From nobody Thu Feb 06 00:50:09 2025 X-Original-To: pkg-fallout@mlmmj.nyi.freebsd.org Received: from mx1.freebsd.org (mx1.freebsd.org [IPv6:2610:1c1:1:606c::19:1]) by mlmmj.nyi.freebsd.org (Postfix) with ESMTP id 4YpJRQ1xv5z5mj5V for ; Thu, 06 Feb 2025 00:50:10 +0000 (UTC) (envelope-from pkg-fallout@FreeBSD.org) Received: from mxrelay.nyi.freebsd.org (mxrelay.nyi.freebsd.org [IPv6:2610:1c1:1:606c::19:3]) (using TLSv1.3 with cipher TLS_AES_256_GCM_SHA384 (256/256 bits) key-exchange X25519 server-signature RSA-PSS (4096 bits) server-digest SHA256 client-signature RSA-PSS (4096 bits) client-digest SHA256) (Client CN "mxrelay.nyi.freebsd.org", Issuer "R11" (verified OK)) by mx1.freebsd.org (Postfix) with ESMTPS id 4YpJRQ0Csgz3F4k for ; Thu, 06 Feb 2025 00:50:10 +0000 (UTC) (envelope-from pkg-fallout@FreeBSD.org) ARC-Message-Signature: i=1; a=rsa-sha256; c=relaxed/relaxed; d=freebsd.org; s=dkim; t=1738803010; h=from:from:reply-to:subject:subject:date:date:message-id:message-id: to:to:cc:cc; bh=fLbrlsIUNPqPnysfvXXk553oDQK0efZjhZh/SlwrgZU=; b=EGHJde9rZ6f6CVmIjgksHaTtqnUoxE1pF0SZdwb3hH4TQlElWDP1jgxWKPPDj8KQu+oCHg I10dtChurOTLUk2CCEHazTV/vPGWlIYQDLPgf9wRi8fWx+M8n7GUh7RhtmxMCHgvNqc/BX G1UWFEoWXOPjz0KpQt44bvZw2gTeqK5and3eekKa2R3ZTZHc79KcRftWtbKAauElkTzRGx iQDU5hEu7Tapl7S9N8xo8hjrL/X6bjHqdtJtpcUHSXX6ABjD8ZP58d8QPuj2/BtPXzQyZe W8ukdn3wNZPCGYyWzh0S7PxmmrFjdhyQCwxuq8oPaGssb43mve3pnvnqRQMmDA== ARC-Seal: i=1; s=dkim; d=freebsd.org; t=1738803010; a=rsa-sha256; cv=none; b=iEPWtIJS6anmBmHgPPZUyp8TnBARXxUwbvmRdZ6spudjFH1NAa+XRKemvP1sEqddi5Rht8 vdsPh+HPD2KjZI7iQdhLIrwfhEUjjO3hE4ho3s6suuUBSHpztGu2u/5jZNv9qFsRTaKvMx Uwm+X01O0q5vtr3i2dn8or30H84xhIH0DqdvD8LLWPAnHTwYOtC6SAz316EmUBUzkUwGhZ hewTZfJUCzCcnfI13e98vseCgyKAkzpBWaBwUNRSXGNRxfsF1C4ctySPDUKwgtvQp2Ut/0 gN7OcwhmZS2IfUmm9hgGCaxTr4sPoRlJp22sQmnJl7lS+CHjgj/ljJMNi6qVvg== ARC-Authentication-Results: i=1; mx1.freebsd.org; none Received: from beefy18.nyi.freebsd.org (beefy18.nyi.freebsd.org [IPv6:2610:1c1:1:6080::16:21]) by mxrelay.nyi.freebsd.org (Postfix) with ESMTP id 4YpJRP6v51z132 for ; Thu, 06 Feb 2025 00:50:09 +0000 (UTC) (envelope-from pkg-fallout@FreeBSD.org) Received: from root (uid 0) (envelope-from pkg-fallout@FreeBSD.org) id 7537 by beefy18.nyi.freebsd.org (DragonFly Mail Agent v0.13+ on beefy18.nyi.freebsd.org); Thu, 06 Feb 2025 00:50:09 +0000 To: yuri@FreeBSD.org Subject: [package - main-amd64-default][biology/gatk] Failed for gatk-4.6.1.0_1 in build Cc: pkg-fallout@FreeBSD.org Date: Thu, 06 Feb 2025 00:50:09 +0000 Message-Id: <67a40741.7537.316aa86c@beefy18.nyi.freebsd.org> From: List-Id: Fallout logs from package building List-Archive: https://lists.freebsd.org/archives/freebsd-pkg-fallout List-Help: List-Post: List-Subscribe: List-Unsubscribe: Sender: owner-freebsd-pkg-fallout@FreeBSD.org You are receiving this mail as a port that you maintain is failing to build on the FreeBSD package build server. Please investigate the failure and submit a PR to fix build. Maintainer: yuri@FreeBSD.org Log URL: https://pkg-status.freebsd.org/beefy18/data/main-amd64-default/p5beddb013d54_s078e8b34b13/logs/gatk-4.6.1.0_1.log Build URL: https://pkg-status.freebsd.org/beefy18/build.html?mastername=main-amd64-default&build=p5beddb013d54_s078e8b34b13 Log: =>> Building biology/gatk build started at Thu Feb 6 00:48:10 UTC 2025 port directory: /usr/ports/biology/gatk package name: gatk-4.6.1.0_1 building for: FreeBSD main-amd64-default-job-12 15.0-CURRENT FreeBSD 15.0-CURRENT 1500031 amd64 maintained by: yuri@FreeBSD.org Makefile datestamp: -rw-r--r-- 1 root wheel 5047 Jan 2 01:01 /usr/ports/biology/gatk/Makefile Ports top last git commit: 5beddb013d5 Ports top unclean checkout: no Port dir last git commit: 0835676e361 Port dir unclean checkout: no Poudriere version: poudriere-git-3.4.2 Host OSVERSION: 1500028 Jail OSVERSION: 1500031 Job Id: 12 !!! Jail is newer than host. (Jail: 1500031, Host: 1500028) !!! !!! This is not supported. !!! !!! Host kernel must be same or newer than jail. !!! !!! Expect build failures. !!! ---Begin Environment--- SHELL=/bin/sh OSVERSION=1500031 UNAME_v=FreeBSD 15.0-CURRENT 1500031 UNAME_r=15.0-CURRENT 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/main-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/main-amd64-default/12/.p OUTPUT_REDIRECTED_STDOUT=3 P_PORTS_FEATURES=FLAVORS SUBPACKAGES SELECTED_OPTIONS MASTERNAME=main-amd64-default SCRIPTPREFIX=/usr/local/share/poudriere SCRIPTNAME=bulk.sh OLDPWD=/usr/local/poudriere/data/.m/main-amd64-default/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--- ===> The following configuration options are available for gatk-4.6.1.0_1: WITH_LARGE_FILES=on: Download large LFS files needed for build and tests ===> Use 'make config' to modify these settings ---End OPTIONS List--- --MAINTAINER-- yuri@FreeBSD.org --End MAINTAINER-- --CONFIGURE_ARGS-- --End CONFIGURE_ARGS-- --CONFIGURE_ENV-- PYTHON="/usr/local/bin/python3.11" XDG_DATA_HOME=/wrkdirs/usr/ports/biology/gatk/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/gatk/work XDG_CACHE_HOME=/wrkdirs/usr/ports/biology/gatk/work/.cache HOME=/wrkdirs/usr/ports/biology/gatk/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/gatk/work/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin PKG_CONFIG_LIBDIR=/wrkdirs/usr/ports/biology/gatk/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/gatk/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/gatk/work XDG_CACHE_HOME=/wrkdirs/usr/ports/biology/gatk/work/.cache HOME=/wrkdirs/usr/ports/biology/gatk/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/gatk/work/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin PKG_CONFIG_LIBDIR=/wrkdirs/usr/ports/biology/gatk/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" --End MAKE_ENV-- --PLIST_SUB-- JAVASHAREDIR="share/java" JAVAJARDIR="share/java/classes" PYTHON_INCLUDEDIR=include/python3.11 PYTHON_LIBDIR=lib/python3.11 PYTHON_PLATFORM=freebsd15 PYTHON_SITELIBDIR=lib/python3.11/site-packages PYTHON_SUFFIX=311 PYTHON_EXT_SUFFIX=.cpython-311 PYTHON_VER=3.11 PYTHON_VERSION=python3.11 PYTHON2="@comment " PYTHON3="" OSREL=15.0 PREFIX=%D LOCALBASE=/usr/local RESETPREFIX=/usr/local LIB32DIR=lib DOCSDIR="share/doc/gatk" EXAMPLESDIR="share/examples/gatk" DATADIR="share/gatk" WWWDIR="www/gatk" ETCDIR="etc/gatk" --End PLIST_SUB-- --SUB_LIST-- PORTVERSION=4.6.1.0 JAVA=/usr/local/openjdk17/bin/java JAVASHAREDIR="/usr/local/share/java" JAVAJARDIR="/usr/local/share/java/classes" JAVALIBDIR="/usr/local/share/java/classes" JAVA_VERSION="17" PYTHON_INCLUDEDIR=/usr/local/include/python3.11 PYTHON_LIBDIR=/usr/local/lib/python3.11 PYTHON_PLATFORM=freebsd15 PYTHON_SITELIBDIR=/usr/local/lib/python3.11/site-packages PYTHON_SUFFIX=311 PYTHON_EXT_SUFFIX=.cpython-311 PYTHON_VER=3.11 PYTHON_VERSION=python3.11 PYTHON2="@comment " PYTHON3="" PREFIX=/usr/local LOCALBASE=/usr/local DATADIR=/usr/local/share/gatk DOCSDIR=/usr/local/share/doc/gatk EXAMPLESDIR=/usr/local/share/examples/gatk WWWDIR=/usr/local/www/gatk ETCDIR=/usr/local/etc/gatk --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) 2048 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 ===> License BSD3CLAUSE accepted by the user =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 ===> gatk-4.6.1.0_1 depends on file: /usr/local/sbin/pkg - not found ===> Installing existing package /packages/All/pkg-2.0.5.pkg [main-amd64-default-job-12] Installing pkg-2.0.5... [main-amd64-default-job-12] Extracting pkg-2.0.5: .......... done ===> gatk-4.6.1.0_1 depends on file: /usr/local/sbin/pkg - found ===> Returning to build of gatk-4.6.1.0_1 =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 ===> gatk-4.6.1.0_1 depends on executable: git - not found ===> Installing existing package /packages/All/git-2.48.1.pkg [main-amd64-default-job-12] Installing git-2.48.1... [main-amd64-default-job-12] `-- Installing curl-8.11.1_1... [main-amd64-default-job-12] | `-- Installing brotli-1.1.0,1... [main-amd64-default-job-12] | `-- Extracting brotli-1.1.0,1: .......... done [main-amd64-default-job-12] | `-- Installing libidn2-2.3.7... [main-amd64-default-job-12] | | `-- Installing indexinfo-0.3.1... [main-amd64-default-job-12] | | `-- Extracting indexinfo-0.3.1: .... done [main-amd64-default-job-12] | | `-- Installing libunistring-1.3... [main-amd64-default-job-12] | | `-- Extracting libunistring-1.3: .......... done [main-amd64-default-job-12] | `-- Extracting libidn2-2.3.7: .......... done [main-amd64-default-job-12] | `-- Installing libnghttp2-1.64.0... [main-amd64-default-job-12] | `-- Extracting libnghttp2-1.64.0: .......... done [main-amd64-default-job-12] | `-- Installing libpsl-0.21.5_1... [main-amd64-default-job-12] | `-- Extracting libpsl-0.21.5_1: .......... done [main-amd64-default-job-12] | `-- Installing libssh2-1.11.1,3... [main-amd64-default-job-12] | `-- Extracting libssh2-1.11.1,3: .......... done [main-amd64-default-job-12] | `-- Installing zstd-1.5.6... [main-amd64-default-job-12] | | `-- Installing liblz4-1.10.0,1... [main-amd64-default-job-12] | | `-- Extracting liblz4-1.10.0,1: .......... done [main-amd64-default-job-12] | `-- Extracting zstd-1.5.6: .......... done [main-amd64-default-job-12] `-- Extracting curl-8.11.1_1: .......... done [main-amd64-default-job-12] `-- Installing expat-2.6.4... [main-amd64-default-job-12] `-- Extracting expat-2.6.4: .......... done [main-amd64-default-job-12] `-- Installing gettext-runtime-0.23.1... [main-amd64-default-job-12] `-- Extracting gettext-runtime-0.23.1: .......... done [main-amd64-default-job-12] `-- Installing p5-Authen-SASL-2.17_1... [main-amd64-default-job-12] | `-- Installing p5-Digest-HMAC-1.05... [main-amd64-default-job-12] | | `-- Installing perl5-5.36.3_2... [main-amd64-default-job-12] | | `-- Extracting perl5-5.36.3_2: .......... done [main-amd64-default-job-12] | `-- Extracting p5-Digest-HMAC-1.05: .......... done [main-amd64-default-job-12] `-- Extracting p5-Authen-SASL-2.17_1: .......... done [main-amd64-default-job-12] `-- Installing p5-CGI-4.67... [main-amd64-default-job-12] | `-- Installing p5-HTML-Parser-3.83... [main-amd64-default-job-12] | | `-- Installing p5-HTML-Tagset-3.24... [main-amd64-default-job-12] | | `-- Extracting p5-HTML-Tagset-3.24: ....... done -- 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: -- 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 openjdk8-8.432.06.1: -- This OpenJDK implementation may require fdescfs(5) mounted on /dev/fd and procfs(5) mounted on /proc for some applications. 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 gradle-8.12.1: -- ===> NOTICE: The gradle 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 ===> gatk-4.6.1.0_1 depends on executable: gradle - found ===> Returning to build of gatk-4.6.1.0_1 ===> gatk-4.6.1.0_1 depends on package: gettext-runtime>=0.22_1 - found ===> gatk-4.6.1.0_1 depends on file: /usr/local/openjdk17/bin/java - not found ===> Installing existing package /packages/All/openjdk17-17.0.13+11.1.pkg [main-amd64-default-job-12] Installing openjdk17-17.0.13+11.1... [main-amd64-default-job-12] `-- Installing harfbuzz-10.2.0... [main-amd64-default-job-12] | `-- Installing glib-2.80.5_1,2... [main-amd64-default-job-12] | | `-- Installing libiconv-1.17_1... [main-amd64-default-job-12] | | `-- Extracting libiconv-1.17_1: .......... done [main-amd64-default-job-12] | | `-- Installing py311-packaging-24.2... [main-amd64-default-job-12] | | `-- Extracting py311-packaging-24.2: .......... done [main-amd64-default-job-12] | `-- Extracting glib-2.80.5_1,2: .......... done [main-amd64-default-job-12] | `-- Installing graphite2-1.3.14... [main-amd64-default-job-12] | `-- Extracting graphite2-1.3.14: .......... done [main-amd64-default-job-12] `-- Extracting harfbuzz-10.2.0: .......... done [main-amd64-default-job-12] `-- Installing jpeg-turbo-3.1.0... [main-amd64-default-job-12] `-- Extracting jpeg-turbo-3.1.0: .......... done [main-amd64-default-job-12] `-- Installing lcms2-2.16_2... [main-amd64-default-job-12] | `-- Installing tiff-4.7.0... [main-amd64-default-job-12] | | `-- Installing jbigkit-2.1_3... [main-amd64-default-job-12] | | `-- Extracting jbigkit-2.1_3: .......... done [main-amd64-default-job-12] | | `-- Installing lerc-4.0.0... [main-amd64-default-job-12] | | `-- Extracting lerc-4.0.0: ........ done [main-amd64-default-job-12] | | `-- Installing libdeflate-1.22... [main-amd64-default-job-12] | | `-- Extracting libdeflate-1.22: .......... done [main-amd64-default-job-12] | `-- Extracting tiff-4.7.0: .......... done [main-amd64-default-job-12] `-- Extracting lcms2-2.16_2: .......... done [main-amd64-default-job-12] `-- Installing libXrandr-1.5.4... [main-amd64-default-job-12] `-- Extracting libXrandr-1.5.4: .......... done [main-amd64-default-job-12] `-- Installing xorg-fonts-truetype-7.7_1... [main-amd64-default-job-12] | `-- Installing encodings-1.1.0,1... [main-amd64-default-job-12] | `-- Extracting encodings-1.1.0,1: .......... done [main-amd64-default-job-12] | `-- Installing font-bh-ttf-1.0.3_5... [main-amd64-default-job-12] | `-- Extracting font-bh-ttf-1.0.3_5: .......... done [main-amd64-default-job-12] | `-- Installing font-misc-ethiopic-1.0.4... [main-amd64-default-job-12] | `-- Extracting font-misc-ethiopic-1.0.4: ...... done [main-amd64-default-job-12] | `-- Installing font-misc-meltho-1.0.3_5... [main-amd64-default-job-12] | `-- Extracting font-misc-meltho-1.0.3_5: .......... done [main-amd64-default-job-12] `-- Extracting xorg-fonts-truetype-7.7_1: ... done [main-amd64-default-job-12] Extracting openjdk17-17.0.13+11.1: .......... 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 openjdk17-17.0.13+11.1: -- This OpenJDK implementation may require fdescfs(5) mounted on /dev/fd and procfs(5) mounted on /proc for some applications. 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 ===> gatk-4.6.1.0_1 depends on file: /usr/local/openjdk17/bin/java - found ===> Returning to build of gatk-4.6.1.0_1 =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 ===> gatk-4.6.1.0_1 depends on shared library: libintl.so - found (/usr/local/lib/libintl.so) =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Configuring for gatk-4.6.1.0_1 =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Building for gatk-4.6.1.0_1 Welcome to Gradle 8.12.1! Here are the highlights of this release: - Enhanced error and warning reporting with the Problems API - File-system watching support on Alpine Linux - Build and test Swift 6 libraries and apps For more details see https://docs.gradle.org/8.12.1/release-notes.html Starting a Gradle Daemon (subsequent builds will be faster) FAILURE: Build failed with an exception. * Where: Build file '/wrkdirs/usr/ports/biology/gatk/work/gatk-4.6.1.0/build.gradle' line: 15 * What went wrong: Plugin [id: 'de.undercouch.download', version: '5.6.0'] was not found in any of the following sources: - Gradle Core Plugins (plugin is not in 'org.gradle' namespace) - Included Builds (No included builds contain this plugin) - Plugin Repositories (could not resolve plugin artifact 'de.undercouch.download:de.undercouch.download.gradle.plugin:5.6.0') Searched in the following repositories: Gradle Central Plugin Repository * Try: > Run with --stacktrace option to get the stack trace. > Run with --info or --debug option to get more log output. > Run with --scan to get full insights. > Get more help at https://help.gradle.org. BUILD FAILED in 10s *** Error code 1 Stop. make: stopped making "build" in /usr/ports/biology/gatk