From nobody Fri Oct 06 11:32:54 2023 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 4S25rk59cDz4wBGj for ; Fri, 6 Oct 2023 11:32:54 +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 "R3" (verified OK)) by mx1.freebsd.org (Postfix) with ESMTPS id 4S25rk3W9Sz4TD3 for ; Fri, 6 Oct 2023 11:32:54 +0000 (UTC) (envelope-from pkg-fallout@FreeBSD.org) ARC-Seal: i=1; s=dkim; d=freebsd.org; t=1696591974; a=rsa-sha256; cv=none; b=D4zPN1ClScJvt91gxmpW9DrQ+FIh6+uafBuZsPY6VT8epD0xVBwq3wO5L87YFc5IFqMdvm 3G7mQXUJCjX585hLafqdoyTu1rdILi74mUFWrr9tRFKXPl7fJLmuYLMtQgIgSIBrF1dcEQ Vr5380KHVBNoeEa81NUbyv7WsO5PikLMr8pPWENhIwf5+4h7rN9n+pCYh7/KgWKbglR5Ar 832heBs5XlHsDPp707U8QsEBM6ATvBcH2JhzxvAnVw8MxBcY17fDw4zobe81bQcfg2GQw5 EjoNJAbDfiRQPLxR50nxczrFdOY/tFyTCLRLonzem0H+2ie7/+YTJlxVBPGEaQ== 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=1696591974; h=from:from:reply-to:subject:subject:date:date:message-id:message-id: to:to:cc:cc; bh=zeYXRgyjfgdWOY3FCkfRQnoJoN40YmKe65uNUczAxBk=; b=ELgVq5xn1OP+cLsRLoAEZ09saRGy/ivcAaV69ykR1biMgzQ6MZhi5vv63O5e1bm4d3gBGO kxkHMGNZeW0gTgwS6LbiPOWObIcqGpyG/wq5D0YWM2W0DP9YDtQT+nw/HDBVL5TZnAPCTC MJca22Heg0UqoegTZFv4h75Mdv2RxAJRIDmb+dgL6Q2p1RZjjdoadoYm/5POVIeM1ETdLs njC0MxygStqzCaMLU7Uji9Dlriyx25/mWyRuWeGzw6h8KGbmLIyjsAdQw16wnd65zpRBx2 h7aU70rNtj5aHt2Bw2kS1DDnwt9APQvu3yFaLxUvOgTLqJKE+BnnDoLJ4qTioA== Received: from beefy18.nyi.freebsd.org (beefy18.nyi.freebsd.org [IPv6:2610:1c1:1:6080::16:21]) by mxrelay.nyi.freebsd.org (Postfix) with ESMTP id 4S25rk2YsKzmbM for ; Fri, 6 Oct 2023 11:32:54 +0000 (UTC) (envelope-from pkg-fallout@FreeBSD.org) Received: from root (uid 0) (envelope-from pkg-fallout@FreeBSD.org) id 2065 by beefy18.nyi.freebsd.org (DragonFly Mail Agent v0.13+ on beefy18.nyi.freebsd.org); Fri, 06 Oct 2023 11:32:54 +0000 To: jwb@FreeBSD.org Subject: [package - main-amd64-default][biology/gcta] Failed for gcta-1.26.0_4 in build Cc: pkg-fallout@FreeBSD.org Date: Fri, 06 Oct 2023 11:32:54 +0000 Message-Id: <651ff066.2065.147f561c@beefy18.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/beefy18/data/main-amd64-default/pecb3f8a4918b_s8818f0f112/logs/gcta-1.26.0_4.log Build URL: https://pkg-status.freebsd.org/beefy18/build.html?mastername=main-amd64-default&build=pecb3f8a4918b_s8818f0f112 Log: =>> Building biology/gcta build started at Fri Oct 6 11:31:31 UTC 2023 port directory: /usr/ports/biology/gcta package name: gcta-1.26.0_4 building for: FreeBSD main-amd64-default-job-01 15.0-CURRENT FreeBSD 15.0-CURRENT 1500001 amd64 maintained by: jwb@FreeBSD.org Makefile ident: Poudriere version: 3.2.8-23-ga7f8d188 Host OSVERSION: 1500000 Jail OSVERSION: 1500001 Job Id: 01 !!! Jail is newer than host. (Jail: 1500001, Host: 1500000) !!! !!! This is not supported. !!! !!! Host kernel must be same or newer than jail. !!! !!! Expect build failures. !!! ---Begin Environment--- SHELL=/bin/sh OSVERSION=1500001 UNAME_v=FreeBSD 15.0-CURRENT 1500001 UNAME_r=15.0-CURRENT 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 LOCALBASE=/usr/local USER=root LIBEXECPREFIX=/usr/local/libexec/poudriere POUDRIERE_VERSION=3.2.8-23-ga7f8d188 MASTERMNT=/usr/local/poudriere/data/.m/main-amd64-default/ref POUDRIERE_BUILD_TYPE=bulk PACKAGE_BUILDING=yes SAVED_TERM= PWD=/usr/local/poudriere/data/.m/main-amd64-default/ref/.p/pool P_PORTS_FEATURES=FLAVORS SELECTED_OPTIONS MASTERNAME=main-amd64-default SCRIPTPREFIX=/usr/local/share/poudriere OLDPWD=/usr/local/poudriere/data/.m/main-amd64-default/ref/.p SCRIPTPATH=/usr/local/share/poudriere/bulk.sh POUDRIEREPATH=/usr/local/bin/poudriere ---End Environment--- ---Begin Poudriere Port Flags/Env--- PORT_FLAGS= PKGENV= FLAVOR= DEPENDS_ARGS= 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-- MAKE=gmake 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-- 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 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=" -lopenblas -fstack-protector-strong -L/usr/local/lib " LIBS="" CXX="c++" CXXFLAGS="-O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/gcta/work/eigen-3.3.9 -fopenmp -isys tem /usr/local/include " MANPREFIX="/usr/local" 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-- OSREL=15.0 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--- USE_PACKAGE_DEPENDS=yes BATCH=yes WRKDIRPREFIX=/wrkdirs PORTSDIR=/usr/ports PACKAGES=/packages DISTDIR=/distfiles PACKAGE_BUILDING=yes PACKAGE_BUILDING_FLAVORS=yes #### /usr/local/etc/poudriere.d/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 2 jobs MAKE_JOBS_NUMBER=3 #### /usr/ports/Mk/Scripts/ports_env.sh #### _CCVERSION_921dbbb2=FreeBSD clang version 16.0.6 (https://github.com/llvm/llvm-project.git llvmorg-16.0.6-0-g7cbf1a259152) Target: x86_64-unknown-freebsd15.0 Thread model: posix InstalledDir: /usr/bin _ALTCCVERSION_921dbbb2=none _CXXINTERNAL_acaad9ca=FreeBSD clang version 16.0.6 (https://github.com/llvm/llvm-project.git llvmorg-16.0.6-0-g7cbf1a259152) Target: x86_64-unknown-freebsd15.0 Thread model: posix InstalledDir: /usr/bin "/usr/bin/ld" "--eh-frame-hdr" "-dynamic-linker" "/libexec/ld-elf.so.1" "--hash-style=both" "--enable-new-dtags" "-o" "a.out" "/usr/lib/crt1.o" "/usr/lib/crti.o" "/usr/lib/crtbegin.o" "-L/usr/lib" "/dev/null" "-lc++" "-lm" "-lgcc" "--as-needed" "-lgcc_s" "--no-as-needed" "-lc" "-lgcc" "--as-needed" "-lgcc_s" "--no-as-needed" "/usr/lib/crtend.o" "/usr/lib/crtn.o" CC_OUTPUT_921dbbb2_58173849=yes CC_OUTPUT_921dbbb2_9bdba57c=yes CC_OUTPUT_921dbbb2_6a4fe7f5=yes CC_OUTPUT_921dbbb2_6bcac02b=yes CC_OUTPUT_921dbbb2_67d20829=yes CC_OUTPUT_921dbbb2_bfa62e83=yes CC_OUTPUT_921dbbb2_f0b4d593=yes CC_OUTPUT_921dbbb2_308abb44=yes CC_OUTPUT_921dbbb2_f00456e5=yes CC_OUTPUT_921dbbb2_65ad290d=yes CC_OUTPUT_921dbbb2_f2776b26=yes CC_OUTPUT_921dbbb2_53255a77=yes CC_OUTPUT_921dbbb2_911cfe02=yes CC_OUTPUT_921dbbb2_b2657cc3=yes CC_OUTPUT_921dbbb2_380987f7=yes CC_OUTPUT_921dbbb2_160933ec=yes CC_OUTPUT_921dbbb2_fb62803b=yes CC_OUTPUT_921dbbb2_af59ad06=yes CC_OUTPUT_921dbbb2_a15f3fcf=yes _OBJC_CCVERSION_921dbbb2=FreeBSD clang version 16.0.6 (https://github.com/llvm/llvm-project.git llvmorg-16.0.6-0-g7cbf1a259152) Target: x86_64-unknown-freebsd15.0 Thread model: posix InstalledDir: /usr/bin _OBJC_ALTCCVERSION_921dbbb2=none ARCH=amd64 OPSYS=FreeBSD _OSRELEASE=15.0-CURRENT OSREL=15.0 OSVERSION=1500001 PYTHONBASE=/usr/local HAVE_COMPAT_IA32_KERN=YES CONFIGURE_MAX_CMD_LEN=524288 HAVE_PORTS_ENV=1 #### Misc Poudriere #### 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) 33554432 stack size (kbytes, -s) 524288 core file size (512-blocks, -c) unlimited max memory size (kbytes, -m) unlimited locked memory (kbytes, -l) unlimited max user processes (-u) 89999 open files (-n) 1024 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-- =================================================== ===> License GPLv3 accepted by the user =========================================================================== =================================================== ===> gcta-1.26.0_4 depends on file: /usr/local/sbin/pkg - not found ===> Installing existing package /packages/All/pkg-1.20.7.pkg [main-amd64-default-job-01] Installing pkg-1.20.7... [main-amd64-default-job-01] Extracting pkg-1.20.7: .......... done ===> gcta-1.26.0_4 depends on file: /usr/local/sbin/pkg - found ===> Returning to build of gcta-1.26.0_4 =========================================================================== =================================================== =========================================================================== =================================================== ===> License GPLv3 accepted by the user ===> Fetching all distfiles required by gcta-1.26.0_4 for building =========================================================================== =================================================== ===> License GPLv3 accepted by the user ===> Fetching all distfiles required by gcta-1.26.0_4 for building => SHA256 Checksum OK for gcta_1.26.0_src.zip. => SHA256 Checksum OK for eigen-3.3.9.tar.gz. =========================================================================== =================================================== =========================================================================== =================================================== ===> License GPLv3 accepted by the user ===> Fetching all distfiles required by gcta-1.26.0_4 for building ===> Extracting for gcta-1.26.0_4 => SHA256 Checksum OK for gcta_1.26.0_src.zip. => SHA256 Checksum OK for eigen-3.3.9.tar.gz. Archive: /portdistfiles/gcta_1.26.0_src.zip extracting: /wrkdirs/usr/ports/biology/gcta/work/gcta-1.26.0/bivar_reml.cpp extracting: /wrkdirs/usr/ports/biology/gcta/work/gcta-1.26.0/cdflib.h extracting: /wrkdirs/usr/ports/biology/gcta/work/gcta-1.26.0/CommFunc.cpp extracting: /wrkdirs/usr/ports/biology/gcta/work/gcta-1.26.0/CommFunc.h extracting: /wrkdirs/usr/ports/biology/gcta/work/gcta-1.26.0/Copyright.txt extracting: /wrkdirs/usr/ports/biology/gcta/work/gcta-1.26.0/data.cpp extracting: /wrkdirs/usr/ports/biology/gcta/work/gcta-1.26.0/dcdflib.cpp extracting: /wrkdirs/usr/ports/biology/gcta/work/gcta-1.26.0/dcdflib.h extracting: /wrkdirs/usr/ports/biology/gcta/work/gcta-1.26.0/edata.cpp ^ joint_meta.cpp:766:12: note: in instantiation of member function 'Eigen::SimplicialLDLT, 1, Eigen::AMDOrdering>::compute' requested here solver.compute(B); ^ /usr/include/c++/v1/__type_traits/result_of.h:24:34: note: 'result_of (const double &, const double &)>' has been explicitly marked deprecated here template class _LIBCPP_DEPRECATED_IN_CXX17 result_of; ^ /usr/include/c++/v1/__config:808:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX17' # define _LIBCPP_DEPRECATED_IN_CXX17 _LIBCPP_DEPRECATED ^ /usr/include/c++/v1/__config:781:49: note: expanded from macro '_LIBCPP_DEPRECATED' # define _LIBCPP_DEPRECATED __attribute__((deprecated)) ^ In file included from joint_meta.cpp:1: In file included from ./gcta.h:26: In file included from ./StatFunc.h:19: In file included from /wrkdirs/usr/ports/biology/gcta/work/eigen-3.3.9/Eigen/Dense:1: In file included from /wrkdirs/usr/ports/biology/gcta/work/eigen-3.3.9/Eigen/Core:367: /wrkdirs/usr/ports/biology/gcta/work/eigen-3.3.9/Eigen/src/Core/util/Meta.h:320:25: warning: 'result_of (const double &)>' is deprecated [-Wdeprecated-declarations] typedef typename std::result_of::type type1; ^ /wrkdirs/usr/ports/biology/gcta/work/eigen-3.3.9/Eigen/src/Core/CwiseUnaryOp.h:21:20: note: in instantiation of template class 'Eigen::internal::result_of (const double &)>' requested here typedef typename result_of< ^ /wrkdirs/usr/ports/biology/gcta/work/eigen-3.3.9/Eigen/src/Core/util/XprHelper.h:497:56: note: in instantiation of template class 'Eigen::internal::traits, const Eigen::Matrix>>' requested here template::XprKind, typename StorageKind = typename traits::StorageKind> ^ /wrkdirs/usr/ports/biology/gcta/work/eigen-3.3.9/Eigen/src/Core/CwiseUnaryOp.h:95:22: note: in instantiation of default argument for 'generic_xpr_base, const Matrix>>' required here : public internal::generic_xpr_base >::type ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /wrkdirs/usr/ports/biology/gcta/work/eigen-3.3.9/Eigen/src/Core/CwiseUnaryOp.h:55:29: note: in instantiation of template class 'Eigen::CwiseUnaryOpImpl, const Eigen::Matrix, Eigen::Dense>' requested here class CwiseUnaryOp : public CwiseUnaryOpImpl::StorageKind>, internal::no_assignment_operator ^ /wrkdirs/usr/ports/biology/gcta/work/eigen-3.3.9/Eigen/src/Core/DiagonalMatrix.h:230:20: note: in instantiation of template class 'Eigen::CwiseUnaryOp, const Eigen::Matrix>' requested here typedef typename DiagonalVectorType::Scalar Scalar; ^ /wrkdirs/usr/ports/biology/gcta/work/eigen-3.3.9/Eigen/src/Core/EigenBase.h:41:30: note: (skipping 6 contexts in backtrace; use -ftemplate-backtrace-limit=0 to see all) typedef typename internal::traits::StorageKind StorageKind; ^ /wrkdirs/usr/ports/biology/gcta/work/eigen-3.3.9/Eigen/src/Core/AssignEvaluator.h:804:3: note: in instantiation of function template specialization 'Eigen::internal::call_assignment_no_alias, Eigen::Solve, 1, Eigen::AMDOrdering>, Eigen::Matrix>, Eigen::internal::assign_op>' requested here call_assignment_no_alias(dst, src, func); ^ /wrkdirs/usr/ports/biology/gcta/work/eigen-3.3.9/Eigen/src/Core/AssignEvaluator.h:782:3: note: in instantiation of function template specialization 'Eigen::internal::call_assignment, Eigen::Solve, 1, Eigen::AMDOrdering>, Eigen::Matrix>, Eigen::internal::assign_op>' requested here call_assignment(dst, src, internal::assign_op()); ^ /wrkdirs/usr/ports/biology/gcta/work/eigen-3.3.9/Eigen/src/Core/PlainObjectBase.h:714:17: note: in instantiation of function template specialization 'Eigen::internal::call_assignment, Eigen::Solve, 1, Eigen::AMDOrdering>, Eigen::Matrix>>' requested here internal::call_assignment(this->derived(), other.derived()); ^ /wrkdirs/usr/ports/biology/gcta/work/eigen-3.3.9/Eigen/src/Core/Matrix.h:225:20: note: in instantiation of function template specialization 'Eigen::PlainObjectBase>::_set, 1, Eigen::AMDOrdering>, Eigen::Matrix>>' requested here return Base::_set(other); ^ joint_meta.cpp:770:8: note: in instantiation of function template specialization 'Eigen::Matrix::operator=, 1, Eigen::AMDOrdering>, Eigen::Matrix>>' requested here bJ = solver.solve(Xty); ^ /usr/include/c++/v1/__type_traits/result_of.h:24:34: note: 'result_of (const double &)>' has been explicitly marked deprecated here template class _LIBCPP_DEPRECATED_IN_CXX17 result_of; ^ /usr/include/c++/v1/__config:808:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX17' # define _LIBCPP_DEPRECATED_IN_CXX17 _LIBCPP_DEPRECATED ^ /usr/include/c++/v1/__config:781:49: note: expanded from macro '_LIBCPP_DEPRECATED' # define _LIBCPP_DEPRECATED __attribute__((deprecated)) ^ 13 warnings generated. c++ -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/gcta/work/eigen-3.3.9 -fopenmp -isystem /usr/local/include -c mlm_assoc.cpp 12 warnings generated. c++ -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/gcta/work/eigen-3.3.9 -fopenmp -isystem /usr/local/include -c mkl.cpp In file included from mlm_assoc.cpp:13: In file included from ./gcta.h:26: In file included from ./StatFunc.h:19: In file included from /wrkdirs/usr/ports/biology/gcta/work/eigen-3.3.9/Eigen/Dense:1: In file included from /wrkdirs/usr/ports/biology/gcta/work/eigen-3.3.9/Eigen/Core:367: /wrkdirs/usr/ports/biology/gcta/work/eigen-3.3.9/Eigen/src/Core/util/Meta.h:320:25: warning: 'result_of (const double &, const double &)>' is deprecated [-Wdeprecated-declarations] typedef typename std::result_of::type type1; ^ /wrkdirs/usr/ports/biology/gcta/work/eigen-3.3.9/Eigen/src/Core/CwiseBinaryOp.h:33:20: note: in instantiation of template class 'Eigen::internal::result_of (const double &, const double &)>' requested here typedef typename result_of< ^ /wrkdirs/usr/ports/biology/gcta/work/eigen-3.3.9/Eigen/src/Core/util/XprHelper.h:497:56: note: in instantiation of template class 'Eigen::internal::traits, const Eigen::ArrayWrapper>, const Eigen::ArrayWrapper, Eigen::Matrix>>>>' requested here template::XprKind, typename StorageKind = typename traits::StorageKind> ^ /wrkdirs/usr/ports/biology/gcta/work/eigen-3.3.9/Eigen/src/Core/CwiseBinaryOp.h:149:22: note: in instantiation of default argument for 'generic_xpr_base, const ArrayWrapper>, const ArrayWrapper, Matrix, 0>>>>' required here : public internal::generic_xpr_base >::type ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /wrkdirs/usr/ports/biology/gcta/work/eigen-3.3.9/Eigen/src/Core/CwiseBinaryOp.h:78:10: note: in instantiation of template class 'Eigen::CwiseBinaryOpImpl, const Eigen::ArrayWrapper>, const Eigen::ArrayWrapper, Eigen::Matrix>>, Eigen::Dense>' requested here public CwiseBinaryOpImpl< ^ mlm_assoc.cpp:197:39: note: in instantiation of template class 'Eigen::CwiseBinaryOp, const Eigen::ArrayWrapper>, const Eigen::ArrayWrapper, Eigen::Matrix>>>' requested here if(!no_adj_covar) y_buf=_y.array()-(_X*_b).array(); // adjust phenotype for covariates ^ /usr/include/c++/v1/__type_traits/result_of.h:24:34: note: 'result_of (const double &, const double &)>' has been explicitly marked deprecated here template class _LIBCPP_DEPRECATED_IN_CXX17 result_of; ^ /usr/include/c++/v1/__config:808:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX17' # define _LIBCPP_DEPRECATED_IN_CXX17 _LIBCPP_DEPRECATED ^ /usr/include/c++/v1/__config:781:49: note: expanded from macro '_LIBCPP_DEPRECATED' # define _LIBCPP_DEPRECATED __attribute__((deprecated)) ^ In file included from mlm_assoc.cpp:13: In file included from ./gcta.h:26: In file included from ./StatFunc.h:19: In file included from /wrkdirs/usr/ports/biology/gcta/work/eigen-3.3.9/Eigen/Dense:1: In file included from /wrkdirs/usr/ports/biology/gcta/work/eigen-3.3.9/Eigen/Core:367: /wrkdirs/usr/ports/biology/gcta/work/eigen-3.3.9/Eigen/src/Core/util/Meta.h:320:25: warning: 'result_of (const double &, const double &)>' is deprecated [-Wdeprecated-declarations] typedef typename std::result_of::type type1; ^ /wrkdirs/usr/ports/biology/gcta/work/eigen-3.3.9/Eigen/src/Core/CwiseBinaryOp.h:33:20: note: in instantiation of template class 'Eigen::internal::result_of (const double &, const double &)>' requested here typedef typename result_of< ^ /wrkdirs/usr/ports/biology/gcta/work/eigen-3.3.9/Eigen/src/Core/util/XprHelper.h:497:56: note: in instantiation of template class 'Eigen::internal::traits, const Eigen::CwiseNullaryOp, const Eigen::Matrix>, const Eigen::Map, 2>>>' requested here template::XprKind, typename StorageKind = typename traits::StorageKind> ^ /wrkdirs/usr/ports/biology/gcta/work/eigen-3.3.9/Eigen/src/Core/CwiseBinaryOp.h:149:22: note: in instantiation of default argument for 'generic_xpr_base, const CwiseNullaryOp, const Matrix>, const Map, 2, Stride<0, 0>>>>' required here : public internal::generic_xpr_base >::type ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /wrkdirs/usr/ports/biology/gcta/work/eigen-3.3.9/Eigen/src/Core/CwiseBinaryOp.h:78:10: note: in instantiation of template class 'Eigen::CwiseBinaryOpImpl, const Eigen::CwiseNullaryOp, const Eigen::Matrix>, const Eigen::Map, 2>, Eigen::Dense>' requested here public CwiseBinaryOpImpl< ^ /wrkdirs/usr/ports/biology/gcta/work/eigen-3.3.9/Eigen/src/Core/GeneralProduct.h:287:40: note: in instantiation of template class 'Eigen::CwiseBinaryOp, const Eigen::CwiseNullaryOp, const Eigen::Matrix>, const Eigen::Map, 2>>' requested here dest.matrix() += actualAlpha * MappedDest(actualDestPtr, dest.size()); ^ /wrkdirs/usr/ports/biology/gcta/work/eigen-3.3.9/Eigen/src/Core/ProductEvaluators.h:383:31: note: (skipping 14 contexts in backtrace; use -ftemplate-backtrace-limit=0 to see all) >::run(actual_lhs, actual_rhs, dst, alpha); ^ /wrkdirs/usr/ports/biology/gcta/work/eigen-3.3.9/Eigen/src/Core/AssignEvaluator.h:804:3: note: in instantiation of function template specialization 'Eigen::internal::call_assignment_no_alias, Eigen::CwiseBinaryOp, const Eigen::ArrayWrapper>, const Eigen::ArrayWrapper, Eigen::Matrix>>>, Eigen::internal::assign_op>' requested here call_assignment_no_alias(dst, src, func); ^ /wrkdirs/usr/ports/biology/gcta/work/eigen-3.3.9/Eigen/src/Core/AssignEvaluator.h:782:3: note: in instantiation of function template specialization 'Eigen::internal::call_assignment, Eigen::CwiseBinaryOp, const Eigen::ArrayWrapper>, const Eigen::ArrayWrapper, Eigen::Matrix>>>, Eigen::internal::assign_op>' requested here call_assignment(dst, src, internal::assign_op()); ^ /wrkdirs/usr/ports/biology/gcta/work/eigen-3.3.9/Eigen/src/Core/PlainObjectBase.h:714:17: note: in instantiation of function template specialization 'Eigen::internal::call_assignment, Eigen::CwiseBinaryOp, const Eigen::ArrayWrapper>, const Eigen::ArrayWrapper, Eigen::Matrix>>>>' requested here internal::call_assignment(this->derived(), other.derived()); ^ /wrkdirs/usr/ports/biology/gcta/work/eigen-3.3.9/Eigen/src/Core/Matrix.h:225:20: note: in instantiation of function template specialization 'Eigen::PlainObjectBase>::_set, const Eigen::ArrayWrapper>, const Eigen::ArrayWrapper, Eigen::Matrix>>>>' requested here return Base::_set(other); ^ mlm_assoc.cpp:197:28: note: in instantiation of function template specialization 'Eigen::Matrix::operator=, const Eigen::ArrayWrapper>, const Eigen::ArrayWrapper, Eigen::Matrix>>>>' requested here if(!no_adj_covar) y_buf=_y.array()-(_X*_b).array(); // adjust phenotype for covariates ^ /usr/include/c++/v1/__type_traits/result_of.h:24:34: note: 'result_of (const double &, const double &)>' has been explicitly marked deprecated here template class _LIBCPP_DEPRECATED_IN_CXX17 result_of; ^ /usr/include/c++/v1/__config:808:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX17' # define _LIBCPP_DEPRECATED_IN_CXX17 _LIBCPP_DEPRECATED ^ /usr/include/c++/v1/__config:781:49: note: expanded from macro '_LIBCPP_DEPRECATED' # define _LIBCPP_DEPRECATED __attribute__((deprecated)) ^ 7 warnings generated. c++ -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/gcta/work/eigen-3.3.9 -fopenmp -isystem /usr/local/include -c option.cpp mkl.cpp:360:5: error: no matching function for call to 'dpotrf_' dpotrf_(&uplo, &int_n, Vi_mkl, &int_n, &info); ^~~~~~~ /usr/local/include/lapack.h:13624:12: note: candidate function not viable: requires 6 arguments, but 5 were provided lapack_int LAPACK_dpotrf_base( ^ /usr/local/include/lapack.h:13623:28: note: expanded from macro 'LAPACK_dpotrf_base' #define LAPACK_dpotrf_base LAPACK_GLOBAL(dpotrf,DPOTRF) ^ /usr/local/include/lapacke_mangling.h:12:39: note: expanded from macro 'LAPACK_GLOBAL' #define LAPACK_GLOBAL(lcname,UCNAME) lcname##_ ^ :346:1: note: expanded from here dpotrf_ ^ mkl.cpp:372:9: error: no matching function for call to 'dpotri_' dpotri_(&uplo, &int_n, Vi_mkl, &int_n, &info); ^~~~~~~ /usr/local/include/lapack.h:13752:6: note: candidate function not viable: requires 6 arguments, but 5 were provided void LAPACK_dpotri_base( ^ /usr/local/include/lapack.h:13751:28: note: expanded from macro 'LAPACK_dpotri_base' #define LAPACK_dpotri_base LAPACK_GLOBAL(dpotri,DPOTRI) ^ /usr/local/include/lapacke_mangling.h:12:39: note: expanded from macro 'LAPACK_GLOBAL' #define LAPACK_GLOBAL(lcname,UCNAME) lcname##_ ^ :354:1: note: expanded from here dpotri_ ^ 2 errors generated. gmake[1]: *** [Makefile:72: mkl.o] Error 1 gmake[1]: *** Waiting for unfinished jobs.... option.cpp:135:24: warning: ISO C++11 does not allow conversion from string literal to 'value_type' (aka 'char *') [-Wwritable-strings] argv[option_num] = "gcta"; ^ option.cpp:136:28: warning: ISO C++11 does not allow conversion from string literal to 'value_type' (aka 'char *') [-Wwritable-strings] argv[option_num + 1] = "gcta"; ^ 2 warnings generated. 2 warnings generated. gmake[1]: Leaving directory '/wrkdirs/usr/ports/biology/gcta/work/gcta-1.26.0' ===> 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