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Maintainer: y...@freebsd.org Log URL: https://pkg-status.freebsd.org/beefy21/data/140i386-default/117e00cbc3d2/logs/fermi-lite-0.1.13.log Build URL: https://pkg-status.freebsd.org/beefy21/build.html?mastername=140i386-default&build=117e00cbc3d2 Log: =>> Building biology/fermi-lite build started at Thu Sep 12 01:09:43 UTC 2024 port directory: /usr/ports/biology/fermi-lite package name: fermi-lite-0.1.13 building for: FreeBSD 140i386-default-job-15 14.0-RELEASE-p10 FreeBSD 14.0-RELEASE-p10 i386 maintained by: y...@freebsd.org Makefile datestamp: -rw-r--r-- 1 root wheel 967 Aug 15 01:01 /usr/ports/biology/fermi-lite/Makefile Ports top last git commit: 117e00cbc3 Ports top unclean checkout: no Port dir last git commit: 80a04a9595 Port dir unclean checkout: no Poudriere version: poudriere-git-3.4.2 Host OSVERSION: 1500023 Jail OSVERSION: 1400097 Job Id: 15 ---Begin Environment--- SHELL=/bin/sh BLOCKSIZE=K MAIL=/var/mail/root MM_CHARSET=UTF-8 LANG=C.UTF-8 OSVERSION=1400097 STATUS=1 HOME=/root PATH=/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin MAKE_OBJDIR_CHECK_WRITABLE=0 UNAME_m=i386 UNAME_p=i386 UNAME_r=14.0-RELEASE-p10 LOCALBASE=/usr/local UNAME_v=FreeBSD 14.0-RELEASE-p10 USER=root POUDRIERE_NAME=poudriere-git LIBEXECPREFIX=/usr/local/libexec/poudriere POUDRIERE_VERSION=3.4.2 MASTERMNT=/usr/local/poudriere/data/.m/140i386-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/140i386-default/15/.p OUTPUT_REDIRECTED_STDOUT=3 P_PORTS_FEATURES=FLAVORS SUBPACKAGES SELECTED_OPTIONS MASTERNAME=140i386-default SCRIPTPREFIX=/usr/local/share/poudriere SCRIPTNAME=bulk.sh OLDPWD=/usr/local/poudriere/data/.m/140i386-default/ref/.p/pool POUDRIERE_PKGNAME=poudriere-git-3.4.2 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-- y...@freebsd.org --End MAINTAINER-- --CONFIGURE_ARGS-- --End CONFIGURE_ARGS-- --CONFIGURE_ENV-- MAKE=gmake XDG_DATA_HOME=/wrkdirs/usr/ports/biology/fermi-lite/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/fermi-lite/work XDG_CACHE_HOME=/wrkdirs/usr/ports/biology/fermi-lite/work/.cache HOME=/wrkdirs/usr/ports/biology/fermi-lite/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/fermi-lite/work/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin PKG_CONFIG_LIBDIR=/wrkdirs/usr/ports/biology/fermi-lite/work/.pkgconfig:/usr/local/libdata/pkgconfig:/usr/local/share/pkgconfig:/usr/libdata/pkgconfig SHELL=/bin/sh CONFIG_SHELL=/bin/sh --End CONFIGURE_ENV-- --MAKE_ENV-- XDG_DATA_HOME=/wrkdirs/usr/ports/biology/fermi-lite/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/fermi-lite/work XDG_CACHE_HOME=/wrkdirs/usr/ports/biology/fermi-lite/work/.cache HOME=/wrkdirs/usr/ports/biology/fermi-lite/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/fermi-lite/work/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin PKG_CONFIG_LIBDIR=/wrkdirs/usr/ports/biology/fermi-lite/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 -fno-strict-aliasing " CPP="cpp" CPPFLAGS="" LDFLAGS=" -fstack-protector-strong " LIBS="" CXX="c++" CXXFLAGS="-O2 -pipe -fstack-protector-strong -fno-strict-aliasing " BSD_INSTALL_PROGRAM="install -s -m 555" BSD_INSTALL_LIB="install -s -m 0644" BSD_INSTALL_SCRIPT="install -m 555" BSD_INSTALL_DATA="i nstall -m 0644" BSD_INSTALL_MAN="install -m 444" --End MAKE_ENV-- --PLIST_SUB-- OSREL=14.0 PREFIX=%D LOCALBASE=/usr/local RESETPREFIX=/usr/local LIB32DIR=lib DOCSDIR="share/doc/fermi-lite" EXAMPLESDIR="share/examples/fermi-lite" DATADIR="share/fermi-lite" WWWDIR="www/fermi-lite" ETCDIR="etc/fermi-lite" --End PLIST_SUB-- --SUB_LIST-- PREFIX=/usr/local LOCALBASE=/usr/local DATADIR=/usr/local/share/fermi-lite DOCSDIR=/usr/local/share/doc/fermi-lite EXAMPLESDIR=/usr/local/share/examples/fermi-lite WWWDIR=/usr/local/www/fermi-lite ETCDIR=/usr/local/etc/fermi-lite --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 MACHINE=i386 MACHINE_ARCH=i386 ARCH=${MACHINE_ARCH} #### #### # 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 DISABLE_MAKE_JOBS=poudriere ---End make.conf--- --Resource limits-- cpu time (seconds, -t) unlimited file size (512-blocks, -f) unlimited data seg size (kbytes, -d) 524288 stack size (kbytes, -s) 65536 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 ===> fermi-lite-0.1.13 depends on file: /usr/local/sbin/pkg - not found ===> Installing existing package /packages/All/pkg-1.21.3.pkg [140i386-default-job-15] Installing pkg-1.21.3... [140i386-default-job-15] Extracting pkg-1.21.3: .......... done ===> fermi-lite-0.1.13 depends on file: /usr/local/sbin/pkg - found ===> Returning to build of fermi-lite-0.1.13 =========================================================================== =======================<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 fermi-lite-0.1.13 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 fermi-lite-0.1.13 for building => SHA256 Checksum OK for lh3-fermi-lite-v0.1-13-g85f159e_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 fermi-lite-0.1.13 for building ===> Extracting for fermi-lite-0.1.13 => SHA256 Checksum OK for lh3-fermi-lite-v0.1-13-g85f159e_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 fermi-lite-0.1.13 =========================================================================== =======================<phase: build-depends >============================ ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 ===> fermi-lite-0.1.13 depends on package: gmake>=4.4.1 - not found ===> Installing existing package /packages/All/gmake-4.4.1.pkg [140i386-default-job-15] Installing gmake-4.4.1... [140i386-default-job-15] `-- Installing gettext-runtime-0.22.5... [140i386-default-job-15] | `-- Installing indexinfo-0.3.1... [140i386-default-job-15] | `-- Extracting indexinfo-0.3.1: .... done [140i386-default-job-15] `-- Extracting gettext-runtime-0.22.5: .......... done [140i386-default-job-15] Extracting gmake-4.4.1: .......... done ===> fermi-lite-0.1.13 depends on package: gmake>=4.4.1 - found ===> Returning to build of fermi-lite-0.1.13 =========================================================================== =======================<phase: lib-depends >============================ ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 =========================================================================== =======================<phase: configure >============================ ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Configuring for fermi-lite-0.1.13 =========================================================================== =======================<phase: build >============================ ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Building for fermi-lite-0.1.13 gcc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing kthread.c -o kthread.o gcc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing misc.c -o misc.o gcc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing bseq.c -o bseq.o gcc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing htab.c -o htab.o gcc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing bfc.c -o bfc.o gcc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing rle.c -o rle.o gcc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing rope.c -o rope.o gcc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing mrope.c -o mrope.o gcc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing rld0.c -o rld0.o gcc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing unitig.c -o unitig.o gcc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing mag.c -o mag.o mag.c:418:84: warning: format specifies type 'long' but the argument has type 'size_t' (aka 'unsigned int') [-Wformat] fprintf(stderr, "[M::%s] removed %ld tips (min_len=%d, min_nsr=%d)\n", __func__, a.n, min_len, min_nsr); ~~~ ^~~ %zu mag.c:436:97: warning: format specifies type 'long' but the argument has type 'size_t' (aka 'unsigned int') [-Wformat] fprintf(stderr, "[M::%s] removed %ld internal vertices (min_len=%d, min_nsr=%d)\n", __func__, a.n, min_len, min_nsr); ~~~ ^~~ %zu 2 warnings generated. gcc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing bubble.c -o bubble.o gcc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing ksw.c -o ksw.o ksw.c:126:9: error: always_inline function '_mm_set1_epi32' requires target feature 'sse2', but would be inlined into function 'ksw_u8' that is compiled without support for 'sse2' zero = _mm_set1_epi32(0); ^ ksw.c:127:10: error: always_inline function '_mm_set1_epi8' requires target feature 'sse2', but would be inlined into function 'ksw_u8' that is compiled without support for 'sse2' gapoe = _mm_set1_epi8(_gapo + _gape); ^ ksw.c:128:9: error: always_inline function '_mm_set1_epi8' requires target feature 'sse2', but would be inlined into function 'ksw_u8' that is compiled without support for 'sse2' gape = _mm_set1_epi8(_gape); ^ ksw.c:129:10: error: always_inline function '_mm_set1_epi8' requires target feature 'sse2', but would be inlined into function 'ksw_u8' that is compiled without support for 'sse2' shift = _mm_set1_epi8(q->shift); ^ ksw.c:133:3: error: always_inline function '_mm_store_si128' requires target feature 'sse2', but would be inlined into function 'ksw_u8' that is compiled without support for 'sse2' _mm_store_si128(E + i, zero); ^ ksw.c:134:3: error: always_inline function '_mm_store_si128' requires target feature 'sse2', but would be inlined into function 'ksw_u8' that is compiled without support for 'sse2' _mm_store_si128(H0 + i, zero); ^ ksw.c:135:3: error: always_inline function '_mm_store_si128' requires target feature 'sse2', but would be inlined into function 'ksw_u8' that is compiled without support for 'sse2' _mm_store_si128(Hmax + i, zero); ^ ksw.c:141:7: error: always_inline function '_mm_load_si128' requires target feature 'sse2', but would be inlined into function 'ksw_u8' that is compiled without support for 'sse2' h = _mm_load_si128(H0 + slen - 1); // h={2,5,8,11,14,17,-1,-1} in the above example ^ ksw.c:142:7: error: '__builtin_ia32_pslldqi128_byteshift' needs target feature sse2 h = _mm_slli_si128(h, 1); // h=H(i-1,-1); << instead of >> because x64 is little-endian ^ /usr/lib/clang/16/include/emmintrin.h:2686:13: note: expanded from macro '_mm_slli_si128' ((__m128i)__builtin_ia32_pslldqi128_byteshift((__v2di)(__m128i)(a), \ ^ ksw.c:150:25: error: always_inline function '_mm_load_si128' requires target feature 'sse2', but would be inlined into function 'ksw_u8' that is compiled without support for 'sse2' h = _mm_adds_epu8(h, _mm_load_si128(S + j)); ^ ksw.c:150:8: error: always_inline function '_mm_adds_epu8' requires target feature 'sse2', but would be inlined into function 'ksw_u8' that is compiled without support for 'sse2' h = _mm_adds_epu8(h, _mm_load_si128(S + j)); ^ ksw.c:151:8: error: always_inline function '_mm_subs_epu8' requires target feature 'sse2', but would be inlined into function 'ksw_u8' that is compiled without support for 'sse2' h = _mm_subs_epu8(h, shift); // h=H'(i-1,j-1)+S(i,j) ^ ksw.c:152:8: error: always_inline function '_mm_load_si128' requires target feature 'sse2', but would be inlined into function 'ksw_u8' that is compiled without support for 'sse2' e = _mm_load_si128(E + j); // e=E'(i,j) ^ ksw.c:153:8: error: always_inline function '_mm_max_epu8' requires target feature 'sse2', but would be inlined into function 'ksw_u8' that is compiled without support for 'sse2' h = _mm_max_epu8(h, e); ^ ksw.c:154:8: error: always_inline function '_mm_max_epu8' requires target feature 'sse2', but would be inlined into function 'ksw_u8' that is compiled without support for 'sse2' h = _mm_max_epu8(h, f); // h=H'(i,j) ^ ksw.c:155:10: error: always_inline function '_mm_max_epu8' requires target feature 'sse2', but would be inlined into function 'ksw_u8' that is compiled without support for 'sse2' max = _mm_max_epu8(max, h); // set max ^ ksw.c:156:4: error: always_inline function '_mm_store_si128' requires target feature 'sse2', but would be inlined into function 'ksw_u8' that is compiled without support for 'sse2' _mm_store_si128(H1 + j, h); // save to H'(i,j) ^ ksw.c:158:8: error: always_inline function '_mm_subs_epu8' requires target feature 'sse2', but would be inlined into function 'ksw_u8' that is compiled without support for 'sse2' h = _mm_subs_epu8(h, gapoe); // h=H'(i,j)-gapo ^ ksw.c:159:8: error: always_inline function '_mm_subs_epu8' requires target feature 'sse2', but would be inlined into function 'ksw_u8' that is compiled without support for 'sse2' e = _mm_subs_epu8(e, gape); // e=E'(i,j)-gape ^ fatal error: too many errors emitted, stopping now [-ferror-limit=] 20 errors generated. gmake: *** [Makefile:15: ksw.o] Error 1 *** Error code 1 Stop. make: stopped in /usr/ports/biology/fermi-lite