From nobody Sun Feb 02 09:07:24 2025 X-Original-To: pkg-fallout@mlmmj.nyi.freebsd.org Received: from mx1.freebsd.org (mx1.freebsd.org [IPv6:2610:1c1:1:606c::19:1]) by mlmmj.nyi.freebsd.org (Postfix) with ESMTP id 4Ym3g15xdMz5m5gx for ; Sun, 02 Feb 2025 09:07:25 +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 "R11" (verified OK)) by mx1.freebsd.org (Postfix) with ESMTPS id 4Ym3g10GnGz3DKQ for ; Sun, 02 Feb 2025 09:07:25 +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=1738487245; h=from:from:reply-to:subject:subject:date:date:message-id:message-id: to:to:cc; bh=+JayvXUrdPMpwLyJOhTqDBd8RGfZh8N0Q1zt7xQBMNQ=; b=coORoefryyOpRe02eAWm5fhH5NQrAaG6UAlAwcRpWiGNDGGn3jgdd6STeY8IaIoBeG26ez vpL6W6k/ZIeLopL9/wUNTfQU8z9QxSf4bapFa1bofSYdgEXh26bd/bS4Kz+6PRj1vpnKnG RwS3zZt2tmKOz8F+r7vk0b7cRE4zeXj4A5HZjO2je110/Os36extMpBYcp3zPjC+h1h7pj GFmCX2pNJcM1f8f9GPQuXgxlJFOXjSlE3m6kjyQWJtvC88s1R3MJJb0A7rlOtuuvaX53yT gCKP2cJhrTGTl9sQWx6n5zG46cRXYYlRWXmB1FGNfWo6Uo6ZcsJ/WuZEHWFbkg== ARC-Seal: i=1; s=dkim; d=freebsd.org; t=1738487245; a=rsa-sha256; cv=none; b=F+9Iugn5LSdOjoHzqt+yJL+EAtEYbVoOusHJWMVbbBpVEW3QsILACEE037GMQvxzwWeY6y AFoYFgBKvYoiycnP31LxqC7v8ZAW0jRFPw3/uMyeZdBj8eRlWfLtdiHOyHdxE0epBDnXl4 ZAbC4C59tL+ZbI2Zr/hetdXxpbMEGUh2WsDaVjHoiOlD3QQaFtHxcecWSscv0p4B+qNoBB 45Cqiajc811bmZ2Cqg2zSzs2tAxOqep91TZNfpIpJ4gcfKisE7ND1tixfQbGVrJTUZvTVr ZzLOBvoxqtjHNEKe9ikHO63qTm3I+aoAWKsAS9Rzne3lk2skMzPneEyN2bX/3Q== ARC-Authentication-Results: i=1; mx1.freebsd.org; none Received: from ampere3.nyi.freebsd.org (ampere3.nyi.freebsd.org [IPv6:2610:1c1:1:6080::16:26]) by mxrelay.nyi.freebsd.org (Postfix) with ESMTP id 4Ym3g06nKNzkgQ for ; Sun, 02 Feb 2025 09:07:24 +0000 (UTC) (envelope-from pkg-fallout@FreeBSD.org) Received: from root (uid 0) (envelope-from pkg-fallout@FreeBSD.org) id 14be by ampere3.nyi.freebsd.org (DragonFly Mail Agent v0.13+ on ampere3.nyi.freebsd.org); Sun, 02 Feb 2025 09:07:24 +0000 To: pkg-fallout@FreeBSD.org Subject: [package - 141releng-armv7-default][biology/gcta] Failed for gcta-1.94.1_2 in build Date: Sun, 02 Feb 2025 09:07:24 +0000 Message-Id: <679f35cc.14be.391f7956@ampere3.nyi.freebsd.org> From: List-Id: Fallout logs from package building List-Archive: https://lists.freebsd.org/archives/freebsd-pkg-fallout List-Help: List-Post: List-Subscribe: List-Unsubscribe: Sender: owner-freebsd-pkg-fallout@FreeBSD.org You are receiving this mail as a port that you maintain is failing to build on the FreeBSD package build server. Please investigate the failure and submit a PR to fix build. Maintainer: jwb@FreeBSD.org Log URL: https://pkg-status.freebsd.org/ampere3/data/141releng-armv7-default/86e28c84a7e0/logs/gcta-1.94.1_2.log Build URL: https://pkg-status.freebsd.org/ampere3/build.html?mastername=141releng-armv7-default&build=86e28c84a7e0 Log: =>> Building biology/gcta build started at Sun Feb 2 09:06:57 UTC 2025 port directory: /usr/ports/biology/gcta package name: gcta-1.94.1_2 building for: FreeBSD 141releng-armv7-default-job-10 14.1-RELEASE-p6 FreeBSD 14.1-RELEASE-p6 1401000 arm maintained by: jwb@FreeBSD.org Makefile datestamp: -rw-r--r-- 1 root wheel 1581 Jun 27 2024 /usr/ports/biology/gcta/Makefile Ports top last git commit: 86e28c84a7e Ports top unclean checkout: no Port dir last git commit: 84a6e7ec36e Port dir unclean checkout: no Poudriere version: poudriere-git-3.4.2 Host OSVERSION: 1500028 Jail OSVERSION: 1401000 Job Id: 10 ---Begin Environment--- SHELL=/bin/sh OSVERSION=1401000 UNAME_v=FreeBSD 14.1-RELEASE-p6 1401000 UNAME_r=14.1-RELEASE-p6 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/141releng-armv7-default/ref LC_COLLATE=C POUDRIERE_BUILD_TYPE=bulk PACKAGE_BUILDING=yes SAVED_TERM= OUTPUT_REDIRECTED_STDERR=4 OUTPUT_REDIRECTED=1 PWD=/usr/local/poudriere/data/.m/141releng-armv7-default/10/.p OUTPUT_REDIRECTED_STDOUT=3 P_PORTS_FEATURES=FLAVORS SUBPACKAGES SELECTED_OPTIONS MASTERNAME=141releng-armv7-default SCRIPTPREFIX=/usr/local/share/poudriere SCRIPTNAME=bulk.sh OLDPWD=/usr/local/poudriere/data/.m/141releng-armv7-default/ref/.p/pool POUDRIERE_PKGNAME=poudriere-git-3.4.2 SCRIPTPATH=/usr/local/share/poudriere/bulk.sh POUDRIEREPATH=/usr/local/bin/poudriere ---End Environment--- ---Begin Poudriere Port Flags/Env--- PORT_FLAGS= PKGENV= FLAVOR= MAKE_ARGS= ---End Poudriere Port Flags/Env--- ---Begin OPTIONS List--- ---End OPTIONS List--- --MAINTAINER-- jwb@FreeBSD.org --End MAINTAINER-- --CONFIGURE_ARGS-- --End CONFIGURE_ARGS-- --CONFIGURE_ENV-- EIGEN3_INCLUDE_DIR=/usr/local/include/eigen3 BOOST_INCLUDE_DIR=/usr/local/include/boost OPENBLAS=/usr/local SPECTRA_INCLUDE_DIR=/usr/local/include/Spectra XDG_DATA_HOME=/wrkdirs/usr/ports/biology/gcta/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/gcta/work XDG_CACHE_HOME=/wrkdirs/usr/ports/biology/gcta/work/.cache HOME=/wrkdirs/usr/ports/biology/gcta/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/gcta/work/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin PKG_CONFIG_LIBDIR=/wrkdirs/usr/ports/biology/gcta/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-- NINJA_STATUS="[%p %s/%t] " XDG_DATA_HOME=/wrkdirs/usr/ports/biology/gcta/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/gcta/work XDG_CACHE_HOME=/wrkdirs/usr/ports/biology/gcta/work/.cache HOME=/wrkdirs/usr/ports/biology/gcta/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/gcta/work/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin PKG_CONFIG_LIBDIR=/wrkdirs/usr/ports/biology/gcta/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 DESTDIR=/wrkdirs/usr/ports/biology/gcta/work/stage 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=" -fopenmp -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" OSREL=14.1 PREFIX=%D LOCALBASE=/usr/local RESETPREFIX=/usr/local LIB32DIR=lib DOCSDIR="share/doc/gcta" EXAMPLESDIR="share/examples/gcta" DATADIR="share/gcta" WWWDIR="www/gcta" ETCDIR="etc/gcta" --End PLIST_SUB-- --SUB_LIST-- PREFIX=/usr/local LOCALBASE=/usr/local DATADIR=/usr/local/share/gcta DOCSDIR=/usr/local/share/doc/gcta EXAMPLESDIR=/usr/local/share/examples/gcta WWWDIR=/usr/local/www/gcta ETCDIR=/usr/local/etc/gcta --End SUB_LIST-- ---Begin make.conf--- # XXX: We really need this but cannot use it while 'make checksum' does not # try the next mirror on checksum failure. It currently retries the same # failed mirror and then fails rather then trying another. It *does* # try the next if the size is mismatched though. #MASTER_SITE_FREEBSD=yes # Build ALLOW_MAKE_JOBS_PACKAGES with 3 jobs MAKE_JOBS_NUMBER=3 USE_PACKAGE_DEPENDS=yes BATCH=yes WRKDIRPREFIX=/wrkdirs PORTSDIR=/usr/ports PACKAGES=/packages DISTDIR=/distfiles PACKAGE_BUILDING=yes PACKAGE_BUILDING_FLAVORS=yes #### #### # XXX: We really need this but cannot use it while 'make checksum' does not # try the next mirror on checksum failure. It currently retries the same # failed mirror and then fails rather then trying another. It *does* # try the next if the size is mismatched though. #MASTER_SITE_FREEBSD=yes # Build ALLOW_MAKE_JOBS_PACKAGES with 3 jobs MAKE_JOBS_NUMBER=3 #### Misc Poudriere #### .include "/etc/make.conf.ports_env" GID=0 UID=0 ---End make.conf--- --Resource limits-- cpu time (seconds, -t) unlimited file size (512-blocks, -f) unlimited data seg size (kbytes, -d) 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) 8192 virtual mem size (kbytes, -v) unlimited swap limit (kbytes, -w) unlimited socket buffer size (bytes, -b) unlimited pseudo-terminals (-p) unlimited kqueues (-k) unlimited umtx shared locks (-o) unlimited --End resource limits-- =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> License GPLv3 accepted by the user =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 ===> gcta-1.94.1_2 depends on file: /usr/local/sbin/pkg - not found ===> Installing existing package /packages/All/pkg-1.21.3.pkg [141releng-armv7-default-job-10] Installing pkg-1.21.3... [141releng-armv7-default-job-10] Extracting pkg-1.21.3: .......... done ===> gcta-1.94.1_2 depends on file: /usr/local/sbin/pkg - found ===> Returning to build of gcta-1.94.1_2 =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> License GPLv3 accepted by the user ===> Fetching all distfiles required by gcta-1.94.1_2 for building =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> License GPLv3 accepted by the user ===> Fetching all distfiles required by gcta-1.94.1_2 for building => SHA256 Checksum OK for jianyangqt-gcta-v1.94.1_GH0.tar.gz. => SHA256 Checksum OK for zhilizheng-plink-ng-3744540_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 ===> License GPLv3 accepted by the user ===> Fetching all distfiles required by gcta-1.94.1_2 for building ===> Extracting for gcta-1.94.1_2 => SHA256 Checksum OK for jianyangqt-gcta-v1.94.1_GH0.tar.gz. => SHA256 Checksum OK for zhilizheng-plink-ng-3744540_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 gcta-1.94.1_2 ===> Applying FreeBSD patches for gcta-1.94.1_2 from /usr/ports/biology/gcta/files =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 ===> gcta-1.94.1_2 depends on package: boost-libs>0 - not found ===> Installing existing package /packages/All/boost-libs-1.86.0_1.pkg [141releng-armv7-default-job-10] Installing boost-libs-1.86.0_1... [141releng-armv7-default-job-10] `-- Installing icu-74.2_1,1... [141releng-armv7-default-job-10] `-- Extracting icu-74.2_1,1: .......... done [141releng-armv7-default-job-10] Extracting boost-libs-1.86.0_1: .......... done ===== Message from boost-libs-1.86.0_1: -- You have built the Boost library with thread support. Don't forget to add -pthread to your linker options when linking your code. ===> gcta-1.94.1_2 depends on package: boost-libs>0 - found ===> Returning to build of gcta-1.94.1_2 ===> gcta-1.94.1_2 depends on package: spectra>0 - not found ===> Installing existing package /packages/All/spectra-1.1.0.pkg [141releng-armv7-default-job-10] Installing spectra-1.1.0... [141releng-armv7-default-job-10] `-- Installing eigen-3.4.0_3... [141releng-armv7-default-job-10] | `-- Installing blas-3.12.0_1... [141releng-armv7-default-job-10] | | `-- Installing gcc13-13.3.0... [141releng-armv7-default-job-10] | | `-- Installing binutils-2.43.1,1... [141releng-armv7-default-job-10] | | | `-- Installing indexinfo-0.3.1... [141releng-armv7-default-job-10] | | | `-- Extracting indexinfo-0.3.1: .... done [141releng-armv7-default-job-10] | | | `-- Installing zstd-1.5.6... [141releng-armv7-default-job-10] | | | `-- Installing liblz4-1.10.0,1... [141releng-armv7-default-job-10] | | | `-- Extracting liblz4-1.10.0,1: .......... done [141releng-armv7-default-job-10] | | | `-- Extracting zstd-1.5.6: .......... done [141releng-armv7-default-job-10] | | `-- Extracting binutils-2.43.1,1: .......... done [141releng-armv7-default-job-10] | | `-- Installing gmp-6.3.0... [141releng-armv7-default-job-10] | | `-- Extracting gmp-6.3.0: .......... done [141releng-armv7-default-job-10] | | `-- Installing mpc-1.3.1_1... [141releng-armv7-default-job-10] | | | `-- Installing mpfr-4.2.1,1... [141releng-armv7-default-job-10] | | | `-- Extracting mpfr-4.2.1,1: .......... done [141releng-armv7-default-job-10] | | `-- Extracting mpc-1.3.1_1: ......... done [141releng-armv7-default-job-10] | | `-- Extracting gcc13-13.3.0: .......... done [141releng-armv7-default-job-10] | `-- Extracting blas-3.12.0_1: ........ done [141releng-armv7-default-job-10] | `-- Installing lapack-3.12.0_2... [141releng-armv7-default-job-10] | `-- Extracting lapack-3.12.0_2: .......... done [141releng-armv7-default-job-10] `-- Extracting eigen-3.4.0_3: .......... done [141releng-armv7-default-job-10] Extracting spectra-1.1.0: .......... done ===== Message from gcc13-13.3.0: -- To ensure binaries built with this toolchain find appropriate versions of the necessary run-time libraries, you may want to link using -Wl,-rpath=/usr/local/lib/gcc13 For ports leveraging USE_GCC, USES=compiler, or USES=fortran this happens transparently. ===> gcta-1.94.1_2 depends on package: spectra>0 - found ===> Returning to build of gcta-1.94.1_2 ===> gcta-1.94.1_2 depends on file: /usr/local/bin/cmake - not found ===> Installing existing package /packages/All/cmake-core-3.31.4.pkg [141releng-armv7-default-job-10] Installing cmake-core-3.31.4... [141releng-armv7-default-job-10] `-- Installing expat-2.6.4... [141releng-armv7-default-job-10] `-- Extracting expat-2.6.4: .......... done [141releng-armv7-default-job-10] `-- Installing jsoncpp-1.9.6_1... [141releng-armv7-default-job-10] `-- Extracting jsoncpp-1.9.6_1: .......... done [141releng-armv7-default-job-10] `-- Installing libidn2-2.3.7... [141releng-armv7-default-job-10] | `-- Installing libunistring-1.3... [141releng-armv7-default-job-10] | `-- Extracting libunistring-1.3: .......... done [141releng-armv7-default-job-10] `-- Extracting libidn2-2.3.7: .......... done [141releng-armv7-default-job-10] `-- Installing libuv-1.50.0... [141releng-armv7-default-job-10] `-- Extracting libuv-1.50.0: .......... done [141releng-armv7-default-job-10] `-- Installing rhash-1.4.4_1... [141releng-armv7-default-job-10] | `-- Installing gettext-runtime-0.23.1... [141releng-armv7-default-job-10] | `-- Extracting gettext-runtime-0.23.1: .......... done [141releng-armv7-default-job-10] `-- Extracting rhash-1.4.4_1: .......... done [141releng-armv7-default-job-10] Extracting cmake-core-3.31.4: .......... done ===> gcta-1.94.1_2 depends on file: /usr/local/bin/cmake - found ===> Returning to build of gcta-1.94.1_2 ===> gcta-1.94.1_2 depends on executable: ninja - not found ===> Installing existing package /packages/All/ninja-1.11.1,4.pkg [141releng-armv7-default-job-10] Installing ninja-1.11.1,4... [141releng-armv7-default-job-10] `-- Installing python311-3.11.11... [141releng-armv7-default-job-10] | `-- Installing libffi-3.4.6... [141releng-armv7-default-job-10] | `-- Extracting libffi-3.4.6: .......... done [141releng-armv7-default-job-10] | `-- Installing mpdecimal-4.0.0... [141releng-armv7-default-job-10] | `-- Extracting mpdecimal-4.0.0: .......... done [141releng-armv7-default-job-10] | `-- Installing readline-8.2.13_2... [141releng-armv7-default-job-10] | `-- Extracting readline-8.2.13_2: .......... done [141releng-armv7-default-job-10] `-- Extracting python311-3.11.11: .......... done [141releng-armv7-default-job-10] Extracting ninja-1.11.1,4: ........ done ===== Message from python311-3.11.11: -- 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 ===> gcta-1.94.1_2 depends on executable: ninja - found ===> Returning to build of gcta-1.94.1_2 ===> gcta-1.94.1_2 depends on file: /usr/local/libdata/pkgconfig/eigen3.pc - found =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 ===> gcta-1.94.1_2 depends on shared library: libgsl.so - not found ===> Installing existing package /packages/All/gsl-2.7.1_1.pkg [141releng-armv7-default-job-10] Installing gsl-2.7.1_1... [141releng-armv7-default-job-10] Extracting gsl-2.7.1_1: .......... done ===> gcta-1.94.1_2 depends on shared library: libgsl.so - found (/usr/local/lib/libgsl.so) ===> Returning to build of gcta-1.94.1_2 ===> gcta-1.94.1_2 depends on shared library: libopenblas.so - not found ===> Installing existing package /packages/All/openblas-0.3.27,2.pkg [141releng-armv7-default-job-10] Installing openblas-0.3.27,2... [141releng-armv7-default-job-10] Extracting openblas-0.3.27,2: .......... done ===> gcta-1.94.1_2 depends on shared library: libopenblas.so - found (/usr/local/lib/libopenblas.so) ===> Returning to build of gcta-1.94.1_2 ===> gcta-1.94.1_2 depends on shared library: libsqlite3.so - not found ===> Installing existing package /packages/All/sqlite3-3.46.1,1.pkg [141releng-armv7-default-job-10] Installing sqlite3-3.46.1,1... [141releng-armv7-default-job-10] `-- Installing libedit-3.1.20240808,1... [141releng-armv7-default-job-10] `-- Extracting libedit-3.1.20240808,1: .......... done [141releng-armv7-default-job-10] Extracting sqlite3-3.46.1,1: .......... done ===> gcta-1.94.1_2 depends on shared library: libsqlite3.so - found (/usr/local/lib/libsqlite3.so) ===> Returning to build of gcta-1.94.1_2 ===> gcta-1.94.1_2 depends on shared library: libzstd.so - found (/usr/local/lib/libzstd.so) =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Configuring for gcta-1.94.1_2 ===> Performing out-of-source build /bin/mkdir -p /wrkdirs/usr/ports/biology/gcta/work/.build CMake Deprecation Warning at CMakeLists.txt:1 (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. -- The C compiler identification is Clang 18.1.5 -- The CXX compiler identification is Clang 18.1.5 -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Check for working C compiler: /usr/bin/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/bin/c++ - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done FreeBSD, Linux and Mac are supported. Compiling by Clang18.1.5 -- ARCHITECTURE:arm -- Configuring done (1.2s) -- Generating done (0.1s) CMake Warning: Manually-specified variables were not used by the project: CMAKE_COLOR_MAKEFILE CMAKE_MODULE_LINKER_FLAGS CMAKE_SHARED_LINKER_FLAGS CMAKE_VERBOSE_MAKEFILE FETCHCONTENT_FULLY_DISCONNECTED THREADS_HAVE_PTHREAD_ARG -- Build files have been written to: /wrkdirs/usr/ports/biology/gcta/work/.build =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Building for gcta-1.94.1_2 [ 1% 3/67] /usr/bin/c++ -I/wrkdirs/usr/ports/biology/gcta/work/.build -I/wrkdirs/usr/ports/biology/gcta/work/gcta-1.94.1 -I/usr/local/include/eigen3 -I/usr/local/include/Spectra -I/usr/local/include/boost -I/wrkdirs/usr/ports/biology/gcta/work/gcta-1.94.1/submods/plink-ng/2.0 -I/wrkdirs/usr/ports/biology/gcta/work/gcta-1.94.1/submods/plink-ng/2.0/simde -I/wrkdirs/usr/ports/biology/gcta/work/gcta-1.94.1/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -pthread -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNDEBUG -DNDEBUG -std=gnu++14 -fopenmp -MD -MT CMakeFiles/grm.dir/src/GRM.cpp.o -MF CMakeFiles/grm.dir/src/GRM.cpp.o.d -o CMakeFiles/grm.dir/src/GRM.cpp.o -c /wrkdirs/usr/ports/biology/gcta/work/gcta-1.94.1/src/GRM.cpp FAILED: CMakeFiles/grm.dir/src/GRM.cpp.o /usr/bin/c++ -I/wrkdirs/usr/ports/biology/gcta/work/.build -I/wrkdirs/usr/ports/biology/gcta/work/gcta-1.94.1 -I/usr/local/include/eigen3 -I/usr/local/include/Spectra -I/usr/local/include/boost -I/wrkdirs/usr/ports/biology/gcta/work/gcta-1.94.1/submods/plink-ng/2.0 -I/wrkdirs/usr/ports/biology/gcta/work/gcta-1.94.1/submods/plink-ng/2.0/simde -I/wrkdirs/usr/ports/biology/gcta/work/gcta-1.94.1/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -pthread -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNDEBUG -DNDEBUG -std=gnu++14 -fopenmp -MD -MT CMakeFiles/grm.dir/src/GRM.cpp.o -MF CMakeFiles/grm.dir/src/GRM.cpp.o.d -o CMakeFiles/grm.dir/src/GRM.cpp.o -c /wrkdirs/usr/ports/biology/gcta/work/gcta-1.94.1/src/GRM.cpp /wrkdirs/usr/ports/biology/gcta/work/gcta-1.94.1/src/GRM.cpp:32:10: fatal error: 'omp.h' file not found 32 | #include | ^~~~~~~ 1 error generated. [ 2% 3/67] /usr/bin/c++ -I/wrkdirs/usr/ports/biology/gcta/work/.build -I/wrkdirs/usr/ports/biology/gcta/work/gcta-1.94.1 -I/usr/local/include/eigen3 -I/usr/local/include/Spectra -I/usr/local/include/boost -I/wrkdirs/usr/ports/biology/gcta/work/gcta-1.94.1/submods/plink-ng/2.0 -I/wrkdirs/usr/ports/biology/gcta/work/gcta-1.94.1/submods/plink-ng/2.0/simde -I/wrkdirs/usr/ports/biology/gcta/work/gcta-1.94.1/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -pthread -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNDEBUG -DNDEBUG -std=gnu++14 -fopenmp -MD -MT CMakeFiles/covar.dir/src/Covar.cpp.o -MF CMakeFiles/covar.dir/src/Covar.cpp.o.d -o CMakeFiles/covar.dir/src/Covar.cpp.o -c /wrkdirs/usr/ports/biology/gcta/work/gcta-1.94.1/src/Covar.cpp FAILED: CMakeFiles/covar.dir/src/Covar.cpp.o /usr/bin/c++ -I/wrkdirs/usr/ports/biology/gcta/work/.build -I/wrkdirs/usr/ports/biology/gcta/work/gcta-1.94.1 -I/usr/local/include/eigen3 -I/usr/local/include/Spectra -I/usr/local/include/boost -I/wrkdirs/usr/ports/biology/gcta/work/gcta-1.94.1/submods/plink-ng/2.0 -I/wrkdirs/usr/ports/biology/gcta/work/gcta-1.94.1/submods/plink-ng/2.0/simde -I/wrkdirs/usr/ports/biology/gcta/work/gcta-1.94.1/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -pthread -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNDEBUG -DNDEBUG -std=gnu++14 -fopenmp -MD -MT CMakeFiles/covar.dir/src/Covar.cpp.o -MF CMakeFiles/covar.dir/src/Covar.cpp.o.d -o CMakeFiles/covar.dir/src/Covar.cpp.o -c /wrkdirs/usr/ports/biology/gcta/work/gcta-1.94.1/src/Covar.cpp In file included from /wrkdirs/usr/ports/biology/gcta/work/gcta-1.94.1/src/Covar.cpp:26: In file included from /wrkdirs/usr/ports/biology/gcta/work/gcta-1.94.1/include/StatLib.h:19: In file included from /usr/local/include/eigen3/Eigen/Eigen:1: In file included from /usr/local/include/eigen3/Eigen/Dense:1: /usr/local/include/eigen3/Eigen/Core:70:10: fatal error: 'omp.h' file not found 70 | #include | ^~~~~~~ 1 error generated. [ 4% 3/67] /usr/bin/c++ -I/wrkdirs/usr/ports/biology/gcta/work/.build -I/wrkdirs/usr/ports/biology/gcta/work/gcta-1.94.1 -I/usr/local/include/eigen3 -I/usr/local/include/Spectra -I/usr/local/include/boost -I/wrkdirs/usr/ports/biology/gcta/work/gcta-1.94.1/submods/plink-ng/2.0 -I/wrkdirs/usr/ports/biology/gcta/work/gcta-1.94.1/submods/plink-ng/2.0/simde -I/wrkdirs/usr/ports/biology/gcta/work/gcta-1.94.1/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -pthread -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNDEBUG -DNDEBUG -std=gnu++14 -fopenmp -MD -MT CMakeFiles/fastfam.dir/src/FastFAM.cpp.o -MF CMakeFiles/fastfam.dir/src/FastFAM.cpp.o.d -o CMakeFiles/fastfam.dir/src/FastFAM.cpp.o -c /wrkdirs/usr/ports/biology/gcta/work/gcta-1.94.1/src/FastFAM.cpp FAILED: CMakeFiles/fastfam.dir/src/FastFAM.cpp.o /usr/bin/c++ -I/wrkdirs/usr/ports/biology/gcta/work/.build -I/wrkdirs/usr/ports/biology/gcta/work/gcta-1.94.1 -I/usr/local/include/eigen3 -I/usr/local/include/Spectra -I/usr/local/include/boost -I/wrkdirs/usr/ports/biology/gcta/work/gcta-1.94.1/submods/plink-ng/2.0 -I/wrkdirs/usr/ports/biology/gcta/work/gcta-1.94.1/submods/plink-ng/2.0/simde -I/wrkdirs/usr/ports/biology/gcta/work/gcta-1.94.1/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -pthread -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNDEBUG -DNDEBUG -std=gnu++14 -fopenmp -MD -MT CMakeFiles/fastfam.dir/src/FastFAM.cpp.o -MF CMakeFiles/fastfam.dir/src/FastFAM.cpp.o.d -o CMakeFiles/fastfam.dir/src/FastFAM.cpp.o -c /wrkdirs/usr/ports/biology/gcta/work/gcta-1.94.1/src/FastFAM.cpp In file included from /wrkdirs/usr/ports/biology/gcta/work/gcta-1.94.1/src/FastFAM.cpp:18: In file included from /wrkdirs/usr/ports/biology/gcta/work/gcta-1.94.1/include/FastFAM.h:27: In file included from /usr/local/include/eigen3/Eigen/Dense:1: /usr/local/include/eigen3/Eigen/Core:70:10: fatal error: 'omp.h' file not found 70 | #include | ^~~~~~~ 1 error generated. ninja: build stopped: subcommand failed. ===> Compilation failed unexpectedly. Try to set MAKE_JOBS_UNSAFE=yes and rebuild before reporting the failure to the maintainer. *** Error code 1 Stop. make: stopped in /usr/ports/biology/gcta