From nobody Sat Oct 14 11:16:19 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 4S715w05Nxz4xcym for ; Sat, 14 Oct 2023 11:16:20 +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 4S715v57xCz3Jn2 for ; Sat, 14 Oct 2023 11:16:19 +0000 (UTC) (envelope-from pkg-fallout@FreeBSD.org) ARC-Seal: i=1; s=dkim; d=freebsd.org; t=1697282179; a=rsa-sha256; cv=none; b=f0lMhsILxTHWxilTqSS3ZocHMFBypbJhw/11C1R8Pv3sft3gQn+e3hO1dc0Akwy9P9p91a nDuFuhleYgqBihlAWb1bRQgtlXeOLfh5kK0vStKJJaiLCuoKZREe6SBoQFD3Sle1vjKdT8 BVvfV2QfohlJB9HzTJ1ywhJub8LL2AY40gGHLLxX/psKicGSVhmiI2N8k3fx3fTzYLlXFI eabMRu0LbIGItgMjUHKFjXfWNB9GnpmHYKLsCEhrJa4FvPVgDCn4ZBWvqKFGBE5iOxTNE4 6bUIZ3kLDFCLkXhcuQ8xLqy3p/8YdavRDl3Jke1b5zVinGSFWhY0fFxwdPCD1A== 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=1697282179; h=from:from:reply-to:subject:subject:date:date:message-id:message-id: to:to:cc:cc; bh=Z2lfbJ+jcz2zbAoSP1ZNpJaIoFwmnJVLWawA+4iJlQ0=; b=uHN3tOenf3Istjrj7i6YTlgUyHz2n0BACIBLQ6Piy7wts5PqUp/0mdPCoViaTjh3FpMN7Z vcQGZ9LgRDqYtb2sUbwIRyV10hc+tN2qDClcu8pl2VtznsgcBN+CwRAlzUdqSz+nJKHHMN rUpJaj3wxYhXeCXQKiDyItKOkUu8L1vaNvl6L2jOyl2/5kYfrIC8k9vgXHd9l6hUOGeUFd 1gpsdn6TD7WaC4yvVq7lbxChwFCimPj0ziK+dIM1K5kqzevZV4whzK3U8mxks//+ihdWNH 5ORSzxRzFOobew1satlifmkYR3oukAnClnN4n+4GXFn19l/bP+TXu3+r2MfSvA== 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 4S715v3xWLzD06 for ; Sat, 14 Oct 2023 11:16:19 +0000 (UTC) (envelope-from pkg-fallout@FreeBSD.org) Received: from root (uid 0) (envelope-from pkg-fallout@FreeBSD.org) id 4131 by ampere3.nyi.freebsd.org (DragonFly Mail Agent v0.13+ on ampere3.nyi.freebsd.org); Sat, 14 Oct 2023 11:16:19 +0000 To: jwb@FreeBSD.org Subject: [package - 132arm64-default][biology/gcta] Failed for gcta-1.26.0_4 in build Cc: pkg-fallout@FreeBSD.org Date: Sat, 14 Oct 2023 11:16:19 +0000 Message-Id: <652a7883.4131.101dc9f9@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/132arm64-default/08943441f26e/logs/gcta-1.26.0_4.log Build URL: https://pkg-status.freebsd.org/ampere3/build.html?mastername=132arm64-default&build=08943441f26e Log: =>> Building biology/gcta build started at Sat Oct 14 11:14:35 UTC 2023 port directory: /usr/ports/biology/gcta package name: gcta-1.26.0_4 building for: FreeBSD 132arm64-default-job-12 13.2-RELEASE-p4 FreeBSD 13.2-RELEASE-p4 arm64 maintained by: jwb@FreeBSD.org Makefile ident: Poudriere version: 3.2.8-23-ga7f8d188 Host OSVERSION: 1500000 Jail OSVERSION: 1302001 Job Id: 12 ---Begin Environment--- SHELL=/bin/csh OSVERSION=1302001 UNAME_v=FreeBSD 13.2-RELEASE-p4 UNAME_r=13.2-RELEASE-p4 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/132arm64-default/ref POUDRIERE_BUILD_TYPE=bulk PACKAGE_BUILDING=yes SAVED_TERM= PWD=/usr/local/poudriere/data/.m/132arm64-default/ref/.p/pool P_PORTS_FEATURES=FLAVORS SELECTED_OPTIONS MASTERNAME=132arm64-default SCRIPTPREFIX=/usr/local/share/poudriere OLDPWD=/usr/local/poudriere/data/.m/132arm64-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=13.2 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--- 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 14.0.5 (https://github.com/llvm/llvm-project.git llvmorg-14.0.5-0-gc12386ae247c) Target: aarch64-unknown-freebsd13.2 Thread model: posix InstalledDir: /usr/bin _ALTCCVERSION_921dbbb2=none _CXXINTERNAL_acaad9ca=FreeBSD clang version 14.0.5 (https://github.com/llvm/llvm-project.git llvmorg-14.0.5-0-gc12386ae247c) Target: aarch64-unknown-freebsd13.2 Thread model: posix InstalledDir: /usr/bin "/usr/bin/ld" "--eh-frame-hdr" "-dynamic-linker" "/libexec/ld-elf.so.1" "--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 14.0.5 (https://github.com/llvm/llvm-project.git llvmorg-14.0.5-0-gc12386ae247c) Target: aarch64-unknown-freebsd13.2 Thread model: posix InstalledDir: /usr/bin _OBJC_ALTCCVERSION_921dbbb2=none ARCH=aarch64 OPSYS=FreeBSD _OSRELEASE=13.2-RELEASE-p4 OSREL=13.2 OSVERSION=1302001 PYTHONBASE=/usr/local 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) 1048576 stack size (kbytes, -s) 1048576 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 [132arm64-default-job-12] Installing pkg-1.20.7... [132arm64-default-job-12] 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 extracting: /wrkdirs/usr/ports/biology/gcta/work/gcta-1.26.0/eigen_func.cpp extracting: /wrkdirs/usr/ports/biology/gcta/work/gcta-1.26.0/eigen_func.h extracting: /wrkdirs/usr/ports/biology/gcta/work/gcta-1.26.0/ejma.cpp extracting: /wrkdirs/usr/ports/biology/gcta/work/gcta-1.26.0/est_hsq.cpp extracting: /wrkdirs/usr/ports/biology/gcta/work/gcta-1.26.0/gbat.cpp extracting: /wrkdirs/usr/ports/biology/gcta/work/gcta-1.26.0/gcta.h extracting: /wrkdirs/usr/ports/biology/gcta/work/gcta-1.26.0/GNU_General_Public_License_v3.txt extracting: /wrkdirs/usr/ports/biology/gcta/work/gcta-1.26.0/grm.cpp extracting: /wrkdirs/usr/ports/biology/gcta/work/gcta-1.26.0/gwas_simu.cpp extracting: /wrkdirs/usr/ports/biology/gcta/work/gcta-1.26.0/HowToCompile.txt extracting: /wrkdirs/usr/ports/biology/gcta/work/gcta-1.26.0/ipmpar.h extracting: /wrkdirs/usr/ports/biology/gcta/work/gcta-1.26.0/joint_meta.cpp extracting: /wrkdirs/usr/ports/biology/gcta/work/gcta-1.26.0/ld.cpp extracting: /wrkdirs/usr/ports/biology/gcta/work/gcta-1.26.0/Makefile extracting: /wrkdirs/usr/ports/biology/gcta/work/gcta-1.26.0/mkl.cpp extracting: /wrkdirs/usr/ports/biology/gcta/work/gcta-1.26.0/mlm_assoc.cpp extracting: /wrkdirs/usr/ports/biology/gcta/work/gcta-1.26.0/option.cpp extracting: /wrkdirs/usr/ports/biology/gcta/work/gcta-1.26.0/popu_genet.cpp extracting: /wrkdirs/usr/ports/biology/gcta/work/gcta-1.26.0/raw_geno.cpp extracting: /wrkdirs/usr/ports/biology/gcta/work/gcta-1.26.0/read_imput.cpp extracting: /wrkdirs/usr/ports/biology/gcta/work/gcta-1.26.0/README.txt extracting: /wrkdirs/usr/ports/biology/gcta/work/gcta-1.26.0/reml_within_family.cpp extracting: /wrkdirs/usr/ports/biology/gcta/work/gcta-1.26.0/sbat.cpp extracting: /wrkdirs/usr/ports/biology/gcta/work/gcta-1.26.0/StatFunc.cpp extracting: /wrkdirs/usr/ports/biology/gcta/work/gcta-1.26.0/StatFunc.h extracting: /wrkdirs/usr/ports/biology/gcta/work/gcta-1.26.0/StrFunc.cpp extracting: /wrkdirs/usr/ports/biology/gcta/work/gcta-1.26.0/StrFunc.h extracting: /wrkdirs/usr/ports/biology/gcta/work/gcta-1.26.0/UnusedCode.cpp extracting: /wrkdirs/usr/ports/biology/gcta/work/gcta-1.26.0/zfstream.cpp extracting: /wrkdirs/usr/ports/biology/gcta/work/gcta-1.26.0/zfstream.h =========================================================================== =================================================== =========================================================================== =================================================== ===> Patching for gcta-1.26.0_4 ===> Converting DOS text files to UNIX text files ===> Applying FreeBSD patches for gcta-1.26.0_4 from /usr/ports/biology/gcta/files =========================================================================== =================================================== ===> gcta-1.26.0_4 depends on package: gmake>=4.3 - not found ===> Installing existing package /packages/All/gmake-4.3_2.pkg [132arm64-default-job-12] Installing gmake-4.3_2... [132arm64-default-job-12] `-- Installing gettext-runtime-0.22_1... [132arm64-default-job-12] | `-- Installing indexinfo-0.3.1... [132arm64-default-job-12] | `-- Extracting indexinfo-0.3.1: .... done [132arm64-default-job-12] `-- Extracting gettext-runtime-0.22_1: .......... done [132arm64-default-job-12] Extracting gmake-4.3_2: .......... done ===> gcta-1.26.0_4 depends on package: gmake>=4.3 - found ===> Returning to build of gcta-1.26.0_4 =========================================================================== =================================================== ===> gcta-1.26.0_4 depends on shared library: libopenblas.so - not found ===> Installing existing package /packages/All/openblas-0.3.24,1.pkg [132arm64-default-job-12] Installing openblas-0.3.24,1... [132arm64-default-job-12] `-- Installing gcc12-12.2.0_6... [132arm64-default-job-12] | `-- Installing binutils-2.40_4,1... [132arm64-default-job-12] | | `-- Installing zstd-1.5.5... [132arm64-default-job-12] | | `-- Installing liblz4-1.9.4,1... [132arm64-default-job-12] | | `-- Extracting liblz4-1.9.4,1: .......... done [132arm64-default-job-12] | | `-- Extracting zstd-1.5.5: .......... done [132arm64-default-job-12] | `-- Extracting binutils-2.40_4,1: .......... done [132arm64-default-job-12] | `-- Installing gmp-6.3.0... [132arm64-default-job-12] | `-- Extracting gmp-6.3.0: .......... done [132arm64-default-job-12] | `-- Installing mpc-1.3.1_1... [132arm64-default-job-12] | | `-- Installing mpfr-4.2.1,1... [132arm64-default-job-12] | | `-- Extracting mpfr-4.2.1,1: .......... done [132arm64-default-job-12] | `-- Extracting mpc-1.3.1_1: ......... done [132arm64-default-job-12] `-- Extracting gcc12-12.2.0_6: .......... done [132arm64-default-job-12] Extracting openblas-0.3.24,1: .......... done ===== Message from gcc12-12.2.0_6: -- 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/gcc12 For ports leveraging USE_GCC, USES=compiler, or USES=fortran this happens transparently. ===> gcta-1.26.0_4 depends on shared library: libopenblas.so - found (/usr/local/lib/libopenblas.so) ===> Returning to build of gcta-1.26.0_4 =========================================================================== =================================================== ===> Configuring for gcta-1.26.0_4 =========================================================================== =================================================== ===> Building for gcta-1.26.0_4 gmake[1]: Entering directory '/wrkdirs/usr/ports/biology/gcta/work/gcta-1.26.0' 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 bivar_reml.cpp 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 CommFunc.cpp 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 eigen_func.cpp 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 data.cpp bivar_reml.cpp:321:1: warning: non-void function does not return a value in all control paths [-Wreturn-type] } ^ 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 dcdflib.cpp dcdflib.cpp:6027:23: warning: ISO C++11 does not allow conversion from string literal to 'char *' [-Wwritable-strings] if(qcond) ftnstop(" SMALL, X, BIG not monotone in INVR"); ^ dcdflib.cpp:6403:28: warning: ISO C++11 does not allow conversion from string literal to 'char *' [-Wwritable-strings] if(xx < 5.0e0) ftnstop(" Argument too small in DLANOR"); ^ dcdflib.cpp:6784:29: warning: ISO C++11 does not allow conversion from string literal to 'char *' [-Wwritable-strings] if(*z <= 0.0e0) ftnstop("Zero or negative argument in DSTREM"); ^ 3 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 edata.cpp 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 ejma.cpp 1 warning 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 est_hsq.cpp 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 grm.cpp est_hsq.cpp:893:25: warning: ISO C++11 does not allow conversion from string literal to 'char *' [-Wwritable-strings] char *mtd_str[3] = {"AI-REML algorithm", "Fisher-scoring ...", "EM-REML algorithm ..."}; ^ est_hsq.cpp:893:46: warning: ISO C++11 does not allow conversion from string literal to 'char *' [-Wwritable-strings] char *mtd_str[3] = {"AI-REML algorithm", "Fisher-scoring ...", "EM-REML algorithm ..."}; ^ est_hsq.cpp:893:68: warning: ISO C++11 does not allow conversion from string literal to 'char *' [-Wwritable-strings] char *mtd_str[3] = {"AI-REML algorithm", "Fisher-scoring ...", "EM-REML algorithm ..."}; ^ 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 gwas_simu.cpp 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 ld.cpp 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 joint_meta.cpp joint_meta.cpp:179:34: warning: implicit conversion of out of range value from 'double' to 'int' is undefined [-Wliteral-conversion] if (top_SNPs < 0) top_SNPs = 1e30; ~ ^~~~ joint_meta.cpp:218:24: warning: logical not is only applied to the left hand side of this comparison [-Wlogical-not-parentheses] if (!joint_only && !mld_slct_alg==2) { ^ ~~ joint_meta.cpp:218:24: note: add parentheses after the '!' to evaluate the comparison first if (!joint_only && !mld_slct_alg==2) { ^ ( ) joint_meta.cpp:218:24: note: add parentheses around left hand side expression to silence this warning if (!joint_only && !mld_slct_alg==2) { ^ ( ) joint_meta.cpp:218:37: warning: result of comparison of constant 2 with expression of type 'bool' is always false [-Wtautological-constant-out-of-range-compare] if (!joint_only && !mld_slct_alg==2) { ~~~~~~~~~~~~~^ ~ 3 warnings generated. 3 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 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 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##_ ^ :10:1: 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##_ ^ :18:1: 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 'std::vector::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 'std::vector::value_type' (aka 'char *') [-Wwritable-strings] argv[option_num + 1] = "gcta"; ^ 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