Date: Thu, 29 Jun 2017 02:39:46 GMT From: pkg-fallout@FreeBSD.org To: pkg-fallout@FreeBSD.org Subject: [package - 110mips64-quarterly][biology/bwa] Failed for bwa-0.7.9a in build Message-ID: <201706290239.v5T2dkSf066229@beefy16.nyi.freebsd.org>
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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: linimon@FreeBSD.org Ident: $FreeBSD: branches/2017Q2/biology/bwa/Makefile 432897 2017-01-31 03:40:46Z linimon $ Log URL: http://beefy16.nyi.freebsd.org/data/110mips64-quarterly/444601/logs/bwa-0.7.9a.log Build URL: http://beefy16.nyi.freebsd.org/build.html?mastername=110mips64-quarterly&build=444601 Log: ====>> Building biology/bwa build started at Thu Jun 29 02:39:31 UTC 2017 port directory: /usr/ports/biology/bwa building for: FreeBSD 110mips64-quarterly-job-23 11.0-RELEASE-p10 FreeBSD 11.0-RELEASE-p10 r317487 mips maintained by: bacon4000@gmail.com Makefile ident: $FreeBSD: branches/2017Q2/biology/bwa/Makefile 432897 2017-01-31 03:40:46Z linimon $ Poudriere version: 3.1.19-40-ga434dff0 Host OSVERSION: 1200033 Jail OSVERSION: 1100122 Job Id: 23 ---Begin Environment--- SHELL=/bin/csh UNAME_p=mips64 UNAME_m=mips ABI_FILE=/usr/lib/crt1.o OSVERSION=1100122 UNAME_v=FreeBSD 11.0-RELEASE-p10 r317487 UNAME_r=11.0-RELEASE-p10 BLOCKSIZE=K MAIL=/var/mail/root STATUS=1 SAVED_TERM= MASTERMNT=/usr/local/poudriere/data/.m/110mips64-quarterly/ref QEMU_EMULATING=1 PATH=/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin POUDRIERE_BUILD_TYPE=bulk PKGNAME=bwa-0.7.9a OLDPWD=/ PWD=/usr/local/poudriere/data/.m/110mips64-quarterly/ref/.p/pool MASTERNAME=110mips64-quarterly SCRIPTPREFIX=/usr/local/share/poudriere USER=root HOME=/root POUDRIERE_VERSION=3.1.19-40-ga434dff0 SCRIPTPATH=/usr/local/share/poudriere/bulk.sh LIBEXECPREFIX=/usr/local/libexec/poudriere LOCALBASE=/usr/local POUDRIEREPATH=/usr/local/bin/poudriere ---End Environment--- ---Begin Poudriere Port Flags/Env--- PORT_FLAGS= PKGENV= ---End Poudriere Port Flags/Env--- ---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 PERL_USE_UNSAFE_INC=1 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-- PERL_USE_UNSAFE_INC=1 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 MK_DEBUG_FILES=no MK_KERNEL_SYMBOLS=no SHELL=/bin/sh NO_LINT=YES PREFIX=/usr/local LOCALBASE=/usr/local LIBDIR="/usr/lib" CC="/nxb-bin/usr/bin/cc" CFLAGS="-O2 -pipe -G0 -fno-strict-aliasing" CPP="/nxb-bin/usr/bin/cpp" CPPFLAGS="" LDFLAGS="" LIBS="" CXX="/nxb-bin/usr/bin/c++" CXXFLAGS="-O2 -pipe -G0 -fno-strict-aliasing " MANPREFIX="/usr/local" BSD_INSTALL_PROGRAM="install -s -m 555" BSD_INSTALL_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-- OSREL=11.0 PREFIX=%D LOCALBASE=/usr/local RESETPREFIX=/usr/local PORTDOCS="" PORTEXAMPLES="" LIB32DIR=lib PERL_VERSION=5.24.1 PERL_VER=5.24 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/5.24 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--- .sinclude "/etc/make.nxb.conf" USE_PACKAGE_DEPENDS=yes BATCH=yes WRKDIRPREFIX=/wrkdirs PORTSDIR=/usr/ports PACKAGES=/packages DISTDIR=/distfiles PACKAGE_BUILDING=yes MACHINE=mips MACHINE_ARCH=mips64 ARCH=${MACHINE_ARCH} #### /usr/local/etc/poudriere.d/make.conf #### # 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 2 jobs MAKE_JOBS_NUMBER=2 #### /usr/ports/Mk/Scripts/ports_env.sh #### ARCH=mips64 CONFIGURE_MAX_CMD_LEN=262144 OPSYS=FreeBSD OSREL=11.0 OSVERSION=1100122 PYTHONBASE=/usr/local UID=0 _JAVA_OS_LIST_REGEXP=native\|linux _JAVA_VENDOR_LIST_REGEXP=openjdk\|oracle\|sun _JAVA_VERSION_LIST_REGEXP=1.6\|1.7\|1.8\|1.6+\|1.7+\|1.8+ _OSRELEASE=11.0-RELEASE-p10 #### Misc Poudriere #### GID=0 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--- --Resource limits-- cpu time (seconds, -t) unlimited file size (512-blocks, -f) unlimited data seg size (kbytes, -d) 131072 stack size (kbytes, -s) 8192 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) 1024 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 >============================ ===> License GPLv3 accepted by the user =========================================================================== =======================<phase: pkg-depends >============================ ===> bwa-0.7.9a depends on file: /usr/local/sbin/pkg - not found ===> Installing existing package /packages/All/pkg-1.10.1.txz [110mips64-quarterly-job-23] Installing pkg-1.10.1... [110mips64-quarterly-job-23] Extracting pkg-1.10.1: .......... done ===> bwa-0.7.9a depends on file: /usr/local/sbin/pkg - found ===> Returning to build of bwa-0.7.9a =========================================================================== =======================<phase: fetch-depends >============================ =========================================================================== =======================<phase: fetch >============================ ===> License GPLv3 accepted by the user ===> Fetching all distfiles required by bwa-0.7.9a for building =========================================================================== =======================<phase: checksum >============================ ===> 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. =========================================================================== =======================<phase: extract-depends>============================ =========================================================================== =======================<phase: extract >============================ ===> 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. =========================================================================== =======================<phase: patch-depends >============================ =========================================================================== =======================<phase: patch >============================ ===> Patching for bwa-0.7.9a ===> Applying FreeBSD patches for bwa-0.7.9a =========================================================================== =======================<phase: build-depends >============================ =========================================================================== =======================<phase: lib-depends >============================ =========================================================================== =======================<phase: configure >============================ ===> Configuring for bwa-0.7.9a =========================================================================== =======================<phase: build >============================ ===> Building for bwa-0.7.9a /nxb-bin/usr/bin/cc -c -O2 -pipe -G0 -fno-strict-aliasing -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS utils.c -o utils.o /nxb-bin/usr/bin/cc -c -O2 -pipe -G0 -fno-strict-aliasing -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS kthread.c -o kthread.o /nxb-bin/usr/bin/cc -c -O2 -pipe -G0 -fno-strict-aliasing -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS kstring.c -o kstring.o /nxb-bin/usr/bin/cc -c -O2 -pipe -G0 -fno-strict-aliasing -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS ksw.c -o ksw.o ksw.c:29:23: error: emmintrin.h: No such file or directory ksw.c:49: error: expected specifier-qualifier-list before '__m128i' ksw.c: In function 'ksw_qinit': ksw.c:72: error: 'kswq_t' has no member named 'qp' ksw.c:72: error: '__m128i' undeclared (first use in this function) ksw.c:72: error: (Each undeclared identifier is reported only once ksw.c:72: error: for each function it appears in.) ksw.c:72: error: expected expression before ')' token ksw.c:73: error: 'kswq_t' has no member named 'H0' ksw.c:73: error: 'kswq_t' has no member named 'qp' ksw.c:74: error: 'kswq_t' has no member named 'H1' ksw.c:74: error: 'kswq_t' has no member named 'H0' ksw.c:75: error: 'kswq_t' has no member named 'E' ksw.c:75: error: 'kswq_t' has no member named 'H1' ksw.c:76: error: 'kswq_t' has no member named 'Hmax' ksw.c:76: error: 'kswq_t' has no member named 'E' ksw.c:90: error: 'kswq_t' has no member named 'qp' ksw.c:99: error: 'kswq_t' has no member named 'qp' ksw.c: In function 'ksw_u8': ksw.c:115: error: '__m128i' undeclared (first use in this function) ksw.c:115: error: expected ';' before 'zero' ksw.c:131: error: 'zero' undeclared (first use in this function) ksw.c:132: error: 'oe_del' undeclared (first use in this function) ksw.c:133: error: 'e_del' undeclared (first use in this function) ksw.c:134: error: 'oe_ins' undeclared (first use in this function) ksw.c:135: error: 'e_ins' undeclared (first use in this function) ksw.c:136: error: 'shift' undeclared (first use in this function) ksw.c:137: error: 'H0' undeclared (first use in this function) ksw.c:137: error: 'kswq_t' has no member named 'H0' ksw.c:137: error: 'H1' undeclared (first use in this function) ksw.c:137: error: 'kswq_t' has no member named 'H1' ksw.c:137: error: 'E' undeclared (first use in this function) ksw.c:137: error: 'kswq_t' has no member named 'E' ksw.c:137: error: 'Hmax' undeclared (first use in this function) ksw.c:137: error: 'kswq_t' has no member named 'Hmax' ksw.c:147: error: expected ';' before 'e' ksw.c:148: error: 'h' undeclared (first use in this function) ksw.c:157: error: 'S' undeclared (first use in this function) ksw.c:159: error: 'e' undeclared (first use in this function) ksw.c:161: error: 'f' undeclared (first use in this function) ksw.c:162: error: 'max' undeclared (first use in this function) ksw.c:166: error: 't' undeclared (first use in this function) ksw.c: In function 'ksw_i16': ksw.c:236: error: '__m128i' undeclared (first use in this function) ksw.c:236: error: expected ';' before 'zero' ksw.c:251: error: 'zero' undeclared (first use in this function) ksw.c:252: error: 'oe_del' undeclared (first use in this function) ksw.c:253: error: 'e_del' undeclared (first use in this function) ksw.c:254: error: 'oe_ins' undeclared (first use in this function) ksw.c:255: error: 'e_ins' undeclared (first use in this function) ksw.c:256: error: 'H0' undeclared (first use in this function) ksw.c:256: error: 'kswq_t' has no member named 'H0' ksw.c:256: error: 'H1' undeclared (first use in this function) ksw.c:256: error: 'kswq_t' has no member named 'H1' ksw.c:256: error: 'E' undeclared (first use in this function) ksw.c:256: error: 'kswq_t' has no member named 'E' ksw.c:256: error: 'Hmax' undeclared (first use in this function) ksw.c:256: error: 'kswq_t' has no member named 'Hmax' ksw.c:266: error: expected ';' before 'e' ksw.c:267: error: 'h' undeclared (first use in this function) ksw.c:270: error: 'S' undeclared (first use in this function) ksw.c:271: error: 'e' undeclared (first use in this function) ksw.c:273: error: 'f' undeclared (first use in this function) ksw.c:274: error: 'max' undeclared (first use in this function) ksw.c:277: error: 't' undeclared (first use in this function) *** 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
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