mastername=140amd64-default&build=43e3af5f5763 Log: =>> Building biology/igv build started at Sun Feb 25 23:52:29 UTC 2024 port directory: /usr/ports/biology/igv package name: igv-2.16.0_1 building for: FreeBSD 140amd64-default-job-05 14.0-RELEASE-p5 FreeBSD 14.0-RELEASE-p5 amd64 maintained by: [email protected] Makefile datestamp: -rw-r--r-- 1 root wheel 2403 Aug 26 2023 /usr/ports/biology/igv/Makefile Ports top last git commit: 43e3af5f57 Ports top unclean checkout: no Port dir last git commit: 157c391cc1 Port dir unclean checkout: no Poudriere version: poudriere-git-3.4.1-1-g1e9f97d6 Host OSVERSION: 1500006 Jail OSVERSION: 1400097 Job Id: 05 ---Begin Environment--- SHELL=/bin/sh OSVERSION=1400097 UNAME_v=FreeBSD 14.0-RELEASE-p5 UNAME_r=14.0-RELEASE-p5 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=3.4.1-1-g1e9f97d6 MASTERMNT=/usr/local/poudriere/data/.m/140amd64-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/140amd64-default/05/.p OUTPUT_REDIRECTED_STDOUT=3 P_PORTS_FEATURES=FLAVORS SUBPACKAGES SELECTED_OPTIONS MASTERNAME=140amd64-default SCRIPTPREFIX=/usr/local/share/poudriere SCRIPTNAME=bulk.sh OLDPWD=/usr/local/poudriere/data/.m/140amd64-default/ref/.p/pool POUDRIERE_PKGNAME=poudriere-git-3.4.1-1-g1e9f97d6 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-- XDG_DATA_HOME=/wrkdirs/usr/ports/biology/igv/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/igv/work XDG_CACHE_HOME=/wrkdirs/usr/ports/biology/igv/work/.cache HOME=/wrkdirs/usr/ports/biology/igv/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/igv/work/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin PKG_CONFIG_LIBDIR=/wrkdirs/usr/ports/biology/igv/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-- GRADLE_USER_HOME=/wrkdirs/usr/ports/biology/igv/work JAVA_HOME=/usr/local/openjdk11 XDG_DATA_HOME=/wrkdirs/usr/ports/biology/igv/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/igv/work XDG_CACHE_HOME=/wrkdirs/usr/ports/biology/igv/work/.cache HOME=/wrkdirs/usr/ports/biology/igv/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/igv/work/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin PKG_CONFIG_LIBDIR=/wrkdirs/usr/ports/biology/igv/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=" -fstack-protector-strong " 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_SCR IPT="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=14.0 PREFIX=%D LOCALBASE=/usr/local RESETPREFIX=/usr/local LIB32DIR=lib DOCSDIR="share/doc/igv" EXAMPLESDIR="share/examples/igv" DATADIR="share/igv" WWWDIR="www/igv" ETCDIR="etc/igv" --End PLIST_SUB-- --SUB_LIST-- JAVA_HOME=/usr/local/openjdk11 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/igv DOCSDIR=/usr/local/share/doc/igv EXAMPLESDIR=/usr/local/share/examples/igv WWWDIR=/usr/local/www/igv ETCDIR=/usr/local/etc/igv --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 #### #### # 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 --End resource limits-- =======================<phase: check-sanity >============================ ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 igv-2.16.0_1: Makefile warning: in desktop entry #1 (igv): category Biology is not a valid desktop category ===> License MIT accepted by the user =========================================================================== =======================<phase: pkg-depends >============================ ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 ===> igv-2.16.0_1 depends on file: /usr/local/sbin/pkg - not found ===> Installing existing package /packages/All/pkg-1.20.9_1.pkg [140amd64-default-job-05] Installing pkg-1.20.9_1... [140amd64-default-job-05] Extracting pkg-1.20.9_1: .......... done ===> igv-2.16.0_1 depends on file: /usr/local/sbin/pkg - found ===> Returning to build of igv-2.16.0_1 =========================================================================== =======================<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 MIT accepted by the user ===> Fetching all distfiles required by igv-2.16.0_1 for building =========================================================================== =======================<phase: checksum >============================ ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 igv-2.16.0_1: Makefile warning: in desktop entry #1 (igv): category Biology is not a valid desktop category igv-2.16.0_1: Makefile warning: in desktop entry #1 (igv): category Science is not a valid desktop category ===> License MIT accepted by the user ===> Fetching all distfiles required by igv-2.16.0_1 for building => SHA256 Checksum OK for igv-2.16.0/tools.png. => SHA256 Checksum OK for igv-2.16.0/igv-2.16.0-deps.tar.gz. => SHA256 Checksum OK for igv-2.16.0/igvteam-igv-v2.16.0_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 MIT accepted by the user ===> Fetching all distfiles required by igv-2.16.0_1 for building ===> Extracting for igv-2.16.0_1 => SHA256 Checksum OK for igv-2.16.0/tools.png. => SHA256 Checksum OK for igv-2.16.0/igv-2.16.0-deps.tar.gz. => SHA256 Checksum OK for igv-2.16.0/igvteam-igv-v2.16.0_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 igv-2.16.0_1 =========================================================================== =======================<phase: build-depends >============================ ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 ===> igv-2.16.0_1 depends on package: openjfx14>0 - not found ===> Installing existing package /packages/All/openjfx14-14.0.2.1+1_15.pkg [140amd64-default-job-05] Installing openjfx14-14.0.2.1+1_15... [140amd64-default-job-05] `-- Installing alsa-lib-1.2.10_1... [140amd64-default-job-05] `-- Extracting alsa-lib-1.2.10_1: .......... done [140amd64-default-job-05] `-- Installing at-spi2-core-2.50.1... [140amd64-default-job-05] | `-- Installing dbus-1.14.10_4,1... [140amd64-default-job-05] | | `-- Installing expat-2.6.0... [140amd64-default-job-05] | | `-- Extracting expat-2.6.0: .......... done [140amd64-default-job-05] | | `-- Installing libICE-1.1.0_2,1... [140amd64-default-job-05] | | `-- Extracting libICE-1.1.0_2,1: .......... done [140amd64-default-job-05] | | `-- Installing libSM-1.2.3_1,1... [140amd64-default-job-05] | | `-- Extracting libSM-1.2.3_1,1: .......... done [140amd64-default-job-05] | | `-- Installing libX11-1.8.7_1,1... [140amd64-default-job-05] | | `-- Installing libxcb-1.15_2... [140amd64-default-job-05] | | | `-- Installing libXau-1.0.9_1... [140amd64-default-job-05] | | | `-- Extracting libXau-1.0.9_1: .......... done [140amd64-default-job-05] | | | `-- Installing libXdmcp-1.1.3... [140amd64-default-job-05] | | | `-- Installing xorgproto-2023.2... [140amd64-default-job-05] | | | `-- Extracting xorgproto-2023.2: .......... done <snip> 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 wayland-1.22.0: -- Wayland requires XDG_RUNTIME_DIR to be defined to a path that will contain "wayland-%d" unix(4) sockets. This is usually handled by consolekit2 (via ck-launch-session) or pam_xdg (via login). ===== 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 duktape-lib-2.7.0: -- ===> NOTICE: The duktape-lib 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 ===== Message from libxkbcommon-1.6.0_2: -- If arrow keys don't work under X11 switch to legacy rules e.g., For sh/bash/ksh/zsh run and (optionally) add into ~/.profile: export XKB_DEFAULT_RULES=xorg For csh/tcsh run and (optionally) add into ~/.login: setenv XKB_DEFAULT_RULES xorg ===== Message from openjdk11-11.0.22+7.1_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 ===== Message from openjfx14-14.0.2.1+1_15: -- ===> NOTICE: The openjfx14 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 ===> igv-2.16.0_1 depends on package: openjfx14>0 - found ===> Returning to build of igv-2.16.0_1 ===> igv-2.16.0_1 depends on executable: gradle - not found ===> Installing existing package /packages/All/gradle6-6.9.4.pkg [140amd64-default-job-05] Installing gradle6-6.9.4... [140amd64-default-job-05] `-- Installing openjdk8-8.402.06.1_1... [140amd64-default-job-05] | `-- Installing java-zoneinfo-2021.e... [140amd64-default-job-05] | `-- Extracting java-zoneinfo-2021.e: .......... done [140amd64-default-job-05] | `-- Installing libinotify-20211018_1... [140amd64-default-job-05] | `-- Extracting libinotify-20211018_1: .......... done [140amd64-default-job-05] `-- Extracting openjdk8-8.402.06.1_1: .......... done [140amd64-default-job-05] Extracting gradle6-6.9.4: .......... done ===== Message from libinotify-20211018_1: -- 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 openjdk8-8.402.06.1_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 ===> igv-2.16.0_1 depends on executable: gradle - found ===> Returning to build of igv-2.16.0_1 ===> igv-2.16.0_1 depends on file: /usr/local/openjdk11/bin/java - found ===> igv-2.16.0_1 depends on package: gettext-runtime>=0.22_1 - found =========================================================================== =======================<phase: lib-depends >============================ ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 ===> igv-2.16.0_1 depends on shared library: libintl.so - found (/usr/local/lib/libintl.so) =========================================================================== =======================<phase: configure >============================ ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Configuring for igv-2.16.0_1 =========================================================================== =======================<phase: build >============================ ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Building for igv-2.16.0_1 cd /wrkdirs/usr/ports/biology/igv/work/igv-2.16.0 && /usr/bin/env GRADLE_USER_HOME=/wrkdirs/usr/ports/biology/igv/work JAVA_HOME=/usr/local/openjdk11 XDG_DATA_HOME=/wrkdirs/usr/ports/biology/igv/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/igv/work XDG_CACHE_HOME=/wrkdirs/usr/ports/biology/igv/work/.cache HOME=/wrkdirs/usr/ports/biology/igv/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/igv/work/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin PKG_CONFIG_LIBDIR=/wrkdirs/usr/ports/biology/igv/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=" -fstack-protector-strong " 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" gradle --gradle-user-home /wrkdirs/usr/ports/biology/igv/work/gradle-igv --project-cache-dir /wrkdirs/usr/ports/biology/igv/work/gradle-igv --offline --build-cache --stacktrace createDist Welcome to Gradle 6.9.4! Here are the highlights of this release: - This is a small backport release. - Java 16 can be used to compile when used with Java toolchains - Dynamic versions can be used within plugin declarations - Native support for Apple Silicon processors For more details see https://docs.gradle.org/6.9.4/release-notes.html Starting a Gradle Daemon (subsequent builds will be faster) > Task :compileJava 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 > Task :classes > Task :jar > Task :createDist Deprecated Gradle features were used in this build, making it incompatible with Gradle 7.0. Use '--warning-mode all' to show the individual deprecation warnings. See https://docs.gradle.org/6.9.4/userguide/command_line_interface.html#sec:command_line_warnings BUILD SUCCESSFUL in 1m 39s 4 actionable tasks: 4 executed =========================================================================== =======================<phase: run-depends >============================ ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 ===> igv-2.16.0_1 depends on package: openjfx14>0 - found ===> igv-2.16.0_1 depends on file: /usr/local/openjdk11/bin/java - found =========================================================================== =======================<phase: stage >============================ ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Staging for igv-2.16.0_1 ===> Generating temporary packing list install -m 555 /wrkdirs/usr/ports/biology/igv/work/igv.sh /wrkdirs/usr/ports/biology/igv/work/stage/usr/local/bin/igv cd /wrkdirs/usr/ports/biology/igv/work/igv-2.16.0/build/IGV-dist/lib && /bin/sh -c '(/usr/bin/find -Ed $1 $3 | /usr/bin/cpio -dumpl $2 >/dev/null 2>&1) && /usr/bin/find -Ed $1 $3 \( -type d -exec /bin/sh -c '\''cd '\''$2'\'' && chmod 755 "$@"'\'' . {} + -o -type f -exec /bin/sh -c '\''cd '\''$2'\'' && chmod 0644 "$@"'\'' . {} + \)' COPYTREE_SHARE ./ /wrkdirs/usr/ports/biology/igv/work/stage/usr/local/share/java/classes/igv install -m 0644 /portdistfiles/igv-2.16.0/tools.png /wrkdirs/usr/ports/biology/igv/work/stage/usr/local/share/pixmaps/igv.png install: /wrkdirs/usr/ports/biology/igv/work/stage/usr/local/share/pixmaps/igv.png: No such file or directory *** Error code 71 Stop. make: stopped in /usr/ports/biology/igv
