From nobody Sat May 25 07:36:03 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 4VmYcM3gLdz5MNxX for ; Sat, 25 May 2024 07:36:03 +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 "R3" (verified OK)) by mx1.freebsd.org (Postfix) with ESMTPS id 4VmYcM154Vz4XhC for ; Sat, 25 May 2024 07:36:03 +0000 (UTC) (envelope-from pkg-fallout@FreeBSD.org) ARC-Seal: i=1; s=dkim; d=freebsd.org; t=1716622563; a=rsa-sha256; cv=none; b=lmsltnpdwQGlKT2c0JPl8Cxvrjid0yre+5a4MxKmFFlsRczuj8PB0xceXkAkBdXYXTM6Fa ZYTyjk2Bjxfn0Fst/LbF1+Wdqs7yTu9Y6d86VBynb5vUOVhzCegOJcGUY87i61vOEH1geg 0UvBE8g9Ar5Issmw3MD2cPR6ZzkkZcOioEV2xZI2nqLU4tYg5tLB5RkgxLFrvcrzJyEPTe REMdRPqn4HnkGxL2HZdiQ0jwBayuFrfvye4fHIL94vXhETunX9ztq+ZN/P2wnXYN5Zrz+Q vmnje1m2mqQ8CuChGi3zeFDPQK7w++BaRmcd+97VHMwkk907TNGmz/aI2/yLaQ== 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=1716622563; h=from:from:reply-to:subject:subject:date:date:message-id:message-id: to:to:cc:cc; bh=Qk96kuDUSDzXMNP2oqNHNGPzx2H9OHIJ+XtngMlB+kk=; b=qGsuVvBztdX49CPAvum4naeWJSZ9Rla7vbHBcJwS7byyUfqHW1M7hvsMr+CuAHZw52w2EC ZFVHbLIHeEz7On1A+zqgaRCfkjGeJ/OTAGxQ5Mvt4syxbBaS9JWgOC9/EQ2vDWshqMYP0+ XC0ZDXdjmfZi0poxArc4J7DsxuaDksqZYoRwGxsg3FSsdTifE4ujmIxF8s8tZBg+/SAZUO Cg4LHlGpiRM3vD+E8Wd8TwfO45vux8NodRO/twvMo5bh/G7utc7Lo+0R/sMlXxE1cZVQrb 48RmXl92/bZ9qNkDApayuOGrIlXo3EPhKhhT9QKtpfwU9OsiIB3HKlDrfjurCA== 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 4VmYcM0hlTz17Sq for ; Sat, 25 May 2024 07:36:03 +0000 (UTC) (envelope-from pkg-fallout@FreeBSD.org) Received: from root (uid 0) (envelope-from pkg-fallout@FreeBSD.org) id 28e6 by ampere1.nyi.freebsd.org (DragonFly Mail Agent v0.13+ on ampere1.nyi.freebsd.org); Sat, 25 May 2024 07:36:03 +0000 To: jwb@FreeBSD.org Subject: [package - 132arm64-quarterly][biology/gcta] Failed for gcta-1.94.1_1 in build Cc: pkg-fallout@FreeBSD.org Date: Sat, 25 May 2024 07:36:03 +0000 Message-Id: <665194e3.28e6.16050af9@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/132arm64-quarterly/39da018952c2/logs/gcta-1.94.1_1.log Build URL: https://pkg-status.freebsd.org/ampere1/build.html?mastername=132arm64-quarterly&build=39da018952c2 Log: =>> Building biology/gcta build started at Sat May 25 07:33:19 UTC 2024 port directory: /usr/ports/biology/gcta package name: gcta-1.94.1_1 building for: FreeBSD 132arm64-quarterly-job-01 13.2-RELEASE-p11 FreeBSD 13.2-RELEASE-p11 arm64 maintained by: jwb@FreeBSD.org Makefile datestamp: -rw-r--r-- 1 root wheel 1581 Apr 14 01:02 /usr/ports/biology/gcta/Makefile Ports top last git commit: 39da01895 Ports top unclean checkout: no Port dir last git commit: 1b931669d Port dir unclean checkout: no Poudriere version: poudriere-git-3.4.1-30-g79e3edcd Host OSVERSION: 1500018 Jail OSVERSION: 1302001 Job Id: 01 ---Begin Environment--- SHELL=/bin/csh OSVERSION=1302001 UNAME_v=FreeBSD 13.2-RELEASE-p11 UNAME_r=13.2-RELEASE-p11 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=3.4.1-30-g79e3edcd MASTERMNT=/usr/local/poudriere/data/.m/132arm64-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/132arm64-quarterly/01/.p OUTPUT_REDIRECTED_STDOUT=3 P_PORTS_FEATURES=FLAVORS SUBPACKAGES SELECTED_OPTIONS MASTERNAME=132arm64-quarterly SCRIPTPREFIX=/usr/local/share/poudriere SCRIPTNAME=bulk.sh OLDPWD=/usr/local/poudriere/data/.m/132arm64-quarterly/ref/.p/pool POUDRIERE_PKGNAME=poudriere-git-3.4.1-30-g79e3edcd 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 ADDR2LINE="/usr/local/bin/addr2line" AR="/usr/local/bin/ar" AS="/usr/local/bin/as" CPPFILT="/usr/local/bin/c++filt" GPROF="/usr/local/bin/gprof" LD="/usr/local/bin/ld" NM="/usr/local/bin/nm" OBJCOPY="/usr/local/bin/objcopy" OBJDUMP="/usr/local/bin/objdump" RANLIB="/usr/local/bin/ranlib" READELF="/usr/local/bin/readelf" SIZE="/usr/local/bin/size" STRINGS="/usr/local/bin/strings" DESTDIR=/wrkdirs/usr/ports/biol ogy/gcta/work/stage PREFIX=/usr/local LOCALBASE=/usr/local CC="gcc13" CFLAGS="-O2 -pipe -fstack-protector-strong -Wl,-rpath=/usr/local/lib/gcc13 -isystem /usr/local/include -fno-strict-aliasing " CPP="cpp13" CPPFLAGS="-isystem /usr/local/include" LDFLAGS=" -fopenmp -fstack-protector-strong -Wl,-rpath=/usr/local/lib/gcc13 -L/usr/local/lib/gcc13 -L/usr/local/lib " LIBS="" CXX="g++13" CXXFLAGS="-O2 -pipe -fstack-protector-strong -Wl,-rpath=/usr/local/lib/gcc13 -Wl,-rpath=/usr/local/lib/gcc13 -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=13.2 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 #### #### # 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) 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) 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_1 depends on file: /usr/local/sbin/pkg - not found ===> Installing existing package /packages/All/pkg-1.21.3.pkg [132arm64-quarterly-job-01] Installing pkg-1.21.3... [132arm64-quarterly-job-01] Extracting pkg-1.21.3: .......... done ===> gcta-1.94.1_1 depends on file: /usr/local/sbin/pkg - found ===> Returning to build of gcta-1.94.1_1 =========================================================================== =================================================== ===== 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_1 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_1 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_1 for building ===> Extracting for gcta-1.94.1_1 => 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_1 ===> Applying FreeBSD patches for gcta-1.94.1_1 from /usr/ports/biology/gcta/files =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 ===> gcta-1.94.1_1 depends on package: boost-libs>0 - not found ===> Installing existing package /packages/All/boost-libs-1.84.0.pkg [132arm64-quarterly-job-01] Installing boost-libs-1.84.0... [132arm64-quarterly-job-01] `-- Installing icu-74.2_1,1... [132arm64-quarterly-job-01] `-- Extracting icu-74.2_1,1: .......... done [132arm64-quarterly-job-01] 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_1 depends on package: boost-libs>0 - found ===> Returning to build of gcta-1.94.1_1 ===> gcta-1.94.1_1 depends on package: spectra>0 - not found ===> Installing existing package /packages/All/spectra-1.0.1_1.pkg [132arm64-quarterly-job-01] Installing spectra-1.0.1_1... [132arm64-quarterly-job-01] `-- Installing eigen-3.4.0_3... [132arm64-quarterly-job-01] | `-- Installing blas-3.12.0_1... [132arm64-quarterly-job-01] | | `-- Installing gcc13-13.2.0_4... [132arm64-quarterly-job-01] | | `-- Installing binutils-2.40_5,1... [132arm64-quarterly-job-01] | | | `-- Installing gettext-runtime-0.22.5... /wrkdirs/usr/ports/biology/gcta/work/gcta-1.94.1/include/Pheno.h:54:25: error: 'uint64_t' has not been declared 54 | void getMaskBitMale(uint64_t *maskp); | ^~~~~~~~ /wrkdirs/usr/ports/biology/gcta/work/gcta-1.94.1/include/Pheno.h:55:5: error: 'uint32_t' does not name a type 55 | uint32_t getSeed(); | ^~~~~~~~ /wrkdirs/usr/ports/biology/gcta/work/gcta-1.94.1/include/Pheno.h:55:5: note: 'uint32_t' is defined in header ''; did you forget to '#include '? /wrkdirs/usr/ports/biology/gcta/work/gcta-1.94.1/include/Pheno.h:57:12: error: 'uint32_t' was not declared in this scope 57 | vector& getSexValidRawIndex(); | ^~~~~~~~ /wrkdirs/usr/ports/biology/gcta/work/gcta-1.94.1/include/Pheno.h:57:12: note: 'uint32_t' is defined in header ''; did you forget to '#include '? /wrkdirs/usr/ports/biology/gcta/work/gcta-1.94.1/include/Pheno.h:57:20: error: template argument 1 is invalid 57 | vector& getSexValidRawIndex(); | ^ /wrkdirs/usr/ports/biology/gcta/work/gcta-1.94.1/include/Pheno.h:57:20: error: template argument 2 is invalid /wrkdirs/usr/ports/biology/gcta/work/gcta-1.94.1/include/Pheno.h:58:12: error: 'uint32_t' was not declared in this scope 58 | vector& getMaleRawIndex(); | ^~~~~~~~ /wrkdirs/usr/ports/biology/gcta/work/gcta-1.94.1/include/Pheno.h:58:12: note: 'uint32_t' is defined in header ''; did you forget to '#include '? /wrkdirs/usr/ports/biology/gcta/work/gcta-1.94.1/include/Pheno.h:58:20: error: template argument 1 is invalid 58 | vector& getMaleRawIndex(); | ^ /wrkdirs/usr/ports/biology/gcta/work/gcta-1.94.1/include/Pheno.h:58:20: error: template argument 2 is invalid /wrkdirs/usr/ports/biology/gcta/work/gcta-1.94.1/include/Pheno.h:59:12: error: 'uint32_t' was not declared in this scope 59 | vector& getMaleExtractIndex(); | ^~~~~~~~ /wrkdirs/usr/ports/biology/gcta/work/gcta-1.94.1/include/Pheno.h:59:12: note: 'uint32_t' is defined in header ''; did you forget to '#include '? /wrkdirs/usr/ports/biology/gcta/work/gcta-1.94.1/include/Pheno.h:59:20: error: template argument 1 is invalid 59 | vector& getMaleExtractIndex(); | ^ /wrkdirs/usr/ports/biology/gcta/work/gcta-1.94.1/include/Pheno.h:59:20: error: template argument 2 is invalid /wrkdirs/usr/ports/biology/gcta/work/gcta-1.94.1/include/Pheno.h:71:12: error: 'int8_t' was not declared in this scope 71 | vector sex; | ^~~~~~ /wrkdirs/usr/ports/biology/gcta/work/gcta-1.94.1/include/Pheno.h:71:12: note: 'int8_t' is defined in header ''; did you forget to '#include '? /wrkdirs/usr/ports/biology/gcta/work/gcta-1.94.1/include/Pheno.h:71:18: error: template argument 1 is invalid 71 | vector sex; | ^ /wrkdirs/usr/ports/biology/gcta/work/gcta-1.94.1/include/Pheno.h:71:18: error: template argument 2 is invalid /wrkdirs/usr/ports/biology/gcta/work/gcta-1.94.1/include/Pheno.h:73:12: error: 'uint32_t' was not declared in this scope 73 | vector index_keep; | ^~~~~~~~ /wrkdirs/usr/ports/biology/gcta/work/gcta-1.94.1/include/Pheno.h:73:12: note: 'uint32_t' is defined in header ''; did you forget to '#include '? /wrkdirs/usr/ports/biology/gcta/work/gcta-1.94.1/include/Pheno.h:73:20: error: template argument 1 is invalid 73 | vector index_keep; | ^ /wrkdirs/usr/ports/biology/gcta/work/gcta-1.94.1/include/Pheno.h:73:20: error: template argument 2 is invalid /wrkdirs/usr/ports/biology/gcta/work/gcta-1.94.1/include/Pheno.h:74:12: error: 'uint32_t' was not declared in this scope 74 | vector index_rm; | ^~~~~~~~ /wrkdirs/usr/ports/biology/gcta/work/gcta-1.94.1/include/Pheno.h:74:12: note: 'uint32_t' is defined in header ''; did you forget to '#include '? /wrkdirs/usr/ports/biology/gcta/work/gcta-1.94.1/include/Pheno.h:74:20: error: template argument 1 is invalid 74 | vector index_rm; | ^ /wrkdirs/usr/ports/biology/gcta/work/gcta-1.94.1/include/Pheno.h:74:20: error: template argument 2 is invalid /wrkdirs/usr/ports/biology/gcta/work/gcta-1.94.1/include/Pheno.h:76:12: error: 'uint32_t' was not declared in this scope 76 | vector index_keep_sex; | ^~~~~~~~ /wrkdirs/usr/ports/biology/gcta/work/gcta-1.94.1/include/Pheno.h:76:12: note: 'uint32_t' is defined in header ''; did you forget to '#include '? /wrkdirs/usr/ports/biology/gcta/work/gcta-1.94.1/include/Pheno.h:76:20: error: template argument 1 is invalid 76 | vector index_keep_sex; | ^ /wrkdirs/usr/ports/biology/gcta/work/gcta-1.94.1/include/Pheno.h:76:20: error: template argument 2 is invalid /wrkdirs/usr/ports/biology/gcta/work/gcta-1.94.1/include/Pheno.h:77:12: error: 'uint32_t' was not declared in this scope 77 | vector index_keep_male; | ^~~~~~~~ /wrkdirs/usr/ports/biology/gcta/work/gcta-1.94.1/include/Pheno.h:77:12: note: 'uint32_t' is defined in header ''; did you forget to '#include '? /wrkdirs/usr/ports/biology/gcta/work/gcta-1.94.1/include/Pheno.h:77:20: error: template argument 1 is invalid 77 | vector index_keep_male; | ^ /wrkdirs/usr/ports/biology/gcta/work/gcta-1.94.1/include/Pheno.h:77:20: error: template argument 2 is invalid /wrkdirs/usr/ports/biology/gcta/work/gcta-1.94.1/include/Pheno.h:78:12: error: 'uint32_t' was not declared in this scope 78 | vector index_keep_male_extract; // in the sex valid | ^~~~~~~~ /wrkdirs/usr/ports/biology/gcta/work/gcta-1.94.1/include/Pheno.h:78:12: note: 'uint32_t' is defined in header ''; did you forget to '#include '? /wrkdirs/usr/ports/biology/gcta/work/gcta-1.94.1/include/Pheno.h:78:20: error: template argument 1 is invalid 78 | vector index_keep_male_extract; // in the sex valid | ^ /wrkdirs/usr/ports/biology/gcta/work/gcta-1.94.1/include/Pheno.h:78:20: error: template argument 2 is invalid /wrkdirs/usr/ports/biology/gcta/work/gcta-1.94.1/include/Pheno.h:81:12: error: 'uint8_t' was not declared in this scope 81 | vector mask_rm; | ^~~~~~~ /wrkdirs/usr/ports/biology/gcta/work/gcta-1.94.1/include/Pheno.h:81:12: note: 'uint8_t' is defined in header ''; did you forget to '#include '? /wrkdirs/usr/ports/biology/gcta/work/gcta-1.94.1/include/Pheno.h:81:19: error: template argument 1 is invalid 81 | vector mask_rm; | ^ /wrkdirs/usr/ports/biology/gcta/work/gcta-1.94.1/include/Pheno.h:81:19: error: template argument 2 is invalid /wrkdirs/usr/ports/biology/gcta/work/gcta-1.94.1/include/Pheno.h:99:12: error: 'uint32_t' was not declared in this scope 99 | vector keep_block_index; | ^~~~~~~~ /wrkdirs/usr/ports/biology/gcta/work/gcta-1.94.1/include/Pheno.h:99:12: note: 'uint32_t' is defined in header ''; did you forget to '#include '? /wrkdirs/usr/ports/biology/gcta/work/gcta-1.94.1/include/Pheno.h:99:20: error: template argument 1 is invalid 99 | vector keep_block_index; | ^ /wrkdirs/usr/ports/biology/gcta/work/gcta-1.94.1/include/Pheno.h:99:20: error: template argument 2 is invalid /wrkdirs/usr/ports/biology/gcta/work/gcta-1.94.1/include/Pheno.h:100:12: error: 'uint64_t' was not declared in this scope 100 | vector mask_items; | ^~~~~~~~ /wrkdirs/usr/ports/biology/gcta/work/gcta-1.94.1/include/Pheno.h:100:12: note: 'uint64_t' is defined in header ''; did you forget to '#include '? /wrkdirs/usr/ports/biology/gcta/work/gcta-1.94.1/include/Pheno.h:100:20: error: template argument 1 is invalid 100 | vector mask_items; | ^ /wrkdirs/usr/ports/biology/gcta/work/gcta-1.94.1/include/Pheno.h:100:20: error: template argument 2 is invalid /wrkdirs/usr/ports/biology/gcta/work/gcta-1.94.1/include/Pheno.h:101:12: error: 'uint64_t' was not declared in this scope 101 | vector mask_add_items; | ^~~~~~~~ /wrkdirs/usr/ports/biology/gcta/work/gcta-1.94.1/include/Pheno.h:101:12: note: 'uint64_t' is defined in header ''; did you forget to '#include '? /wrkdirs/usr/ports/biology/gcta/work/gcta-1.94.1/include/Pheno.h:101:20: error: template argument 1 is invalid 101 | vector mask_add_items; | ^ /wrkdirs/usr/ports/biology/gcta/work/gcta-1.94.1/include/Pheno.h:101:20: error: template argument 2 is invalid /wrkdirs/usr/ports/biology/gcta/work/gcta-1.94.1/include/Covar.h:32:71: error: 'uint32_t' was not declared in this scope 32 | bool getCommonSampleIndex(const vector &sampleIDs, vector &keep_index, vector &covar_index); | ^~~~~~~~ /wrkdirs/usr/ports/biology/gcta/work/gcta-1.94.1/include/Covar.h:24:1: note: 'uint32_t' is defined in header ''; did you forget to '#include '? 23 | #include "Pheno.h" +++ |+#include 24 | /wrkdirs/usr/ports/biology/gcta/work/gcta-1.94.1/include/Covar.h:32:79: error: template argument 1 is invalid 32 | bool getCommonSampleIndex(const vector &sampleIDs, vector &keep_index, vector &covar_index); | ^ /wrkdirs/usr/ports/biology/gcta/work/gcta-1.94.1/include/Covar.h:32:79: error: template argument 2 is invalid /wrkdirs/usr/ports/biology/gcta/work/gcta-1.94.1/include/Covar.h:32:101: error: 'uint32_t' was not declared in this scope 32 | bool getCommonSampleIndex(const vector &sampleIDs, vector &keep_index, vector &covar_index); | ^~~~~~~~ /wrkdirs/usr/ports/biology/gcta/work/gcta-1.94.1/include/Covar.h:32:101: note: 'uint32_t' is defined in header ''; did you forget to '#include '? /wrkdirs/usr/ports/biology/gcta/work/gcta-1.94.1/include/Covar.h:32:109: error: template argument 1 is invalid 32 | bool getCommonSampleIndex(const vector &sampleIDs, vector &keep_index, vector &covar_index); | ^ /wrkdirs/usr/ports/biology/gcta/work/gcta-1.94.1/include/Covar.h:32:109: error: template argument 2 is invalid /wrkdirs/usr/ports/biology/gcta/work/gcta-1.94.1/include/Covar.h:34:82: error: 'uint32_t' was not declared in this scope 34 | bool getCovarXRaw(const vector &sampleIDs, vector &X, vector &keep_index); | ^~~~~~~~ /wrkdirs/usr/ports/biology/gcta/work/gcta-1.94.1/include/Covar.h:34:82: note: 'uint32_t' is defined in header ''; did you forget to '#include '? /wrkdirs/usr/ports/biology/gcta/work/gcta-1.94.1/include/Covar.h:34:90: error: template argument 1 is invalid 34 | bool getCovarXRaw(const vector &sampleIDs, vector &X, vector &keep_index); | ^ /wrkdirs/usr/ports/biology/gcta/work/gcta-1.94.1/include/Covar.h:34:90: error: template argument 2 is invalid /wrkdirs/usr/ports/biology/gcta/work/gcta-1.94.1/include/Covar.h:35:79: error: 'uint32_t' was not declared in this scope 35 | bool getCovarX(const vector &sampleIDs, vector &X, vector &keep_index); | ^~~~~~~~ /wrkdirs/usr/ports/biology/gcta/work/gcta-1.94.1/include/Covar.h:35:79: note: 'uint32_t' is defined in header ''; did you forget to '#include '? /wrkdirs/usr/ports/biology/gcta/work/gcta-1.94.1/include/Covar.h:35:87: error: template argument 1 is invalid 35 | bool getCovarX(const vector &sampleIDs, vector &X, vector &keep_index); | ^ /wrkdirs/usr/ports/biology/gcta/work/gcta-1.94.1/include/Covar.h:35:87: error: template argument 2 is invalid /wrkdirs/usr/ports/biology/gcta/work/gcta-1.94.1/src/Covar.cpp:333:6: error: no declaration matches 'bool Covar::getCommonSampleIndex(const std::vector >&, std::vector&, std::vector&)' 333 | bool Covar::getCommonSampleIndex(const vector &sampleIDs, vector &keep_index, vector &covar_index){ | ^~~~~ /wrkdirs/usr/ports/biology/gcta/work/gcta-1.94.1/include/Covar.h:32:10: note: candidate is: 'bool Covar::getCommonSampleIndex(const std::vector >&, int&, int&)' 32 | bool getCommonSampleIndex(const vector &sampleIDs, vector &keep_index, vector &covar_index); | ^~~~~~~~~~~~~~~~~~~~ /wrkdirs/usr/ports/biology/gcta/work/gcta-1.94.1/include/Covar.h:29:7: note: 'class Covar' defined here 29 | class Covar{ | ^~~~~ /wrkdirs/usr/ports/biology/gcta/work/gcta-1.94.1/src/Covar.cpp:354:6: error: no declaration matches 'bool Covar::getCovarX(const std::vector >&, std::vector&, std::vector&)' 354 | bool Covar::getCovarX(const vector &sampleIDs, vector &X, vector &keep_index){ | ^~~~~ /wrkdirs/usr/ports/biology/gcta/work/gcta-1.94.1/include/Covar.h:35:10: note: candidate is: 'bool Covar::getCovarX(const std::vector >&, std::vector&, int&)' 35 | bool getCovarX(const vector &sampleIDs, vector &X, vector &keep_index); | ^~~~~~~~~ /wrkdirs/usr/ports/biology/gcta/work/gcta-1.94.1/include/Covar.h:29:7: note: 'class Covar' defined here 29 | class Covar{ | ^~~~~ /wrkdirs/usr/ports/biology/gcta/work/gcta-1.94.1/src/Covar.cpp:420:6: error: no declaration matches 'bool Covar::getCovarXRaw(const std::vector >&, std::vector&, std::vector&)' 420 | bool Covar::getCovarXRaw(const vector &sampleIDs, vector &X, vector &keep_index){ | ^~~~~ /wrkdirs/usr/ports/biology/gcta/work/gcta-1.94.1/include/Covar.h:34:10: note: candidate is: 'bool Covar::getCovarXRaw(const std::vector >&, std::vector&, int&)' 34 | bool getCovarXRaw(const vector &sampleIDs, vector &X, vector &keep_index); | ^~~~~~~~~~~~ /wrkdirs/usr/ports/biology/gcta/work/gcta-1.94.1/include/Covar.h:29:7: note: 'class Covar' defined here 29 | class Covar{ | ^~~~~ /wrkdirs/usr/ports/biology/gcta/work/gcta-1.94.1/src/Covar.cpp: In static member function 'static int Covar::registerOption(std::map, std::vector > >&)': /wrkdirs/usr/ports/biology/gcta/work/gcta-1.94.1/src/Covar.cpp:616:40: error: cannot convert 'std::vector' to 'int&' 616 | covar.getCovarXRaw(samples, X, sample_index); | ^~~~~~~~~~~~ | | | std::vector /wrkdirs/usr/ports/biology/gcta/work/gcta-1.94.1/include/Covar.h:34:93: note: initializing argument 3 of 'bool Covar::getCovarXRaw(const std::vector >&, std::vector&, int&)' 34 | bool getCovarXRaw(const vector &sampleIDs, vector &X, vector &keep_index); | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /wrkdirs/usr/ports/biology/gcta/work/gcta-1.94.1/src/Covar.cpp:627:37: error: cannot convert 'std::vector' to 'int&' 627 | covar.getCovarX(samples, X, sample_index); | ^~~~~~~~~~~~ | | | std::vector /wrkdirs/usr/ports/biology/gcta/work/gcta-1.94.1/include/Covar.h:35:90: note: initializing argument 3 of 'bool Covar::getCovarX(const std::vector >&, std::vector&, int&)' 35 | bool getCovarX(const vector &sampleIDs, vector &X, vector &keep_index); | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~ [ 2% 3/67] /usr/local/bin/g++13 -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 -Wl,-rpath=/usr/local/lib/gcc13 -Wl,-rpath=/usr/local/lib/gcc13 -isystem /usr/local/include -pthread -O2 -pipe -fstack-protector-strong -Wl,-rpath=/usr/local/lib/gcc13 -Wl,-rpath=/usr/local/lib/gcc13 -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 [ 4% 3/67] /usr/local/bin/g++13 -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 -Wl,-rpath=/usr/local/lib/gcc13 -Wl,-rpath=/usr/local/lib/gcc13 -isystem /usr/local/include -pthread -O2 -pipe -fstack-protector-strong -Wl,-rpath=/usr/local/lib/gcc13 -Wl,-rpath=/usr/local/lib/gcc13 -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 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