[package - 110mips64-quarterly][biology/bwa] Failed for bwa-0.7.9a in build
pkg-fallout at FreeBSD.org
pkg-fallout at FreeBSD.org
Sat Jul 1 02:44:31 UTC 2017
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 at gmail.com
Last committer: linimon at 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/444712/logs/bwa-0.7.9a.log
Build URL: http://beefy16.nyi.freebsd.org/build.html?mastername=110mips64-quarterly&build=444712
Log:
====>> Building biology/bwa
build started at Sat Jul 1 02:44:14 UTC 2017
port directory: /usr/ports/biology/bwa
building for: FreeBSD 110mips64-quarterly-job-07 11.0-RELEASE-p10 FreeBSD 11.0-RELEASE-p10 r317487 mips
maintained by: bacon4000 at 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: 07
---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-07] Installing pkg-1.10.1...
[110mips64-quarterly-job-07] 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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