=>> Building biology/gkl build started at Fri May 2 15:50:26 BST 2025 port directory: /usr/ports/biology/gkl package name: gkl-0.8.11.9 building for: FreeBSD pkg-builder.dan.net.uk 14.2-RELEASE FreeBSD 14.2-RELEASE amd64 maintained by: yuri@FreeBSD.org Makefile datestamp: -rw-r--r-- 1 root wheel 496 Jan 27 13:48 /usr/ports/biology/gkl/Makefile Ports top last git commit: 5529c5919b Ports top unclean checkout: yes Port dir last git commit: 0835676e36 Port dir unclean checkout: no Poudriere version: poudriere-git-3.4.2 Host OSVERSION: 1402000 Jail OSVERSION: 1402000 Job Id: 06 ---Begin Environment--- SHELL=/bin/sh OSVERSION=1402000 UNAME_v=FreeBSD 14.2-RELEASE UNAME_r=14.2-RELEASE 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/14-amd64-default-dan/ref LC_COLLATE=C POUDRIERE_BUILD_TYPE=bulk PACKAGE_BUILDING=yes SAVED_TERM=screen OUTPUT_REDIRECTED_STDERR=4 OUTPUT_REDIRECTED=1 PWD=/usr/local/poudriere/data/.m/14-amd64-default-dan/06/.p OUTPUT_REDIRECTED_STDOUT=3 P_PORTS_FEATURES=FLAVORS SUBPACKAGES SELECTED_OPTIONS MASTERNAME=14-amd64-default-dan SCRIPTPREFIX=/usr/local/share/poudriere SCRIPTNAME=bulk.sh OLDPWD=/usr/local/poudriere/data/.m/14-amd64-default-dan/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--- ---End OPTIONS List--- --MAINTAINER-- yuri@FreeBSD.org --End MAINTAINER-- --CONFIGURE_ARGS-- --End CONFIGURE_ARGS-- --CONFIGURE_ENV-- XDG_DATA_HOME=/wrkdirs/usr/ports/biology/gkl/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/gkl/work XDG_CACHE_HOME=/wrkdirs/usr/ports/biology/gkl/work/.cache HOME=/wrkdirs/usr/ports/biology/gkl/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/gkl/work/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin PKG_CONFIG_LIBDIR=/wrkdirs/usr/ports/biology/gkl/work/.pkgconfig:/usr/local/libdata/pkgconfig:/usr/local/share/pkgconfig:/usr/libdata/pkgconfig SHELL=/bin/sh CONFIG_SHELL=/bin/sh CMAKE_PREFIX_PATH="/usr/local" --End CONFIGURE_ENV-- --MAKE_ENV-- XDG_DATA_HOME=/wrkdirs/usr/ports/biology/gkl/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/gkl/work XDG_CACHE_HOME=/wrkdirs/usr/ports/biology/gkl/work/.cache HOME=/wrkdirs/usr/ports/biology/gkl/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/gkl/work/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin PKG_CONFIG_LIBDIR=/wrkdirs/usr/ports/biology/gkl/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 -isystem /usr/local/include -fno-strict-aliasing " CPP="cpp" CPPFLAGS="-isystem /usr/local/include" LDFLAGS=" -fstack-protector-strong -L/usr/local/lib " LIBS="" CXX="c++" CXXFLAGS="-O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include " 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-- CMAKE_BUILD_TYPE="release" JAVASHAREDIR="share/java" JAVAJARDIR="share/java/classes" OSREL=14.2 PREFIX=%D LOCALBASE=/usr/local RESETPREFIX=/usr/local LIB32DIR=lib DOCSDIR="share/doc/gkl" EXAMPLESDIR="share/examples/gkl" DATADIR="share/gkl" WWWDIR="www/gkl" ETCDIR="etc/gkl" --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/gkl DOCSDIR=/usr/local/share/doc/gkl EXAMPLESDIR=/usr/local/share/examples/gkl WWWDIR=/usr/local/www/gkl ETCDIR=/usr/local/etc/gkl --End SUB_LIST-- ---Begin make.conf--- 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 #### #### CCACHE_CPP2=1 WITH_SSP_PORTS=yes WITH_SSP=yes #WITH_LTO=yes DISABLE_LICENSES=yes LICENSES_ACCEPTED=AGPLv3 APACHE10 APACHE11 APACHE20 ART10 ARTPERL10 ART20 BSD BSD2CLAUSE BSD3CLAUSE BSD4CLAUSE BSL CC0-1.0 CDDL ClArtistic EPL GFDL GMGPL GPLv1 GPLv2 GPLv3 GPLv3RLE ISCL LGPL20 LGPL21 LGPL3 LPPL10 LPPL11 LPPL12 LPPL13 LPPL13a LPPL13b LPPL13c MIT MPL OpenSSL OFL10 OFL11 OWL PostgreSQL PHP202 PHP30 PHP301 PSFL RUBY ZLIB ZPL21 SVM-Light EULA ALASIR Microsoft-exFAT SIMIAN UDEVGAME unknown MTA COMMERCIAL teamspeak NO_LICENSES_DIALOGS=yes #### #### NO_IGNORE=yes DEFAULT_VERSIONS+=ssl=openssl apache=2.4 imagemagick=7 java=21 linux=c7 mysql=8.0 php=8.3 samba=4.19 varnish=7 WITH_SETID_MODE=force PHP_ZTS=enabled OPTIONS_UNSET+=OPENJPEG OPTIONS_UNSET+=GSSAPI_BASE OPTIONS_SET+=ZTS OPTIONS_SET+=GSSAPI_NONE ALLOW_UNSUPPORTED_SYSTEM=yes WITH_CCACHE_BUILD=yes CCACHE_DIR=/root/.ccache #### Misc Poudriere #### .include "/etc/make.conf.ports_env" GID=0 UID=0 DISABLE_MAKE_JOBS=poudriere ---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 ===> gkl-0.8.11.9 depends on file: /usr/local/sbin/pkg - not found ===> Installing existing package /packages/All/pkg-2.1.2.pkg [pkg-builder.dan.net.uk] Installing pkg-2.1.2... [pkg-builder.dan.net.uk] Extracting pkg-2.1.2: .......... done ===> gkl-0.8.11.9 depends on file: /usr/local/sbin/pkg - found ===> Returning to build of gkl-0.8.11.9 =========================================================================== =================================================== ===== 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 gkl-0.8.11.9 for building =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Fetching all distfiles required by gkl-0.8.11.9 for building => SHA256 Checksum OK for Intel-HLS-GKL-0.8.11-9-g25670d8_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 gkl-0.8.11.9 for building ===> Extracting for gkl-0.8.11.9 => SHA256 Checksum OK for Intel-HLS-GKL-0.8.11-9-g25670d8_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 gkl-0.8.11.9 ===> Applying FreeBSD patches for gkl-0.8.11.9 from /usr/ports/biology/gkl/files =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 ===> gkl-0.8.11.9 depends on executable: gmake - not found ===> Installing existing package /packages/All/gmake-4.4.1.pkg [pkg-builder.dan.net.uk] Installing gmake-4.4.1... [pkg-builder.dan.net.uk] `-- Installing gettext-runtime-0.23.1... [pkg-builder.dan.net.uk] | `-- Installing indexinfo-0.3.1_1... [pkg-builder.dan.net.uk] | `-- Extracting indexinfo-0.3.1_1: . done [pkg-builder.dan.net.uk] `-- Extracting gettext-runtime-0.23.1: .......... done [pkg-builder.dan.net.uk] Extracting gmake-4.4.1: .......... done ===> gkl-0.8.11.9 depends on executable: gmake - found ===> Returning to build of gkl-0.8.11.9 ===> gkl-0.8.11.9 depends on file: /usr/local/bin/cmake - not found ===> Installing existing package /packages/All/cmake-core-3.31.6.pkg [pkg-builder.dan.net.uk] Installing cmake-core-3.31.6... [pkg-builder.dan.net.uk] `-- Installing expat-2.7.1... [pkg-builder.dan.net.uk] `-- Extracting expat-2.7.1: .......... done [pkg-builder.dan.net.uk] `-- Installing jsoncpp-1.9.6_1... [pkg-builder.dan.net.uk] `-- Extracting jsoncpp-1.9.6_1: .......... done [pkg-builder.dan.net.uk] `-- Installing libidn2-2.3.8... [pkg-builder.dan.net.uk] | `-- Installing libunistring-1.3... [pkg-builder.dan.net.uk] | `-- Extracting libunistring-1.3: .......... done [pkg-builder.dan.net.uk] `-- Extracting libidn2-2.3.8: .......... done [pkg-builder.dan.net.uk] `-- Installing libuv-1.51.0... [pkg-builder.dan.net.uk] `-- Extracting libuv-1.51.0: .......... done [pkg-builder.dan.net.uk] `-- Installing openssl-3.0.16,1... [pkg-builder.dan.net.uk] `-- Extracting openssl-3.0.16,1: .......... done [pkg-builder.dan.net.uk] `-- Installing rhash-1.4.4_1... [pkg-builder.dan.net.uk] `-- Extracting rhash-1.4.4_1: .......... done [pkg-builder.dan.net.uk] Extracting cmake-core-3.31.6: .......... done ===> gkl-0.8.11.9 depends on file: /usr/local/bin/cmake - found ===> Returning to build of gkl-0.8.11.9 ===> gkl-0.8.11.9 depends on file: /usr/local/openjdk21/bin/java - not found ===> Installing existing package /packages/All/openjdk21-21.0.7+6.1.pkg [pkg-builder.dan.net.uk] Installing openjdk21-21.0.7+6.1... [pkg-builder.dan.net.uk] `-- Installing alsa-lib-1.2.13... [pkg-builder.dan.net.uk] `-- Extracting alsa-lib-1.2.13: .......... done [pkg-builder.dan.net.uk] `-- Installing fontconfig-2.15.0_3,1... [pkg-builder.dan.net.uk] | `-- Installing freetype2-2.13.3... [pkg-builder.dan.net.uk] | `-- Extracting freetype2-2.13.3: .......... done [pkg-builder.dan.net.uk] `-- Extracting fontconfig-2.15.0_3,1: .......... done [pkg-builder.dan.net.uk] `-- Installing giflib-5.2.2... [pkg-builder.dan.net.uk] `-- Extracting giflib-5.2.2: .......... done [pkg-builder.dan.net.uk] `-- Installing harfbuzz-10.3.0... [pkg-builder.dan.net.uk] | `-- Installing glib-2.84.1_2,2... [pkg-builder.dan.net.uk] | | `-- Installing libffi-3.4.8... [pkg-builder.dan.net.uk] | | `-- Extracting libffi-3.4.8: .......... done [pkg-builder.dan.net.uk] | | `-- Installing libiconv-1.17_1... [pkg-builder.dan.net.uk] | | `-- Extracting libiconv-1.17_1: .......... done [pkg-builder.dan.net.uk] | | `-- Installing libinotify-20240724_1... [pkg-builder.dan.net.uk] | | `-- Extracting libinotify-20240724_1: .......... done [pkg-builder.dan.net.uk] | | `-- Installing pcre2-10.45_1... [pkg-builder.dan.net.uk] | | `-- Installing readline-8.2.13_2... [pkg-builder.dan.net.uk] | | `-- Extracting readline-8.2.13_2: .......... done [pkg-builder.dan.net.uk] | | `-- Extracting pcre2-10.45_1: .......... done [pkg-builder.dan.net.uk] | | `-- Installing py311-packaging-24.2... [pkg-builder.dan.net.uk] | | `-- Installing python311-3.11.12... [pkg-builder.dan.net.uk] | | | `-- Installing mpdecimal-4.0.0... [pkg-builder.dan.net.uk] | | | `-- Extracting mpdecimal-4.0.0: .......... done [pkg-builder.dan.net.uk] | | `-- Extracting python311-3.11.12: .......... done [pkg-builder.dan.net.uk] | | `-- Extracting py311-packaging-24.2: .......... done [pkg-builder.dan.net.uk] | `-- Extracting glib-2.84.1_2,2: .......... done [pkg-builder.dan.net.uk] | `-- Installing graphite2-1.3.14... [pkg-builder.dan.net.uk] | `-- Extracting graphite2-1.3.14: .......... done [pkg-builder.dan.net.uk] `-- Extracting harfbuzz-10.3.0: .......... done [pkg-builder.dan.net.uk] `-- Installing javavmwrapper-2.7.10... [pkg-builder.dan.net.uk] `-- Extracting javavmwrapper-2.7.10: .......... done [pkg-builder.dan.net.uk] `-- Installing jpeg-turbo-3.1.0... [pkg-builder.dan.net.uk] `-- Extracting jpeg-turbo-3.1.0: .......... done [pkg-builder.dan.net.uk] `-- Installing lcms2-2.17... [pkg-builder.dan.net.uk] | `-- Installing tiff-4.7.0... [pkg-builder.dan.net.uk] | | `-- Installing jbigkit-2.1_3... [pkg-builder.dan.net.uk] | | `-- Extracting jbigkit-2.1_3: .......... done [pkg-builder.dan.net.uk] | | `-- Installing lerc-4.0.0... [pkg-builder.dan.net.uk] | | `-- Extracting lerc-4.0.0: ..... done [pkg-builder.dan.net.uk] | | `-- Installing libdeflate-1.22... [pkg-builder.dan.net.uk] | | `-- Extracting libdeflate-1.22: .......... done [pkg-builder.dan.net.uk] | | `-- Installing zstd-1.5.7... [pkg-builder.dan.net.uk] | | `-- Installing liblz4-1.10.0,1... [pkg-builder.dan.net.uk] | | `-- Extracting liblz4-1.10.0,1: .......... done [pkg-builder.dan.net.uk] | | `-- Extracting zstd-1.5.7: .......... done [pkg-builder.dan.net.uk] | `-- Extracting tiff-4.7.0: .......... done [pkg-builder.dan.net.uk] `-- Extracting lcms2-2.17: .......... done [pkg-builder.dan.net.uk] `-- Installing libX11-1.8.12,1... [pkg-builder.dan.net.uk] | `-- Installing libxcb-1.17.0... [pkg-builder.dan.net.uk] | | `-- Installing libXau-1.0.11... [pkg-builder.dan.net.uk] | | `-- Extracting libXau-1.0.11: .......... done [pkg-builder.dan.net.uk] | | `-- Installing libXdmcp-1.1.5... [pkg-builder.dan.net.uk] | | `-- Installing xorgproto-2024.1... [pkg-builder.dan.net.uk] | | `-- Extracting xorgproto-2024.1: .......... done [pkg-builder.dan.net.uk] | | `-- Extracting libXdmcp-1.1.5: ...... done [pkg-builder.dan.net.uk] | `-- Extracting libxcb-1.17.0: .......... done [pkg-builder.dan.net.uk] `-- Extracting libX11-1.8.12,1: .......... done [pkg-builder.dan.net.uk] `-- Installing libXext-1.3.6,1... [pkg-builder.dan.net.uk] `-- Extracting libXext-1.3.6,1: .......... done [pkg-builder.dan.net.uk] `-- Installing libXi-1.8.1,1... [pkg-builder.dan.net.uk] | `-- Installing libXfixes-6.0.1... [pkg-builder.dan.net.uk] | `-- Extracting libXfixes-6.0.1: ....... done [pkg-builder.dan.net.uk] `-- Extracting libXi-1.8.1,1: .......... done [pkg-builder.dan.net.uk] `-- Installing libXrandr-1.5.4... [pkg-builder.dan.net.uk] | `-- Installing libXrender-0.9.12... [pkg-builder.dan.net.uk] | `-- Extracting libXrender-0.9.12: ....... done [pkg-builder.dan.net.uk] `-- Extracting libXrandr-1.5.4: .......... done [pkg-builder.dan.net.uk] `-- Installing libXt-1.3.0,1... [pkg-builder.dan.net.uk] | `-- Installing libICE-1.1.1,1... [pkg-builder.dan.net.uk] | `-- Extracting libICE-1.1.1,1: .......... done [pkg-builder.dan.net.uk] | `-- Installing libSM-1.2.6,1... [pkg-builder.dan.net.uk] | `-- Extracting libSM-1.2.6,1: ........ done [pkg-builder.dan.net.uk] `-- Extracting libXt-1.3.0,1: .......... done [pkg-builder.dan.net.uk] `-- Installing libXtst-1.2.4... [pkg-builder.dan.net.uk] `-- Extracting libXtst-1.2.4: .......... done [pkg-builder.dan.net.uk] `-- Installing png-1.6.47... [pkg-builder.dan.net.uk] `-- Extracting png-1.6.47: .......... done [pkg-builder.dan.net.uk] `-- Installing xorg-fonts-truetype-7.7_1... [pkg-builder.dan.net.uk] | `-- Installing dejavu-2.37_3... [pkg-builder.dan.net.uk] | | `-- Installing mkfontscale-1.2.3... [pkg-builder.dan.net.uk] | | `-- Installing libfontenc-1.1.8... [pkg-builder.dan.net.uk] | | `-- Extracting libfontenc-1.1.8: ...... done [pkg-builder.dan.net.uk] | | `-- Extracting mkfontscale-1.2.3: .... done [pkg-builder.dan.net.uk] | `-- Extracting dejavu-2.37_3: .......... done [pkg-builder.dan.net.uk] | `-- Installing encodings-1.1.0,1... [pkg-builder.dan.net.uk] | `-- Extracting encodings-1.1.0,1: .......... done [pkg-builder.dan.net.uk] | `-- Installing font-bh-ttf-1.0.3_5... [pkg-builder.dan.net.uk] | `-- Extracting font-bh-ttf-1.0.3_5: .......... done [pkg-builder.dan.net.uk] | `-- Installing font-misc-ethiopic-1.0.4... [pkg-builder.dan.net.uk] | `-- Extracting font-misc-ethiopic-1.0.4: ... done [pkg-builder.dan.net.uk] | `-- Installing font-misc-meltho-1.0.3_5... [pkg-builder.dan.net.uk] | `-- Extracting font-misc-meltho-1.0.3_5: .......... done [pkg-builder.dan.net.uk] Extracting openjdk21-21.0.7+6.1: .......... 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 freetype2-2.13.3: -- 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_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 python311-3.11.12: -- 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 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 openjdk21-21.0.7+6.1: -- 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 ===> gkl-0.8.11.9 depends on file: /usr/local/openjdk21/bin/java - found ===> Returning to build of gkl-0.8.11.9 ===> gkl-0.8.11.9 depends on file: /usr/local/bin/ccache - not found ===> Installing existing package /packages/All/ccache-3.7.12_8.pkg [pkg-builder.dan.net.uk] Installing ccache-3.7.12_8... [pkg-builder.dan.net.uk] 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. ===> gkl-0.8.11.9 depends on file: /usr/local/bin/ccache - found ===> Returning to build of gkl-0.8.11.9 =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 ===> gkl-0.8.11.9 depends on shared library: libisal.so - not found ===> Installing existing package /packages/All/isa-l-2.31.1.pkg [pkg-builder.dan.net.uk] Installing isa-l-2.31.1... [pkg-builder.dan.net.uk] Extracting isa-l-2.31.1: .......... done ===> gkl-0.8.11.9 depends on shared library: libisal.so - found (/usr/local/lib/libisal.so) ===> Returning to build of gkl-0.8.11.9 =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Configuring for gkl-0.8.11.9 ===> Performing out-of-source build /bin/mkdir -p /wrkdirs/usr/ports/biology/gkl/work/.build CMake Warning (dev) at CMakeLists.txt:1 (project): cmake_minimum_required() should be called prior to this top-level project() call. Please see the cmake-commands(7) manual for usage documentation of both commands. This warning is for project developers. Use -Wno-dev to suppress it. -- The C compiler identification is Clang 18.1.6 -- The CXX compiler identification is Clang 18.1.6 -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Check for working C compiler: /usr/local/libexec/ccache/cc - skipped -- Detecting C compile features -- Detecting C compile features - done -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Check for working CXX compiler: /usr/local/libexec/ccache/c++ - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done CMake Deprecation Warning at CMakeLists.txt:2 (cmake_minimum_required): Compatibility with CMake < 3.10 will be removed from a future version of CMake. Update the VERSION argument value. Or, use the ... syntax to tell CMake that the project requires at least but has been updated to work with policies introduced by or earlier. -- Found Java: /usr/local/bin/java (found suitable version "21.0.7", minimum required is "1.8") -- Could NOT find JNI (missing: JAVA_INCLUDE_PATH JAVA_INCLUDE_PATH2 AWT JVM) -- Found OpenMP_C: -fopenmp=libomp (found version "5.1") -- Found OpenMP_CXX: -fopenmp=libomp (found version "5.1") -- Found OpenMP: TRUE (found version "5.1") -- Configuring done (1.4s) CMake Error: The following variables are used in this project, but they are set to NOTFOUND. Please set them or make sure they are set and tested correctly in the CMake files: JAVA_AWT_INCLUDE_PATH (ADVANCED) used as include directory in directory /wrkdirs/usr/ports/biology/gkl/work/GKL-0.8.11-9-g25670d8 used as include directory in directory /wrkdirs/usr/ports/biology/gkl/work/GKL-0.8.11-9-g25670d8 used as include directory in directory /wrkdirs/usr/ports/biology/gkl/work/GKL-0.8.11-9-g25670d8 used as include directory in directory /wrkdirs/usr/ports/biology/gkl/work/GKL-0.8.11-9-g25670d8 used as include directory in directory /wrkdirs/usr/ports/biology/gkl/work/GKL-0.8.11-9-g25670d8 used as include directory in directory /wrkdirs/usr/ports/biology/gkl/work/GKL-0.8.11-9-g25670d8 used as include directory in directory /wrkdirs/usr/ports/biology/gkl/work/GKL-0.8.11-9-g25670d8/src/main/native/compression used as include directory in directory /wrkdirs/usr/ports/biology/gkl/work/GKL-0.8.11-9-g25670d8/src/main/native/compression used as include directory in directory /wrkdirs/usr/ports/biology/gkl/work/GKL-0.8.11-9-g25670d8/src/main/native/compression used as include directory in directory /wrkdirs/usr/ports/biology/gkl/work/GKL-0.8.11-9-g25670d8/src/main/native/compression used as include directory in directory /wrkdirs/usr/ports/biology/gkl/work/GKL-0.8.11-9-g25670d8/src/main/native/compression used as include directory in directory /wrkdirs/usr/ports/biology/gkl/work/GKL-0.8.11-9-g25670d8/src/main/native/compression used as include directory in directory /wrkdirs/usr/ports/biology/gkl/work/GKL-0.8.11-9-g25670d8/src/main/native/compression used as include directory in directory /wrkdirs/usr/ports/biology/gkl/work/GKL-0.8.11-9-g25670d8/src/main/native/compression used as include directory in directory /wrkdirs/usr/ports/biology/gkl/work/GKL-0.8.11-9-g25670d8/src/main/native/pairhmm used as include directory in directory /wrkdirs/usr/ports/biology/gkl/work/GKL-0.8.11-9-g25670d8/src/main/native/pairhmm used as include directory in directory /wrkdirs/usr/ports/biology/gkl/work/GKL-0.8.11-9-g25670d8/src/main/native/pairhmm used as include directory in directory /wrkdirs/usr/ports/biology/gkl/work/GKL-0.8.11-9-g25670d8/src/main/native/pairhmm used as include directory in directory /wrkdirs/usr/ports/biology/gkl/work/GKL-0.8.11-9-g25670d8/src/main/native/pairhmm used as include directory in directory /wrkdirs/usr/ports/biology/gkl/work/GKL-0.8.11-9-g25670d8/src/main/native/pairhmm used as include directory in directory /wrkdirs/usr/ports/biology/gkl/work/GKL-0.8.11-9-g25670d8/src/main/native/pairhmm used as include directory in directory /wrkdirs/usr/ports/biology/gkl/work/GKL-0.8.11-9-g25670d8/src/main/native/pairhmm used as include directory in directory /wrkdirs/usr/ports/biology/gkl/work/GKL-0.8.11-9-g25670d8/src/main/native/utils used as include directory in directory /wrkdirs/usr/ports/biology/gkl/work/GKL-0.8.11-9-g25670d8/src/main/native/utils used as include directory in directory /wrkdirs/usr/ports/biology/gkl/work/GKL-0.8.11-9-g25670d8/src/main/native/utils used as include directory in directory /wrkdirs/usr/ports/biology/gkl/work/GKL-0.8.11-9-g25670d8/src/main/native/utils used as include directory in directory /wrkdirs/usr/ports/biology/gkl/work/GKL-0.8.11-9-g25670d8/src/main/native/utils used as include directory in directory /wrkdirs/usr/ports/biology/gkl/work/GKL-0.8.11-9-g25670d8/src/main/native/utils used as include directory in directory /wrkdirs/usr/ports/biology/gkl/work/GKL-0.8.11-9-g25670d8/src/main/native/utils used as include directory in directory /wrkdirs/usr/ports/biology/gkl/work/GKL-0.8.11-9-g25670d8/src/main/native/smithwaterman used as include directory in directory /wrkdirs/usr/ports/biology/gkl/work/GKL-0.8.11-9-g25670d8/src/main/native/smithwaterman used as include directory in directory /wrkdirs/usr/ports/biology/gkl/work/GKL-0.8.11-9-g25670d8/src/main/native/smithwaterman used as include directory in directory /wrkdirs/usr/ports/biology/gkl/work/GKL-0.8.11-9-g25670d8/src/main/native/smithwaterman used as include directory in directory /wrkdirs/usr/ports/biology/gkl/work/GKL-0.8.11-9-g25670d8/src/main/native/smithwaterman used as include directory in directory /wrkdirs/usr/ports/biology/gkl/work/GKL-0.8.11-9-g25670d8/src/main/native/smithwaterman used as include directory in directory /wrkdirs/usr/ports/biology/gkl/work/GKL-0.8.11-9-g25670d8/src/main/native/smithwaterman used as include directory in directory /wrkdirs/usr/ports/biology/gkl/work/GKL-0.8.11-9-g25670d8/src/main/native/pdhmm used as include directory in directory /wrkdirs/usr/ports/biology/gkl/work/GKL-0.8.11-9-g25670d8/src/main/native/pdhmm used as include directory in directory /wrkdirs/usr/ports/biology/gkl/work/GKL-0.8.11-9-g25670d8/src/main/native/pdhmm used as include directory in directory /wrkdirs/usr/ports/biology/gkl/work/GKL-0.8.11-9-g25670d8/src/main/native/pdhmm used as include directory in directory /wrkdirs/usr/ports/biology/gkl/work/GKL-0.8.11-9-g25670d8/src/main/native/pdhmm used as include directory in directory /wrkdirs/usr/ports/biology/gkl/work/GKL-0.8.11-9-g25670d8/src/main/native/pdhmm used as include directory in directory /wrkdirs/usr/ports/biology/gkl/work/GKL-0.8.11-9-g25670d8/src/main/native/pdhmm JAVA_INCLUDE_PATH (ADVANCED) used as include directory in directory /wrkdirs/usr/ports/biology/gkl/work/GKL-0.8.11-9-g25670d8 used as include directory in directory /wrkdirs/usr/ports/biology/gkl/work/GKL-0.8.11-9-g25670d8 used as include directory in directory /wrkdirs/usr/ports/biology/gkl/work/GKL-0.8.11-9-g25670d8 used as include directory in directory /wrkdirs/usr/ports/biology/gkl/work/GKL-0.8.11-9-g25670d8 used as include directory in directory /wrkdirs/usr/ports/biology/gkl/work/GKL-0.8.11-9-g25670d8 used as include directory in directory /wrkdirs/usr/ports/biology/gkl/work/GKL-0.8.11-9-g25670d8 used as include directory in directory /wrkdirs/usr/ports/biology/gkl/work/GKL-0.8.11-9-g25670d8/src/main/native/compression used as include directory in directory /wrkdirs/usr/ports/biology/gkl/work/GKL-0.8.11-9-g25670d8/src/main/native/compression used as include directory in directory /wrkdirs/usr/ports/biology/gkl/work/GKL-0.8.11-9-g25670d8/src/main/native/compression used as include directory in directory /wrkdirs/usr/ports/biology/gkl/work/GKL-0.8.11-9-g25670d8/src/main/native/compression used as include directory in directory /wrkdirs/usr/ports/biology/gkl/work/GKL-0.8.11-9-g25670d8/src/main/native/compression used as include directory in directory /wrkdirs/usr/ports/biology/gkl/work/GKL-0.8.11-9-g25670d8/src/main/native/compression used as include directory in directory /wrkdirs/usr/ports/biology/gkl/work/GKL-0.8.11-9-g25670d8/src/main/native/compression used as include directory in directory /wrkdirs/usr/ports/biology/gkl/work/GKL-0.8.11-9-g25670d8/src/main/native/compression used as include directory in directory /wrkdirs/usr/ports/biology/gkl/work/GKL-0.8.11-9-g25670d8/src/main/native/pairhmm used as include directory in directory /wrkdirs/usr/ports/biology/gkl/work/GKL-0.8.11-9-g25670d8/src/main/native/pairhmm used as include directory in directory /wrkdirs/usr/ports/biology/gkl/work/GKL-0.8.11-9-g25670d8/src/main/native/pairhmm used as include directory in directory /wrkdirs/usr/ports/biology/gkl/work/GKL-0.8.11-9-g25670d8/src/main/native/pairhmm used as include directory in directory /wrkdirs/usr/ports/biology/gkl/work/GKL-0.8.11-9-g25670d8/src/main/native/pairhmm used as include directory in directory /wrkdirs/usr/ports/biology/gkl/work/GKL-0.8.11-9-g25670d8/src/main/native/pairhmm used as include directory in directory /wrkdirs/usr/ports/biology/gkl/work/GKL-0.8.11-9-g25670d8/src/main/native/pairhmm used as include directory in directory /wrkdirs/usr/ports/biology/gkl/work/GKL-0.8.11-9-g25670d8/src/main/native/pairhmm used as include directory in directory /wrkdirs/usr/ports/biology/gkl/work/GKL-0.8.11-9-g25670d8/src/main/native/utils used as include directory in directory /wrkdirs/usr/ports/biology/gkl/work/GKL-0.8.11-9-g25670d8/src/main/native/utils used as include directory in directory /wrkdirs/usr/ports/biology/gkl/work/GKL-0.8.11-9-g25670d8/src/main/native/utils used as include directory in directory /wrkdirs/usr/ports/biology/gkl/work/GKL-0.8.11-9-g25670d8/src/main/native/utils used as include directory in directory /wrkdirs/usr/ports/biology/gkl/work/GKL-0.8.11-9-g25670d8/src/main/native/utils used as include directory in directory /wrkdirs/usr/ports/biology/gkl/work/GKL-0.8.11-9-g25670d8/src/main/native/utils used as include directory in directory /wrkdirs/usr/ports/biology/gkl/work/GKL-0.8.11-9-g25670d8/src/main/native/utils used as include directory in directory /wrkdirs/usr/ports/biology/gkl/work/GKL-0.8.11-9-g25670d8/src/main/native/smithwaterman used as include directory in directory /wrkdirs/usr/ports/biology/gkl/work/GKL-0.8.11-9-g25670d8/src/main/native/smithwaterman used as include directory in directory /wrkdirs/usr/ports/biology/gkl/work/GKL-0.8.11-9-g25670d8/src/main/native/smithwaterman used as include directory in directory /wrkdirs/usr/ports/biology/gkl/work/GKL-0.8.11-9-g25670d8/src/main/native/smithwaterman used as include directory in directory /wrkdirs/usr/ports/biology/gkl/work/GKL-0.8.11-9-g25670d8/src/main/native/smithwaterman used as include directory in directory /wrkdirs/usr/ports/biology/gkl/work/GKL-0.8.11-9-g25670d8/src/main/native/smithwaterman used as include directory in directory /wrkdirs/usr/ports/biology/gkl/work/GKL-0.8.11-9-g25670d8/src/main/native/smithwaterman used as include directory in directory /wrkdirs/usr/ports/biology/gkl/work/GKL-0.8.11-9-g25670d8/src/main/native/pdhmm used as include directory in directory /wrkdirs/usr/ports/biology/gkl/work/GKL-0.8.11-9-g25670d8/src/main/native/pdhmm used as include directory in directory /wrkdirs/usr/ports/biology/gkl/work/GKL-0.8.11-9-g25670d8/src/main/native/pdhmm used as include directory in directory /wrkdirs/usr/ports/biology/gkl/work/GKL-0.8.11-9-g25670d8/src/main/native/pdhmm used as include directory in directory /wrkdirs/usr/ports/biology/gkl/work/GKL-0.8.11-9-g25670d8/src/main/native/pdhmm used as include directory in directory /wrkdirs/usr/ports/biology/gkl/work/GKL-0.8.11-9-g25670d8/src/main/native/pdhmm used as include directory in directory /wrkdirs/usr/ports/biology/gkl/work/GKL-0.8.11-9-g25670d8/src/main/native/pdhmm JAVA_INCLUDE_PATH2 (ADVANCED) used as include directory in directory /wrkdirs/usr/ports/biology/gkl/work/GKL-0.8.11-9-g25670d8 used as include directory in directory /wrkdirs/usr/ports/biology/gkl/work/GKL-0.8.11-9-g25670d8 used as include directory in directory /wrkdirs/usr/ports/biology/gkl/work/GKL-0.8.11-9-g25670d8 used as include directory in directory /wrkdirs/usr/ports/biology/gkl/work/GKL-0.8.11-9-g25670d8 used as include directory in directory /wrkdirs/usr/ports/biology/gkl/work/GKL-0.8.11-9-g25670d8 used as include directory in directory /wrkdirs/usr/ports/biology/gkl/work/GKL-0.8.11-9-g25670d8 used as include directory in directory /wrkdirs/usr/ports/biology/gkl/work/GKL-0.8.11-9-g25670d8/src/main/native/compression used as include directory in directory /wrkdirs/usr/ports/biology/gkl/work/GKL-0.8.11-9-g25670d8/src/main/native/compression used as include directory in directory /wrkdirs/usr/ports/biology/gkl/work/GKL-0.8.11-9-g25670d8/src/main/native/compression used as include directory in directory /wrkdirs/usr/ports/biology/gkl/work/GKL-0.8.11-9-g25670d8/src/main/native/compression used as include directory in directory /wrkdirs/usr/ports/biology/gkl/work/GKL-0.8.11-9-g25670d8/src/main/native/compression used as include directory in directory /wrkdirs/usr/ports/biology/gkl/work/GKL-0.8.11-9-g25670d8/src/main/native/compression used as include directory in directory /wrkdirs/usr/ports/biology/gkl/work/GKL-0.8.11-9-g25670d8/src/main/native/compression used as include directory in directory /wrkdirs/usr/ports/biology/gkl/work/GKL-0.8.11-9-g25670d8/src/main/native/compression used as include directory in directory /wrkdirs/usr/ports/biology/gkl/work/GKL-0.8.11-9-g25670d8/src/main/native/pairhmm used as include directory in directory /wrkdirs/usr/ports/biology/gkl/work/GKL-0.8.11-9-g25670d8/src/main/native/pairhmm used as include directory in directory /wrkdirs/usr/ports/biology/gkl/work/GKL-0.8.11-9-g25670d8/src/main/native/pairhmm used as include directory in directory /wrkdirs/usr/ports/biology/gkl/work/GKL-0.8.11-9-g25670d8/src/main/native/pairhmm used as include directory in directory /wrkdirs/usr/ports/biology/gkl/work/GKL-0.8.11-9-g25670d8/src/main/native/pairhmm used as include directory in directory /wrkdirs/usr/ports/biology/gkl/work/GKL-0.8.11-9-g25670d8/src/main/native/pairhmm used as include directory in directory /wrkdirs/usr/ports/biology/gkl/work/GKL-0.8.11-9-g25670d8/src/main/native/pairhmm used as include directory in directory /wrkdirs/usr/ports/biology/gkl/work/GKL-0.8.11-9-g25670d8/src/main/native/pairhmm used as include directory in directory /wrkdirs/usr/ports/biology/gkl/work/GKL-0.8.11-9-g25670d8/src/main/native/utils used as include directory in directory /wrkdirs/usr/ports/biology/gkl/work/GKL-0.8.11-9-g25670d8/src/main/native/utils used as include directory in directory /wrkdirs/usr/ports/biology/gkl/work/GKL-0.8.11-9-g25670d8/src/main/native/utils used as include directory in directory /wrkdirs/usr/ports/biology/gkl/work/GKL-0.8.11-9-g25670d8/src/main/native/utils used as include directory in directory /wrkdirs/usr/ports/biology/gkl/work/GKL-0.8.11-9-g25670d8/src/main/native/utils used as include directory in directory /wrkdirs/usr/ports/biology/gkl/work/GKL-0.8.11-9-g25670d8/src/main/native/utils used as include directory in directory /wrkdirs/usr/ports/biology/gkl/work/GKL-0.8.11-9-g25670d8/src/main/native/utils used as include directory in directory /wrkdirs/usr/ports/biology/gkl/work/GKL-0.8.11-9-g25670d8/src/main/native/smithwaterman used as include directory in directory /wrkdirs/usr/ports/biology/gkl/work/GKL-0.8.11-9-g25670d8/src/main/native/smithwaterman used as include directory in directory /wrkdirs/usr/ports/biology/gkl/work/GKL-0.8.11-9-g25670d8/src/main/native/smithwaterman used as include directory in directory /wrkdirs/usr/ports/biology/gkl/work/GKL-0.8.11-9-g25670d8/src/main/native/smithwaterman used as include directory in directory /wrkdirs/usr/ports/biology/gkl/work/GKL-0.8.11-9-g25670d8/src/main/native/smithwaterman used as include directory in directory /wrkdirs/usr/ports/biology/gkl/work/GKL-0.8.11-9-g25670d8/src/main/native/smithwaterman used as include directory in directory /wrkdirs/usr/ports/biology/gkl/work/GKL-0.8.11-9-g25670d8/src/main/native/smithwaterman used as include directory in directory /wrkdirs/usr/ports/biology/gkl/work/GKL-0.8.11-9-g25670d8/src/main/native/pdhmm used as include directory in directory /wrkdirs/usr/ports/biology/gkl/work/GKL-0.8.11-9-g25670d8/src/main/native/pdhmm used as include directory in directory /wrkdirs/usr/ports/biology/gkl/work/GKL-0.8.11-9-g25670d8/src/main/native/pdhmm used as include directory in directory /wrkdirs/usr/ports/biology/gkl/work/GKL-0.8.11-9-g25670d8/src/main/native/pdhmm used as include directory in directory /wrkdirs/usr/ports/biology/gkl/work/GKL-0.8.11-9-g25670d8/src/main/native/pdhmm used as include directory in directory /wrkdirs/usr/ports/biology/gkl/work/GKL-0.8.11-9-g25670d8/src/main/native/pdhmm used as include directory in directory /wrkdirs/usr/ports/biology/gkl/work/GKL-0.8.11-9-g25670d8/src/main/native/pdhmm CMake Warning (dev) in src/main/native/compression/CMakeLists.txt: Policy CMP0021 is not set: Fatal error on relative paths in INCLUDE_DIRECTORIES target property. Run "cmake --help-policy CMP0021" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Found relative path while evaluating include directories of "gkl_compression": "JAVA_INCLUDE_PATH-NOTFOUND" This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) in src/main/native/compression/CMakeLists.txt: Policy CMP0021 is not set: Fatal error on relative paths in INCLUDE_DIRECTORIES target property. Run "cmake --help-policy CMP0021" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Found relative path while evaluating include directories of "gkl_compression": "JAVA_INCLUDE_PATH2-NOTFOUND" This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) in src/main/native/compression/CMakeLists.txt: Policy CMP0021 is not set: Fatal error on relative paths in INCLUDE_DIRECTORIES target property. Run "cmake --help-policy CMP0021" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Found relative path while evaluating include directories of "gkl_compression": "JAVA_AWT_INCLUDE_PATH-NOTFOUND" This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) in src/main/native/pairhmm/CMakeLists.txt: Policy CMP0021 is not set: Fatal error on relative paths in INCLUDE_DIRECTORIES target property. Run "cmake --help-policy CMP0021" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Found relative path while evaluating include directories of "gkl_pairhmm": "JAVA_INCLUDE_PATH-NOTFOUND" This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) in src/main/native/pairhmm/CMakeLists.txt: Policy CMP0021 is not set: Fatal error on relative paths in INCLUDE_DIRECTORIES target property. Run "cmake --help-policy CMP0021" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Found relative path while evaluating include directories of "gkl_pairhmm": "JAVA_INCLUDE_PATH2-NOTFOUND" This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) in src/main/native/pairhmm/CMakeLists.txt: Policy CMP0021 is not set: Fatal error on relative paths in INCLUDE_DIRECTORIES target property. Run "cmake --help-policy CMP0021" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Found relative path while evaluating include directories of "gkl_pairhmm": "JAVA_AWT_INCLUDE_PATH-NOTFOUND" This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) in src/main/native/pairhmm/CMakeLists.txt: Policy CMP0021 is not set: Fatal error on relative paths in INCLUDE_DIRECTORIES target property. Run "cmake --help-policy CMP0021" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Found relative path while evaluating include directories of "gkl_pairhmm_omp": "JAVA_INCLUDE_PATH-NOTFOUND" This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) in src/main/native/pairhmm/CMakeLists.txt: Policy CMP0021 is not set: Fatal error on relative paths in INCLUDE_DIRECTORIES target property. Run "cmake --help-policy CMP0021" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Found relative path while evaluating include directories of "gkl_pairhmm_omp": "JAVA_INCLUDE_PATH2-NOTFOUND" This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) in src/main/native/pairhmm/CMakeLists.txt: Policy CMP0021 is not set: Fatal error on relative paths in INCLUDE_DIRECTORIES target property. Run "cmake --help-policy CMP0021" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Found relative path while evaluating include directories of "gkl_pairhmm_omp": "JAVA_AWT_INCLUDE_PATH-NOTFOUND" This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) in src/main/native/utils/CMakeLists.txt: Policy CMP0021 is not set: Fatal error on relative paths in INCLUDE_DIRECTORIES target property. Run "cmake --help-policy CMP0021" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Found relative path while evaluating include directories of "gkl_utils": "JAVA_INCLUDE_PATH-NOTFOUND" This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) in src/main/native/utils/CMakeLists.txt: Policy CMP0021 is not set: Fatal error on relative paths in INCLUDE_DIRECTORIES target property. Run "cmake --help-policy CMP0021" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Found relative path while evaluating include directories of "gkl_utils": "JAVA_INCLUDE_PATH2-NOTFOUND" This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) in src/main/native/utils/CMakeLists.txt: Policy CMP0021 is not set: Fatal error on relative paths in INCLUDE_DIRECTORIES target property. Run "cmake --help-policy CMP0021" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Found relative path while evaluating include directories of "gkl_utils": "JAVA_AWT_INCLUDE_PATH-NOTFOUND" This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) in src/main/native/smithwaterman/CMakeLists.txt: Policy CMP0021 is not set: Fatal error on relative paths in INCLUDE_DIRECTORIES target property. Run "cmake --help-policy CMP0021" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Found relative path while evaluating include directories of "gkl_smithwaterman": "JAVA_INCLUDE_PATH-NOTFOUND" This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) in src/main/native/smithwaterman/CMakeLists.txt: Policy CMP0021 is not set: Fatal error on relative paths in INCLUDE_DIRECTORIES target property. Run "cmake --help-policy CMP0021" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Found relative path while evaluating include directories of "gkl_smithwaterman": "JAVA_INCLUDE_PATH2-NOTFOUND" This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) in src/main/native/smithwaterman/CMakeLists.txt: Policy CMP0021 is not set: Fatal error on relative paths in INCLUDE_DIRECTORIES target property. Run "cmake --help-policy CMP0021" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Found relative path while evaluating include directories of "gkl_smithwaterman": "JAVA_AWT_INCLUDE_PATH-NOTFOUND" This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) in src/main/native/pdhmm/CMakeLists.txt: Policy CMP0021 is not set: Fatal error on relative paths in INCLUDE_DIRECTORIES target property. Run "cmake --help-policy CMP0021" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Found relative path while evaluating include directories of "gkl_pdhmm": "JAVA_INCLUDE_PATH-NOTFOUND" This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) in src/main/native/pdhmm/CMakeLists.txt: Policy CMP0021 is not set: Fatal error on relative paths in INCLUDE_DIRECTORIES target property. Run "cmake --help-policy CMP0021" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Found relative path while evaluating include directories of "gkl_pdhmm": "JAVA_INCLUDE_PATH2-NOTFOUND" This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) in src/main/native/pdhmm/CMakeLists.txt: Policy CMP0021 is not set: Fatal error on relative paths in INCLUDE_DIRECTORIES target property. Run "cmake --help-policy CMP0021" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Found relative path while evaluating include directories of "gkl_pdhmm": "JAVA_AWT_INCLUDE_PATH-NOTFOUND" This warning is for project developers. Use -Wno-dev to suppress it. -- Generating done (0.0s) CMake Warning: Manually-specified variables were not used by the project: CMAKE_C_FLAGS_RELEASE CMAKE_EXE_LINKER_FLAGS CMAKE_MODULE_LINKER_FLAGS FETCHCONTENT_FULLY_DISCONNECTED THREADS_HAVE_PTHREAD_ARG CMake Generate step failed. Build files cannot be regenerated correctly. *** Error code 1 Stop. make: stopped in /usr/ports/biology/gkl =>> Cleaning up wrkdir ===> Cleaning for gkl-0.8.11.9 build of biology/gkl | gkl-0.8.11.9 ended at Fri May 2 15:51:33 BST 2025 build time: 00:01:07 !!! build failure encountered !!!