From nobody Fri Nov 08 01:26:02 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 4Xl1VM1D9rz5d12C for ; Fri, 08 Nov 2024 01:26:03 +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 "R10" (verified OK)) by mx1.freebsd.org (Postfix) with ESMTPS id 4Xl1VL6dNnz4ZKg for ; Fri, 8 Nov 2024 01:26:02 +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=1731029162; h=from:from:reply-to:subject:subject:date:date:message-id:message-id: to:to:cc; bh=qJE1ULkce3yQyltd7uCR2JTGx7pWGoNxecz4zOS5bOI=; b=JluBPmzjVBWYC3yDQ+vH3stVsmp7tFrZ6KAVSXWXTTnin7L+sudQbf94BraHEQ28gFlLgK 5nmbXuDDoHX3R3/3sVkHV5S9RVEwgqkGeo7YDS/+TtZVAAqjQwWVT3gooir+Xcs3GiCaxp GkIfN7G73l9eXqv7l7mKBVqzLsCnLf670o08OnYwdLctskbvvYPYsgi/jc+i3QSdW7ohI2 qdt4LYywznuIj8Z9qM/jMNrbRiDJctmVo3YObYgeHxW81LNSW8BVAX2toeoEUuHSzSKyFo KFpi6uQjyYEq0/NEoY6HuglyzwQrpgE/+P1hi2gYKt/n4BxcqEfg6Pb7hkSyow== ARC-Authentication-Results: i=1; mx1.freebsd.org; none ARC-Seal: i=1; s=dkim; d=freebsd.org; t=1731029162; a=rsa-sha256; cv=none; b=n8VHM9ypsXRL/mI/ilBZhnkz60337dG8Xs+Bwc0kXR+kI6tb6gx1NijtzP/MWils2z7MMD BDX96d/gA1dz35ZkBoJG9W9fp86TL/5c4OOxWzr8cMmXl1fZZW9UFZ48UZHJAd2y4B0Io8 tuqBd0uLIXhtD4RhU6iwnq2e7uaqfQJDfFmu3nAllR5hIbO47Uk80sXDGdtjV3V6NY0oKf 0dpzI1ixjScdcD1B+0S/Mvn6PoIHjQPg3NuvCSrzQg5vbmxtWyNV0Oaj4yh88xr1UxjpRu ciCnmZRP7rgWH19/xyPC2Fji57Cf/o1nWKJwyfALrNfCoMJXGoZem7YTD2tOUA== 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 4Xl1VL5wcYz18Vd for ; Fri, 8 Nov 2024 01:26:02 +0000 (UTC) (envelope-from pkg-fallout@FreeBSD.org) Received: from root (uid 0) (envelope-from pkg-fallout@FreeBSD.org) id 5b4b by ampere1.nyi.freebsd.org (DragonFly Mail Agent v0.13+ on ampere1.nyi.freebsd.org); Fri, 08 Nov 2024 01:26:02 +0000 To: pkg-fallout@FreeBSD.org Subject: [package - 133releng-armv7-quarterly][biology/gcta] Failed for gcta-1.94.1_2 in build Date: Fri, 08 Nov 2024 01:26:02 +0000 Message-Id: <672d68aa.5b4b.1fd5772f@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/133releng-armv7-quarterly/2e2d801cf977/logs/gcta-1.94.1_2.log Build URL: https://pkg-status.freebsd.org/ampere1/build.html?mastername=133releng-armv7-quarterly&build=2e2d801cf977 Log: =>> Building biology/gcta build started at Fri Nov 8 01:25:22 UTC 2024 port directory: /usr/ports/biology/gcta package name: gcta-1.94.1_2 building for: FreeBSD 133releng-armv7-quarterly-job-07 13.3-RELEASE-p8 FreeBSD 13.3-RELEASE-p8 1303001 arm maintained by: jwb@FreeBSD.org Makefile datestamp: -rw-r--r-- 1 root wheel 1581 Oct 15 01:02 /usr/ports/biology/gcta/Makefile Ports top last git commit: 2e2d801cf Ports top unclean checkout: no Port dir last git commit: db5128afd Port dir unclean checkout: no Poudriere version: poudriere-git-3.4.2 Host OSVERSION: 1500023 Jail OSVERSION: 1303001 Job Id: 07 ---Begin Environment--- SHELL=/bin/csh OSVERSION=1303001 UNAME_v=FreeBSD 13.3-RELEASE-p8 1303001 UNAME_r=13.3-RELEASE-p8 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-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/133releng-armv7-quarterly/07/.p OUTPUT_REDIRECTED_STDOUT=3 P_PORTS_FEATURES=FLAVORS SUBPACKAGES SELECTED_OPTIONS MASTERNAME=133releng-armv7-quarterly SCRIPTPREFIX=/usr/local/share/poudriere SCRIPTNAME=bulk.sh OLDPWD=/usr/local/poudriere/data/.m/133releng-armv7-quarterly/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-quarterly-job-07] Installing pkg-1.21.3... [133releng-armv7-quarterly-job-07] 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-1.85.0.pkg [133releng-armv7-quarterly-job-07] Installing boost-libs-1.85.0... [133releng-armv7-quarterly-job-07] `-- Installing icu-74.2_1,1... [133releng-armv7-quarterly-job-07] `-- Extracting icu-74.2_1,1: .......... done [133releng-armv7-quarterly-job-07] Extracting boost-libs-1.85.0: .......... done ===== Message from boost-libs-1.85.0: -- 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-quarterly-job-07] Installing spectra-1.0.1_1... [133releng-armv7-quarterly-job-07] `-- Installing eigen-3.4.0_3... [133releng-armv7-quarterly-job-07] | `-- Installing blas-3.12.0_1... [133releng-armv7-quarterly-job-07] | | `-- Installing gcc13-13.3.0... [133releng-armv7-quarterly-job-07] | | `-- Installing binutils-2.43.1,1... [133releng-armv7-quarterly-job-07] | | | `-- Installing indexinfo-0.3.1... [133releng-armv7-quarterly-job-07] | | | `-- Extracting indexinfo-0.3.1: .... done [133releng-armv7-quarterly-job-07] | | | `-- Installing zstd-1.5.6... [133releng-armv7-quarterly-job-07] | | | `-- Installing liblz4-1.10.0,1... [133releng-armv7-quarterly-job-07] | | | `-- Extracting liblz4-1.10.0,1: .......... done [133releng-armv7-quarterly-job-07] | | | `-- Extracting zstd-1.5.6: .......... done [133releng-armv7-quarterly-job-07] | | `-- Extracting binutils-2.43.1,1: .......... done [133releng-armv7-quarterly-job-07] | | `-- Installing gmp-6.3.0... [133releng-armv7-quarterly-job-07] | | `-- Extracting gmp-6.3.0: .......... done [133releng-armv7-quarterly-job-07] | | `-- Installing mpc-1.3.1_1... [133releng-armv7-quarterly-job-07] | | | `-- Installing mpfr-4.2.1,1... [133releng-armv7-quarterly-job-07] | | | `-- Extracting mpfr-4.2.1,1: .......... done [133releng-armv7-quarterly-job-07] | | `-- Extracting mpc-1.3.1_1: ......... done [133releng-armv7-quarterly-job-07] | | `-- Extracting gcc13-13.3.0: .......... done [133releng-armv7-quarterly-job-07] | `-- Extracting blas-3.12.0_1: ........ done [133releng-armv7-quarterly-job-07] | `-- Installing lapack-3.12.0_2... [133releng-armv7-quarterly-job-07] | `-- Extracting lapack-3.12.0_2: .......... done [133releng-armv7-quarterly-job-07] `-- Extracting eigen-3.4.0_3: .......... done [133releng-armv7-quarterly-job-07] Extracting spectra-1.0.1_1: .......... 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-3.30.5.pkg [133releng-armv7-quarterly-job-07] Installing cmake-core-3.30.5... [133releng-armv7-quarterly-job-07] `-- Installing expat-2.6.3... [133releng-armv7-quarterly-job-07] `-- Extracting expat-2.6.3: .......... done [133releng-armv7-quarterly-job-07] `-- Installing jsoncpp-1.9.6_1... [133releng-armv7-quarterly-job-07] `-- Extracting jsoncpp-1.9.6_1: .......... done [133releng-armv7-quarterly-job-07] `-- Installing libuv-1.49.0... [133releng-armv7-quarterly-job-07] `-- Extracting libuv-1.49.0: .......... done [133releng-armv7-quarterly-job-07] `-- Installing rhash-1.4.4_1... [133releng-armv7-quarterly-job-07] | `-- Installing gettext-runtime-0.22.5... [133releng-armv7-quarterly-job-07] | `-- Extracting gettext-runtime-0.22.5: .......... done [133releng-armv7-quarterly-job-07] `-- Extracting rhash-1.4.4_1: .......... done [133releng-armv7-quarterly-job-07] Extracting cmake-core-3.30.5: .......... 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-quarterly-job-07] Installing ninja-1.11.1,4... [133releng-armv7-quarterly-job-07] `-- Installing python311-3.11.10... [133releng-armv7-quarterly-job-07] | `-- Installing libffi-3.4.6... [133releng-armv7-quarterly-job-07] | `-- Extracting libffi-3.4.6: .......... done [133releng-armv7-quarterly-job-07] | `-- Installing mpdecimal-4.0.0... [133releng-armv7-quarterly-job-07] | `-- Extracting mpdecimal-4.0.0: .......... done [133releng-armv7-quarterly-job-07] | `-- Installing readline-8.2.13_1... [133releng-armv7-quarterly-job-07] | `-- Extracting readline-8.2.13_1: .......... done [133releng-armv7-quarterly-job-07] `-- Extracting python311-3.11.10: .......... done [133releng-armv7-quarterly-job-07] Extracting ninja-1.11.1,4: ........ done ===== Message from python311-3.11.10: -- 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-quarterly-job-07] Installing gsl-2.7.1_1... [133releng-armv7-quarterly-job-07] 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-quarterly-job-07] Installing openblas-0.3.27,2... [133releng-armv7-quarterly-job-07] 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-quarterly-job-07] Installing sqlite3-3.46.1,1... [133releng-armv7-quarterly-job-07] `-- Installing libedit-3.1.20240808,1... [133releng-armv7-quarterly-job-07] `-- Extracting libedit-3.1.20240808,1: .......... done [133releng-armv7-quarterly-job-07] 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 (1.1s) -- 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