[package - 132releng-armv6-quarterly][biology/smithwaterman] Failed for smithwaterman-g20160702 in build
- Go to: [ bottom of page ] [ top of archives ] [ this month ]
Date: Sat, 09 Sep 2023 03:26:42 UTC
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: jwb@FreeBSD.org
Log URL: https://pkg-status.freebsd.org/beefy8/data/132releng-armv6-quarterly/c49faaf4fd33/logs/smithwaterman-g20160702.log
Build URL: https://pkg-status.freebsd.org/beefy8/build.html?mastername=132releng-armv6-quarterly&build=c49faaf4fd33
Log:
=>> Building biology/smithwaterman
build started at Sat Sep 9 03:26:24 UTC 2023
port directory: /usr/ports/biology/smithwaterman
package name: smithwaterman-g20160702
building for: FreeBSD 132releng-armv6-quarterly-job-03 13.2-RELEASE-p3 FreeBSD 13.2-RELEASE-p3 1302001 arm
maintained by: jwb@FreeBSD.org
Makefile ident:
Poudriere version: 3.2.8-23-ga7f8d188
Host OSVERSION: 1500000
Jail OSVERSION: 1302001
Job Id: 03
---Begin Environment---
SHELL=/bin/csh
UNAME_p=armv6
UNAME_m=arm
ABI_FILE=/usr/lib/crt1.o
OSVERSION=1302001
UNAME_v=FreeBSD 13.2-RELEASE-p3 1302001
UNAME_r=13.2-RELEASE-p3
BLOCKSIZE=K
MAIL=/var/mail/root
MM_CHARSET=UTF-8
LANG=C.UTF-8
STATUS=1
HOME=/root
PATH=/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin
LOCALBASE=/usr/local
QEMU_EMULATING=1
USER=root
LIBEXECPREFIX=/usr/local/libexec/poudriere
POUDRIERE_VERSION=3.2.8-23-ga7f8d188
MASTERMNT=/usr/local/poudriere/data/.m/132releng-armv6-quarterly/ref
POUDRIERE_BUILD_TYPE=bulk
PACKAGE_BUILDING=yes
SAVED_TERM=
PWD=/usr/local/poudriere/data/.m/132releng-armv6-quarterly/ref/.p/pool
P_PORTS_FEATURES=FLAVORS SELECTED_OPTIONS
MASTERNAME=132releng-armv6-quarterly
SCRIPTPREFIX=/usr/local/share/poudriere
OLDPWD=/usr/local/poudriere/data/.m/132releng-armv6-quarterly/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 XDG_DATA_HOME=/wrkdirs/usr/ports/biology/smithwaterman/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/smithwaterman/work XDG_CACHE_HOME=/wrkdirs/usr/ports/biology/smithwaterman/work/.cache HOME=/wrkdirs/usr/ports/biology/smithwaterman/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/smithwaterman/work/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin PKG_CONFIG_LIBDIR=/wrkdirs/usr/ports/biology/smithwaterman/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/smithwaterman/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/smithwaterman/work XDG_CACHE_HOME=/wrkdirs/usr/ports/biology/smithwaterman/work/.cache HOME=/wrkdirs/usr/ports/biology/smithwaterman/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/smithwaterman/work/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin PKG_CONFIG_LIBDIR=/wrkdirs/usr/ports/biology/smithwaterman/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="/nxb-bin/usr/bin/cc" CFLAGS="-O2 -pipe -fstack-protector-strong -fno-strict-aliasing " CPP="/nxb-bin/usr/bin/cpp" CPPFLAGS="" LDFLAGS=" -fstack-protector-strong " LIBS="" CXX="/nxb-bin/usr/bin/c++" CXXFLAGS="-O2 -pipe -fstack-protector-strong -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=13.2 PREFIX=%D LOCALBASE=/usr/local RESETPREFIX=/usr/local LIB32DIR=lib DOCSDIR="share/doc/smithwaterman" EXAMPLESDIR="share/examples/smithwaterman" DATADIR="share/smithwaterman" WWWDIR="www/smithwaterman" ETCDIR="etc/smithwaterman"
--End PLIST_SUB--
--SUB_LIST--
PREFIX=/usr/local LOCALBASE=/usr/local DATADIR=/usr/local/share/smithwaterman DOCSDIR=/usr/local/share/doc/smithwaterman EXAMPLESDIR=/usr/local/share/examples/smithwaterman WWWDIR=/usr/local/www/smithwaterman ETCDIR=/usr/local/etc/smithwaterman
--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
PACKAGE_BUILDING_FLAVORS=yes
MACHINE=arm
MACHINE_ARCH=armv6
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 ####
_CCVERSION_9d218390=FreeBSD clang version 14.0.5 (https://github.com/llvm/llvm-project.git llvmorg-14.0.5-0-gc12386ae247c) Target: armv6-unknown-freebsd13.2-gnueabihf Thread model: posix InstalledDir: /nxb-bin/usr/bin
_ALTCCVERSION_9d218390=none
_CXXINTERNAL_9c45a5b1=FreeBSD clang version 14.0.5 (https://github.com/llvm/llvm-project.git llvmorg-14.0.5-0-gc12386ae247c) Target: armv6-unknown-freebsd13.2-gnueabihf Thread model: posix InstalledDir: /nxb-bin/usr/bin "/nxb-bin/usr/bin/ld" "--eh-frame-hdr" "-dynamic-linker" "/libexec/ld-elf.so.1" "--hash-style=both" "--enable-new-dtags" "-o" "a.out" "/usr/lib/crt1.o" "/usr/lib/crti.o" "/usr/lib/crtbegin.o" "-L/usr/lib" "/dev/null" "-lc++" "-lm" "-lgcc" "--as-needed" "-lgcc_s" "--no-as-needed" "-lc" "-lgcc" "--as-needed" "-lgcc_s" "--no-as-needed" "/usr/lib/crtend.o" "/usr/lib/crtn.o"
CC_OUTPUT_9d218390_58173849=yes
CC_OUTPUT_9d218390_9bdba57c=yes
CC_OUTPUT_9d218390_6a4fe7f5=yes
CC_OUTPUT_9d218390_6bcac02b=yes
CC_OUTPUT_9d218390_67d20829=yes
CC_OUTPUT_9d218390_bfa62e83=yes
CC_OUTPUT_9d218390_f0b4d593=yes
CC_OUTPUT_9d218390_308abb44=yes
CC_OUTPUT_9d218390_f00456e5=yes
CC_OUTPUT_9d218390_65ad290d=yes
CC_OUTPUT_9d218390_f2776b26=yes
CC_OUTPUT_9d218390_53255a77=yes
CC_OUTPUT_9d218390_911cfe02=yes
CC_OUTPUT_9d218390_b2657cc3=yes
CC_OUTPUT_9d218390_380987f7=yes
CC_OUTPUT_9d218390_160933ec=yes
CC_OUTPUT_9d218390_fb62803b=yes
CC_OUTPUT_9d218390_af59ad06=yes
CC_OUTPUT_9d218390_a15f3fcf=yes
_OBJC_CCVERSION_9d218390=FreeBSD clang version 14.0.5 (https://github.com/llvm/llvm-project.git llvmorg-14.0.5-0-gc12386ae247c) Target: armv6-unknown-freebsd13.2-gnueabihf Thread model: posix InstalledDir: /nxb-bin/usr/bin
_OBJC_ALTCCVERSION_9d218390=none
ARCH=armv6
OPSYS=FreeBSD
_OSRELEASE=13.2-RELEASE-p3
OSREL=13.2
OSVERSION=1302001
PYTHONBASE=/usr/local
CONFIGURE_MAX_CMD_LEN=524288
HAVE_PORTS_ENV=1
#### Misc Poudriere ####
GID=0
UID=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++
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
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) 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--
=======================<phase: check-sanity >============================
===> License GPLv2 accepted by the user
===========================================================================
=======================<phase: pkg-depends >============================
===> smithwaterman-g20160702 depends on file: /usr/local/sbin/pkg - not found
===> Installing existing package /packages/All/pkg-1.19.2.pkg
[132releng-armv6-quarterly-job-03] Installing pkg-1.19.2...
[132releng-armv6-quarterly-job-03] Extracting pkg-1.19.2: .......... done
===> smithwaterman-g20160702 depends on file: /usr/local/sbin/pkg - found
===> Returning to build of smithwaterman-g20160702
===========================================================================
=======================<phase: fetch-depends >============================
===========================================================================
=======================<phase: fetch >============================
===> License GPLv2 accepted by the user
===> Fetching all distfiles required by smithwaterman-g20160702 for building
===========================================================================
=======================<phase: checksum >============================
===> License GPLv2 accepted by the user
===> Fetching all distfiles required by smithwaterman-g20160702 for building
=> SHA256 Checksum OK for ekg-smithwaterman-g20160702-2610e259611ae4cde8f03c72499d28f03f6d38a7_GH0.tar.gz.
===========================================================================
=======================<phase: extract-depends>============================
===========================================================================
=======================<phase: extract >============================
===> License GPLv2 accepted by the user
===> Fetching all distfiles required by smithwaterman-g20160702 for building
===> Extracting for smithwaterman-g20160702
=> SHA256 Checksum OK for ekg-smithwaterman-g20160702-2610e259611ae4cde8f03c72499d28f03f6d38a7_GH0.tar.gz.
===========================================================================
=======================<phase: patch-depends >============================
===========================================================================
=======================<phase: patch >============================
===> Patching for smithwaterman-g20160702
===========================================================================
=======================<phase: build-depends >============================
===> smithwaterman-g20160702 depends on package: gmake>=4.3 - not found
===> Installing existing package /packages/All/gmake-4.3_2.pkg
[132releng-armv6-quarterly-job-03] Installing gmake-4.3_2...
[132releng-armv6-quarterly-job-03] `-- Installing gettext-runtime-0.21.1...
[132releng-armv6-quarterly-job-03] | `-- Installing indexinfo-0.3.1...
[132releng-armv6-quarterly-job-03] | `-- Extracting indexinfo-0.3.1: .... done
[132releng-armv6-quarterly-job-03] `-- Extracting gettext-runtime-0.21.1: .......... done
[132releng-armv6-quarterly-job-03] Extracting gmake-4.3_2: .......... done
===> smithwaterman-g20160702 depends on package: gmake>=4.3 - found
===> Returning to build of smithwaterman-g20160702
===========================================================================
=======================<phase: lib-depends >============================
===========================================================================
=======================<phase: configure >============================
===> Configuring for smithwaterman-g20160702
===========================================================================
=======================<phase: build >============================
===> Building for smithwaterman-g20160702
gmake[1]: Entering directory '/wrkdirs/usr/ports/biology/smithwaterman/work/smithwaterman-2610e259611ae4cde8f03c72499d28f03f6d38a7'
/nxb-bin/usr/bin/c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -c -o disorder.o disorder.cpp -I.
/nxb-bin/usr/bin/c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -c -o smithwaterman.o smithwaterman.cpp -I.
/nxb-bin/usr/bin/c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -c -o BandedSmithWaterman.o BandedSmithWaterman.cpp -I.
/nxb-bin/usr/bin/c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -c -o SmithWatermanGotoh.o SmithWatermanGotoh.cpp -I.
/nxb-bin/usr/bin/c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -c -o Repeats.o Repeats.cpp -I.
/nxb-bin/usr/bin/c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -c -o LeftAlign.o LeftAlign.cpp -I.
/nxb-bin/usr/bin/c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -c -o IndelAllele.o IndelAllele.cpp -I.
/nxb-bin/usr/bin/c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing smithwaterman.o BandedSmithWaterman.o SmithWatermanGotoh.o Repeats.o LeftAlign.o IndelAllele.o disorder.o -I. -o smithwaterman
ar rs libsw.a disorder.o BandedSmithWaterman.o SmithWatermanGotoh.o Repeats.o LeftAlign.o IndelAllele.o
ar: warning: creating libsw.a
/nxb-bin/usr/bin/c++ -shared -Wl,-soname,libsw.so.1 -o libsw.so.1 disorder.o BandedSmithWaterman.o SmithWatermanGotoh.o Repeats.o LeftAlign.o IndelAllele.o
ld -r disorder.o BandedSmithWaterman.o SmithWatermanGotoh.o Repeats.o LeftAlign.o IndelAllele.o -o sw.o -L.
qemu: uncaught target signal 6 (Abort trap) - core dumped
gmake[1]: *** [/usr/ports/biology/smithwaterman/files/Makefile:54: sw.o] Abort trap
gmake[1]: Leaving directory '/wrkdirs/usr/ports/biology/smithwaterman/work/smithwaterman-2610e259611ae4cde8f03c72499d28f03f6d38a7'
*** Error code 1
Stop.
make: stopped in /usr/ports/biology/smithwaterman