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Maintainer: [email protected] Log URL: https://pkg-status.freebsd.org/ampere3/data/135arm64-quarterly/fdcb9cadcbbc/logs/gkl-0.9.1.log Build URL: https://pkg-status.freebsd.org/ampere3/build.html?mastername=135arm64-quarterly&build=fdcb9cadcbbc Log: =>> Building biology/gkl build started at Sat Feb 14 01:29:13 UTC 2026 port directory: /usr/ports/biology/gkl package name: gkl-0.9.1 building for: FreeBSD 135arm64-quarterly-job-12 13.5-RELEASE-p9 FreeBSD 13.5-RELEASE-p9 arm64 maintained by: [email protected] Makefile datestamp: -rw-r--r-- 1 root wheel 464 Jan 29 01:04 /usr/ports/biology/gkl/Makefile Ports top last git commit: fdcb9cadcbbccb1315452eafff742d7b3a0db92c Ports top unclean checkout: no Port dir last git commit: e0a7a5a2edafbcf1649bbeec0d8904d9de277aec Port dir unclean checkout: no Poudriere version: poudriere-git-3.4.4-22-g8faef853 Host OSVERSION: 1600007 Jail OSVERSION: 1305000 Job Id: 12 ---Begin Environment--- SHELL=/bin/csh OSVERSION=1305000 UNAME_v=FreeBSD 13.5-RELEASE-p9 UNAME_r=13.5-RELEASE-p9 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/135arm64-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/135arm64-quarterly/12/.p OUTPUT_REDIRECTED_STDOUT=3 P_PORTS_FEATURES=FLAVORS SUBPACKAGES SELECTED_OPTIONS MASTERNAME=135arm64-quarterly SCRIPTPREFIX=/usr/local/share/poudriere SCRIPTNAME=bulk.sh OLDPWD=/usr/local/poudriere/data/.m/135arm64-quarterly/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=13.5 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 --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 [135arm64-quarterly-job-12] Installing pkg-2.5.1... [135arm64-quarterly-job-12] 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 [135arm64-quarterly-job-12] Installing gmake-4.4.1... [135arm64-quarterly-job-12] `-- Installing gettext-runtime-0.26... [135arm64-quarterly-job-12] | `-- Installing indexinfo-0.3.1_1... [135arm64-quarterly-job-12] | `-- Extracting indexinfo-0.3.1_1: .... done [135arm64-quarterly-job-12] `-- Extracting gettext-runtime-0.26: .......... done [135arm64-quarterly-job-12] 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.pkg [135arm64-quarterly-job-12] Installing cmake-core-3.31.10... [135arm64-quarterly-job-12] `-- Installing expat-2.7.3... [135arm64-quarterly-job-12] `-- Extracting expat-2.7.3: .......... done [135arm64-quarterly-job-12] `-- Installing jsoncpp-1.9.6_1... [135arm64-quarterly-job-12] `-- Extracting jsoncpp-1.9.6_1: .......... done [135arm64-quarterly-job-12] `-- Installing libidn2-2.3.8... [135arm64-quarterly-job-12] | `-- Installing libunistring-1.4.1... [135arm64-quarterly-job-12] | `-- Extracting libunistring-1.4.1: .......... done [135arm64-quarterly-job-12] `-- Extracting libidn2-2.3.8: .......... done [135arm64-quarterly-job-12] `-- Installing libuv-1.51.0... [135arm64-quarterly-job-12] `-- Extracting libuv-1.51.0: .......... done [135arm64-quarterly-job-12] `-- Installing rhash-1.4.6... [135arm64-quarterly-job-12] `-- Extracting rhash-1.4.6: .......... done [135arm64-quarterly-job-12] Extracting cmake-core-3.31.10: .......... done <snip> | ^ /wrkdirs/usr/ports/biology/gkl/work/.build/src/main/native/compression/otc_zlibExternal-prefix/src/otc_zlibExternal/adler32.c:196:15: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype] 196 | uLong ZEXPORT adler32_combine64(adler1, adler2, len2) | ^ 5 warnings generated. --- crc32.o --- cc -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fPIC -O3 -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -include zconf.h -c -o crc32.o /wrkdirs/usr/ports/biology/gkl/work/.build/src/main/native/compression/otc_zlibExternal-prefix/src/otc_zlibExternal/crc32.c /wrkdirs/usr/ports/biology/gkl/work/.build/src/main/native/compression/otc_zlibExternal-prefix/src/otc_zlibExternal/crc32.c:126:16: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype] 126 | local z_word_t byte_swap(word) | ^ /wrkdirs/usr/ports/biology/gkl/work/.build/src/main/native/compression/otc_zlibExternal-prefix/src/otc_zlibExternal/crc32.c:551:15: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype] 551 | local z_crc_t multmodp(a, b) | ^ /wrkdirs/usr/ports/biology/gkl/work/.build/src/main/native/compression/otc_zlibExternal-prefix/src/otc_zlibExternal/crc32.c:575:15: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype] 575 | local z_crc_t x2nmodp(n, k) | ^ /wrkdirs/usr/ports/biology/gkl/work/.build/src/main/native/compression/otc_zlibExternal-prefix/src/otc_zlibExternal/crc32.c:726:15: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype] 726 | local z_crc_t crc_word(data) | ^ /wrkdirs/usr/ports/biology/gkl/work/.build/src/main/native/compression/otc_zlibExternal-prefix/src/otc_zlibExternal/crc32.c:735:16: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype] 735 | local z_word_t crc_word_big(data) | ^ /wrkdirs/usr/ports/biology/gkl/work/.build/src/main/native/compression/otc_zlibExternal-prefix/src/otc_zlibExternal/crc32.c:748:23: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype] 748 | unsigned long ZEXPORT crc32_z(crc, buf, len) | ^ /wrkdirs/usr/ports/biology/gkl/work/.build/src/main/native/compression/otc_zlibExternal-prefix/src/otc_zlibExternal/crc32.c:1072:23: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype] 1072 | unsigned long ZEXPORT crc32(crc, buf, len) | ^ /wrkdirs/usr/ports/biology/gkl/work/.build/src/main/native/compression/otc_zlibExternal-prefix/src/otc_zlibExternal/crc32.c:1081:15: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype] 1081 | uLong ZEXPORT crc32_combine64(crc1, crc2, len2) | ^ /wrkdirs/usr/ports/biology/gkl/work/.build/src/main/native/compression/otc_zlibExternal-prefix/src/otc_zlibExternal/crc32.c:1093:15: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype] 1093 | uLong ZEXPORT crc32_combine(crc1, crc2, len2) | ^ /wrkdirs/usr/ports/biology/gkl/work/.build/src/main/native/compression/otc_zlibExternal-prefix/src/otc_zlibExternal/crc32.c:1102:15: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype] 1102 | uLong ZEXPORT crc32_combine_gen64(len2) | ^ /wrkdirs/usr/ports/biology/gkl/work/.build/src/main/native/compression/otc_zlibExternal-prefix/src/otc_zlibExternal/crc32.c:1112:15: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype] 1112 | uLong ZEXPORT crc32_combine_gen(len2) | ^ /wrkdirs/usr/ports/biology/gkl/work/.build/src/main/native/compression/otc_zlibExternal-prefix/src/otc_zlibExternal/crc32.c:1119:15: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype] 1119 | uLong ZEXPORT crc32_combine_op(crc1, crc2, op) | ^ --- 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/pairhmm/CMakeFiles/gkl_pairhmm.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/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); | ^ --- src/main/native/pairhmm/CMakeFiles/gkl_pairhmm.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); | ^ --- src/main/native/pairhmm/CMakeFiles/gkl_pairhmm_omp.dir/all --- /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); | ^ --- src/main/native/pairhmm/CMakeFiles/gkl_pairhmm.dir/all --- /usr/lib/clang/19/include/ia32intrin.h:408:10: error: use of undeclared identifier '__builtin_ia32_crc32qi' 408 | return __builtin_ia32_crc32qi(__C, __D); | ^ --- src/main/native/pairhmm/CMakeFiles/gkl_pairhmm_omp.dir/all --- /usr/lib/clang/19/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.dir/all --- /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); | ^ --- src/main/native/pairhmm/CMakeFiles/gkl_pairhmm_omp.dir/all --- /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); | ^ ~~~ --- src/main/native/pairhmm/CMakeFiles/gkl_pairhmm.dir/all --- /usr/lib/clang/19/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 --- /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); | ^~~ --- src/main/native/pairhmm/CMakeFiles/gkl_pairhmm.dir/all --- /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); | ^ ~~~ --- src/main/native/pairhmm/CMakeFiles/gkl_pairhmm_omp.dir/all --- /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" | ^ --- src/main/native/pairhmm/CMakeFiles/gkl_pairhmm.dir/all --- /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); | ^~~ --- src/main/native/compression/CMakeFiles/otc_zlibExternal.dir/all --- 12 warnings generated. --- crc_folding.o --- cc -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fPIC -O3 -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -include zconf.h -mpclmul -msse4 -c -o crc_folding.o /wrkdirs/usr/ports/biology/gkl/work/.build/src/main/native/compression/otc_zlibExternal-prefix/src/otc_zlibExternal/crc_folding.c --- 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: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); | ^ --- src/main/native/pairhmm/CMakeFiles/gkl_pairhmm.dir/all --- /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:14: /usr/lib/clang/19/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 --- cc: error: unsupported option '-mpclmul' for target 'aarch64-unknown-freebsd13.5' cc: warning: argument unused during compilation: '-msse4' [-Wunused-command-line-argument] *** [crc_folding.o] Error code 1 make[3]: stopped in /wrkdirs/usr/ports/biology/gkl/work/.build/src/main/native/compression/otc_zlibExternal-prefix/src/otc_zlibExternal-build 1 error make[3]: stopped in /wrkdirs/usr/ports/biology/gkl/work/.build/src/main/native/compression/otc_zlibExternal-prefix/src/otc_zlibExternal-build --- src/main/native/pairhmm/CMakeFiles/gkl_pairhmm_omp.dir/all --- *** [src/main/native/pairhmm/CMakeFiles/gkl_pairhmm_omp.dir/all] Error code 6 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 --- *** [src/main/native/compression/otc_zlibExternal-prefix/src/otc_zlibExternal-stamp/otc_zlibExternal-build] Error code 2 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 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
