From nobody Sat Jun 03 12:38:25 2023 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 4QYKD1523Fz4YdkJ for ; Sat, 3 Jun 2023 12:38:25 +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 "R3" (verified OK)) by mx1.freebsd.org (Postfix) with ESMTPS id 4QYKD11mdtz40Tx; Sat, 3 Jun 2023 12:38:25 +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=1685795905; h=from:from:reply-to:subject:subject:date:date:message-id:message-id: to:to:cc:cc; bh=FmbUEaMX1O+tDSxbiQGoPxk/Bsi5jBr7PbqWnqEa/LY=; b=IqLlVN2SKrsJOYwfWoGthp6l1IWi0Q0BsERrPGW6ZGpVST/Icz0568lf38ZUxZlHxgwLt5 R4mijxLo5CmpEbVRHPg5Yl9Ne7Dm3yxRMcxU3CKunErlJTLv89tDCIfCaLf1mKKQShkXlN oqkncVmtmMT44514K/kybWYpEr9qGnNYT4+/Mu4LMIm+yrSVkfrIVSHVI2/WUP+r6DiNiB 2d5vX59qD0s/SvGdgCOZ6FD0aoTdsoysbQk3cRbudrDcGdsGYsNHq7aUy+THwZ9iln8cv9 nEGngBSdsuD1SLiYzZkWborC1OjUt5syWFI0b5alwmJI6+k0flaOEGEDA7tvrA== ARC-Authentication-Results: i=1; mx1.freebsd.org; none ARC-Seal: i=1; s=dkim; d=freebsd.org; t=1685795905; a=rsa-sha256; cv=none; b=xoRC+4r+FWS8VKUPA3UPURTtNwHq9N3sEeiVRcFGhIjTvlRjvenPkubQfbF/IQ1e/3VqpH GOaXdjBpEYPGpZFvbYAPtBH4ORFitC2sw8nX3Gv0lWzTUaLR1GBV6FCALNZ28Qbu+4vAnK 7yk+dpM9eYi0FQFQRkRpMOopjeO76sqNX7uENFYBXijik+p6eubURgocV77HgPd7hIk4bf bNEskheIzB8orOGd14y05qtEAl++NRyJfPx561zlZF2aI3g2GJItxrVnK/J9Q5PJpC3ogo You7qC/fH5Q08IjCXr87sTtpT4AaLsFH8+tIn50KmuCDurMGzKR5GgGFJbT5Xw== Received: from beefy17.nyi.freebsd.org (beefy17.nyi.freebsd.org [IPv6:2610:1c1:1:6080::16:20]) (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 did not present a certificate) by mxrelay.nyi.freebsd.org (Postfix) with ESMTPS id 4QYKD10rB4zQhT; Sat, 3 Jun 2023 12:38:25 +0000 (UTC) (envelope-from pkg-fallout@FreeBSD.org) Received: from beefy17.nyi.freebsd.org (localhost [127.0.0.1]) by beefy17.nyi.freebsd.org (8.16.1/8.16.1) with ESMTP id 353CcPUU079277; Sat, 3 Jun 2023 12:38:25 GMT (envelope-from pkg-fallout@FreeBSD.org) Received: (from root@localhost) by beefy17.nyi.freebsd.org (8.16.1/8.16.1/Submit) id 353CcPu9079271; Sat, 3 Jun 2023 12:38:25 GMT (envelope-from pkg-fallout@FreeBSD.org) Date: Sat, 3 Jun 2023 12:38:25 GMT From: pkg-fallout@FreeBSD.org Message-Id: <202306031238.353CcPu9079271@beefy17.nyi.freebsd.org> To: yuri@FreeBSD.org Subject: [package - main-i386-default][biology/gatk] Failed for gatk-4.3.0.0 in build Cc: pkg-fallout@FreeBSD.org X-ThisMailContainsUnwantedMimeParts: N 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/beefy17/data/main-i386-default/p7677d0cb38c5_s4f2cc73f34/logs/gatk-4.3.0.0.log Build URL: https://pkg-status.freebsd.org/beefy17/build.html?mastername=main-i386-default&build=p7677d0cb38c5_s4f2cc73f34 Log: =>> Building biology/gatk build started at Sat Jun 3 12:37:57 UTC 2023 port directory: /usr/ports/biology/gatk package name: gatk-4.3.0.0 building for: FreeBSD main-i386-default-job-06 14.0-CURRENT FreeBSD 14.0-CURRENT 1400089 i386 maintained by: yuri@FreeBSD.org Makefile ident: Poudriere version: 3.2.8-23-ga7f8d188 Host OSVERSION: 1400073 Jail OSVERSION: 1400089 Job Id: 06 !!! Jail is newer than host. (Jail: 1400089, Host: 1400073) !!! !!! This is not supported. !!! !!! Host kernel must be same or newer than jail. !!! !!! Expect build failures. !!! ---Begin Environment--- SHELL=/bin/sh UNAME_p=i386 UNAME_m=i386 OSVERSION=1400089 UNAME_v=FreeBSD 14.0-CURRENT 1400089 UNAME_r=14.0-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 LOCALBASE=/usr/local USER=root LIBEXECPREFIX=/usr/local/libexec/poudriere POUDRIERE_VERSION=3.2.8-23-ga7f8d188 MASTERMNT=/usr/local/poudriere/data/.m/main-i386-default/ref POUDRIERE_BUILD_TYPE=bulk PACKAGE_BUILDING=yes SAVED_TERM= PWD=/usr/local/poudriere/data/.m/main-i386-default/ref/.p/pool P_PORTS_FEATURES=FLAVORS SELECTED_OPTIONS MASTERNAME=main-i386-default SCRIPTPREFIX=/usr/local/share/poudriere OLDPWD=/usr/local/poudriere/data/.m/main-i386-default/ref/.p SCRIPTPATH=/usr/local/share/poudriere/bulk.sh POUDRIEREPATH=/usr/local/bin/poudriere ---End Environment--- ---Begin Poudriere Port Flags/Env--- PORT_FLAGS= PKGENV= FLAVOR= DEPENDS_ARGS= MAKE_ARGS= ---End Poudriere Port Flags/Env--- ---Begin OPTIONS List--- ===> The following configuration options are available for gatk-4.3.0.0: WITH_LARGE_FILES=off: 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-- 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 " MANPREFIX="/usr/local" 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=14.0 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=4.3.0.0 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" 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--- USE_PACKAGE_DEPENDS=yes BATCH=yes WRKDIRPREFIX=/wrkdirs PORTSDIR=/usr/ports PACKAGES=/packages DISTDIR=/distfiles PACKAGE_BUILDING=yes PACKAGE_BUILDING_FLAVORS=yes MACHINE=i386 MACHINE_ARCH=i386 ARCH=${MACHINE_ARCH} #### /usr/local/etc/poudriere.d/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 2 jobs MAKE_JOBS_NUMBER=2 #### /usr/ports/Mk/Scripts/ports_env.sh #### _CCVERSION_921dbbb2=FreeBSD clang version 15.0.7 (https://github.com/llvm/llvm-project.git llvmorg-15.0.7-0-g8dfdcc7b7bf6) Target: i386-unknown-freebsd14.0 Thread model: posix InstalledDir: /usr/bin _ALTCCVERSION_921dbbb2=none _CXXINTERNAL_acaad9ca=FreeBSD clang version 15.0.7 (https://github.com/llvm/llvm-project.git llvmorg-15.0.7-0-g8dfdcc7b7bf6) Target: i386-unknown-freebsd14.0 Thread model: posix InstalledDir: /usr/bin "/usr/bin/ld" "--eh-frame-hdr" "-dynamic-linker" "/libexec/ld-elf.so.1" "--hash-style=both" "--enable-new-dtags" "-m" "elf_i386_fbsd" "-o" "a.out" "/usr/lib/crt1.o" "/usr/lib/crti.o" "/usr/lib/crtbegin.o" "-L/usr/lib" "/dev/null" "-lc++" "-lm" "-lgcc" "--as-needed" "-lgcc_s" "--no-as-needed" "-lc" "-lgcc" "--as-needed" "-lgcc_s" "--no-as-needed" "/usr/lib/crtend.o" "/usr/lib/crtn.o" CC_OUTPUT_921dbbb2_58173849=yes CC_OUTPUT_921dbbb2_9bdba57c=yes CC_OUTPUT_921dbbb2_6a4fe7f5=yes CC_OUTPUT_921dbbb2_6bcac02b=yes CC_OUTPUT_921dbbb2_67d20829=yes CC_OUTPUT_921dbbb2_bfa62e83=yes CC_OUTPUT_921dbbb2_f0b4d593=yes CC_OUTPUT_921dbbb2_308abb44=yes CC_OUTPUT_921dbbb2_f00456e5=yes CC_OUTPUT_921dbbb2_65ad290d=yes CC_OUTPUT_921dbbb2_f2776b26=yes CC_OUTPUT_921dbbb2_53255a77=yes CC_OUTPUT_921dbbb2_911cfe02=yes CC_OUTPUT_921dbbb2_b2657cc3=yes CC_OUTPUT_921dbbb2_380987f7=yes CC_OUTPUT_921dbbb2_160933ec=yes CC_OUTPUT_921dbbb2_fb62803b=yes CC_OUTPUT_921dbbb2_af59ad06=yes CC_OUTPUT_921dbbb2_a15f3fcf=yes _OBJC_CCVERSION_921dbbb2=FreeBSD clang version 15.0.7 (https://github.com/llvm/llvm-project.git llvmorg-15.0.7-0-g8dfdcc7b7bf6) Target: i386-unknown-freebsd14.0 Thread model: posix InstalledDir: /usr/bin _OBJC_ALTCCVERSION_921dbbb2=none ARCH=i386 OPSYS=FreeBSD _OSRELEASE=14.0-CURRENT OSREL=14.0 OSVERSION=1400089 PYTHONBASE=/usr/local CONFIGURE_MAX_CMD_LEN=524288 HAVE_PORTS_ENV=1 #### Misc Poudriere #### 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) 524288 stack size (kbytes, -s) 65536 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 --End resource limits-- =================================================== ===> License BSD3CLAUSE accepted by the user =========================================================================== =================================================== ===> gatk-4.3.0.0 depends on file: /usr/local/sbin/pkg - not found ===> Installing existing package /packages/All/pkg-1.19.1_1.pkg [main-i386-default-job-06] Installing pkg-1.19.1_1... [main-i386-default-job-06] Extracting pkg-1.19.1_1: .......... done ===> gatk-4.3.0.0 depends on file: /usr/local/sbin/pkg - found ===> Returning to build of gatk-4.3.0.0 =========================================================================== =================================================== =========================================================================== =================================================== ===> License BSD3CLAUSE accepted by the user ===> Fetching all distfiles required by gatk-4.3.0.0 for building =========================================================================== =================================================== ===> License BSD3CLAUSE accepted by the user ===> Fetching all distfiles required by gatk-4.3.0.0 for building => SHA256 Checksum OK for gatk-4.3.0.0-deps.tar.gz. => SHA256 Checksum OK for broadinstitute-gatk-4.3.0.0_GH0.tar.gz. =========================================================================== =================================================== =========================================================================== =================================================== ===> License BSD3CLAUSE accepted by the user ===> Fetching all distfiles required by gatk-4.3.0.0 for building ===> Extracting for gatk-4.3.0.0 => SHA256 Checksum OK for gatk-4.3.0.0-deps.tar.gz. => SHA256 Checksum OK for broadinstitute-gatk-4.3.0.0_GH0.tar.gz. =========================================================================== =================================================== =========================================================================== 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_1: -- 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-20211018: -- 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 openjdk8-8.372.07.1_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 ===> gatk-4.3.0.0 depends on executable: gradle - found ===> Returning to build of gatk-4.3.0.0 ===> gatk-4.3.0.0 depends on file: /usr/local/openjdk17/bin/java - not found ===> Installing existing package /packages/All/openjdk17-17.0.7+7.1.pkg [main-i386-default-job-06] Installing openjdk17-17.0.7+7.1... [main-i386-default-job-06] `-- Installing harfbuzz-7.3.0... [main-i386-default-job-06] | `-- Installing gettext-runtime-0.21.1... [main-i386-default-job-06] | | `-- Installing indexinfo-0.3.1... [main-i386-default-job-06] | | `-- Extracting indexinfo-0.3.1: .... done [main-i386-default-job-06] | `-- Extracting gettext-runtime-0.21.1: .......... done [main-i386-default-job-06] | `-- Installing glib-2.76.3,2... [main-i386-default-job-06] | | `-- Installing libffi-3.4.4... [main-i386-default-job-06] | | `-- Extracting libffi-3.4.4: .......... done [main-i386-default-job-06] | | `-- Installing libiconv-1.17... [main-i386-default-job-06] | | `-- Extracting libiconv-1.17: .......... done [main-i386-default-job-06] | | `-- Installing libxml2-2.10.4... [main-i386-default-job-06] | | `-- Installing readline-8.2.1... [main-i386-default-job-06] | | `-- Extracting readline-8.2.1: .......... done [main-i386-default-job-06] | | `-- Extracting libxml2-2.10.4: .......... done [main-i386-default-job-06] | | `-- Installing pcre2-10.42... [main-i386-default-job-06] | | `-- Extracting pcre2-10.42: .......... done [main-i386-default-job-06] | | `-- Installing python39-3.9.16_2... [main-i386-default-job-06] | | `-- Installing mpdecimal-2.5.1... [main-i386-default-job-06] | | `-- Extracting mpdecimal-2.5.1: .......... done [main-i386-default-job-06] | | `-- Extracting python39-3.9.16_2: .......... done [main-i386-default-job-06] | `-- Extracting glib-2.76.3,2: .......... done [main-i386-default-job-06] | `-- Installing graphite2-1.3.14... [main-i386-default-job-06] | `-- Extracting graphite2-1.3.14: .......... done [main-i386-default-job-06] `-- Extracting harfbuzz-7.3.0: .......... done [main-i386-default-job-06] `-- Installing jpeg-turbo-2.1.5.1... [main-i386-default-job-06] `-- Extracting jpeg-turbo-2.1.5.1: .......... done [main-i386-default-job-06] `-- Installing lcms2-2.15_1... [main-i386-default-job-06] | `-- Installing tiff-4.4.0_1... [main-i386-default-job-06] | | `-- Installing jbigkit-2.1_1... [main-i386-default-job-06] | | `-- Extracting jbigkit-2.1_1: .......... done [main-i386-default-job-06] | | `-- Installing libdeflate-1.18... [main-i386-default-job-06] | | `-- Extracting libdeflate-1.18: .......... done [main-i386-default-job-06] | | `-- Installing zstd-1.5.5... [main-i386-default-job-06] | | `-- Installing liblz4-1.9.4,1... [main-i386-default-job-06] | | `-- Extracting liblz4-1.9.4,1: .......... done [main-i386-default-job-06] | | `-- Extracting zstd-1.5.5: .......... done [main-i386-default-job-06] | `-- Extracting tiff-4.4.0_1: .......... done [main-i386-default-job-06] `-- Extracting lcms2-2.15_1: .......... done [main-i386-default-job-06] `-- Installing libXrandr-1.5.2... [main-i386-default-job-06] `-- Extracting libXrandr-1.5.2: .......... done [main-i386-default-job-06] `-- Installing xorg-fonts-truetype-7.7_1... [main-i386-default-job-06] | `-- Installing encodings-1.0.5,1... [main-i386-default-job-06] | `-- Extracting encodings-1.0.5,1: .......... done [main-i386-default-job-06] | `-- Installing font-bh-ttf-1.0.3_4... [main-i386-default-job-06] | `-- Extracting font-bh-ttf-1.0.3_4: .......... done [main-i386-default-job-06] | `-- Installing font-misc-ethiopic-1.0.4... [main-i386-default-job-06] | `-- Extracting font-misc-ethiopic-1.0.4: ...... done [main-i386-default-job-06] | `-- Installing font-misc-meltho-1.0.3_4... [main-i386-default-job-06] | `-- Extracting font-misc-meltho-1.0.3_4: .......... done [main-i386-default-job-06] `-- Extracting xorg-fonts-truetype-7.7_1: ... done [main-i386-default-job-06] Extracting openjdk17-17.0.7+7.1: .......... done Running fc-cache to build fontconfig cache... Generating GIO modules cache Compiling glib schemas No schema files found: doing nothing. ===== Message from python39-3.9.16_2: -- Note that some standard Python modules are provided as separate ports as they require additional dependencies. They are available as: py39-gdbm databases/py-gdbm@py39 py39-sqlite3 databases/py-sqlite3@py39 py39-tkinter x11-toolkits/py-tkinter@py39 ===== Message from openjdk17-17.0.7+7.1: -- 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 ===> gatk-4.3.0.0 depends on file: /usr/local/openjdk17/bin/java - found ===> Returning to build of gatk-4.3.0.0 =========================================================================== =================================================== ===> gatk-4.3.0.0 depends on shared library: libintl.so - found (/usr/local/lib/libintl.so) =========================================================================== =================================================== ===> Configuring for gatk-4.3.0.0 =========================================================================== =================================================== ===> Building for gatk-4.3.0.0 Welcome to Gradle 8.0.1! Here are the highlights of this release: - Improvements to the Kotlin DSL - Fine-grained parallelism from the first build with configuration cache - Configurable Gradle user home cache cleanup For more details see https://docs.gradle.org/8.0.1/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-4.3.0.0/build.gradle' line: 15 * What went wrong: Plugin [id: 'de.undercouch.download', version: '4.1.2'] was not found in any of the following sources: - Gradle Core Plugins (plugin is not in 'org.gradle' namespace) - Plugin Repositories (could not resolve plugin artifact 'de.undercouch.download:de.undercouch.download.gradle.plugin:4.1.2') 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 5s *** Error code 1 Stop. make: stopped in /usr/ports/biology/gatk