From nobody Wed Sep 04 18:51:35 2024 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 4WzWmm2Jprz5V9gP for ; Wed, 04 Sep 2024 18:51:36 +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 4WzWmm0WL6z40Xg for ; Wed, 4 Sep 2024 18:51:36 +0000 (UTC) (envelope-from pkg-fallout@FreeBSD.org) ARC-Seal: i=1; s=dkim; d=freebsd.org; t=1725475896; a=rsa-sha256; cv=none; b=ekAkPIGhkfle3PVJaXKgjOcgUwzC4GQjJWpZiuTJ4o4eM0UdFyAR52Xzzy2eYwKdUDu3Ks 8uywL16wqRxQVFtzhUFsTQK1B1+9nj/eBERuOSxNMLrieu8drU7P3PrwDGM5wOpN6IxL+i CwSnn8KD1lpc1ekFPAg8eE/VCAmHb20xct1KCBqimxguYMIiEjCj59I1qqLZB9wyVyozJa oLpHwftK0WUBNPPW6ZZq7xy5OXFOUrm9sfj5ILmi9Eg3Itg8Ux+0kzcDzr8ArEKvUkx0BN 8NNAjq/gq1ZqvM0jx3j9PxlgxMECGk3PcMR2VGF+EjhHcKMjCqH3AFloRAFwCw== ARC-Authentication-Results: i=1; mx1.freebsd.org; none ARC-Message-Signature: i=1; a=rsa-sha256; c=relaxed/relaxed; d=freebsd.org; s=dkim; t=1725475896; h=from:from:reply-to:subject:subject:date:date:message-id:message-id: to:to:cc; bh=Mzkq7vOD2NiyvwbPXMnOWA2XxFVtq4fv7r89RLlYGeA=; b=t38RS5/SM0OR0ztSNRPr5j2a0AHCLvRB54PYDq+FErpCFYR4ChZaHOlbxUKgKHx4haEgDO JNBrjFId0uXSjQ+Id/jVOa7N3Q1NWqNAVcSeCUd7i71BNbpSfqfJRY2M16Fs/BeuLn+CW2 rWb6de21UEzkY55d0aR6bOAe8Wv4xARr6vXlNpkb3ZoZtdyjAZ3Z+omZAQrE9ALjBGGBKp xRItZt6afDPL5dPUYh6noelBo1hWvSaPT+9M4nP4P0lu/0X0yqE5PkcUof4iTdSdZGsGTz e9ScOYducKdSllFi0IbTYXhUrX/tT7NRV8HEJS23YOqrM7iwhnyP2ggz5WqLPA== 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 4WzWml6Y5qzbcV for ; Wed, 4 Sep 2024 18:51:35 +0000 (UTC) (envelope-from pkg-fallout@FreeBSD.org) Received: from root (uid 0) (envelope-from pkg-fallout@FreeBSD.org) id 4850 by ampere3.nyi.freebsd.org (DragonFly Mail Agent v0.13+ on ampere3.nyi.freebsd.org); Wed, 04 Sep 2024 18:51:35 +0000 To: pkg-fallout@FreeBSD.org Subject: [package - 133releng-armv7-default][biology/gcta] Failed for gcta-1.94.1_2 in build Date: Wed, 04 Sep 2024 18:51:35 +0000 Message-Id: <66d8ac37.4850.f253ed6@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/133releng-armv7-default/1b6eada811a7/logs/gcta-1.94.1_2.log Build URL: https://pkg-status.freebsd.org/ampere3/build.html?mastername=133releng-armv7-default&build=1b6eada811a7 Log: =>> Building biology/gcta build started at Wed Sep 4 18:50:26 UTC 2024 port directory: /usr/ports/biology/gcta package name: gcta-1.94.1_2 building for: FreeBSD 133releng-armv7-default-job-08 13.3-RELEASE-p5 FreeBSD 13.3-RELEASE-p5 1303001 arm maintained by: jwb@FreeBSD.org Makefile datestamp: -rw-r--r-- 1 root wheel 1581 Jun 27 01:08 /usr/ports/biology/gcta/Makefile Ports top last git commit: 1b6eada811a 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: 1500019 Jail OSVERSION: 1303001 Job Id: 08 ---Begin Environment--- SHELL=/bin/csh OSVERSION=1303001 UNAME_v=FreeBSD 13.3-RELEASE-p5 1303001 UNAME_r=13.3-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=3.4.2 MASTERMNT=/usr/local/poudriere/data/.m/133releng-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/133releng-armv7-default/08/.p OUTPUT_REDIRECTED_STDOUT=3 P_PORTS_FEATURES=FLAVORS SUBPACKAGES SELECTED_OPTIONS MASTERNAME=133releng-armv7-default SCRIPTPREFIX=/usr/local/share/poudriere SCRIPTNAME=bulk.sh OLDPWD=/usr/local/poudriere/data/.m/133releng-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=13.3 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 [133releng-armv7-default-job-08] Installing pkg-1.21.3... [133releng-armv7-default-job-08] 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-1.84.0.pkg [133releng-armv7-default-job-08] Installing boost-libs-1.84.0... [133releng-armv7-default-job-08] `-- Installing icu-74.2_1,1... [133releng-armv7-default-job-08] `-- Extracting icu-74.2_1,1: .......... done [133releng-armv7-default-job-08] Extracting boost-libs-1.84.0: .......... done ===== Message from boost-libs-1.84.0: -- 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-1.0.1_1.pkg [133releng-armv7-default-job-08] Installing spectra-1.0.1_1... [133releng-armv7-default-job-08] `-- Installing eigen-3.4.0_3... [133releng-armv7-default-job-08] | `-- Installing blas-3.12.0_1... [133releng-armv7-default-job-08] | | `-- Installing gcc13-13.2.0_4... [133releng-armv7-default-job-08] | | `-- Installing binutils-2.40_7,1... [133releng-armv7-default-job-08] | | | `-- Installing indexinfo-0.3.1... [133releng-armv7-default-job-08] | | | `-- Extracting indexinfo-0.3.1: .... done [133releng-armv7-default-job-08] | | | `-- Installing zstd-1.5.6... [133releng-armv7-default-job-08] | | | `-- Installing liblz4-1.10.0,1... [133releng-armv7-default-job-08] | | | `-- Extracting liblz4-1.10.0,1: .......... done [133releng-armv7-default-job-08] | | | `-- Extracting zstd-1.5.6: .......... done [133releng-armv7-default-job-08] | | `-- Extracting binutils-2.40_7,1: .......... done [133releng-armv7-default-job-08] | | `-- Installing gmp-6.3.0... [133releng-armv7-default-job-08] | | `-- Extracting gmp-6.3.0: .......... done [133releng-armv7-default-job-08] | | `-- Installing mpc-1.3.1_1... [133releng-armv7-default-job-08] | | | `-- Installing mpfr-4.2.1,1... [133releng-armv7-default-job-08] | | | `-- Extracting mpfr-4.2.1,1: .......... done [133releng-armv7-default-job-08] | | `-- Extracting mpc-1.3.1_1: ......... done [133releng-armv7-default-job-08] | | `-- Extracting gcc13-13.2.0_4: .......... done [133releng-armv7-default-job-08] | `-- Extracting blas-3.12.0_1: ........ done [133releng-armv7-default-job-08] | `-- Installing lapack-3.12.0_2... [133releng-armv7-default-job-08] | `-- Extracting lapack-3.12.0_2: .......... done [133releng-armv7-default-job-08] `-- Extracting eigen-3.4.0_3: .......... done [133releng-armv7-default-job-08] Extracting spectra-1.0.1_1: .......... done ===== Message from gcc13-13.2.0_4: -- 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-3.30.2.pkg [133releng-armv7-default-job-08] Installing cmake-core-3.30.2... [133releng-armv7-default-job-08] `-- Installing expat-2.6.2... [133releng-armv7-default-job-08] `-- Extracting expat-2.6.2: .......... done [133releng-armv7-default-job-08] `-- Installing jsoncpp-1.9.5... [133releng-armv7-default-job-08] `-- Extracting jsoncpp-1.9.5: .......... done [133releng-armv7-default-job-08] `-- Installing libuv-1.48.0... [133releng-armv7-default-job-08] `-- Extracting libuv-1.48.0: .......... done [133releng-armv7-default-job-08] `-- Installing rhash-1.4.4_1... [133releng-armv7-default-job-08] | `-- Installing gettext-runtime-0.22.5... [133releng-armv7-default-job-08] | `-- Extracting gettext-runtime-0.22.5: .......... done [133releng-armv7-default-job-08] `-- Extracting rhash-1.4.4_1: .......... done [133releng-armv7-default-job-08] Extracting cmake-core-3.30.2: .......... 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 [133releng-armv7-default-job-08] Installing ninja-1.11.1,4... [133releng-armv7-default-job-08] `-- Installing python311-3.11.9_1... [133releng-armv7-default-job-08] | `-- Installing libffi-3.4.6... [133releng-armv7-default-job-08] | `-- Extracting libffi-3.4.6: .......... done [133releng-armv7-default-job-08] | `-- Installing mpdecimal-4.0.0... [133releng-armv7-default-job-08] | `-- Extracting mpdecimal-4.0.0: .......... done [133releng-armv7-default-job-08] | `-- Installing readline-8.2.10... [133releng-armv7-default-job-08] | `-- Extracting readline-8.2.10: .......... done [133releng-armv7-default-job-08] `-- Extracting python311-3.11.9_1: .......... done [133releng-armv7-default-job-08] Extracting ninja-1.11.1,4: ........ done ===== Message from python311-3.11.9_1: -- 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 [133releng-armv7-default-job-08] Installing gsl-2.7.1_1... [133releng-armv7-default-job-08] 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 [133releng-armv7-default-job-08] Installing openblas-0.3.27,2... [133releng-armv7-default-job-08] 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 [133releng-armv7-default-job-08] Installing sqlite3-3.46.1,1... [133releng-armv7-default-job-08] `-- Installing libedit-3.1.20240808,1... [133releng-armv7-default-job-08] `-- Extracting libedit-3.1.20240808,1: .......... done [133releng-armv7-default-job-08] 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 < 3.5 will be removed from a future version of CMake. Update the VERSION argument value or use a ... suffix to tell CMake that the project does not need compatibility with older versions. -- The C compiler identification is Clang 17.0.6 -- The CXX compiler identification is Clang 17.0.6 -- 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 Clang17.0.6 -- ARCHITECTURE:arm -- Configuring done (3.4s) -- 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