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: [email protected] Log URL: https://pkg-status.freebsd.org/ampere5/data/143arm64-default/fb751ba0f5ab/logs/gkl-0.9.1.log Build URL: https://pkg-status.freebsd.org/ampere5/build.html?mastername=143arm64-default&build=fb751ba0f5ab Log: =>> Building biology/gkl build started at Tue Feb 17 17:47:12 UTC 2026 port directory: /usr/ports/biology/gkl package name: gkl-0.9.1 building for: FreeBSD 143arm64-default-job-05 14.3-RELEASE-p8 FreeBSD 14.3-RELEASE-p8 arm64 maintained by: [email protected] Makefile datestamp: -rw-r--r-- 1 root wheel 483 Jan 22 01:01 /usr/ports/biology/gkl/Makefile Ports top last git commit: fb751ba0f5ab7119faf174266b9ed8617163e70f Ports top unclean checkout: no Port dir last git commit: ed25d4e234ff7deee31c2501b6f910188dd501e8 Port dir unclean checkout: no Poudriere version: poudriere-git-3.4.4-22-g8faef853 Host OSVERSION: 1600007 Jail OSVERSION: 1403000 Job Id: 05 ---Begin Environment--- SHELL=/bin/sh OSVERSION=1403000 UNAME_v=FreeBSD 14.3-RELEASE-p8 UNAME_r=14.3-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=3.4.4-22-g8faef853 MASTERMNT=/usr/local/poudriere/data/.m/143arm64-default/ref LC_COLLATE=C POUDRIERE_BUILD_TYPE=bulk PACKAGE_BUILDING=yes SAVED_TERM= OUTPUT_REDIRECTED_STDERR=4 OUTPUT_REDIRECTED=1 PWD=/usr/local/poudriere/data/.m/143arm64-default/05/.p OUTPUT_REDIRECTED_STDOUT=3 P_PORTS_FEATURES=FLAVORS SUBPACKAGES SELECTED_OPTIONS MASTERNAME=143arm64-default SCRIPTPREFIX=/usr/local/share/poudriere SCRIPTNAME=bulk.sh OLDPWD=/usr/local/poudriere/data/.m/143arm64-default/ref/.p/pool POUDRIERE_PKGNAME=poudriere-git-3.4.4-22-g8faef853 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-- [email protected] --End MAINTAINER-- --CONFIGURE_ARGS-- --End CONFIGURE_ARGS-- --CONFIGURE_ENV-- XDG_DATA_HOME=/wrkdirs/usr/ports/biology/gkl/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/gkl/work XDG_CACHE_HOME=/wrkdirs/usr/ports/biology/gkl/work/.cache HOME=/wrkdirs/usr/ports/biology/gkl/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/gkl/work/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin PKG_CONFIG_LIBDIR=/wrkdirs/usr/ports/biology/gkl/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/gkl/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/gkl/work XDG_CACHE_HOME=/wrkdirs/usr/ports/biology/gkl/work/.cache HOME=/wrkdirs/usr/ports/biology/gkl/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/gkl/work/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin PKG_CONFIG_LIBDIR=/wrkdirs/usr/ports/biology/gkl/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=" -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 064 4" 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" JAVASHAREDIR="share/java" JAVAJARDIR="share/java/classes" OSREL=14.3 PREFIX=%D LOCALBASE=/usr/local RESETPREFIX=/usr/local LIB32DIR=lib DOCSDIR="share/doc/gkl" EXAMPLESDIR="share/examples/gkl" DATADIR="share/gkl" WWWDIR="www/gkl" ETCDIR="etc/gkl" --End PLIST_SUB-- --SUB_LIST-- JAVASHAREDIR="/usr/local/share/java" JAVAJARDIR="/usr/local/share/java/classes" JAVALIBDIR="/usr/local/share/java/classes" JAVA_VERSION="8 11" PREFIX=/usr/local LOCALBASE=/usr/local DATADIR=/usr/local/share/gkl DOCSDIR=/usr/local/share/doc/gkl EXAMPLESDIR=/usr/local/share/examples/gkl WWWDIR=/usr/local/www/gkl ETCDIR=/usr/local/etc/gkl --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 pipebuf (-y) unlimited --End resource limits-- =======================<phase: check-sanity >============================ ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> License MIT accepted by the user =========================================================================== =======================<phase: pkg-depends >============================ ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 ===> gkl-0.9.1 depends on file: /usr/local/sbin/pkg - not found ===> Installing existing package /packages/All/pkg-2.5.1.pkg [143arm64-default-job-05] Installing pkg-2.5.1... [143arm64-default-job-05] Extracting pkg-2.5.1: .......... done ===> gkl-0.9.1 depends on file: /usr/local/sbin/pkg - found ===> Returning to build of gkl-0.9.1 =========================================================================== =======================<phase: fetch-depends >============================ ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 =========================================================================== =======================<phase: fetch >============================ ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> License MIT accepted by the user ===> Fetching all distfiles required by gkl-0.9.1 for building =========================================================================== =======================<phase: checksum >============================ ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> License MIT accepted by the user ===> Fetching all distfiles required by gkl-0.9.1 for building => SHA256 Checksum OK for Intel-HLS-GKL-0.9.1_GH0.tar.gz. =========================================================================== =======================<phase: extract-depends>============================ ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 =========================================================================== =======================<phase: extract >============================ ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> License MIT accepted by the user ===> Fetching all distfiles required by gkl-0.9.1 for building ===> Extracting for gkl-0.9.1 => SHA256 Checksum OK for Intel-HLS-GKL-0.9.1_GH0.tar.gz. =========================================================================== =======================<phase: patch-depends >============================ ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 =========================================================================== =======================<phase: patch >============================ ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Patching for gkl-0.9.1 ===> Applying FreeBSD patches for gkl-0.9.1 from /usr/ports/biology/gkl/files =========================================================================== =======================<phase: build-depends >============================ ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 ===> gkl-0.9.1 depends on executable: gmake - not found ===> Installing existing package /packages/All/gmake-4.4.1.pkg [143arm64-default-job-05] Installing gmake-4.4.1... [143arm64-default-job-05] `-- Installing gettext-runtime-0.26... [143arm64-default-job-05] | `-- Installing indexinfo-0.3.1_1... [143arm64-default-job-05] | `-- Extracting indexinfo-0.3.1_1: .... done [143arm64-default-job-05] `-- Extracting gettext-runtime-0.26: .......... done [143arm64-default-job-05] Extracting gmake-4.4.1: .......... done ===> gkl-0.9.1 depends on executable: gmake - found ===> Returning to build of gkl-0.9.1 ===> gkl-0.9.1 depends on file: /usr/local/bin/cmake - not found ===> Installing existing package /packages/All/cmake-core-3.31.10_1.pkg [143arm64-default-job-05] Installing cmake-core-3.31.10_1... [143arm64-default-job-05] `-- Installing expat-2.7.4... [143arm64-default-job-05] `-- Extracting expat-2.7.4: .......... done [143arm64-default-job-05] `-- Installing jsoncpp-1.9.6_1... [143arm64-default-job-05] `-- Extracting jsoncpp-1.9.6_1: .......... done [143arm64-default-job-05] `-- Installing libidn2-2.3.8... [143arm64-default-job-05] | `-- Installing libunistring-1.4.1... [143arm64-default-job-05] | `-- Extracting libunistring-1.4.1: .......... done [143arm64-default-job-05] `-- Extracting libidn2-2.3.8: .......... done [143arm64-default-job-05] `-- Installing libuv-1.52.0... [143arm64-default-job-05] `-- Extracting libuv-1.52.0: .......... done [143arm64-default-job-05] `-- Installing rhash-1.4.6... [143arm64-default-job-05] `-- Extracting rhash-1.4.6: .......... done <snip> --- src/main/native/pairhmm/CMakeFiles/gkl_pairhmm.dir/all --- --- src/main/native/pairhmm/CMakeFiles/gkl_pairhmm.dir/depend --- --- src/main/native/pairhmm/CMakeFiles/gkl_pairhmm_omp.dir/all --- --- src/main/native/pairhmm/CMakeFiles/gkl_pairhmm_omp.dir/depend --- --- src/main/native/pairhmm/CMakeFiles/gkl_pairhmm.dir/all --- cd /wrkdirs/usr/ports/biology/gkl/work/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1 /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm /wrkdirs/usr/ports/biology/gkl/work/.build /wrkdirs/usr/ports/biology/gkl/work/.build/src/main/native/pairhmm /wrkdirs/usr/ports/biology/gkl/work/.build/src/main/native/pairhmm/CMakeFiles/gkl_pairhmm.dir/DependInfo.cmake --- src/main/native/compression/CMakeFiles/otc_zlibExternal.dir/all --- cd /wrkdirs/usr/ports/biology/gkl/work/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1 /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/compression /wrkdirs/usr/ports/biology/gkl/work/.build /wrkdirs/usr/ports/biology/gkl/work/.build/src/main/native/compression /wrkdirs/usr/ports/biology/gkl/work/.build/src/main/native/compression/CMakeFiles/otc_zlibExternal.dir/DependInfo.cmake --- src/main/native/pairhmm/CMakeFiles/gkl_pairhmm_omp.dir/all --- cd /wrkdirs/usr/ports/biology/gkl/work/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1 /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm /wrkdirs/usr/ports/biology/gkl/work/.build /wrkdirs/usr/ports/biology/gkl/work/.build/src/main/native/pairhmm /wrkdirs/usr/ports/biology/gkl/work/.build/src/main/native/pairhmm/CMakeFiles/gkl_pairhmm_omp.dir/DependInfo.cmake --- src/main/native/compression/CMakeFiles/otc_zlibExternal.dir/all --- /usr/bin/make -f src/main/native/compression/CMakeFiles/otc_zlibExternal.dir/build.make src/main/native/compression/CMakeFiles/otc_zlibExternal.dir/build --- src/main/native/pairhmm/CMakeFiles/gkl_pairhmm.dir/all --- /usr/bin/make -f src/main/native/pairhmm/CMakeFiles/gkl_pairhmm.dir/build.make src/main/native/pairhmm/CMakeFiles/gkl_pairhmm.dir/build --- src/main/native/pairhmm/CMakeFiles/gkl_pairhmm_omp.dir/all --- /usr/bin/make -f src/main/native/pairhmm/CMakeFiles/gkl_pairhmm_omp.dir/build.make src/main/native/pairhmm/CMakeFiles/gkl_pairhmm_omp.dir/build --- src/main/native/compression/CMakeFiles/otc_zlibExternal.dir/all --- --- src/main/native/compression/otc_zlibExternal-prefix/src/otc_zlibExternal-stamp/otc_zlibExternal-mkdir --- --- src/main/native/pairhmm/CMakeFiles/gkl_pairhmm.dir/all --- --- src/main/native/pairhmm/CMakeFiles/gkl_pairhmm.dir/IntelPairHmm.cc.o --- --- src/main/native/pairhmm/CMakeFiles/gkl_pairhmm_omp.dir/all --- --- src/main/native/pairhmm/CMakeFiles/gkl_pairhmm_omp.dir/IntelPairHmm.cc.o --- --- src/main/native/compression/CMakeFiles/otc_zlibExternal.dir/all --- [ 2%] Creating directories for 'otc_zlibExternal' cd /wrkdirs/usr/ports/biology/gkl/work/.build/src/main/native/compression && /usr/local/bin/cmake -Dcfgdir= -P /wrkdirs/usr/ports/biology/gkl/work/.build/src/main/native/compression/otc_zlibExternal-prefix/tmp/otc_zlibExternal-mkdirs.cmake --- src/main/native/pairhmm/CMakeFiles/gkl_pairhmm.dir/all --- [ 5%] Building CXX object src/main/native/pairhmm/CMakeFiles/gkl_pairhmm.dir/IntelPairHmm.cc.o --- src/main/native/pairhmm/CMakeFiles/gkl_pairhmm_omp.dir/all --- [ 8%] Building CXX object src/main/native/pairhmm/CMakeFiles/gkl_pairhmm_omp.dir/IntelPairHmm.cc.o --- src/main/native/pairhmm/CMakeFiles/gkl_pairhmm.dir/all --- cd /wrkdirs/usr/ports/biology/gkl/work/.build/src/main/native/pairhmm && /usr/bin/c++ -Dgkl_pairhmm_EXPORTS -I/usr/local/openjdk8/include -I/usr/local/openjdk8/include/freebsd -I/wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/../common -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -D_FORTIFY_SOURCE=2 -O3 -Wformat -Werror=format-security -Wconversion -Wfloat-conversion -Wbool-compare -fstack-protector-all -fno-strict-overflow -fno-delete-null-pointer-checks -fwrapv -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNDEBUG -std=gnu++11 -fPIC -MD -MT src/main/native/pairhmm/CMakeFiles/gkl_pairhmm.dir/IntelPairHmm.cc.o -MF CMakeFiles/gkl_pairhmm.dir/IntelPairHmm.cc.o.d -o CMakeFiles/gkl_pairhmm.dir/IntelPairHmm.cc.o -c /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/IntelPairHmm.cc --- src/main/native/pairhmm/CMakeFiles/gkl_pairhmm_omp.dir/all --- cd /wrkdirs/usr/ports/biology/gkl/work/.build/src/main/native/pairhmm && /usr/bin/c++ -Dgkl_pairhmm_omp_EXPORTS -I/usr/local/openjdk8/include -I/usr/local/openjdk8/include/freebsd -I/wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/../common -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -D_FORTIFY_SOURCE=2 -O3 -Wformat -Werror=format-security -Wconversion -Wfloat-conversion -Wbool-compare -fstack-protector-all -fno-strict-overflow -fno-delete-null-pointer-checks -fwrapv -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNDEBUG -std=gnu++11 -fPIC -fopenmp=libomp -MD -MT src/main/native/pairhmm/CMakeFiles/gkl_pairhmm_omp.dir/IntelPairHmm.cc.o -MF CMakeFiles/gkl_pairhmm_omp.dir/IntelPairHmm.cc.o.d -o CMakeFiles/gkl_pairhmm_omp.dir/IntelPairHmm.cc.o -c /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/Inte lPairHmm.cc --- src/main/native/compression/CMakeFiles/otc_zlibExternal.dir/all --- cd /wrkdirs/usr/ports/biology/gkl/work/.build/src/main/native/compression && /usr/local/bin/cmake -E touch /wrkdirs/usr/ports/biology/gkl/work/.build/src/main/native/compression/otc_zlibExternal-prefix/src/otc_zlibExternal-stamp/otc_zlibExternal-mkdir --- src/main/native/compression/otc_zlibExternal-prefix/src/otc_zlibExternal-stamp/otc_zlibExternal-download --- [ 11%] Performing download step (DIR copy) for 'otc_zlibExternal' cd /wrkdirs/usr/ports/biology/gkl/work/.build/src/main/native/compression/otc_zlibExternal-prefix/src && /usr/local/bin/cmake -E rm -rf /wrkdirs/usr/ports/biology/gkl/work/.build/src/main/native/compression/otc_zlibExternal-prefix/src/otc_zlibExternal --- src/main/native/pairhmm/CMakeFiles/gkl_pairhmm_omp.dir/all --- c++: warning: argument unused during compilation: '-fno-strict-overflow' [-Wunused-command-line-argument] warning: unknown warning option '-Wbool-compare' [-Wunknown-warning-option] --- src/main/native/pairhmm/CMakeFiles/gkl_pairhmm.dir/all --- c++: warning: argument unused during compilation: '-fno-strict-overflow' [-Wunused-command-line-argument] warning: unknown warning option '-Wbool-compare' [-Wunknown-warning-option] --- src/main/native/compression/CMakeFiles/otc_zlibExternal.dir/all --- cd /wrkdirs/usr/ports/biology/gkl/work/.build/src/main/native/compression/otc_zlibExternal-prefix/src && /usr/local/bin/cmake -E copy_directory /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/compression/otc_zlib /wrkdirs/usr/ports/biology/gkl/work/.build/src/main/native/compression/otc_zlibExternal-prefix/src/otc_zlibExternal cd /wrkdirs/usr/ports/biology/gkl/work/.build/src/main/native/compression/otc_zlibExternal-prefix/src && /usr/local/bin/cmake -E touch /wrkdirs/usr/ports/biology/gkl/work/.build/src/main/native/compression/otc_zlibExternal-prefix/src/otc_zlibExternal-stamp/otc_zlibExternal-download --- src/main/native/compression/otc_zlibExternal-prefix/src/otc_zlibExternal-stamp/otc_zlibExternal-update --- [ 14%] No update step for 'otc_zlibExternal' cd /wrkdirs/usr/ports/biology/gkl/work/.build/src/main/native/compression && /usr/local/bin/cmake -E echo_append cd /wrkdirs/usr/ports/biology/gkl/work/.build/src/main/native/compression && /usr/local/bin/cmake -E touch /wrkdirs/usr/ports/biology/gkl/work/.build/src/main/native/compression/otc_zlibExternal-prefix/src/otc_zlibExternal-stamp/otc_zlibExternal-update --- src/main/native/compression/otc_zlibExternal-prefix/src/otc_zlibExternal-stamp/otc_zlibExternal-patch --- [ 17%] Performing patch step for 'otc_zlibExternal' cd /wrkdirs/usr/ports/biology/gkl/work/.build/src/main/native/compression/otc_zlibExternal-prefix/src/otc_zlibExternal && patch < /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/compression/otc_zlib.patch Hmm... Looks like a new-style context diff to me... The text leading up to this was: -------------------------- |*** configure 2023-05-18 15:55:05.049975110 -0800 |--- configure_new 2023-05-18 15:53:58.853492011 -0800 -------------------------- Patching file configure using Plan A... Hunk #1 succeeded at 194. done cd /wrkdirs/usr/ports/biology/gkl/work/.build/src/main/native/compression/otc_zlibExternal-prefix/src/otc_zlibExternal && /usr/local/bin/cmake -E touch /wrkdirs/usr/ports/biology/gkl/work/.build/src/main/native/compression/otc_zlibExternal-prefix/src/otc_zlibExternal-stamp/otc_zlibExternal-patch --- src/main/native/compression/otc_zlibExternal-prefix/src/otc_zlibExternal-stamp/otc_zlibExternal-configure --- [ 20%] Performing configure step for 'otc_zlibExternal' cd /wrkdirs/usr/ports/biology/gkl/work/.build/src/main/native/compression/otc_zlibExternal-prefix/src/otc_zlibExternal-build && /wrkdirs/usr/ports/biology/gkl/work/.build/src/main/native/compression/otc_zlibExternal-prefix/src/otc_zlibExternal/configure --static --prefix=/wrkdirs/usr/ports/biology/gkl/work/.build/src/main/native/compression/otc_zlibExternal-prefix Building static library libz.a version 1.2.13 with cc. Checking for size_t... Yes. --- src/main/native/pairhmm/CMakeFiles/gkl_pairhmm_omp.dir/all --- In file included from /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/IntelPairHmm.cc:33: In file included from /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/../common/avx.h:32: In file included from /usr/lib/clang/19/include/x86intrin.h:13: /usr/lib/clang/19/include/ia32intrin.h:312:10: error: use of undeclared identifier '__builtin_ia32_readeflags_u32' 312 | return __builtin_ia32_readeflags_u32(); | ^ --- src/main/native/compression/CMakeFiles/otc_zlibExternal.dir/all --- Checking for off64_t... Yes. Checking for fseeko... Yes. --- src/main/native/pairhmm/CMakeFiles/gkl_pairhmm_omp.dir/all --- /usr/lib/clang/19/include/ia32intrin.h:327:3: error: use of undeclared identifier '__builtin_ia32_writeeflags_u32' 327 | __builtin_ia32_writeeflags_u32(__f); | ^ /usr/lib/clang/19/include/ia32intrin.h:408:10: error: use of undeclared identifier '__builtin_ia32_crc32qi' 408 | return __builtin_ia32_crc32qi(__C, __D); | ^ /usr/lib/clang/19/include/ia32intrin.h:428:10: error: use of undeclared identifier '__builtin_ia32_crc32hi'; did you mean '__builtin_arm_crc32h'? 428 | return __builtin_ia32_crc32hi(__C, __D); | ^ /usr/lib/clang/19/include/ia32intrin.h:448:10: error: use of undeclared identifier '__builtin_ia32_crc32si' 448 | return __builtin_ia32_crc32si(__C, __D); | ^ /usr/lib/clang/19/include/ia32intrin.h:487:10: error: use of undeclared identifier '__builtin_ia32_rdpmc'; did you mean '__builtin_arm_dmb'? 487 | return __builtin_ia32_rdpmc(__A); | ^ /usr/lib/clang/19/include/ia32intrin.h:487:10: error: argument to '__builtin_arm_dmb' must be a constant integer 487 | return __builtin_ia32_rdpmc(__A); | ^ ~~~ /usr/lib/clang/19/include/ia32intrin.h:502:10: error: use of undeclared identifier '__builtin_ia32_rdtscp'; did you mean '__builtin_arm_rsrp'? 502 | return __builtin_ia32_rdtscp(__A); | ^ /usr/lib/clang/19/include/ia32intrin.h:502:32: error: cannot initialize a parameter of type 'const char *' with an lvalue of type 'unsigned int *' 502 | return __builtin_ia32_rdtscp(__A); | ^~~ /usr/lib/clang/19/include/ia32intrin.h:538:3: error: use of undeclared identifier '__builtin_ia32_wbinvd' 538 | __builtin_ia32_wbinvd(); | ^ In file included from /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/IntelPairHmm.cc:33: In file included from /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/../common/avx.h:32: In file included from /usr/lib/clang/19/include/x86intrin.h:15: /usr/lib/clang/19/include/immintrin.h:14:2: error: "This header is only meant to be used on x86 and x64 architecture" 14 | #error "This header is only meant to be used on x86 and x64 architecture" | ^ In file included from /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/IntelPairHmm.cc:33: In file included from /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/../common/avx.h:32: In file included from /usr/lib/clang/19/include/x86intrin.h:15: In file included from /usr/lib/clang/19/include/immintrin.h:17: In file included from /usr/lib/clang/19/include/x86gprintrin.h:26: /usr/lib/clang/19/include/crc32intrin.h:33:10: error: use of undeclared identifier '__builtin_ia32_crc32qi' 33 | return __builtin_ia32_crc32qi(__C, __D); | ^ /usr/lib/clang/19/include/crc32intrin.h:53:10: error: use of undeclared identifier '__builtin_ia32_crc32hi'; did you mean '__builtin_arm_crc32h'? 53 | return __builtin_ia32_crc32hi(__C, __D); | ^ /usr/lib/clang/19/include/ia32intrin.h:428:10: note: '__builtin_arm_crc32h' declared here 428 | return __builtin_ia32_crc32hi(__C, __D); | ^ In file included from /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/IntelPairHmm.cc:33: In file included from /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/../common/avx.h:32: In file included from /usr/lib/clang/19/include/x86intrin.h:15: In file included from /usr/lib/clang/19/include/immintrin.h:17: In file included from /usr/lib/clang/19/include/x86gprintrin.h:26: /usr/lib/clang/19/include/crc32intrin.h:73:10: error: use of undeclared identifier '__builtin_ia32_crc32si' 73 | return __builtin_ia32_crc32si(__C, __D); | ^ In file included from /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/IntelPairHmm.cc:33: In file included from /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/../common/avx.h:32: In file included from /usr/lib/clang/19/include/x86intrin.h:15: In file included from /usr/lib/clang/19/include/immintrin.h:17: In file included from /usr/lib/clang/19/include/x86gprintrin.h:34: /usr/lib/clang/19/include/raointintrin.h:39:3: error: use of undeclared identifier '__builtin_ia32_aadd32'; did you mean '__builtin_arm_addg'? 39 | __builtin_ia32_aadd32((int *)__A, __B); | ^ /usr/lib/clang/19/include/raointintrin.h:39:3: error: argument to '__builtin_arm_addg' must be a constant integer 39 | __builtin_ia32_aadd32((int *)__A, __B); | ^ ~~~ /usr/lib/clang/19/include/raointintrin.h:61:3: error: use of undeclared identifier '__builtin_ia32_aand32' 61 | __builtin_ia32_aand32((int *)__A, __B); | ^ /usr/lib/clang/19/include/raointintrin.h:83:3: error: use of undeclared identifier '__builtin_ia32_aor32' 83 | __builtin_ia32_aor32((int *)__A, __B); | ^ /usr/lib/clang/19/include/raointintrin.h:105:3: error: use of undeclared identifier '__builtin_ia32_axor32' 105 | __builtin_ia32_axor32((int *)__A, __B); | ^ fatal error: too many errors emitted, stopping now [-ferror-limit=] --- src/main/native/compression/CMakeFiles/otc_zlibExternal.dir/all --- Checking for strerror... Yes. Checking for unistd.h... Yes. Checking for stdarg.h... Yes. --- src/main/native/pairhmm/CMakeFiles/gkl_pairhmm_omp.dir/all --- 1 warning and 20 errors generated. *** [src/main/native/pairhmm/CMakeFiles/gkl_pairhmm_omp.dir/IntelPairHmm.cc.o] Error code 1 make[2]: stopped in /wrkdirs/usr/ports/biology/gkl/work/.build 1 error make[2]: stopped in /wrkdirs/usr/ports/biology/gkl/work/.build *** [src/main/native/pairhmm/CMakeFiles/gkl_pairhmm_omp.dir/all] Error code 2 make[1]: stopped in /wrkdirs/usr/ports/biology/gkl/work/.build --- src/main/native/pairhmm/CMakeFiles/gkl_pairhmm.dir/all --- *** [src/main/native/pairhmm/CMakeFiles/gkl_pairhmm.dir/all] Error code 6 make[1]: stopped in /wrkdirs/usr/ports/biology/gkl/work/.build --- src/main/native/compression/CMakeFiles/otc_zlibExternal.dir/all --- Checking whether to use vs[n]printf() or s[n]printf()... using vs[n]printf(). Checking for vsnprintf() in stdio.h... Yes. Checking for return value of vsnprintf()... Yes. Checking for attribute(visibility) support... Yes. cd /wrkdirs/usr/ports/biology/gkl/work/.build/src/main/native/compression/otc_zlibExternal-prefix/src/otc_zlibExternal-build && /usr/local/bin/cmake -E touch /wrkdirs/usr/ports/biology/gkl/work/.build/src/main/native/compression/otc_zlibExternal-prefix/src/otc_zlibExternal-stamp/otc_zlibExternal-configure *** [src/main/native/compression/CMakeFiles/otc_zlibExternal.dir/all] Error code 6 make[1]: stopped in /wrkdirs/usr/ports/biology/gkl/work/.build 3 errors make[1]: stopped in /wrkdirs/usr/ports/biology/gkl/work/.build *** [all] Error code 2 make: stopped in /wrkdirs/usr/ports/biology/gkl/work/.build 1 error make: stopped in /wrkdirs/usr/ports/biology/gkl/work/.build ===> 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/gkl
