=>> Building biology/bwa build started at Fri Apr 12 01:50:17 UTC 2019 port directory: /usr/ports/biology/bwa package name: bwa-0.7.17 building for: FreeBSD ppcports 13.0-CURRENT FreeBSD 13.0-CURRENT 1300013 powerpc maintained by: jwb@FreeBSD.org Makefile ident: $FreeBSD: head/biology/bwa/Makefile 460452 2018-01-31 01:07:07Z jwb $ Poudriere version: 3.2.8 Host OSVERSION: 1300012 Jail OSVERSION: 1300013 Job Id: 74 !!! Jail is newer than host. (Jail: 1300013, Host: 1300012) !!! !!! This is not supported. !!! !!! Host kernel must be same or newer than jail. !!! !!! Expect build failures. !!! ---Begin Environment--- SHELL=/bin/csh OSVERSION=1300013 UNAME_v=FreeBSD 13.0-CURRENT 1300013 UNAME_r=13.0-CURRENT BLOCKSIZE=K MAIL=/var/mail/root STATUS=1 HOME=/root PATH=/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin LOCALBASE=/usr/local USER=root TRYBROKEN=yes LIBEXECPREFIX=/usr/local/libexec/poudriere POUDRIERE_VERSION=3.2.8 MASTERMNT=/zfs/poudriere/data/.m/head-head-powerpc64-default/ref POUDRIERE_BUILD_TYPE=bulk PACKAGE_BUILDING=yes SAVED_TERM=screen GID=0 UID=0 PWD=/zfs/poudriere/data/.m/head-head-powerpc64-default/ref/.p/pool P_PORTS_FEATURES=FLAVORS SELECTED_OPTIONS MASTERNAME=head-head-powerpc64-default SCRIPTPREFIX=/usr/local/share/poudriere OLDPWD=/zfs/poudriere/data/.m/head-head-powerpc64-default/ref/.p SCRIPTPATH=/usr/local/share/poudriere/bulk.sh POUDRIEREPATH=/usr/local/bin/poudriere ---End Environment--- ---Begin Poudriere Port Flags/Env--- PORT_FLAGS= PKGENV= FLAVOR= DEPENDS_ARGS= MAKE_ARGS= ---End Poudriere Port Flags/Env--- ---Begin OPTIONS List--- ---End OPTIONS List--- --MAINTAINER-- jwb@FreeBSD.org --End MAINTAINER-- --CONFIGURE_ARGS-- --End CONFIGURE_ARGS-- --CONFIGURE_ENV-- MAKE=gmake 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" PATH=/wrkdirs/usr/ports/biology/bwa/work/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin 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" PATH=/wrkdirs/usr/ports/biology/bwa/work/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin NO_PIE=yes 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 -fno-strict-aliasing " CPP="cpp" CPPFLAGS="" LDFLAGS=" " LIBS="" CXX="c++" CXXFLAGS="-O2 -pipe -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=13.0 PREFIX=%D LOCALBASE=/usr/local RESETPREFIX=/usr/local LIB32DIR=lib PERL_VERSION=5.28.1 PERL_VER=5.28 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/5.28 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--- USE_PACKAGE_DEPENDS=yes BATCH=yes WRKDIRPREFIX=/wrkdirs PORTSDIR=/usr/ports PACKAGES=/packages DISTDIR=/distfiles FORCE_PACKAGE=yes PACKAGE_BUILDING=yes PACKAGE_BUILDING_FLAVORS=yes #### /usr/ports/Mk/Scripts/ports_env.sh #### _CCVERSION_921dbbb2=cc (GCC) 4.2.1 20070831 patched [FreeBSD] Copyright (C) 2007 Free Software Foundation, Inc. This is free software; see the source for copying conditions. There is NO warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. _ALTCCVERSION_921dbbb2=none _CXXINTERNAL_acaad9ca=Using built-in specs. Target: powerpc64-undermydesk-freebsd Configured with: FreeBSD/powerpc64 system compiler Thread model: posix gcc version 4.2.1 20070831 patched [FreeBSD] "/usr/bin/ld" "--eh-frame-hdr" "-Qy" "-melf64ppc_fbsd" "--enable-new-dtags" "-dynamic-linker" "/libexec/ld-elf.so.1" "/usr/lib/crt1.o" "/usr/lib/crti.o" "/usr/lib/crtbegin.o" "-L/usr/lib" "-L/usr/lib" "/dev/null" "-lstdc++" "-lm" "-lgcc_s" "-lgcc" "-lc" "-lgcc_s" "-lgcc" "/usr/lib/crtsavres.o" "/usr/lib/crtend.o" "/usr/lib/crtn.o" CC_OUTPUT_921dbbb2_58173849=yes CC_OUTPUT_921dbbb2_9bdba57c=yes CC_OUTPUT_921dbbb2_6a4fe7f5=cc1: error: unrecognized command line option "-std=c11" CC_OUTPUT_921dbbb2_6bcac02b=yes CC_OUTPUT_921dbbb2_67d20829=yes CC_OUTPUT_921dbbb2_bfa62e83=cc1: error: unrecognized command line option "-std=gnu11" CC_OUTPUT_921dbbb2_f0b4d593=yes CC_OUTPUT_921dbbb2_308abb44=cc1plus: error: unrecognized command line option "-std=c++0x" CC_OUTPUT_921dbbb2_f00456e5=cc1plus: error: unrecognized command line option "-std=c++11" CC_OUTPUT_921dbbb2_65ad290d=cc1plus: error: unrecognized command line option "-std=c++14" CC_OUTPUT_921dbbb2_f2776b26=cc1plus: error: unrecognized command line option "-std=c++17" CC_OUTPUT_921dbbb2_b2657cc3=yes CC_OUTPUT_921dbbb2_380987f7=cc1plus: error: unrecognized command line option "-std=gnu++11" CC_OUTPUT_921dbbb2_160933ec=cc1plus: error: unrecognized command line option "-std=gnu++14" CC_OUTPUT_921dbbb2_fb62803b=cc1plus: error: unrecognized command line option "-std=gnu++17" _OBJC_CCVERSION_921dbbb2=cc (GCC) 4.2.1 20070831 patched [FreeBSD] Copyright (C) 2007 Free Software Foundation, Inc. This is free software; see the source for copying conditions. There is NO warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. _OBJC_ALTCCVERSION_921dbbb2=none ARCH=powerpc64 OPSYS=FreeBSD _OSRELEASE=13.0-CURRENT OSREL=13.0 OSVERSION=1300013 PYTHONBASE=/usr/local _SMP_CPUS=80 CONFIGURE_MAX_CMD_LEN=262144 HAVE_PORTS_ENV=1 #### Misc Poudriere #### 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) 33554432 stack size (kbytes, -s) 524288 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-- =================================================== ===> License GPLv3 accepted by the user =========================================================================== =================================================== ===> bwa-0.7.17 depends on file: /usr/local/sbin/pkg - not found ===> Installing existing package /packages/All/pkg-1.10.5_5.txz [ppcports] Installing pkg-1.10.5_5... [ppcports] Extracting pkg-1.10.5_5: .......... done ===> bwa-0.7.17 depends on file: /usr/local/sbin/pkg - found ===> Returning to build of bwa-0.7.17 =========================================================================== =================================================== =========================================================================== =================================================== ===> License GPLv3 accepted by the user => lh3-bwa-v0.7.17_GH0.tar.gz doesn't seem to exist in /portdistfiles/. => Attempting to fetch https://codeload.github.com/lh3/bwa/tar.gz/v0.7.17?dummy=/lh3-bwa-v0.7.17_GH0.tar.gz fetch: https://codeload.github.com/lh3/bwa/tar.gz/v0.7.17?dummy=/lh3-bwa-v0.7.17_GH0.tar.gz: size unknown fetch: https://codeload.github.com/lh3/bwa/tar.gz/v0.7.17?dummy=/lh3-bwa-v0.7.17_GH0.tar.gz: size of remote file is not known lh3-bwa-v0.7.17_GH0.tar.gz 227 kB 4070 kBps 00s ===> Fetching all distfiles required by bwa-0.7.17 for building =========================================================================== =================================================== ===> License GPLv3 accepted by the user ===> Fetching all distfiles required by bwa-0.7.17 for building => SHA256 Checksum OK for lh3-bwa-v0.7.17_GH0.tar.gz. =========================================================================== =================================================== =========================================================================== =================================================== ===> License GPLv3 accepted by the user ===> Fetching all distfiles required by bwa-0.7.17 for building ===> Extracting for bwa-0.7.17 => SHA256 Checksum OK for lh3-bwa-v0.7.17_GH0.tar.gz. =========================================================================== =================================================== =========================================================================== =================================================== ===> Patching for bwa-0.7.17 ===> Applying FreeBSD patches for bwa-0.7.17 =========================================================================== =================================================== ===> bwa-0.7.17 depends on executable: gmake - not found ===> Installing existing package /packages/All/gmake-4.2.1_3.txz [ppcports] Installing gmake-4.2.1_3... [ppcports] `-- Installing gettext-runtime-0.19.8.1_2... [ppcports] | `-- Installing indexinfo-0.3.1... [ppcports] | `-- Extracting indexinfo-0.3.1: .... done [ppcports] `-- Extracting gettext-runtime-0.19.8.1_2: .......... done [ppcports] Extracting gmake-4.2.1_3: .......... done ===> bwa-0.7.17 depends on executable: gmake - found ===> Returning to build of bwa-0.7.17 =========================================================================== =================================================== =========================================================================== =================================================== ===> Configuring for bwa-0.7.17 =========================================================================== =================================================== ===> Building for bwa-0.7.17 gmake[1]: Entering directory '/wrkdirs/usr/ports/biology/bwa/work/bwa-0.7.17' cc -c -O2 -pipe -fno-strict-aliasing -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS utils.c -o utils.o cc -c -O2 -pipe -fno-strict-aliasing -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS kthread.c -o kthread.o cc -c -O2 -pipe -fno-strict-aliasing -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS kstring.c -o kstring.o cc -c -O2 -pipe -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) gmake[1]: *** [Makefile:25: ksw.o] Error 1 gmake[1]: Leaving directory '/wrkdirs/usr/ports/biology/bwa/work/bwa-0.7.17' *** Error code 1 Stop. make: stopped in /usr/ports/biology/bwa =>> Cleaning up wrkdir ===> Cleaning for bwa-0.7.17 build of biology/bwa | bwa-0.7.17 ended at Fri Apr 12 01:51:15 UTC 2019 build time: 00:01:01 !!! build failure encountered !!!