From owner-freebsd-pkg-fallout@freebsd.org Mon Mar 28 13:08:39 2016 Return-Path: Delivered-To: freebsd-pkg-fallout@mailman.ysv.freebsd.org Received: from mx1.freebsd.org (mx1.freebsd.org [IPv6:2001:1900:2254:206a::19:1]) by mailman.ysv.freebsd.org (Postfix) with ESMTP id C5B6EAE05F7 for ; Mon, 28 Mar 2016 13:08:39 +0000 (UTC) (envelope-from pkg-fallout@FreeBSD.org) Received: from mailman.ysv.freebsd.org (unknown [127.0.1.3]) by mx1.freebsd.org (Postfix) with ESMTP id B5622160C for ; Mon, 28 Mar 2016 13:08:39 +0000 (UTC) (envelope-from pkg-fallout@FreeBSD.org) Received: by mailman.ysv.freebsd.org (Postfix) id B0F2FAE05F5; Mon, 28 Mar 2016 13:08:39 +0000 (UTC) Delivered-To: pkg-fallout@mailman.ysv.freebsd.org Received: from mx1.freebsd.org (mx1.freebsd.org [IPv6:2001:1900:2254:206a::19:1]) by mailman.ysv.freebsd.org (Postfix) with ESMTP id B089FAE05F4 for ; Mon, 28 Mar 2016 13:08:39 +0000 (UTC) (envelope-from pkg-fallout@FreeBSD.org) Received: from beefy8.nyi.freebsd.org (beefy8.nyi.freebsd.org [IPv6:2610:1c1:1:6080::16:eb]) (using TLSv1.2 with cipher ECDHE-RSA-AES256-GCM-SHA384 (256/256 bits)) (Client did not present a certificate) by mx1.freebsd.org (Postfix) with ESMTPS id 7C89C160B for ; Mon, 28 Mar 2016 13:08:39 +0000 (UTC) (envelope-from pkg-fallout@FreeBSD.org) Received: from beefy8.nyi.freebsd.org (localhost [127.0.0.1]) by beefy8.nyi.freebsd.org (8.15.2/8.15.2) with ESMTP id u2SD8cTA093828 for ; Mon, 28 Mar 2016 13:08:38 GMT (envelope-from pkg-fallout@FreeBSD.org) Received: (from root@localhost) by beefy8.nyi.freebsd.org (8.15.2/8.15.2/Submit) id u2SD8cRx093827; Mon, 28 Mar 2016 13:08:38 GMT (envelope-from pkg-fallout@FreeBSD.org) Date: Mon, 28 Mar 2016 13:08:38 GMT From: pkg-fallout@FreeBSD.org Message-Id: <201603281308.u2SD8cRx093827@beefy8.nyi.freebsd.org> To: pkg-fallout@FreeBSD.org Subject: [package - head-armv6-default][biology/bwa] Failed for bwa-0.7.9a in build X-BeenThere: freebsd-pkg-fallout@freebsd.org X-Mailman-Version: 2.1.21 Precedence: list List-Id: Fallout logs from package building List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , X-List-Received-Date: Mon, 28 Mar 2016 13:08:39 -0000 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: bacon4000@gmail.com Last committer: swills@FreeBSD.org Ident: $FreeBSD: head/biology/bwa/Makefile 403676 2015-12-13 16:07:27Z swills $ Log URL: http://beefy8.nyi.freebsd.org/data/head-armv6-default/p411721_s297210/logs/bwa-0.7.9a.log Build URL: http://beefy8.nyi.freebsd.org/build.html?mastername=head-armv6-default&build=p411721_s297210 Log: ====>> Building biology/bwa build started at Mon Mar 28 13:08:33 UTC 2016 port directory: /usr/ports/biology/bwa building for: FreeBSD head-armv6-default-job-12 11.0-CURRENT FreeBSD 11.0-CURRENT r297210 arm maintained by: bacon4000@gmail.com Makefile ident: $FreeBSD: head/biology/bwa/Makefile 403676 2015-12-13 16:07:27Z swills $ Poudriere version: 3.1.12 Host OSVERSION: 1100100 Jail OSVERSION: 1100104 !!! Jail is newer than host. (Jail: 1100104, Host: 1100100) !!! !!! This is not supported. !!! !!! Host kernel must be same or newer than jail. !!! !!! Expect build failures. !!! ---Begin Environment--- SHELL=/bin/csh UNAME_p=armv6 UNAME_m=arm ABI_FILE=/usr/lib/crt1.o UNAME_v=FreeBSD 11.0-CURRENT r297210 UNAME_r=11.0-CURRENT BLOCKSIZE=K MAIL=/var/mail/root STATUS=1 OPSYS=FreeBSD ARCH=armv6 LINUX_OSRELEASE=2.6.32 SAVED_TERM=screen QEMU_EMULATING=1 MASTERMNT=/usr/local/poudriere/data/.m/head-armv6-default/ref UID=0 PATH=/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin _JAVA_VERSION_LIST_REGEXP=1.6\|1.7\|1.8\|1.6+\|1.7+\|1.8+ POUDRIERE_BUILD_TYPE=bulk PKGNAME=bwa-0.7.9a OSREL=11.0 _OSRELEASE=11.0-CURRENT PYTHONBASE=/usr/local OLDPWD=/ _SMP_CPUS=24 PWD=/usr/local/poudriere/data/.m/head-armv6-default/ref/.p/pool MASTERNAME=head-armv6-default SCRIPTPREFIX=/usr/local/share/poudriere _JAVA_VENDOR_LIST_REGEXP=openjdk\|oracle\|sun USER=root HOME=/root POUDRIERE_VERSION=3.1.12 SCRIPTPATH=/usr/local/share/poudriere/bulk.sh CONFIGURE_MAX_CMD_LEN=262144 LIBEXECPREFIX=/usr/local/libexec/poudriere LOCALBASE=/usr/local PACKAGE_BUILDING=yes _JAVA_OS_LIST_REGEXP=native\|linux OSVERSION=1100104 ---End Environment--- ---Begin OPTIONS List--- ---End OPTIONS List--- --CONFIGURE_ARGS-- --End CONFIGURE_ARGS-- --CONFIGURE_ENV-- ac_cv_path_PERL=/usr/local/bin/perl ac_cv_path_PERL_PATH=/usr/local/bin/perl XDG_DATA_HOME=/wrkdirs/usr/ports/biology/bwa/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/bwa/work HOME=/wrkdirs/usr/ports/biology/bwa/work TMPDIR="/tmp" SHELL=/bin/sh CONFIG_SHELL=/bin/sh --End CONFIGURE_ENV-- --MAKE_ENV-- XDG_DATA_HOME=/wrkdirs/usr/ports/biology/bwa/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/bwa/work HOME=/wrkdirs/usr/ports/biology/bwa/work TMPDIR="/tmp" NO_PIE=yes WITHOUT_DEBUG_FILES=yes WITHOUT_KERNEL_SYMBOLS=yes SHELL=/bin/sh NO_LINT=YES PREFIX=/usr/local LOCALBASE=/usr/local LIBDIR="/usr/lib" CC="/nxb-bin/usr/bin/cc" CFLAGS="-O2 -pipe -mfloat-abi=softfp -msse2 -fno-strict-aliasing" CPP="/nxb-bin/usr/bin/cpp" CPPFLAGS="" LDFLAGS="" LIBS="" CXX="/nxb-bin/usr/bin/c++" CXXFLAGS="-O2 -pipe -mfloat-abi=softfp -msse2 -fno-strict-aliasing " MANPREFIX="/usr/local" BSD_INSTALL_PROGRAM="install -s -m 555" BSD_INSTALL_LIB="install -s -m 444" BSD_INSTALL_SCRIPT="install -m 555" BSD_INSTALL_DATA="install -m 0644" BSD_INSTALL_MAN="install -m 444" --End MAKE_ENV-- --PLIST_SUB-- OSREL=11.0 PREFIX=%D LOCALBASE=/usr/local RESETPREFIX=/usr/local PORTDOCS="" PORTEXAMPLES="" LIB32DIR=lib PERL_VERSION=5.20.3 PERL_VER=5.20 PERL5_MAN1=lib/perl5/site_perl/man/man1 PERL5_MAN3=lib/perl5/site_perl/man/man3 SITE_PERL=lib/perl5/site_perl SITE_ARCH=lib/perl5/site_perl/mach/5.20 DOCSDIR="share/doc/bwa" EXAMPLESDIR="share/examples/bwa" DATADIR="share/bwa" WWWDIR="www/bwa" ETCDIR="etc/bwa" --End PLIST_SUB-- --SUB_LIST-- PREFIX=/usr/local LOCALBASE=/usr/local DATADIR=/usr/local/share/bwa DOCSDIR=/usr/local/share/doc/bwa EXAMPLESDIR=/usr/local/share/examples/bwa WWWDIR=/usr/local/www/bwa ETCDIR=/usr/local/etc/bwa --End SUB_LIST-- ---Begin make.conf--- CC=/nxb-bin/usr/bin/cc CPP=/nxb-bin/usr/bin/cpp CXX=/nxb-bin/usr/bin/c++ AS=/nxb-bin/usr/bin/as NM=/nxb-bin/usr/bin/nm LD=/nxb-bin/usr/bin/ld OBJCOPY=/nxb-bin/usr/bin/objcopy SIZE=/nxb-bin/usr/bin/size STRIPBIN=/nxb-bin/usr/bin/strip SED=/nxb-bin/usr/bin/sed READELF=/nxb-bin/usr/bin/readelf RANLIB=/nxb-bin/usr/bin/ranlib YACC=/nxb-bin/usr/bin/yacc NM=/nxb-bin/usr/bin/nm MAKE=/nxb-bin/usr/bin/make STRINGS=/nxb-bin/usr/bin/strings AWK=/nxb-bin/usr/bin/awk FLEX=/nxb-bin/usr/bin/flex CC=/nxb-bin/usr/bin/cc CPP=/nxb-bin/usr/bin/cpp CXX=/nxb-bin/usr/bin/c++ AS=/nxb-bin/usr/bin/as NM=/nxb-bin/usr/bin/nm LD=/nxb-bin/usr/bin/ld OBJCOPY=/nxb-bin/usr/bin/objcopy SIZE=/nxb-bin/usr/bin/size STRIPBIN=/nxb-bin/usr/bin/strip SED=/nxb-bin/usr/bin/sed READELF=/nxb-bin/usr/bin/readelf RANLIB=/nxb-bin/usr/bin/ranlib YACC=/nxb-bin/usr/bin/yacc NM=/nxb-bin/usr/bin/nm MAKE=/nxb-bin/usr/bin/make STRINGS=/nxb-bin/usr/bin/strings AWK=/nxb-bin/usr/bin/awk FLEX=/nxb-bin/usr/bin/flex CC=/nxb-bin/usr/bin/cc CPP=/nxb-bin/usr/bin/cpp CXX=/nxb-bin/usr/bin/c++ AS=/nxb-bin/usr/bin/as NM=/nxb-bin/usr/bin/nm LD=/nxb-bin/usr/bin/ld OBJCOPY=/nxb-bin/usr/bin/objcopy SIZE=/nxb-bin/usr/bin/size STRIPBIN=/nxb-bin/usr/bin/strip SED=/nxb-bin/usr/bin/sed READELF=/nxb-bin/usr/bin/readelf RANLIB=/nxb-bin/usr/bin/ranlib YACC=/nxb-bin/usr/bin/yacc NM=/nxb-bin/usr/bin/nm MAKE=/nxb-bin/usr/bin/make STRINGS=/nxb-bin/usr/bin/strings AWK=/nxb-bin/usr/bin/awk FLEX=/nxb-bin/usr/bin/flex CC=/nxb-bin/usr/bin/cc CPP=/nxb-bin/usr/bin/cpp CXX=/nxb-bin/usr/bin/c++ AS=/nxb-bin/usr/bin/as NM=/nxb-bin/usr/bin/nm LD=/nxb-bin/usr/bin/ld OBJCOPY=/nxb-bin/usr/bin/objcopy SIZE=/nxb-bin/usr/bin/size STRIPBIN=/nxb-bin/usr/bin/strip SED=/nxb-bin/usr/bin/sed READELF=/nxb-bin/usr/bin/readelf RANLIB=/nxb-bin/usr/bin/ranlib YACC=/nxb-bin/usr/bin/yacc NM=/nxb-bin/usr/bin/nm MAKE=/nxb-bin/usr/bin/make STRINGS=/nxb-bin/usr/bin/strings AWK=/nxb-bin/usr/bin/awk FLEX=/nxb-bin/usr/bin/flex CC=/nxb-bin/usr/bin/cc CPP=/nxb-bin/usr/bin/cpp CXX=/nxb-bin/usr/bin/c++ AS=/nxb-bin/usr/bin/as NM=/nxb-bin/usr/bin/nm LD=/nxb-bin/usr/bin/ld OBJCOPY=/nxb-bin/usr/bin/objcopy SIZE=/nxb-bin/usr/bin/size STRIPBIN=/nxb-bin/usr/bin/strip SED=/nxb-bin/usr/bin/sed READELF=/nxb-bin/usr/bin/readelf RANLIB=/nxb-bin/usr/bin/ranlib YACC=/nxb-bin/usr/bin/yacc NM=/nxb-bin/usr/bin/nm MAKE=/nxb-bin/usr/bin/make STRINGS=/nxb-bin/usr/bin/strings AWK=/nxb-bin/usr/bin/awk FLEX=/nxb-bin/usr/bin/flex STRIPBIN=/nxb-bin/usr/bin/strip SED=/nxb-bin/usr/bin/sed READELF=/nxb-bin/usr/bin/readelf RANLIB=/nxb-bin/usr/bin/ranlib YACC=/nxb-bin/usr/bin/yacc NM=/nxb-bin/usr/bin/nm MAKE=/nxb-bin/usr/bin/make STRINGS=/nxb-bin/usr/bin/strings AWK=/nxb-bin/usr/bin/awk FLEX=/nxb-bin/usr/bin/flex MACHINE=arm MACHINE_ARCH=armv6 ARCH=${MACHINE_ARCH} .sinclude "/etc/make.nxb.conf" USE_PACKAGE_DEPENDS=yes BATCH=yes WRKDIRPREFIX=/wrkdirs PORTSDIR=/usr/ports PACKAGES=/packages DISTDIR=/distfiles #### /usr/local/etc/poudriere.d/make.conf #### DISABLE_MAKE_JOBS=poudriere ---End make.conf--- ---Begin make.nxb.conf--- CC=/nxb-bin/usr/bin/cc CPP=/nxb-bin/usr/bin/cpp CXX=/nxb-bin/usr/bin/c++ AS=/nxb-bin/usr/bin/as NM=/nxb-bin/usr/bin/nm LD=/nxb-bin/usr/bin/ld OBJCOPY=/nxb-bin/usr/bin/objcopy SIZE=/nxb-bin/usr/bin/size STRIPBIN=/nxb-bin/usr/bin/strip SED=/nxb-bin/usr/bin/sed READELF=/nxb-bin/usr/bin/readelf RANLIB=/nxb-bin/usr/bin/ranlib YACC=/nxb-bin/usr/bin/yacc MAKE=/nxb-bin/usr/bin/make STRINGS=/nxb-bin/usr/bin/strings AWK=/nxb-bin/usr/bin/awk FLEX=/nxb-bin/usr/bin/flex ---End make.nxb.conf--- =================================================== ===> License GPLv3 accepted by the user =========================================================================== =================================================== ===> bwa-0.7.9a depends on file: /usr/local/sbin/pkg - not found ===> Installing existing package /packages/All/pkg-1.6.4_1.txz [head-armv6-default-job-12] Installing pkg-1.6.4_1... [head-armv6-default-job-12] Extracting pkg-1.6.4_1: .......... done ===> bwa-0.7.9a depends on file: /usr/local/sbin/pkg - found ===> Returning to build of bwa-0.7.9a =========================================================================== =================================================== =========================================================================== =================================================== ===> License GPLv3 accepted by the user ===> Fetching all distfiles required by bwa-0.7.9a for building =========================================================================== =================================================== ===> License GPLv3 accepted by the user ===> Fetching all distfiles required by bwa-0.7.9a for building => SHA256 Checksum OK for bwa-0.7.9a.tar.bz2. =========================================================================== =================================================== =========================================================================== =================================================== ===> License GPLv3 accepted by the user ===> Fetching all distfiles required by bwa-0.7.9a for building ===> Extracting for bwa-0.7.9a => SHA256 Checksum OK for bwa-0.7.9a.tar.bz2. =========================================================================== =================================================== =========================================================================== =================================================== ===> Patching for bwa-0.7.9a ===> Applying FreeBSD patches for bwa-0.7.9a =========================================================================== =================================================== =========================================================================== =================================================== =========================================================================== =================================================== ===> Configuring for bwa-0.7.9a =========================================================================== =================================================== ===> Building for bwa-0.7.9a /nxb-bin/usr/bin/cc -c -O2 -pipe -mfloat-abi=softfp -msse2 -fno-strict-aliasing -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS utils.c -o utils.o cc: warning: argument unused during compilation: '-msse2' /nxb-bin/usr/bin/cc -c -O2 -pipe -mfloat-abi=softfp -msse2 -fno-strict-aliasing -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS kthread.c -o kthread.o cc: warning: argument unused during compilation: '-msse2' /nxb-bin/usr/bin/cc -c -O2 -pipe -mfloat-abi=softfp -msse2 -fno-strict-aliasing -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS kstring.c -o kstring.o cc: warning: argument unused during compilation: '-msse2' /nxb-bin/usr/bin/cc -c -O2 -pipe -mfloat-abi=softfp -msse2 -fno-strict-aliasing -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS ksw.c -o ksw.o cc: warning: argument unused during compilation: '-msse2' In file included from ksw.c:29: /nxb-bin/usr/bin/../lib/clang/3.7.1/include/emmintrin.h:28:2: error: "SSE2 instruction set not enabled" #error "SSE2 instruction set not enabled" ^ ksw.c:49:2: error: unknown type name '__m128i' __m128i *qp, *H0, *H1, *E, *Hmax; ^ ksw.c:72:19: error: expected expression q->qp = (__m128i*)(((size_t)q + sizeof(kswq_t) + 15) >> 4 << 4); // align memory ^ ksw.c:72:11: error: use of undeclared identifier '__m128i' q->qp = (__m128i*)(((size_t)q + sizeof(kswq_t) + 15) >> 4 << 4); // align memory ^ ksw.c:115:2: error: use of undeclared identifier '__m128i' __m128i zero, oe_del, e_del, oe_ins, e_ins, shift, *H0, *H1, *E, *Hmax; ^ ksw.c:131:2: error: use of undeclared identifier 'zero' zero = _mm_set1_epi32(0); ^ ksw.c:131:9: warning: implicit declaration of function '_mm_set1_epi32' is invalid in C99 [-Wimplicit-function-declaration] zero = _mm_set1_epi32(0); ^ ksw.c:132:2: error: use of undeclared identifier 'oe_del'; did you mean '_e_del'? oe_del = _mm_set1_epi8(_o_del + _e_del); ^~~~~~ _e_del ksw.c:111:75: note: '_e_del' declared here kswr_t ksw_u8(kswq_t *q, int tlen, const uint8_t *target, int _o_del, int _e_del, int _o_ins, int _e_ins, int xtra) // the first gap costs -(_o+_e) ^ ksw.c:132:11: warning: implicit declaration of function '_mm_set1_epi8' is invalid in C99 [-Wimplicit-function-declaration] oe_del = _mm_set1_epi8(_o_del + _e_del); ^ ksw.c:133:2: error: use of undeclared identifier 'e_del'; did you mean '_e_del'? e_del = _mm_set1_epi8(_e_del); ^~~~~ _e_del ksw.c:111:75: note: '_e_del' declared here kswr_t ksw_u8(kswq_t *q, int tlen, const uint8_t *target, int _o_del, int _e_del, int _o_ins, int _e_ins, int xtra) // the first gap costs -(_o+_e) ^ ksw.c:134:2: error: use of undeclared identifier 'oe_ins'; did you mean '_e_ins'? oe_ins = _mm_set1_epi8(_o_ins + _e_ins); ^~~~~~ _e_ins ksw.c:111:99: note: '_e_ins' declared here kswr_t ksw_u8(kswq_t *q, int tlen, const uint8_t *target, int _o_del, int _e_del, int _o_ins, int _e_ins, int xtra) // the first gap costs -(_o+_e) ^ ksw.c:135:2: error: use of undeclared identifier 'e_ins'; did you mean '_e_ins'? e_ins = _mm_set1_epi8(_e_ins); ^~~~~ _e_ins ksw.c:111:99: note: '_e_ins' declared here kswr_t ksw_u8(kswq_t *q, int tlen, const uint8_t *target, int _o_del, int _e_del, int _o_ins, int _e_ins, int xtra) // the first gap costs -(_o+_e) ^ ksw.c:136:2: error: use of undeclared identifier 'shift' shift = _mm_set1_epi8(q->shift); ^ ksw.c:137:2: error: use of undeclared identifier 'H0' H0 = q->H0; H1 = q->H1; E = q->E; Hmax = q->Hmax; ^ ksw.c:137:14: error: use of undeclared identifier 'H1' H0 = q->H0; H1 = q->H1; E = q->E; Hmax = q->Hmax; ^ ksw.c:137:26: error: use of undeclared identifier 'E' H0 = q->H0; H1 = q->H1; E = q->E; Hmax = q->Hmax; ^ ksw.c:137:36: error: use of undeclared identifier 'Hmax'; did you mean 'gmax'? H0 = q->H0; H1 = q->H1; E = q->E; Hmax = q->Hmax; ^~~~ gmax ksw.c:113:34: note: 'gmax' declared here int slen, i, m_b, n_b, te = -1, gmax = 0, minsc, endsc; ^ ksw.c:140:3: warning: implicit declaration of function '_mm_store_si128' is invalid in C99 [-Wimplicit-function-declaration] _mm_store_si128(E + i, zero); ^ ksw.c:140:19: error: use of undeclared identifier 'E' _mm_store_si128(E + i, zero); ^ ksw.c:140:26: error: use of undeclared identifier 'zero'; did you mean 'bzero'? _mm_store_si128(E + i, zero); ^~~~ bzero /usr/include/strings.h:44:7: note: 'bzero' declared here void bzero(void *, size_t); /* LEGACY */ ^ ksw.c:141:19: error: use of undeclared identifier 'H0' _mm_store_si128(H0 + i, zero); ^ ksw.c:141:27: error: use of undeclared identifier 'zero'; did you mean 'bzero'? _mm_store_si128(H0 + i, zero); ^~~~ bzero /usr/include/strings.h:44:7: note: 'bzero' declared here void bzero(void *, size_t); /* LEGACY */ ^ fatal error: too many errors emitted, stopping now [-ferror-limit=] 3 warnings and 20 errors generated. *** Error code 1 Stop. make[1]: stopped in /wrkdirs/usr/ports/biology/bwa/work/bwa-0.7.9a *** Error code 1 Stop. make: stopped in /usr/ports/biology/bwa