From nobody Wed Sep 03 09:27:07 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 4cGy1S0knFz65nfv for ; Wed, 03 Sep 2025 09:27:08 +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 "R12" (verified OK)) by mx1.freebsd.org (Postfix) with ESMTPS id 4cGy1R68sCz3FYw for ; Wed, 03 Sep 2025 09:27:07 +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=1756891627; h=from:from:reply-to:subject:subject:date:date:message-id:message-id: to:to:cc; bh=40i7tGz+YWs3WyzvvO5mmb0OWop13wXYwkbH8j5uans=; b=mVTs/JEaRyQJ050IkOFlQDm3Bj6334RqSpPkNIp9jm06mCNQ0hGBbOAkya68aTq3+KdZGD 11oQaw5M5HBRQziWx6LLAjD12LScLeH5ewSfk3tcm3rnFDKK6BHO4438UpLH7dluBcJ1B+ xAAQ12SMkl6hzE6lf6ZQSUEviPEvdM3vLFdd8sBmbp+H+DQFumMiyXvN/Yt8SWW/76gdYa uvHsQjzYK1MJwuJXwjIW2mLXpzGb1rq9Qn7aAtivgmin5I0v2AxAOsCqnffKDFLwZUB+9k PqZDgLt1Hu6QkxMmQW4mfUcO0VTd9dCr4dXgqtk5DjZ4I5re0PEQL5a2IWgLNw== ARC-Seal: i=1; s=dkim; d=freebsd.org; t=1756891627; a=rsa-sha256; cv=none; b=YkoV7Fquk//P4o1LRX0Q8yhaYi8QiroquIJFqjWkbCwsANrebNCpYF4k8zU0wo/bh6r3fO B93gTvaQ6pmyyvFZ5ivDLp3gvLAMRAvnBCcHYb7x1m+gt8NbUdAMqoYcHGYjU55QQF7XV7 O08oKmUwfD1CllXjfghk/oTkVlfTHjZp98gPodaBiBht7VJgv2HFN/Fu2taFKpOHJPHMiy GGhKR75Aw1x8rajQ4x7axjn1nvkb1QXs0ialQkTaV2oLudPQxj+rlt6nZuFChvYFMxwUl6 i29jrXTy7avj3P8hW6qi+kgs594zoC6I6tteaOSkFgp3rTbF/RiXQsEHQOyoTA== ARC-Authentication-Results: i=1; mx1.freebsd.org; none Received: from ampere1.nyi.freebsd.org (ampere1.nyi.freebsd.org [IPv6:2610:1c1:1:6080::16:23]) by mxrelay.nyi.freebsd.org (Postfix) with ESMTP id 4cGy1R5SV3z1Pr2 for ; Wed, 03 Sep 2025 09:27:07 +0000 (UTC) (envelope-from pkg-fallout@FreeBSD.org) Received: from root (uid 0) (envelope-from pkg-fallout@FreeBSD.org) id 62f by ampere1.nyi.freebsd.org (DragonFly Mail Agent v0.13+ on ampere1.nyi.freebsd.org); Wed, 03 Sep 2025 09:27:07 +0000 To: pkg-fallout@FreeBSD.org Subject: [package - 142releng-armv7-quarterly][biology/gcta] Failed for gcta-1.94.1_3 in build Date: Wed, 03 Sep 2025 09:27:07 +0000 Message-Id: <68b809eb.62f.3c0eda0c@ampere1.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/ampere1/data/142releng-armv7-quarterly/260a422233fc/logs/gcta-1.94.1_3.log Build URL: https://pkg-status.freebsd.org/ampere1/build.html?mastername=142releng-armv7-quarterly&build=260a422233fc Log: =>> Building biology/gcta build started at Wed Sep 3 09:24:10 UTC 2025 port directory: /usr/ports/biology/gcta package name: gcta-1.94.1_3 building for: FreeBSD 142releng-armv7-quarterly-job-12 14.2-RELEASE-p5 FreeBSD 14.2-RELEASE-p5 1402000 arm maintained by: jwb@FreeBSD.org Makefile datestamp: -rw-r--r-- 1 root wheel 1581 Jul 3 01:02 /usr/ports/biology/gcta/Makefile Ports top last git commit: 260a42223 Ports top unclean checkout: no Port dir last git commit: d7951ee86 Port dir unclean checkout: no Poudriere version: poudriere-git-3.4.3 Host OSVERSION: 1500052 Jail OSVERSION: 1402000 Job Id: 12 ---Begin Environment--- SHELL=/bin/sh OSVERSION=1402000 UNAME_v=FreeBSD 14.2-RELEASE-p5 1402000 UNAME_r=14.2-RELEASE-p5 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=3.4.3 MASTERMNT=/usr/local/poudriere/data/.m/142releng-armv7-quarterly/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/142releng-armv7-quarterly/12/.p OUTPUT_REDIRECTED_STDOUT=3 P_PORTS_FEATURES=FLAVORS SUBPACKAGES SELECTED_OPTIONS MASTERNAME=142releng-armv7-quarterly SCRIPTPREFIX=/usr/local/share/poudriere SCRIPTNAME=bulk.sh OLDPWD=/usr/local/poudriere/data/.m/142releng-armv7-quarterly/ref/.p/pool POUDRIERE_PKGNAME=poudriere-git-3.4.3 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=14.2 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 pipebuf (-y) 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_3 depends on file: /usr/local/sbin/pkg - not found ===> Installing existing package /packages/All/pkg-2.2.2.pkg [142releng-armv7-quarterly-job-12] Installing pkg-2.2.2... [142releng-armv7-quarterly-job-12] Extracting pkg-2.2.2: .......... done ===> gcta-1.94.1_3 depends on file: /usr/local/sbin/pkg - found ===> Returning to build of gcta-1.94.1_3 =========================================================================== =================================================== ===== 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_3 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_3 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_3 for building ===> Extracting for gcta-1.94.1_3 => 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_3 ===> Applying FreeBSD patches for gcta-1.94.1_3 from /usr/ports/biology/gcta/files =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 ===> gcta-1.94.1_3 depends on package: boost-libs>0 - not found ===> Installing existing package /packages/All/boost-libs-1.88.0_1.pkg [142releng-armv7-quarterly-job-12] Installing boost-libs-1.88.0_1... [142releng-armv7-quarterly-job-12] `-- Installing icu-76.1,1... [142releng-armv7-quarterly-job-12] `-- Extracting icu-76.1,1: .......... done [142releng-armv7-quarterly-job-12] `-- Installing zstd-1.5.7... [142releng-armv7-quarterly-job-12] | `-- Installing liblz4-1.10.0,1... [142releng-armv7-quarterly-job-12] | `-- Extracting liblz4-1.10.0,1: .......... done [142releng-armv7-quarterly-job-12] `-- Extracting zstd-1.5.7: .......... done [142releng-armv7-quarterly-job-12] Extracting boost-libs-1.88.0_1: .......... done ===== Message from boost-libs-1.88.0_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_3 depends on package: boost-libs>0 - found ===> Returning to build of gcta-1.94.1_3 ===> gcta-1.94.1_3 depends on package: spectra>0 - not found ===> Installing existing package /packages/All/spectra-1.1.0.pkg [142releng-armv7-quarterly-job-12] Installing spectra-1.1.0... [142releng-armv7-quarterly-job-12] `-- Installing eigen-3.4.0_4... [142releng-armv7-quarterly-job-12] | `-- Installing blas-3.12.1... [142releng-armv7-quarterly-job-12] | | `-- Installing gcc13-13.3.0_3... [142releng-armv7-quarterly-job-12] | | `-- Installing binutils-2.44,1... [142releng-armv7-quarterly-job-12] | | | `-- Installing indexinfo-0.3.1_1... [142releng-armv7-quarterly-job-12] | | | `-- Extracting indexinfo-0.3.1_1: .... done [142releng-armv7-quarterly-job-12] | | `-- Extracting binutils-2.44,1: .......... done [142releng-armv7-quarterly-job-12] | | `-- Installing gmp-6.3.0... [142releng-armv7-quarterly-job-12] | | `-- Extracting gmp-6.3.0: .......... done [142releng-armv7-quarterly-job-12] | | `-- Installing mpc-1.3.1_1... [142releng-armv7-quarterly-job-12] | | | `-- Installing mpfr-4.2.2,1... [142releng-armv7-quarterly-job-12] | | | `-- Extracting mpfr-4.2.2,1: .......... done [142releng-armv7-quarterly-job-12] | | `-- Extracting mpc-1.3.1_1: ......... done [142releng-armv7-quarterly-job-12] | | `-- Extracting gcc13-13.3.0_3: .......... done [142releng-armv7-quarterly-job-12] | `-- Extracting blas-3.12.1: ........ done [142releng-armv7-quarterly-job-12] | `-- Installing lapack-3.12.1... [142releng-armv7-quarterly-job-12] | `-- Extracting lapack-3.12.1: .......... done [142releng-armv7-quarterly-job-12] `-- Extracting eigen-3.4.0_4: .......... done [142releng-armv7-quarterly-job-12] Extracting spectra-1.1.0: .......... done ===== Message from gcc13-13.3.0_3: -- 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_3 depends on package: spectra>0 - found ===> Returning to build of gcta-1.94.1_3 ===> gcta-1.94.1_3 depends on file: /usr/local/bin/cmake - not found ===> Installing existing package /packages/All/cmake-core-3.31.7.pkg [142releng-armv7-quarterly-job-12] Installing cmake-core-3.31.7... [142releng-armv7-quarterly-job-12] `-- Installing expat-2.7.1... [142releng-armv7-quarterly-job-12] `-- Extracting expat-2.7.1: .......... done [142releng-armv7-quarterly-job-12] `-- Installing jsoncpp-1.9.6_1... [142releng-armv7-quarterly-job-12] `-- Extracting jsoncpp-1.9.6_1: .......... done [142releng-armv7-quarterly-job-12] `-- Installing libidn2-2.3.8... [142releng-armv7-quarterly-job-12] | `-- Installing libunistring-1.3... [142releng-armv7-quarterly-job-12] | `-- Extracting libunistring-1.3: .......... done [142releng-armv7-quarterly-job-12] `-- Extracting libidn2-2.3.8: .......... done [142releng-armv7-quarterly-job-12] `-- Installing libuv-1.51.0... [142releng-armv7-quarterly-job-12] `-- Extracting libuv-1.51.0: .......... done [142releng-armv7-quarterly-job-12] `-- Installing rhash-1.4.4_1... [142releng-armv7-quarterly-job-12] | `-- Installing gettext-runtime-0.23.1... [142releng-armv7-quarterly-job-12] | `-- Extracting gettext-runtime-0.23.1: .......... done [142releng-armv7-quarterly-job-12] `-- Extracting rhash-1.4.4_1: .......... done [142releng-armv7-quarterly-job-12] Extracting cmake-core-3.31.7: .......... done ===> gcta-1.94.1_3 depends on file: /usr/local/bin/cmake - found ===> Returning to build of gcta-1.94.1_3 ===> gcta-1.94.1_3 depends on executable: ninja - not found ===> Installing existing package /packages/All/ninja-1.11.1,4.pkg [142releng-armv7-quarterly-job-12] Installing ninja-1.11.1,4... [142releng-armv7-quarterly-job-12] `-- Installing python311-3.11.13... [142releng-armv7-quarterly-job-12] | `-- Installing libffi-3.5.1... [142releng-armv7-quarterly-job-12] | `-- Extracting libffi-3.5.1: .......... done [142releng-armv7-quarterly-job-12] | `-- Installing mpdecimal-4.0.1... [142releng-armv7-quarterly-job-12] | `-- Extracting mpdecimal-4.0.1: .......... done [142releng-armv7-quarterly-job-12] | `-- Installing readline-8.2.13_2... [142releng-armv7-quarterly-job-12] | `-- Extracting readline-8.2.13_2: .......... done [142releng-armv7-quarterly-job-12] `-- Extracting python311-3.11.13: .......... done [142releng-armv7-quarterly-job-12] Extracting ninja-1.11.1,4: ........ done ===== Message from python311-3.11.13: -- 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_3 depends on executable: ninja - found ===> Returning to build of gcta-1.94.1_3 ===> gcta-1.94.1_3 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_3 depends on shared library: libgsl.so - not found ===> Installing existing package /packages/All/gsl-2.7.1_1.pkg [142releng-armv7-quarterly-job-12] Installing gsl-2.7.1_1... [142releng-armv7-quarterly-job-12] Extracting gsl-2.7.1_1: .......... done ===> gcta-1.94.1_3 depends on shared library: libgsl.so - found (/usr/local/lib/libgsl.so) ===> Returning to build of gcta-1.94.1_3 ===> gcta-1.94.1_3 depends on shared library: libopenblas.so - not found ===> Installing existing package /packages/All/openblas-0.3.30,2.pkg [142releng-armv7-quarterly-job-12] Installing openblas-0.3.30,2... [142releng-armv7-quarterly-job-12] Extracting openblas-0.3.30,2: .......... done ===> gcta-1.94.1_3 depends on shared library: libopenblas.so - found (/usr/local/lib/libopenblas.so) ===> Returning to build of gcta-1.94.1_3 ===> gcta-1.94.1_3 depends on shared library: libsqlite3.so - not found ===> Installing existing package /packages/All/sqlite3-3.50.2_1,1.pkg [142releng-armv7-quarterly-job-12] Installing sqlite3-3.50.2_1,1... [142releng-armv7-quarterly-job-12] `-- Installing libedit-3.1.20250104,1... [142releng-armv7-quarterly-job-12] `-- Extracting libedit-3.1.20250104,1: .......... done [142releng-armv7-quarterly-job-12] Extracting sqlite3-3.50.2_1,1: .......... done ===> gcta-1.94.1_3 depends on shared library: libsqlite3.so - found (/usr/local/lib/libsqlite3.so) ===> Returning to build of gcta-1.94.1_3 ===> gcta-1.94.1_3 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_3 ===> 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 18.1.6 -- 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/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 Clang18.1.6 -- ARCHITECTURE:arm -- Configuring done (1.1s) -- Generating done (0.0s) 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_3 [ 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