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Maintainer: [email protected] Log URL: https://pkg-status.freebsd.org/ampere1/data/142arm64-quarterly/ae4b9c5a1177/logs/gkl-0.8.11.9.log Build URL: https://pkg-status.freebsd.org/ampere1/build.html?mastername=142arm64-quarterly&build=ae4b9c5a1177 Log: =>> Building biology/gkl build started at Sun Aug 10 21:22:18 UTC 2025 port directory: /usr/ports/biology/gkl package name: gkl-0.8.11.9 building for: FreeBSD 142arm64-quarterly-job-12 14.2-RELEASE-p5 FreeBSD 14.2-RELEASE-p5 arm64 maintained by: [email protected] Makefile datestamp: -rw-r--r-- 1 root wheel 496 Jul 3 01:02 /usr/ports/biology/gkl/Makefile Ports top last git commit: ae4b9c5a1 Ports top unclean checkout: no Port dir last git commit: d7951ee86 Port dir unclean checkout: no Poudriere version: poudriere-git-3.4.3 Host OSVERSION: 1500052 Jail OSVERSION: 1402000 Job Id: 12 ---Begin Environment--- SHELL=/bin/sh OSVERSION=1402000 UNAME_v=FreeBSD 14.2-RELEASE-p5 UNAME_r=14.2-RELEASE-p5 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=3.4.3 MASTERMNT=/usr/local/poudriere/data/.m/142arm64-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/142arm64-quarterly/12/.p OUTPUT_REDIRECTED_STDOUT=3 P_PORTS_FEATURES=FLAVORS SUBPACKAGES SELECTED_OPTIONS MASTERNAME=142arm64-quarterly SCRIPTPREFIX=/usr/local/share/poudriere SCRIPTNAME=bulk.sh OLDPWD=/usr/local/poudriere/data/.m/142arm64-quarterly/ref/.p/pool POUDRIERE_PKGNAME=poudriere-git-3.4.3 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=" -fstack-protector-strong -L/usr/local/lib " LIBS="" CXX="c++" CXXFLAGS="-O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include " BSD_INSTALL_PROGRAM="install -s -m 555" BSD_INSTAL L_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" JAVASHAREDIR="share/java" JAVAJARDIR="share/java/classes" OSREL=14.2 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" 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-0.8.11.9 depends on file: /usr/local/sbin/pkg - not found ===> Installing existing package /packages/All/pkg-2.2.2.pkg [142arm64-quarterly-job-12] Installing pkg-2.2.2... [142arm64-quarterly-job-12] Extracting pkg-2.2.2: .......... done ===> gkl-0.8.11.9 depends on file: /usr/local/sbin/pkg - found ===> Returning to build of gkl-0.8.11.9 =========================================================================== =======================<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-0.8.11.9 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-0.8.11.9 for building => SHA256 Checksum OK for Intel-HLS-GKL-0.8.11-9-g25670d8_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-0.8.11.9 for building ===> Extracting for gkl-0.8.11.9 => SHA256 Checksum OK for Intel-HLS-GKL-0.8.11-9-g25670d8_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-0.8.11.9 ===> Applying FreeBSD patches for gkl-0.8.11.9 from /usr/ports/biology/gkl/files =========================================================================== =======================<phase: build-depends >============================ ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 ===> gkl-0.8.11.9 depends on executable: gmake - not found ===> Installing existing package /packages/All/gmake-4.4.1.pkg [142arm64-quarterly-job-12] Installing gmake-4.4.1... [142arm64-quarterly-job-12] `-- Installing gettext-runtime-0.23.1... [142arm64-quarterly-job-12] | `-- Installing indexinfo-0.3.1_1... [142arm64-quarterly-job-12] | `-- Extracting indexinfo-0.3.1_1: .... done [142arm64-quarterly-job-12] `-- Extracting gettext-runtime-0.23.1: .......... done [142arm64-quarterly-job-12] Extracting gmake-4.4.1: .......... done ===> gkl-0.8.11.9 depends on executable: gmake - found ===> Returning to build of gkl-0.8.11.9 ===> gkl-0.8.11.9 depends on file: /usr/local/bin/cmake - not found ===> Installing existing package /packages/All/cmake-core-3.31.7.pkg [142arm64-quarterly-job-12] Installing cmake-core-3.31.7... [142arm64-quarterly-job-12] `-- Installing expat-2.7.1... [142arm64-quarterly-job-12] `-- Extracting expat-2.7.1: .......... done [142arm64-quarterly-job-12] `-- Installing jsoncpp-1.9.6_1... [142arm64-quarterly-job-12] `-- Extracting jsoncpp-1.9.6_1: .......... done [142arm64-quarterly-job-12] `-- Installing libidn2-2.3.8... [142arm64-quarterly-job-12] | `-- Installing libunistring-1.3... [142arm64-quarterly-job-12] | `-- Extracting libunistring-1.3: .......... done [142arm64-quarterly-job-12] `-- Extracting libidn2-2.3.8: .......... done [142arm64-quarterly-job-12] `-- Installing libuv-1.51.0... [142arm64-quarterly-job-12] `-- Extracting libuv-1.51.0: .......... done [142arm64-quarterly-job-12] `-- Installing rhash-1.4.4_1... [142arm64-quarterly-job-12] `-- Extracting rhash-1.4.4_1: .......... done <snip> | ^ In file included from /wrkdirs/usr/ports/biology/gkl/work/GKL-0.8.11-9-g25670d8/src/main/native/pairhmm/IntelPairHmm.cc:33: In file included from /wrkdirs/usr/ports/biology/gkl/work/GKL-0.8.11-9-g25670d8/src/main/native/pairhmm/../common/avx.h:32: In file included from /usr/lib/clang/18/include/x86intrin.h:15: /usr/lib/clang/18/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" | ^ --- src/main/native/pairhmm/CMakeFiles/gkl_pairhmm.dir/all --- /usr/lib/clang/18/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/18/include/ia32intrin.h:428:10: note: '__builtin_arm_crc32h' declared here /usr/lib/clang/18/include/ia32intrin.h:448:10: error: use of undeclared identifier '__builtin_ia32_crc32si' 448 | return __builtin_ia32_crc32si(__C, __D); | ^ --- src/main/native/pairhmm/CMakeFiles/gkl_pairhmm_omp.dir/all --- In file included from /wrkdirs/usr/ports/biology/gkl/work/GKL-0.8.11-9-g25670d8/src/main/native/pairhmm/IntelPairHmm.cc:33: In file included from /wrkdirs/usr/ports/biology/gkl/work/GKL-0.8.11-9-g25670d8/src/main/native/pairhmm/../common/avx.h:32: In file included from /usr/lib/clang/18/include/x86intrin.h:15: In file included from /usr/lib/clang/18/include/immintrin.h:17: In file included from /usr/lib/clang/18/include/x86gprintrin.h:30: /usr/lib/clang/18/include/crc32intrin.h:33:10: error: use of undeclared identifier '__builtin_ia32_crc32qi' 33 | return __builtin_ia32_crc32qi(__C, __D); | ^ --- src/main/native/pairhmm/CMakeFiles/gkl_pairhmm.dir/all --- /usr/lib/clang/18/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/18/include/ia32intrin.h:487:10: note: '__builtin_arm_dmb' declared here /usr/lib/clang/18/include/ia32intrin.h:487:10: error: argument to '__builtin_arm_dmb' must be a constant integer 487 | return __builtin_ia32_rdpmc(__A); | ^ ~~~ --- src/main/native/pairhmm/CMakeFiles/gkl_pairhmm_omp.dir/all --- /usr/lib/clang/18/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/18/include/ia32intrin.h:428:10: note: '__builtin_arm_crc32h' declared here 428 | return __builtin_ia32_crc32hi(__C, __D); | ^ --- src/main/native/pairhmm/CMakeFiles/gkl_pairhmm.dir/all --- /usr/lib/clang/18/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/18/include/ia32intrin.h:502:10: note: '__builtin_arm_rsrp' declared here /usr/lib/clang/18/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); | ^~~ --- src/main/native/pairhmm/CMakeFiles/gkl_pairhmm_omp.dir/all --- In file included from /wrkdirs/usr/ports/biology/gkl/work/GKL-0.8.11-9-g25670d8/src/main/native/pairhmm/IntelPairHmm.cc:33: In file included from /wrkdirs/usr/ports/biology/gkl/work/GKL-0.8.11-9-g25670d8/src/main/native/pairhmm/../common/avx.h:32: In file included from /usr/lib/clang/18/include/x86intrin.h:15: In file included from /usr/lib/clang/18/include/immintrin.h:17: In file included from /usr/lib/clang/18/include/x86gprintrin.h:30: /usr/lib/clang/18/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-0.8.11-9-g25670d8/src/main/native/pairhmm/IntelPairHmm.cc:33: In file included from /wrkdirs/usr/ports/biology/gkl/work/GKL-0.8.11-9-g25670d8/src/main/native/pairhmm/../common/avx.h:32: In file included from /usr/lib/clang/18/include/x86intrin.h:15: In file included from /usr/lib/clang/18/include/immintrin.h:17: In file included from /usr/lib/clang/18/include/x86gprintrin.h:40: /usr/lib/clang/18/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/18/include/raointintrin.h:39:3: note: '__builtin_arm_addg' declared here /usr/lib/clang/18/include/raointintrin.h:39:3: error: argument to '__builtin_arm_addg' must be a constant integer 39 | __builtin_ia32_aadd32((int *)__A, __B); | ^ ~~~ --- src/main/native/pairhmm/CMakeFiles/gkl_pairhmm.dir/all --- /usr/lib/clang/18/include/ia32intrin.h:538:3: error: use of undeclared identifier '__builtin_ia32_wbinvd' 538 | __builtin_ia32_wbinvd(); | ^ --- src/main/native/pairhmm/CMakeFiles/gkl_pairhmm_omp.dir/all --- /usr/lib/clang/18/include/raointintrin.h:61:3: error: use of undeclared identifier '__builtin_ia32_aand32' 61 | __builtin_ia32_aand32((int *)__A, __B); | ^ --- src/main/native/pairhmm/CMakeFiles/gkl_pairhmm.dir/all --- In file included from /wrkdirs/usr/ports/biology/gkl/work/GKL-0.8.11-9-g25670d8/src/main/native/pairhmm/IntelPairHmm.cc:33: In file included from /wrkdirs/usr/ports/biology/gkl/work/GKL-0.8.11-9-g25670d8/src/main/native/pairhmm/../common/avx.h:32: In file included from /usr/lib/clang/18/include/x86intrin.h:15: /usr/lib/clang/18/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-0.8.11-9-g25670d8/src/main/native/pairhmm/IntelPairHmm.cc:33: In file included from /wrkdirs/usr/ports/biology/gkl/work/GKL-0.8.11-9-g25670d8/src/main/native/pairhmm/../common/avx.h:32: In file included from /usr/lib/clang/18/include/x86intrin.h:15: In file included from /usr/lib/clang/18/include/immintrin.h:17: In file included from /usr/lib/clang/18/include/x86gprintrin.h:15: /usr/lib/clang/18/include/hresetintrin.h:42:27: error: invalid input constraint 'a' in asm 42 | __asm__ ("hreset $0" :: "a"(__eax)); | ^ --- src/main/native/compression/CMakeFiles/otc_zlibExternal.dir/all --- Checking for unistd.h... Yes. --- src/main/native/pairhmm/CMakeFiles/gkl_pairhmm_omp.dir/all --- /usr/lib/clang/18/include/raointintrin.h:83:3: error: use of undeclared identifier '__builtin_ia32_aor32' 83 | __builtin_ia32_aor32((int *)__A, __B); | ^ --- src/main/native/pairhmm/CMakeFiles/gkl_pairhmm.dir/all --- In file included from /wrkdirs/usr/ports/biology/gkl/work/GKL-0.8.11-9-g25670d8/src/main/native/pairhmm/IntelPairHmm.cc:33: In file included from /wrkdirs/usr/ports/biology/gkl/work/GKL-0.8.11-9-g25670d8/src/main/native/pairhmm/../common/avx.h:32: In file included from /usr/lib/clang/18/include/x86intrin.h:15: In file included from /usr/lib/clang/18/include/immintrin.h:17: In file included from /usr/lib/clang/18/include/x86gprintrin.h:30: /usr/lib/clang/18/include/crc32intrin.h:33:10: error: use of undeclared identifier '__builtin_ia32_crc32qi' 33 | return __builtin_ia32_crc32qi(__C, __D); | ^ --- src/main/native/pairhmm/CMakeFiles/gkl_pairhmm_omp.dir/all --- /usr/lib/clang/18/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/pairhmm/CMakeFiles/gkl_pairhmm.dir/all --- /usr/lib/clang/18/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/18/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-0.8.11-9-g25670d8/src/main/native/pairhmm/IntelPairHmm.cc:33: In file included from /wrkdirs/usr/ports/biology/gkl/work/GKL-0.8.11-9-g25670d8/src/main/native/pairhmm/../common/avx.h:32: In file included from /usr/lib/clang/18/include/x86intrin.h:15: In file included from /usr/lib/clang/18/include/immintrin.h:17: In file included from /usr/lib/clang/18/include/x86gprintrin.h:30: /usr/lib/clang/18/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-0.8.11-9-g25670d8/src/main/native/pairhmm/IntelPairHmm.cc:33: In file included from /wrkdirs/usr/ports/biology/gkl/work/GKL-0.8.11-9-g25670d8/src/main/native/pairhmm/../common/avx.h:32: In file included from /usr/lib/clang/18/include/x86intrin.h:15: In file included from /usr/lib/clang/18/include/immintrin.h:17: In file included from /usr/lib/clang/18/include/x86gprintrin.h:40: /usr/lib/clang/18/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/18/include/raointintrin.h:39:3: note: '__builtin_arm_addg' declared here /usr/lib/clang/18/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/18/include/raointintrin.h:61:3: error: use of undeclared identifier '__builtin_ia32_aand32' 61 | __builtin_ia32_aand32((int *)__A, __B); | ^ /usr/lib/clang/18/include/raointintrin.h:83:3: error: use of undeclared identifier '__builtin_ia32_aor32' 83 | __builtin_ia32_aor32((int *)__A, __B); | ^ fatal error: too many errors emitted, stopping now [-ferror-limit=] --- src/main/native/compression/CMakeFiles/otc_zlibExternal.dir/all --- Checking for stdarg.h... Yes. 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/otc_zlibExternal-prefix/src/otc_zlibExternal-stamp/otc_zlibExternal-build --- [ 23%] Performing build step for 'otc_zlibExternal' cd /wrkdirs/usr/ports/biology/gkl/work/.build/src/main/native/compression/otc_zlibExternal-prefix/src/otc_zlibExternal-build && /usr/bin/make --- src/main/native/pairhmm/CMakeFiles/gkl_pairhmm_omp.dir/all --- 1 warning and 20 errors generated. --- src/main/native/compression/CMakeFiles/otc_zlibExternal.dir/all --- --- example64.o --- --- src/main/native/pairhmm/CMakeFiles/gkl_pairhmm_omp.dir/all --- *** [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/compression/CMakeFiles/otc_zlibExternal.dir/all --- cc -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fPIC -O3 -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -I. -I/wrkdirs/usr/ports/biology/gkl/work/.build/src/main/native/compression/otc_zlibExternal-prefix/src/otc_zlibExternal/ -D_FILE_OFFSET_BITS=64 -c -o example64.o /wrkdirs/usr/ports/biology/gkl/work/.build/src/main/native/compression/otc_zlibExternal-prefix/src/otc_zlibExternal/test/example.c *** [src/main/native/compression/otc_zlibExternal-prefix/src/otc_zlibExternal-stamp/otc_zlibExternal-build] Error code 6 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/compression/CMakeFiles/otc_zlibExternal.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 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
