=>> Building biology/gatk build started at Fri Feb 20 15:22:35 EST 2026 port directory: /usr/ports/biology/gatk package name: gatk-4.6.2.0 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 5132 Aug 28 04:44 /usr/ports/biology/gatk/Makefile Ports top last git commit: eac71dbf758c Ports top unclean checkout: no Port dir last git commit: 803f55e390e8 Port dir unclean checkout: no Poudriere version: poudriere-git-3.4.2 Host OSVERSION: 1500068 Jail OSVERSION: 1500068 Job Id: 01 ---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/01/.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--- ===> The following configuration options are available for gatk-4.6.2.0: 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=" " 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_BASESUFFIX=311 PYTHON_TAG=.cpython-311 PYTHON_SOABI=.cpython-311 PYTHON_VER=3.11 PYTHON_BASEVER=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=4.6.2.0 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_BASESUFFIX=311 PYTHON_TAG=.cpython-311 PYTHON_SOABI=.cpython-311 PYTHON_VER=3.11 PYTHON_BASEVER=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--- 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 ===> gatk-4.6.2.0 depends on file: /usr/local/sbin/pkg - not found ===> Installing existing package /packages/All/pkg-2.5.1.pkg [pkg.DaveG.ca] Installing pkg-2.5.1... [pkg.DaveG.ca] Extracting pkg-2.5.1: .......... done ===> gatk-4.6.2.0 depends on file: /usr/local/sbin/pkg - found ===> Returning to build of gatk-4.6.2.0 =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 ===> gatk-4.6.2.0 depends on executable: git - not found ===> Installing existing package /packages/All/git-2.53.0.pkg [pkg.DaveG.ca] Installing git-2.53.0... [pkg.DaveG.ca] `-- Installing curl-8.17.0... [pkg.DaveG.ca] | `-- Installing brotli-1.2.0,1... [pkg.DaveG.ca] | `-- Extracting brotli-1.2.0,1: .......... done [pkg.DaveG.ca] | `-- Installing libidn2-2.3.8... [pkg.DaveG.ca] | | `-- Installing indexinfo-0.3.1_1... [pkg.DaveG.ca] | | `-- Extracting indexinfo-0.3.1_1: . done [pkg.DaveG.ca] | | `-- Installing libunistring-1.4.1... [pkg.DaveG.ca] | | `-- Extracting libunistring-1.4.1: .......... done [pkg.DaveG.ca] | `-- Extracting libidn2-2.3.8: .......... done [pkg.DaveG.ca] | `-- Installing libnghttp2-1.68.0... [pkg.DaveG.ca] | `-- Extracting libnghttp2-1.68.0: ....... done [pkg.DaveG.ca] | `-- Installing libpsl-0.21.5_2... [pkg.DaveG.ca] | `-- Extracting libpsl-0.21.5_2: ........ done [pkg.DaveG.ca] | `-- Installing libssh2-1.11.1,3... [pkg.DaveG.ca] | `-- Extracting libssh2-1.11.1,3: .......... done [pkg.DaveG.ca] | `-- Installing zstd-1.5.7_1... [pkg.DaveG.ca] | `-- Extracting zstd-1.5.7_1: .......... done [pkg.DaveG.ca] `-- Extracting curl-8.17.0: .......... done [pkg.DaveG.ca] `-- Installing expat-2.7.4... [pkg.DaveG.ca] `-- Extracting expat-2.7.4: .......... done [pkg.DaveG.ca] `-- Installing gettext-runtime-0.26... [pkg.DaveG.ca] `-- Extracting gettext-runtime-0.26: .......... done [pkg.DaveG.ca] `-- Installing p5-Authen-SASL-2.1900... [pkg.DaveG.ca] | `-- Installing p5-Crypt-URandom-0.54... [pkg.DaveG.ca] | | `-- Installing perl5-5.42.0_1... [pkg.DaveG.ca] | | `-- Extracting perl5-5.42.0_1: .......... done [pkg.DaveG.ca] | `-- Extracting p5-Crypt-URandom-0.54: .... done [pkg.DaveG.ca] | `-- Installing p5-Digest-HMAC-1.05... [pkg.DaveG.ca] | `-- Extracting p5-Digest-HMAC-1.05: ....... done [pkg.DaveG.ca] `-- Extracting p5-Authen-SASL-2.1900: .......... done [pkg.DaveG.ca] `-- Installing p5-Error-0.17030... [pkg.DaveG.ca] `-- Extracting p5-Error-0.17030: ..... done [pkg.DaveG.ca] `-- Installing p5-IO-Socket-SSL-2.095... [pkg.DaveG.ca] | `-- Installing p5-Mozilla-CA-20250602... [pkg.DaveG.ca] | `-- Extracting p5-Mozilla-CA-20250602: .... done [pkg.DaveG.ca] | `-- Installing p5-Net-SSLeay-1.94... [pkg.DaveG.ca] | `-- Extracting p5-Net-SSLeay-1.94: .......... done [pkg.DaveG.ca] | `-- Installing p5-URI-5.34... [pkg.DaveG.ca] | | `-- Installing p5-MIME-Base32-1.303... [pkg.DaveG.ca] | | `-- Extracting p5-MIME-Base32-1.303: ... done [pkg.DaveG.ca] | | `-- Installing p5-MIME-Base64-3.16... [pkg.DaveG.ca] | | `-- Extracting p5-MIME-Base64-3.16: ...... done [pkg.DaveG.ca] | `-- Extracting p5-URI-5.34: .......... done [pkg.DaveG.ca] `-- Extracting p5-IO-Socket-SSL-2.095: .......... done [pkg.DaveG.ca] `-- Installing pcre2-10.47_1... [pkg.DaveG.ca] `-- Extracting pcre2-10.47_1: .......... done [pkg.DaveG.ca] `-- Installing python311-3.11.14_2... [pkg.DaveG.ca] | `-- Installing libffi-3.5.1... [pkg.DaveG.ca] | `-- Extracting libffi-3.5.1: .......... done [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 python311-3.11.14_2: .......... done ===> Creating groups Creating group 'git_daemon' with gid '964' ===> Creating users Creating user 'git_daemon' with uid '964' [pkg.DaveG.ca] Extracting git-2.53.0: .......... done ===== Message from python311-3.11.14_2: -- 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 git-2.53.0: -- If you installed the GITWEB option please follow these instructions: In the directory /usr/local/share/examples/git/gitweb you can find all files to make gitweb work as a public repository on the web. All you have to do to make gitweb work is: 1) Please be sure you're able to execute CGI scripts in /usr/local/share/examples/git/gitweb. 2) Set the GITWEB_CONFIG variable in your webserver's config to /usr/local/etc/git/gitweb.conf. This variable is passed to gitweb.cgi. 3) Restart server. If you installed the CONTRIB option please note that the scripts are installed in /usr/local/share/git-core/contrib. Some of them require other ports to be installed (perl, python, etc), which you may need to install manually. ===> gatk-4.6.2.0 depends on executable: git - found ===> Returning to build of gatk-4.6.2.0 ===> gatk-4.6.2.0 depends on executable: git-lfs - not found ===> Installing existing package /packages/All/git-lfs-3.6.1_14.pkg [pkg.DaveG.ca] Installing git-lfs-3.6.1_14... [pkg.DaveG.ca] Extracting git-lfs-3.6.1_14: .......... done ===== Message from git-lfs-3.6.1_14: -- To get started with Git LFS, the following commands can be used: 1. Setup Git LFS on your system. You only have to do this once per repository per machine: $ git lfs install 2. Choose the type of files you want to track, for examples all ISO images, with git lfs track: $ git lfs track "*.iso" 3. The above stores this information in gitattributes(5) files, so that file needs to be added to the repository: $ git add .gitattributes 4. Commit, push and work with the files normally: $ git add file.iso $ git commit -m "Add disk image" $ git push ===> gatk-4.6.2.0 depends on executable: git-lfs - found ===> Returning to build of gatk-4.6.2.0 =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Fetching all distfiles required by gatk-4.6.2.0 for building =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Fetching all distfiles required by gatk-4.6.2.0 for building => SHA256 Checksum OK for gatk-4.6.2.0-deps.tar.gz. => SHA256 Checksum OK for broadinstitute-gatk-4.6.2.0_GH0.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 gatk-4.6.2.0 for building ===> Extracting for gatk-4.6.2.0 => SHA256 Checksum OK for gatk-4.6.2.0-deps.tar.gz. => SHA256 Checksum OK for broadinstitute-gatk-4.6.2.0_GH0.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 gatk-4.6.2.0 ===> Applying FreeBSD patches for gatk-4.6.2.0 from /usr/ports/biology/gatk/files =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 ===> gatk-4.6.2.0 depends on executable: gradle8 - not found ===> Installing existing package /packages/All/gradle8-8.8.pkg [pkg.DaveG.ca] Installing gradle8-8.8... [pkg.DaveG.ca] `-- Installing openjdk8-8.482.08.1... [pkg.DaveG.ca] | `-- Installing alsa-lib-1.2.14... [pkg.DaveG.ca] | `-- Extracting alsa-lib-1.2.14: .......... done [pkg.DaveG.ca] | `-- Installing dejavu-2.37_4... [pkg.DaveG.ca] | | `-- Installing fontconfig-2.17.1,1... [pkg.DaveG.ca] | | `-- Installing freetype2-2.14.1... [pkg.DaveG.ca] | | | `-- Installing png-1.6.54... [pkg.DaveG.ca] | | | `-- Extracting png-1.6.54: .......... done [pkg.DaveG.ca] | | `-- Extracting freetype2-2.14.1: .......... done [pkg.DaveG.ca] | | `-- Extracting fontconfig-2.17.1,1: .......... done [pkg.DaveG.ca] | | `-- Installing mkfontscale-1.2.3... [pkg.DaveG.ca] | | `-- Installing libfontenc-1.1.8... [pkg.DaveG.ca] | | `-- Extracting libfontenc-1.1.8: ...... done [pkg.DaveG.ca] | | `-- Extracting mkfontscale-1.2.3: .... done [pkg.DaveG.ca] | `-- Extracting dejavu-2.37_4: .......... done [pkg.DaveG.ca] | `-- Installing giflib-5.2.2... [pkg.DaveG.ca] | `-- Extracting giflib-5.2.2: .......... done [pkg.DaveG.ca] | `-- Installing java-zoneinfo-2021.e... [pkg.DaveG.ca] | `-- Extracting java-zoneinfo-2021.e: .......... done [pkg.DaveG.ca] | `-- Installing javavmwrapper-2.7.10... [pkg.DaveG.ca] | `-- Extracting javavmwrapper-2.7.10: .......... done [pkg.DaveG.ca] | `-- Installing libX11-1.8.12,1... [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 libX11-1.8.12,1: .......... 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 libXrender-0.9.12... [pkg.DaveG.ca] | `-- Extracting libXrender-0.9.12: ....... 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 libinotify-20240724_3... [pkg.DaveG.ca] | `-- Extracting libinotify-20240724_3: .......... done [pkg.DaveG.ca] `-- Extracting openjdk8-8.482.08.1: .......... done [pkg.DaveG.ca] Extracting gradle8-8.8: .......... 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 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 openjdk8-8.482.08.1: -- 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 ===> gatk-4.6.2.0 depends on executable: gradle8 - found ===> Returning to build of gatk-4.6.2.0 ===> gatk-4.6.2.0 depends on package: gettext-runtime>=0.26 - found ===> gatk-4.6.2.0 depends on file: /usr/local/openjdk17/bin/java - not found ===> Installing existing package /packages/All/openjdk17-17.0.18+8.1.pkg [pkg.DaveG.ca] Installing openjdk17-17.0.18+8.1... [pkg.DaveG.ca] `-- Installing harfbuzz-12.3.2... [pkg.DaveG.ca] | `-- Installing glib-2.84.4,2... [pkg.DaveG.ca] | | `-- Installing libiconv-1.18_1... [pkg.DaveG.ca] | | `-- Extracting libiconv-1.18_1: .......... done [pkg.DaveG.ca] | | `-- Installing py311-packaging-26.0... [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 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] | `-- Extracting tiff-4.7.1: .......... done [pkg.DaveG.ca] `-- Extracting lcms2-2.18: .......... done [pkg.DaveG.ca] `-- Installing libXrandr-1.5.4... [pkg.DaveG.ca] `-- Extracting libXrandr-1.5.4: .......... done [pkg.DaveG.ca] `-- Installing xorg-fonts-truetype-7.7_1... [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 openjdk17-17.0.18+8.1: .......... 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 openjdk17-17.0.18+8.1: -- 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 ===> gatk-4.6.2.0 depends on file: /usr/local/openjdk17/bin/java - found ===> Returning to build of gatk-4.6.2.0 ===> gatk-4.6.2.0 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. ===> gatk-4.6.2.0 depends on file: /usr/local/bin/ccache - found ===> Returning to build of gatk-4.6.2.0 =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 ===> gatk-4.6.2.0 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-4.6.2.0 =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Building for gatk-4.6.2.0 Starting a Gradle Daemon, 1 incompatible and 1 stopped Daemons could not be reused, use --status for details > Task :compileJava > Task :compileJava FROM-CACHE > Task :condaStandardEnvironmentDefinition Created standard Conda environment yml file: gatkcondaenv.yml > Task :pythonPackageArchive Created GATK Python package archive in task ':pythonPackageArchive' property 'destinationDirectory'/task ':pythonPackageArchive' property 'archiveFileName' > Task :condaEnvironmentDefinition > Task :sourcesJar > Task :downloadGsaLibFile SKIPPED > Task :processResources > Task :classes > Task :shadowJar FROM-CACHE > Task :localJar UP-TO-DATE BUILD SUCCESSFUL in 5m 54s 6 actionable tasks: 4 executed, 2 from cache =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 ===> gatk-4.6.2.0 depends on file: /usr/local/lib/libfml.so - not found ===> Installing existing package /packages/All/fermi-lite-0.1.13_2.pkg [pkg.DaveG.ca] Installing fermi-lite-0.1.13_2... [pkg.DaveG.ca] Extracting fermi-lite-0.1.13_2: .... done ===> gatk-4.6.2.0 depends on file: /usr/local/lib/libfml.so - found ===> Returning to build of gatk-4.6.2.0 ===> gatk-4.6.2.0 depends on package: gkl>0 - not found ===> Installing existing package /packages/All/gkl-0.9.1.pkg [pkg.DaveG.ca] Installing gkl-0.9.1... [pkg.DaveG.ca] `-- Installing isa-l-2.31.1... [pkg.DaveG.ca] `-- Extracting isa-l-2.31.1: .......... done [pkg.DaveG.ca] Extracting gkl-0.9.1: ...... done ===> gatk-4.6.2.0 depends on package: gkl>0 - found ===> Returning to build of gatk-4.6.2.0 ===> gatk-4.6.2.0 depends on package: mummer>0 - not found ===> Installing existing package /packages/All/mummer-4.0.1.pkg [pkg.DaveG.ca] Installing mummer-4.0.1... [pkg.DaveG.ca] Extracting mummer-4.0.1: .......... done ===> gatk-4.6.2.0 depends on package: mummer>0 - found ===> Returning to build of gatk-4.6.2.0 ===> gatk-4.6.2.0 depends on file: /usr/local/openjdk17/bin/java - found =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Staging for gatk-4.6.2.0 ===> Generating temporary packing list install -m 555 /wrkdirs/usr/ports/biology/gatk/work/gatk.sh /wrkdirs/usr/ports/biology/gatk/work/stage/usr/local/bin/gatk install -m 0644 /wrkdirs/usr/ports/biology/gatk/work/gatk-4.6.2.0/build/libs/gatk-package-1.0-SNAPSHOT-local.jar /wrkdirs/usr/ports/biology/gatk/work/stage/usr/local/share/java/classes/GenomeAnalysisTK-4.6.2.0.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=2026-02-20T20:22:35+0000' 'PKG_NOTE_ports_top_git_hash=eac71dbf758c' 'PKG_NOTE_ports_top_checkout_unclean=no' 'PKG_NOTE_port_git_hash=803f55e390e8' '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 gatk-4.6.2.0 ===> Building gatk-4.6.2.0 =========================================================================== =>> Cleaning up wrkdir ===> Cleaning for gatk-4.6.2.0 build of biology/gatk | gatk-4.6.2.0 ended at Fri Feb 20 15:40:19 EST 2026 build time: 00:17:46