[exp - 122amd64-default-build-as-user][biology/spoa] Failed for spoa-4.0.7 in build
pkg-fallout at FreeBSD.org
pkg-fallout at FreeBSD.org
Sat Feb 20 09:46:28 UTC 2021
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: yuri at FreeBSD.org
Last committer: yuri at FreeBSD.org
Ident: $FreeBSD: head/biology/spoa/Makefile 562036 2021-01-19 09:28:00Z yuri $
Log URL: http://package19.nyi.freebsd.org/data/122amd64-default-build-as-user/566011/logs/spoa-4.0.7.log
Build URL: http://package19.nyi.freebsd.org/build.html?mastername=122amd64-default-build-as-user&build=566011
Log:
=>> Building biology/spoa
build started at Sat Feb 20 09:45:41 UTC 2021
port directory: /usr/ports/biology/spoa
package name: spoa-4.0.7
building for: FreeBSD 122amd64-default-build-as-user-job-03 12.2-RELEASE-p3 FreeBSD 12.2-RELEASE-p3 amd64
maintained by: yuri at FreeBSD.org
Makefile ident: $FreeBSD: head/biology/spoa/Makefile 562036 2021-01-19 09:28:00Z yuri $
Poudriere version: 3.2.8-8-gaf08dbda
Host OSVERSION: 1300121
Jail OSVERSION: 1202000
Job Id: 03
---Begin Environment---
SHELL=/bin/csh
OSVERSION=1202000
UNAME_v=FreeBSD 12.2-RELEASE-p3
UNAME_r=12.2-RELEASE-p3
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
LIBEXECPREFIX=/usr/local/libexec/poudriere
POUDRIERE_VERSION=3.2.8-8-gaf08dbda
MASTERMNT=/poudriere/data/.m/122amd64-default-build-as-user/ref
POUDRIERE_BUILD_TYPE=bulk
PACKAGE_BUILDING=yes
SAVED_TERM=
GID=0
UID=0
PWD=/poudriere/data/.m/122amd64-default-build-as-user/ref/.p/pool
P_PORTS_FEATURES=FLAVORS SELECTED_OPTIONS
MASTERNAME=122amd64-default-build-as-user
SCRIPTPREFIX=/usr/local/share/poudriere
OLDPWD=/poudriere/data/.m/122amd64-default-build-as-user/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--
yuri at FreeBSD.org
--End MAINTAINER--
--CONFIGURE_ARGS--
--End CONFIGURE_ARGS--
--CONFIGURE_ENV--
XDG_DATA_HOME=/wrkdirs/usr/ports/biology/spoa/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/spoa/work HOME=/wrkdirs/usr/ports/biology/spoa/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/spoa/work/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin SHELL=/bin/sh CONFIG_SHELL=/bin/sh CMAKE_PREFIX_PATH="/usr/local"
--End CONFIGURE_ENV--
--MAKE_ENV--
XDG_DATA_HOME=/wrkdirs/usr/ports/biology/spoa/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/spoa/work HOME=/wrkdirs/usr/ports/biology/spoa/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/spoa/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 DESTDIR=/wrkdirs/usr/ports/biology/spoa/work/stage PREFIX=/usr/local LOCALBASE=/usr/local CC="cc" CFLAGS="-O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing " CPP="cpp" CPPFLAGS="-isystem /usr/local/include" LDFLAGS=" -lz -lcpu_features -fstack-protector-strong -L/usr/local/lib " LIBS="" CXX="c++" CXXFLAGS="-O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include " 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--
CMAKE_BUILD_TYPE="release" OSREL=12.2 PREFIX=%D LOCALBASE=/usr/local RESETPREFIX=/usr/local LIB32DIR=lib DOCSDIR="share/doc/spoa" EXAMPLESDIR="share/examples/spoa" DATADIR="share/spoa" WWWDIR="www/spoa" ETCDIR="etc/spoa"
--End PLIST_SUB--
--SUB_LIST--
PREFIX=/usr/local LOCALBASE=/usr/local DATADIR=/usr/local/share/spoa DOCSDIR=/usr/local/share/doc/spoa EXAMPLESDIR=/usr/local/share/examples/spoa WWWDIR=/usr/local/www/spoa ETCDIR=/usr/local/etc/spoa
--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/local/etc/poudriere.d/make.conf ####
# Build ALLOW_MAKE_JOBS_PACKAGES with 2 jobs
MAKE_JOBS_NUMBER=2
#### /usr/ports/Mk/Scripts/ports_env.sh ####
_CCVERSION_921dbbb2=FreeBSD clang version 10.0.1 (git at github.com:llvm/llvm-project.git llvmorg-10.0.1-0-gef32c611aa2) Target: x86_64-unknown-freebsd12.2 Thread model: posix InstalledDir: /usr/bin
_ALTCCVERSION_921dbbb2=none
_CXXINTERNAL_acaad9ca=FreeBSD clang version 10.0.1 (git at github.com:llvm/llvm-project.git llvmorg-10.0.1-0-gef32c611aa2) Target: x86_64-unknown-freebsd12.2 Thread model: posix InstalledDir: /usr/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_921dbbb2_58173849=yes
CC_OUTPUT_921dbbb2_9bdba57c=yes
CC_OUTPUT_921dbbb2_6a4fe7f5=yes
CC_OUTPUT_921dbbb2_6bcac02b=yes
CC_OUTPUT_921dbbb2_67d20829=yes
CC_OUTPUT_921dbbb2_bfa62e83=yes
CC_OUTPUT_921dbbb2_f0b4d593=yes
CC_OUTPUT_921dbbb2_308abb44=yes
CC_OUTPUT_921dbbb2_f00456e5=yes
CC_OUTPUT_921dbbb2_65ad290d=yes
CC_OUTPUT_921dbbb2_f2776b26=yes
CC_OUTPUT_921dbbb2_b2657cc3=yes
CC_OUTPUT_921dbbb2_380987f7=yes
CC_OUTPUT_921dbbb2_160933ec=yes
CC_OUTPUT_921dbbb2_fb62803b=yes
_OBJC_CCVERSION_921dbbb2=FreeBSD clang version 10.0.1 (git at github.com:llvm/llvm-project.git llvmorg-10.0.1-0-gef32c611aa2) Target: x86_64-unknown-freebsd12.2 Thread model: posix InstalledDir: /usr/bin
_OBJC_ALTCCVERSION_921dbbb2=none
ARCH=amd64
OPSYS=FreeBSD
_OSRELEASE=12.2-RELEASE-p3
OSREL=12.2
OSVERSION=1202000
PYTHONBASE=/usr/local
HAVE_COMPAT_IA32_KERN=YES
CONFIGURE_MAX_CMD_LEN=524288
HAVE_PORTS_ENV=1
#### Misc 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--
=======================<phase: check-sanity >============================
===> License MIT accepted by the user
===========================================================================
=======================<phase: pkg-depends >============================
===> spoa-4.0.7 depends on file: /usr/local/sbin/pkg - not found
===> Installing existing package /packages/All/pkg-1.16.3.txz
[122amd64-default-build-as-user-job-03] Installing pkg-1.16.3...
[122amd64-default-build-as-user-job-03] Extracting pkg-1.16.3: .......... done
===> spoa-4.0.7 depends on file: /usr/local/sbin/pkg - found
===> Returning to build of spoa-4.0.7
===========================================================================
=======================<phase: fetch-depends >============================
===========================================================================
=======================<phase: fetch >============================
===> License MIT accepted by the user
===> Fetching all distfiles required by spoa-4.0.7 for building
===========================================================================
=======================<phase: checksum >============================
===> License MIT accepted by the user
===> Fetching all distfiles required by spoa-4.0.7 for building
=> SHA256 Checksum OK for rvaser-spoa-4.0.7_GH0.tar.gz.
===========================================================================
=======================<phase: extract-depends>============================
===========================================================================
=======================<phase: extract >============================
===> License MIT accepted by the user
===> Fetching all distfiles required by spoa-4.0.7 for building
===> Extracting for spoa-4.0.7
=> SHA256 Checksum OK for rvaser-spoa-4.0.7_GH0.tar.gz.
===========================================================================
=======================<phase: patch-depends >============================
===========================================================================
=======================<phase: patch >============================
===> Patching for spoa-4.0.7
===> Applying FreeBSD patches for spoa-4.0.7 from /usr/ports/biology/spoa/files
===========================================================================
=======================<phase: build-depends >============================
===> spoa-4.0.7 depends on package: bioparser>0 - not found
===> Installing existing package /packages/All/bioparser-3.0.12.2.txz
[122amd64-default-build-as-user-job-03] Installing bioparser-3.0.12.2...
[122amd64-default-build-as-user-job-03] Extracting bioparser-3.0.12.2: .......... done
===> spoa-4.0.7 depends on package: bioparser>0 - found
===> Returning to build of spoa-4.0.7
===> spoa-4.0.7 depends on file: /usr/local/include/biosoup/nucleic_acid.hpp - not found
===> Installing existing package /packages/All/biosoup-g20201216.txz
[122amd64-default-build-as-user-job-03] Installing biosoup-g20201216...
[122amd64-default-build-as-user-job-03] Extracting biosoup-g20201216: ........ done
===> spoa-4.0.7 depends on file: /usr/local/include/biosoup/nucleic_acid.hpp - found
===> Returning to build of spoa-4.0.7
===> spoa-4.0.7 depends on package: cereal>0 - not found
===> Installing existing package /packages/All/cereal-1.3.0.10.txz
[122amd64-default-build-as-user-job-03] Installing cereal-1.3.0.10...
[122amd64-default-build-as-user-job-03] `-- Installing boost-libs-1.72.0_3...
[122amd64-default-build-as-user-job-03] | `-- Installing icu-68.2,1...
[122amd64-default-build-as-user-job-03] | `-- Extracting icu-68.2,1: .......... done
[122amd64-default-build-as-user-job-03] `-- Extracting boost-libs-1.72.0_3: .......... done
[122amd64-default-build-as-user-job-03] Extracting cereal-1.3.0.10: .......... done
=====
Message from boost-libs-1.72.0_3:
--
<snip>
[122amd64-default-build-as-user-job-03] | `-- Extracting ca_root_nss-3.61: ........ done
[122amd64-default-build-as-user-job-03] | `-- Installing libnghttp2-1.43.0...
[122amd64-default-build-as-user-job-03] | `-- Extracting libnghttp2-1.43.0: .......... done
[122amd64-default-build-as-user-job-03] `-- Extracting curl-7.75.0: .......... done
[122amd64-default-build-as-user-job-03] `-- Installing expat-2.2.10...
[122amd64-default-build-as-user-job-03] `-- Extracting expat-2.2.10: .......... done
[122amd64-default-build-as-user-job-03] `-- Installing jsoncpp-1.9.4...
[122amd64-default-build-as-user-job-03] `-- Extracting jsoncpp-1.9.4: .......... done
[122amd64-default-build-as-user-job-03] `-- Installing libarchive-3.4.3_1,1...
[122amd64-default-build-as-user-job-03] | `-- Installing liblz4-1.9.3,1...
[122amd64-default-build-as-user-job-03] | `-- Extracting liblz4-1.9.3,1: .......... done
[122amd64-default-build-as-user-job-03] `-- Extracting libarchive-3.4.3_1,1: .......... done
[122amd64-default-build-as-user-job-03] `-- Installing libuv-1.40.0...
[122amd64-default-build-as-user-job-03] `-- Extracting libuv-1.40.0: .......... done
[122amd64-default-build-as-user-job-03] `-- Installing rhash-1.4.1...
[122amd64-default-build-as-user-job-03] | `-- Installing gettext-runtime-0.21...
[122amd64-default-build-as-user-job-03] | | `-- Installing indexinfo-0.3.1...
[122amd64-default-build-as-user-job-03] | | `-- Extracting indexinfo-0.3.1: .... done
[122amd64-default-build-as-user-job-03] | `-- Extracting gettext-runtime-0.21: .......... done
[122amd64-default-build-as-user-job-03] `-- Extracting rhash-1.4.1: .......... done
[122amd64-default-build-as-user-job-03] Extracting cmake-3.19.4_1: .......... done
=====
Message from ca_root_nss-3.61:
--
FreeBSD does not, and can not warrant that the certification authorities
whose certificates are included in this package have in any way been
audited for trustworthiness or RFC 3647 compliance.
Assessment and verification of trust is the complete responsibility of the
system administrator.
This package installs symlinks to support root certificates discovery by
default for software that uses OpenSSL.
This enables SSL Certificate Verification by client software without manual
intervention.
If you prefer to do this manually, replace the following symlinks with
either an empty file or your site-local certificate bundle.
* /etc/ssl/cert.pem
* /usr/local/etc/ssl/cert.pem
* /usr/local/openssl/cert.pem
===> spoa-4.0.7 depends on file: /usr/local/bin/cmake - found
===> Returning to build of spoa-4.0.7
===> spoa-4.0.7 depends on executable: ninja - not found
===> Installing existing package /packages/All/ninja-1.10.2,2.txz
[122amd64-default-build-as-user-job-03] Installing ninja-1.10.2,2...
[122amd64-default-build-as-user-job-03] `-- Installing python37-3.7.9_1...
[122amd64-default-build-as-user-job-03] | `-- Installing libffi-3.3_1...
[122amd64-default-build-as-user-job-03] | `-- Extracting libffi-3.3_1: .......... done
[122amd64-default-build-as-user-job-03] | `-- Installing readline-8.1.0...
[122amd64-default-build-as-user-job-03] | `-- Extracting readline-8.1.0: .......... done
[122amd64-default-build-as-user-job-03] `-- Extracting python37-3.7.9_1: .......... done
[122amd64-default-build-as-user-job-03] Extracting ninja-1.10.2,2: ........ done
=====
Message from python37-3.7.9_1:
--
Note that some standard Python modules are provided as separate ports
as they require additional dependencies. They are available as:
py37-gdbm databases/py-gdbm at py37
py37-sqlite3 databases/py-sqlite3 at py37
py37-tkinter x11-toolkits/py-tkinter at py37
===> spoa-4.0.7 depends on executable: ninja - found
===> Returning to build of spoa-4.0.7
===========================================================================
=======================<phase: lib-depends >============================
===========================================================================
=======================<phase: configure >============================
===> Configuring for spoa-4.0.7
===> Performing out-of-source build
/bin/mkdir -p /wrkdirs/usr/ports/biology/spoa/work/.build
-- The CXX compiler identification is Clang 10.0.1
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Check for working CXX compiler: /usr/bin/c++ - skipped
-- Detecting CXX compile features
-- Detecting CXX compile features - done
-- Configuring done
-- Generating done
CMake Warning:
Manually-specified variables were not used by the project:
CMAKE_COLOR_MAKEFILE
CMAKE_C_FLAGS
CMAKE_C_FLAGS_DEBUG
CMAKE_C_FLAGS_RELEASE
CMAKE_MODULE_LINKER_FLAGS
CMAKE_VERBOSE_MAKEFILE
THREADS_HAVE_PTHREAD_ARG
spoa_optimize_for_native
spoa_optimize_for_portability
-- Build files have been written to: /wrkdirs/usr/ports/biology/spoa/work/.build
===========================================================================
=======================<phase: build >============================
===> Building for spoa-4.0.7
[1/11] /usr/bin/c++ -DGENERATE_DISPATCH -DSIMDE_ENABLE_NATIVE_ALIASES -DSIMDE_ENABLE_OPENMP -DSIMDE_NO_NATIVE -DUSE_SIMDE -Dspoa_EXPORTS -I/wrkdirs/usr/ports/biology/spoa/work/spoa-4.0.7/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -Wall -Wextra -pedantic -fopenmp-simd -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -fPIC -std=c++11 -MD -MT CMakeFiles/spoa.dir/src/alignment_engine.cpp.o -MF CMakeFiles/spoa.dir/src/alignment_engine.cpp.o.d -o CMakeFiles/spoa.dir/src/alignment_engine.cpp.o -c /wrkdirs/usr/ports/biology/spoa/work/spoa-4.0.7/src/alignment_engine.cpp
[2/11] /usr/bin/c++ -DGENERATE_DISPATCH -DSIMDE_ENABLE_NATIVE_ALIASES -DSIMDE_ENABLE_OPENMP -DSIMDE_NO_NATIVE -DUSE_SIMDE -Dspoa_EXPORTS -I/wrkdirs/usr/ports/biology/spoa/work/spoa-4.0.7/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -Wall -Wextra -pedantic -fopenmp-simd -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -fPIC -std=c++11 -MD -MT CMakeFiles/spoa.dir/src/sisd_alignment_engine.cpp.o -MF CMakeFiles/spoa.dir/src/sisd_alignment_engine.cpp.o.d -o CMakeFiles/spoa.dir/src/sisd_alignment_engine.cpp.o -c /wrkdirs/usr/ports/biology/spoa/work/spoa-4.0.7/src/sisd_alignment_engine.cpp
[3/11] /usr/bin/c++ -DGENERATE_DISPATCH -DSIMDE_ENABLE_NATIVE_ALIASES -DSIMDE_ENABLE_OPENMP -DSIMDE_NO_NATIVE -DUSE_SIMDE -Dspoa_EXPORTS -I/wrkdirs/usr/ports/biology/spoa/work/spoa-4.0.7/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -Wall -Wextra -pedantic -fopenmp-simd -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -fPIC -std=c++11 -MD -MT CMakeFiles/spoa.dir/src/graph.cpp.o -MF CMakeFiles/spoa.dir/src/graph.cpp.o.d -o CMakeFiles/spoa.dir/src/graph.cpp.o -c /wrkdirs/usr/ports/biology/spoa/work/spoa-4.0.7/src/graph.cpp
[4/11] /usr/bin/c++ -DGENERATE_DISPATCH -DSIMDE_ENABLE_NATIVE_ALIASES -DSIMDE_ENABLE_OPENMP -DSIMDE_NO_NATIVE -DUSE_SIMDE -I/wrkdirs/usr/ports/biology/spoa/work/spoa-4.0.7/include -I/wrkdirs/usr/ports/biology/spoa/work/spoa-4.0.7/vendor/simde -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -Wall -Wextra -pedantic -fopenmp-simd -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -fPIC -msse2 -std=c++11 -MD -MT CMakeFiles/spoa_sse2.dir/src/simd_alignment_engine_dispatch.cpp.o -MF CMakeFiles/spoa_sse2.dir/src/simd_alignment_engine_dispatch.cpp.o.d -o CMakeFiles/spoa_sse2.dir/src/simd_alignment_engine_dispatch.cpp.o -c /wrkdirs/usr/ports/biology/spoa/work/spoa-4.0.7/src/simd_alignment_engine_dispatch.cpp
[5/11] /usr/bin/c++ -DGENERATE_DISPATCH -DSIMDE_ENABLE_NATIVE_ALIASES -DSIMDE_ENABLE_OPENMP -DSIMDE_NO_NATIVE -DUSE_SIMDE -Dspoa_EXPORTS -I/wrkdirs/usr/ports/biology/spoa/work/spoa-4.0.7/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -Wall -Wextra -pedantic -fopenmp-simd -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -fPIC -std=c++11 -MD -MT CMakeFiles/spoa.dir/src/dispatcher.cpp.o -MF CMakeFiles/spoa.dir/src/dispatcher.cpp.o.d -o CMakeFiles/spoa.dir/src/dispatcher.cpp.o -c /wrkdirs/usr/ports/biology/spoa/work/spoa-4.0.7/src/dispatcher.cpp
[6/11] /usr/bin/c++ -DGENERATE_DISPATCH -DSIMDE_ENABLE_NATIVE_ALIASES -DSIMDE_ENABLE_OPENMP -DSIMDE_NO_NATIVE -DUSE_SIMDE -I/wrkdirs/usr/ports/biology/spoa/work/spoa-4.0.7/include -I/wrkdirs/usr/ports/biology/spoa/work/spoa-4.0.7/vendor/simde -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -Wall -Wextra -pedantic -fopenmp-simd -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -fPIC -msse4.1 -std=c++11 -MD -MT CMakeFiles/spoa_sse4.1.dir/src/simd_alignment_engine_dispatch.cpp.o -MF CMakeFiles/spoa_sse4.1.dir/src/simd_alignment_engine_dispatch.cpp.o.d -o CMakeFiles/spoa_sse4.1.dir/src/simd_alignment_engine_dispatch.cpp.o -c /wrkdirs/usr/ports/biology/spoa/work/spoa-4.0.7/src/simd_alignment_engine_dispatch.cpp
[7/11] /usr/bin/c++ -DGENERATE_DISPATCH -DSIMDE_ENABLE_NATIVE_ALIASES -DSIMDE_ENABLE_OPENMP -DSIMDE_NO_NATIVE -DSPOA_VERSION=\"v4.0.7\" -DUSE_SIMDE -I/wrkdirs/usr/ports/biology/spoa/work/spoa-4.0.7/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -Wall -Wextra -pedantic -fopenmp-simd -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -std=c++11 -MD -MT CMakeFiles/spoa_exe.dir/src/main.cpp.o -MF CMakeFiles/spoa_exe.dir/src/main.cpp.o.d -o CMakeFiles/spoa_exe.dir/src/main.cpp.o -c /wrkdirs/usr/ports/biology/spoa/work/spoa-4.0.7/src/main.cpp
[8/11] /usr/bin/c++ -DGENERATE_DISPATCH -DSIMDE_ENABLE_NATIVE_ALIASES -DSIMDE_ENABLE_OPENMP -DSIMDE_NO_NATIVE -DUSE_SIMDE -I/wrkdirs/usr/ports/biology/spoa/work/spoa-4.0.7/include -I/wrkdirs/usr/ports/biology/spoa/work/spoa-4.0.7/vendor/simde -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -Wall -Wextra -pedantic -fopenmp-simd -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -fPIC -mavx2 -std=c++11 -MD -MT CMakeFiles/spoa_avx2.dir/src/simd_alignment_engine_dispatch.cpp.o -MF CMakeFiles/spoa_avx2.dir/src/simd_alignment_engine_dispatch.cpp.o.d -o CMakeFiles/spoa_avx2.dir/src/simd_alignment_engine_dispatch.cpp.o -c /wrkdirs/usr/ports/biology/spoa/work/spoa-4.0.7/src/simd_alignment_engine_dispatch.cpp
In file included from /wrkdirs/usr/ports/biology/spoa/work/spoa-4.0.7/src/simd_alignment_engine_dispatch.cpp:3:
In file included from /wrkdirs/usr/ports/biology/spoa/work/spoa-4.0.7/src/simd_alignment_engine_implementation.hpp:6:
/wrkdirs/usr/ports/biology/spoa/work/spoa-4.0.7/src/simd_alignment_engine.hpp:103:8: warning: loop not vectorized: the optimizer was unable to perform the requested transformation; the transformation might be disabled or specified as part of an unsupported transformation ordering [-Wpass-failed=transform-warning]
void Initialize(
^
/wrkdirs/usr/ports/biology/spoa/work/spoa-4.0.7/src/simd_alignment_engine.hpp:103:8: warning: loop not vectorized: the optimizer was unable to perform the requested transformation; the transformation might be disabled or specified as part of an unsupported transformation ordering [-Wpass-failed=transform-warning]
/wrkdirs/usr/ports/biology/spoa/work/spoa-4.0.7/src/simd_alignment_engine.hpp:103:8: warning: loop not vectorized: the optimizer was unable to perform the requested transformation; the transformation might be disabled or specified as part of an unsupported transformation ordering [-Wpass-failed=transform-warning]
/wrkdirs/usr/ports/biology/spoa/work/spoa-4.0.7/src/simd_alignment_engine.hpp:103:8: warning: loop not vectorized: the optimizer was unable to perform the requested transformation; the transformation might be disabled or specified as part of an unsupported transformation ordering [-Wpass-failed=transform-warning]
/wrkdirs/usr/ports/biology/spoa/work/spoa-4.0.7/src/simd_alignment_engine.hpp:103:8: warning: loop not vectorized: the optimizer was unable to perform the requested transformation; the transformation might be disabled or specified as part of an unsupported transformation ordering [-Wpass-failed=transform-warning]
/wrkdirs/usr/ports/biology/spoa/work/spoa-4.0.7/src/simd_alignment_engine.hpp:103:8: warning: loop not vectorized: the optimizer was unable to perform the requested transformation; the transformation might be disabled or specified as part of an unsupported transformation ordering [-Wpass-failed=transform-warning]
/wrkdirs/usr/ports/biology/spoa/work/spoa-4.0.7/src/simd_alignment_engine.hpp:103:8: warning: loop not vectorized: the optimizer was unable to perform the requested transformation; the transformation might be disabled or specified as part of an unsupported transformation ordering [-Wpass-failed=transform-warning]
/wrkdirs/usr/ports/biology/spoa/work/spoa-4.0.7/src/simd_alignment_engine.hpp:103:8: warning: loop not vectorized: the optimizer was unable to perform the requested transformation; the transformation might be disabled or specified as part of an unsupported transformation ordering [-Wpass-failed=transform-warning]
/wrkdirs/usr/ports/biology/spoa/work/spoa-4.0.7/src/simd_alignment_engine.hpp:80:13: warning: loop not vectorized: the optimizer was unable to perform the requested transformation; the transformation might be disabled or specified as part of an unsupported transformation ordering [-Wpass-failed=transform-warning]
Alignment Linear(
^
/wrkdirs/usr/ports/biology/spoa/work/spoa-4.0.7/src/simd_alignment_engine.hpp:80:13: warning: loop not vectorized: the optimizer was unable to perform the requested transformation; the transformation might be disabled or specified as part of an unsupported transformation ordering [-Wpass-failed=transform-warning]
/wrkdirs/usr/ports/biology/spoa/work/spoa-4.0.7/src/simd_alignment_engine.hpp:80:13: warning: loop not vectorized: the optimizer was unable to perform the requested transformation; the transformation might be disabled or specified as part of an unsupported transformation ordering [-Wpass-failed=transform-warning]
/wrkdirs/usr/ports/biology/spoa/work/spoa-4.0.7/src/simd_alignment_engine.hpp:80:13: warning: loop not vectorized: the optimizer was unable to perform the requested transformation; the transformation might be disabled or specified as part of an unsupported transformation ordering [-Wpass-failed=transform-warning]
/wrkdirs/usr/ports/biology/spoa/work/spoa-4.0.7/src/simd_alignment_engine.hpp:80:13: warning: loop not vectorized: the optimizer was unable to perform the requested transformation; the transformation might be disabled or specified as part of an unsupported transformation ordering [-Wpass-failed=transform-warning]
/wrkdirs/usr/ports/biology/spoa/work/spoa-4.0.7/src/simd_alignment_engine.hpp:86:13: warning: loop not vectorized: the optimizer was unable to perform the requested transformation; the transformation might be disabled or specified as part of an unsupported transformation ordering [-Wpass-failed=transform-warning]
Alignment Affine(
^
/wrkdirs/usr/ports/biology/spoa/work/spoa-4.0.7/src/simd_alignment_engine.hpp:86:13: warning: loop not vectorized: the optimizer was unable to perform the requested transformation; the transformation might be disabled or specified as part of an unsupported transformation ordering [-Wpass-failed=transform-warning]
/wrkdirs/usr/ports/biology/spoa/work/spoa-4.0.7/src/simd_alignment_engine.hpp:86:13: warning: loop not vectorized: the optimizer was unable to perform the requested transformation; the transformation might be disabled or specified as part of an unsupported transformation ordering [-Wpass-failed=transform-warning]
/wrkdirs/usr/ports/biology/spoa/work/spoa-4.0.7/src/simd_alignment_engine.hpp:86:13: warning: loop not vectorized: the optimizer was unable to perform the requested transformation; the transformation might be disabled or specified as part of an unsupported transformation ordering [-Wpass-failed=transform-warning]
/wrkdirs/usr/ports/biology/spoa/work/spoa-4.0.7/src/simd_alignment_engine.hpp:86:13: warning: loop not vectorized: the optimizer was unable to perform the requested transformation; the transformation might be disabled or specified as part of an unsupported transformation ordering [-Wpass-failed=transform-warning]
/wrkdirs/usr/ports/biology/spoa/work/spoa-4.0.7/src/simd_alignment_engine.hpp:86:13: warning: loop not vectorized: the optimizer was unable to perform the requested transformation; the transformation might be disabled or specified as part of an unsupported transformation ordering [-Wpass-failed=transform-warning]
/wrkdirs/usr/ports/biology/spoa/work/spoa-4.0.7/src/simd_alignment_engine.hpp:86:13: warning: loop not vectorized: the optimizer was unable to perform the requested transformation; the transformation might be disabled or specified as part of an unsupported transformation ordering [-Wpass-failed=transform-warning]
/wrkdirs/usr/ports/biology/spoa/work/spoa-4.0.7/src/simd_alignment_engine.hpp:92:13: warning: loop not vectorized: the optimizer was unable to perform the requested transformation; the transformation might be disabled or specified as part of an unsupported transformation ordering [-Wpass-failed=transform-warning]
Alignment Convex(
^
/wrkdirs/usr/ports/biology/spoa/work/spoa-4.0.7/src/simd_alignment_engine.hpp:92:13: warning: loop not vectorized: the optimizer was unable to perform the requested transformation; the transformation might be disabled or specified as part of an unsupported transformation ordering [-Wpass-failed=transform-warning]
/wrkdirs/usr/ports/biology/spoa/work/spoa-4.0.7/src/simd_alignment_engine.hpp:92:13: warning: loop not vectorized: the optimizer was unable to perform the requested transformation; the transformation might be disabled or specified as part of an unsupported transformation ordering [-Wpass-failed=transform-warning]
/wrkdirs/usr/ports/biology/spoa/work/spoa-4.0.7/src/simd_alignment_engine.hpp:92:13: warning: loop not vectorized: the optimizer was unable to perform the requested transformation; the transformation might be disabled or specified as part of an unsupported transformation ordering [-Wpass-failed=transform-warning]
/wrkdirs/usr/ports/biology/spoa/work/spoa-4.0.7/src/simd_alignment_engine.hpp:92:13: warning: loop not vectorized: the optimizer was unable to perform the requested transformation; the transformation might be disabled or specified as part of an unsupported transformation ordering [-Wpass-failed=transform-warning]
/wrkdirs/usr/ports/biology/spoa/work/spoa-4.0.7/src/simd_alignment_engine.hpp:92:13: warning: loop not vectorized: the optimizer was unable to perform the requested transformation; the transformation might be disabled or specified as part of an unsupported transformation ordering [-Wpass-failed=transform-warning]
/wrkdirs/usr/ports/biology/spoa/work/spoa-4.0.7/src/simd_alignment_engine.hpp:92:13: warning: loop not vectorized: the optimizer was unable to perform the requested transformation; the transformation might be disabled or specified as part of an unsupported transformation ordering [-Wpass-failed=transform-warning]
/wrkdirs/usr/ports/biology/spoa/work/spoa-4.0.7/src/simd_alignment_engine.hpp:92:13: warning: loop not vectorized: the optimizer was unable to perform the requested transformation; the transformation might be disabled or specified as part of an unsupported transformation ordering [-Wpass-failed=transform-warning]
/wrkdirs/usr/ports/biology/spoa/work/spoa-4.0.7/src/simd_alignment_engine.hpp:92:13: warning: loop not vectorized: the optimizer was unable to perform the requested transformation; the transformation might be disabled or specified as part of an unsupported transformation ordering [-Wpass-failed=transform-warning]
/wrkdirs/usr/ports/biology/spoa/work/spoa-4.0.7/src/simd_alignment_engine.hpp:103:8: warning: loop not vectorized: the optimizer was unable to perform the requested transformation; the transformation might be disabled or specified as part of an unsupported transformation ordering [-Wpass-failed=transform-warning]
void Initialize(
^
/wrkdirs/usr/ports/biology/spoa/work/spoa-4.0.7/src/simd_alignment_engine.hpp:103:8: warning: loop not vectorized: the optimizer was unable to perform the requested transformation; the transformation might be disabled or specified as part of an unsupported transformation ordering [-Wpass-failed=transform-warning]
/wrkdirs/usr/ports/biology/spoa/work/spoa-4.0.7/src/simd_alignment_engine.hpp:103:8: warning: loop not vectorized: the optimizer was unable to perform the requested transformation; the transformation might be disabled or specified as part of an unsupported transformation ordering [-Wpass-failed=transform-warning]
/wrkdirs/usr/ports/biology/spoa/work/spoa-4.0.7/src/simd_alignment_engine.hpp:103:8: warning: loop not vectorized: the optimizer was unable to perform the requested transformation; the transformation might be disabled or specified as part of an unsupported transformation ordering [-Wpass-failed=transform-warning]
/wrkdirs/usr/ports/biology/spoa/work/spoa-4.0.7/src/simd_alignment_engine.hpp:103:8: warning: loop not vectorized: the optimizer was unable to perform the requested transformation; the transformation might be disabled or specified as part of an unsupported transformation ordering [-Wpass-failed=transform-warning]
/wrkdirs/usr/ports/biology/spoa/work/spoa-4.0.7/src/simd_alignment_engine.hpp:103:8: warning: loop not vectorized: the optimizer was unable to perform the requested transformation; the transformation might be disabled or specified as part of an unsupported transformation ordering [-Wpass-failed=transform-warning]
/wrkdirs/usr/ports/biology/spoa/work/spoa-4.0.7/src/simd_alignment_engine.hpp:103:8: warning: loop not vectorized: the optimizer was unable to perform the requested transformation; the transformation might be disabled or specified as part of an unsupported transformation ordering [-Wpass-failed=transform-warning]
/wrkdirs/usr/ports/biology/spoa/work/spoa-4.0.7/src/simd_alignment_engine.hpp:103:8: warning: loop not vectorized: the optimizer was unable to perform the requested transformation; the transformation might be disabled or specified as part of an unsupported transformation ordering [-Wpass-failed=transform-warning]
/wrkdirs/usr/ports/biology/spoa/work/spoa-4.0.7/src/simd_alignment_engine.hpp:80:13: warning: loop not vectorized: the optimizer was unable to perform the requested transformation; the transformation might be disabled or specified as part of an unsupported transformation ordering [-Wpass-failed=transform-warning]
Alignment Linear(
^
/wrkdirs/usr/ports/biology/spoa/work/spoa-4.0.7/src/simd_alignment_engine.hpp:80:13: warning: loop not vectorized: the optimizer was unable to perform the requested transformation; the transformation might be disabled or specified as part of an unsupported transformation ordering [-Wpass-failed=transform-warning]
/wrkdirs/usr/ports/biology/spoa/work/spoa-4.0.7/src/simd_alignment_engine.hpp:80:13: warning: loop not vectorized: the optimizer was unable to perform the requested transformation; the transformation might be disabled or specified as part of an unsupported transformation ordering [-Wpass-failed=transform-warning]
/wrkdirs/usr/ports/biology/spoa/work/spoa-4.0.7/src/simd_alignment_engine.hpp:80:13: warning: loop not vectorized: the optimizer was unable to perform the requested transformation; the transformation might be disabled or specified as part of an unsupported transformation ordering [-Wpass-failed=transform-warning]
/wrkdirs/usr/ports/biology/spoa/work/spoa-4.0.7/src/simd_alignment_engine.hpp:80:13: warning: loop not vectorized: the optimizer was unable to perform the requested transformation; the transformation might be disabled or specified as part of an unsupported transformation ordering [-Wpass-failed=transform-warning]
/wrkdirs/usr/ports/biology/spoa/work/spoa-4.0.7/src/simd_alignment_engine.hpp:86:13: warning: loop not vectorized: the optimizer was unable to perform the requested transformation; the transformation might be disabled or specified as part of an unsupported transformation ordering [-Wpass-failed=transform-warning]
Alignment Affine(
^
/wrkdirs/usr/ports/biology/spoa/work/spoa-4.0.7/src/simd_alignment_engine.hpp:86:13: warning: loop not vectorized: the optimizer was unable to perform the requested transformation; the transformation might be disabled or specified as part of an unsupported transformation ordering [-Wpass-failed=transform-warning]
/wrkdirs/usr/ports/biology/spoa/work/spoa-4.0.7/src/simd_alignment_engine.hpp:86:13: warning: loop not vectorized: the optimizer was unable to perform the requested transformation; the transformation might be disabled or specified as part of an unsupported transformation ordering [-Wpass-failed=transform-warning]
/wrkdirs/usr/ports/biology/spoa/work/spoa-4.0.7/src/simd_alignment_engine.hpp:86:13: warning: loop not vectorized: the optimizer was unable to perform the requested transformation; the transformation might be disabled or specified as part of an unsupported transformation ordering [-Wpass-failed=transform-warning]
/wrkdirs/usr/ports/biology/spoa/work/spoa-4.0.7/src/simd_alignment_engine.hpp:86:13: warning: loop not vectorized: the optimizer was unable to perform the requested transformation; the transformation might be disabled or specified as part of an unsupported transformation ordering [-Wpass-failed=transform-warning]
/wrkdirs/usr/ports/biology/spoa/work/spoa-4.0.7/src/simd_alignment_engine.hpp:86:13: warning: loop not vectorized: the optimizer was unable to perform the requested transformation; the transformation might be disabled or specified as part of an unsupported transformation ordering [-Wpass-failed=transform-warning]
/wrkdirs/usr/ports/biology/spoa/work/spoa-4.0.7/src/simd_alignment_engine.hpp:86:13: warning: loop not vectorized: the optimizer was unable to perform the requested transformation; the transformation might be disabled or specified as part of an unsupported transformation ordering [-Wpass-failed=transform-warning]
/wrkdirs/usr/ports/biology/spoa/work/spoa-4.0.7/src/simd_alignment_engine.hpp:92:13: warning: loop not vectorized: the optimizer was unable to perform the requested transformation; the transformation might be disabled or specified as part of an unsupported transformation ordering [-Wpass-failed=transform-warning]
Alignment Convex(
^
/wrkdirs/usr/ports/biology/spoa/work/spoa-4.0.7/src/simd_alignment_engine.hpp:92:13: warning: loop not vectorized: the optimizer was unable to perform the requested transformation; the transformation might be disabled or specified as part of an unsupported transformation ordering [-Wpass-failed=transform-warning]
/wrkdirs/usr/ports/biology/spoa/work/spoa-4.0.7/src/simd_alignment_engine.hpp:92:13: warning: loop not vectorized: the optimizer was unable to perform the requested transformation; the transformation might be disabled or specified as part of an unsupported transformation ordering [-Wpass-failed=transform-warning]
/wrkdirs/usr/ports/biology/spoa/work/spoa-4.0.7/src/simd_alignment_engine.hpp:92:13: warning: loop not vectorized: the optimizer was unable to perform the requested transformation; the transformation might be disabled or specified as part of an unsupported transformation ordering [-Wpass-failed=transform-warning]
/wrkdirs/usr/ports/biology/spoa/work/spoa-4.0.7/src/simd_alignment_engine.hpp:92:13: warning: loop not vectorized: the optimizer was unable to perform the requested transformation; the transformation might be disabled or specified as part of an unsupported transformation ordering [-Wpass-failed=transform-warning]
/wrkdirs/usr/ports/biology/spoa/work/spoa-4.0.7/src/simd_alignment_engine.hpp:92:13: warning: loop not vectorized: the optimizer was unable to perform the requested transformation; the transformation might be disabled or specified as part of an unsupported transformation ordering [-Wpass-failed=transform-warning]
/wrkdirs/usr/ports/biology/spoa/work/spoa-4.0.7/src/simd_alignment_engine.hpp:92:13: warning: loop not vectorized: the optimizer was unable to perform the requested transformation; the transformation might be disabled or specified as part of an unsupported transformation ordering [-Wpass-failed=transform-warning]
/wrkdirs/usr/ports/biology/spoa/work/spoa-4.0.7/src/simd_alignment_engine.hpp:92:13: warning: loop not vectorized: the optimizer was unable to perform the requested transformation; the transformation might be disabled or specified as part of an unsupported transformation ordering [-Wpass-failed=transform-warning]
/wrkdirs/usr/ports/biology/spoa/work/spoa-4.0.7/src/simd_alignment_engine.hpp:92:13: warning: loop not vectorized: the optimizer was unable to perform the requested transformation; the transformation might be disabled or specified as part of an unsupported transformation ordering [-Wpass-failed=transform-warning]
58 warnings generated.
[9/11] : && /usr/bin/c++ -fPIC -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -Wall -Wextra -pedantic -fopenmp-simd -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -lz -lcpu_features -fstack-protector-strong -L/usr/local/lib -shared -Wl,-soname,libspoa.so.7.0.0 -o lib/libspoa.so.7.0.0 CMakeFiles/spoa.dir/src/alignment_engine.cpp.o CMakeFiles/spoa.dir/src/graph.cpp.o CMakeFiles/spoa.dir/src/sisd_alignment_engine.cpp.o CMakeFiles/spoa.dir/src/dispatcher.cpp.o -lcereal && :
FAILED: lib/libspoa.so.7.0.0
: && /usr/bin/c++ -fPIC -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -Wall -Wextra -pedantic -fopenmp-simd -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -lz -lcpu_features -fstack-protector-strong -L/usr/local/lib -shared -Wl,-soname,libspoa.so.7.0.0 -o lib/libspoa.so.7.0.0 CMakeFiles/spoa.dir/src/alignment_engine.cpp.o CMakeFiles/spoa.dir/src/graph.cpp.o CMakeFiles/spoa.dir/src/sisd_alignment_engine.cpp.o CMakeFiles/spoa.dir/src/dispatcher.cpp.o -lcereal && :
ld: error: unable to find library -lcereal
c++: error: linker command failed with exit code 1 (use -v to see invocation)
ninja: build stopped: subcommand failed.
===> Compilation failed unexpectedly.
Try to set MAKE_JOBS_UNSAFE=yes and rebuild before reporting the failure to
the maintainer.
*** Error code 1
Stop.
make: stopped in /usr/ports/biology/spoa
More information about the freebsd-pkg-fallout
mailing list