[package - head-armv6-default][biology/seqan-apps] Failed for seqan-apps-2.2.0_6 in build
pkg-fallout at FreeBSD.org
pkg-fallout at FreeBSD.org
Mon Sep 25 20:04:13 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: h2+fbsdports at fsfe.org
Last committer: gerald at FreeBSD.org
Ident: $FreeBSD: head/biology/seqan-apps/Makefile 449591 2017-09-10 20:55:38Z gerald $
Log URL: http://beefy8.nyi.freebsd.org/data/head-armv6-default/p450418_s323935/logs/seqan-apps-2.2.0_6.log
Build URL: http://beefy8.nyi.freebsd.org/build.html?mastername=head-armv6-default&build=p450418_s323935
Log:
====>> Building biology/seqan-apps
build started at Mon Sep 25 19:26:12 UTC 2017
port directory: /usr/ports/biology/seqan-apps
building for: FreeBSD head-armv6-default-job-18 12.0-CURRENT FreeBSD 12.0-CURRENT 1200046 arm
maintained by: h2+fbsdports at fsfe.org
Makefile ident: $FreeBSD: head/biology/seqan-apps/Makefile 449591 2017-09-10 20:55:38Z gerald $
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!!! Jail is newer than host. (Jail: 1200046, Host: 1200040) !!!
!!! This is not supported. !!!
!!! Host kernel must be same or newer than jail. !!!
!!! Expect build failures. !!!
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=======================<phase: check-sanity >============================
===> License BSD3CLAUSE LGPL3 GPLv3 accepted by the user
===========================================================================
=======================<phase: pkg-depends >============================
===> seqan-apps-2.2.0_6 depends on file: /usr/local/sbin/pkg - not found
===> Installing existing package /packages/All/pkg-1.10.1.txz
[head-armv6-default-job-18] Installing pkg-1.10.1...
[head-armv6-default-job-18] Extracting pkg-1.10.1: .......... done
===> seqan-apps-2.2.0_6 depends on file: /usr/local/sbin/pkg - found
===> Returning to build of seqan-apps-2.2.0_6
===========================================================================
=======================<phase: fetch-depends >============================
===========================================================================
=======================<phase: fetch >============================
===> License BSD3CLAUSE LGPL3 GPLv3 accepted by the user
===> Fetching all distfiles required by seqan-apps-2.2.0_6 for building
===========================================================================
=======================<phase: checksum >============================
===> License BSD3CLAUSE LGPL3 GPLv3 accepted by the user
===> Fetching all distfiles required by seqan-apps-2.2.0_6 for building
=> SHA256 Checksum OK for seqan-seqan-seqan-v2.2.0_GH0.tar.gz.
===========================================================================
=======================<phase: extract-depends>============================
===========================================================================
=======================<phase: extract >============================
===> License BSD3CLAUSE LGPL3 GPLv3 accepted by the user
===> Fetching all distfiles required by seqan-apps-2.2.0_6 for building
===> Extracting for seqan-apps-2.2.0_6
=> SHA256 Checksum OK for seqan-seqan-seqan-v2.2.0_GH0.tar.gz.
<snip>
[head-armv6-default-job-18] `-- Extracting binutils-2.28,1: .......... done
[head-armv6-default-job-18] `-- Installing gmp-6.1.2...
[head-armv6-default-job-18] `-- Extracting gmp-6.1.2: .......... done
[head-armv6-default-job-18] `-- Installing mpc-1.0.3...
[head-armv6-default-job-18] | `-- Installing mpfr-3.1.6...
[head-armv6-default-job-18] | `-- Extracting mpfr-3.1.6: .......... done
[head-armv6-default-job-18] `-- Extracting mpc-1.0.3: ...... done
[head-armv6-default-job-18] Extracting gcc6-6.4.0_1: .......... done
Message from gcc6-6.4.0_1:
To ensure binaries built with this toolchain find appropriate versions
of the necessary run-time libraries, you may want to link using
-Wl,-rpath=/usr/local/lib/gcc6
For ports leveraging USE_GCC, USES=compiler, or USES=fortran this happens
transparently.
===> seqan-apps-2.2.0_6 depends on executable: gcc6 - found
===> Returning to build of seqan-apps-2.2.0_6
===> seqan-apps-2.2.0_6 depends on file: /usr/local/bin/as - found
===========================================================================
=======================<phase: lib-depends >============================
===========================================================================
=======================<phase: configure >============================
===> Configuring for seqan-apps-2.2.0_6
===> Performing out-of-source build
/bin/mkdir -p /wrkdirs/usr/ports/biology/seqan-apps/work/.build
-- The CXX compiler identification is GNU 6.4.0
-- Check for working CXX compiler: /usr/local/bin/g++6
-- Check for working CXX compiler: /usr/local/bin/g++6 -- works
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Detecting CXX compile features
-- Detecting CXX compile features - done
-- Initializing SeqAn Build System...
-- Selected repository dir: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.2.0
-- No revision system found.
-- Repository date not determined.
-- Repository revision not determined.
-- Configuring apps
-- Configuring apps/alf
-- Performing Test CXX14_BUILTIN
-- Performing Test CXX14_BUILTIN - Success
-- Looking for C++ include execinfo.h
-- Looking for C++ include execinfo.h - found
-- Configuring apps/bs_tools
-- Found ZLIB: /usr/lib/libz.so (found version "1.2.11")
-- Boost version: 1.64.0
-- Found PythonInterp: /usr/local/bin/python2.7 (found version "2.7.13")
-- Configuring apps/dfi
-- Configuring apps/fiona
CMake Warning (dev) at /usr/local/share/cmake/Modules/FindOpenMP.cmake:200 (if):
Policy CMP0054 is not set: Only interpret if() arguments as variables or
keywords when unquoted. Run "cmake --help-policy CMP0054" for policy
details. Use the cmake_policy command to set the policy and suppress this
warning.
Quoted variables like "c" will no longer be dereferenced when the policy is
set to NEW. Since the policy is not set the OLD behavior will be used.
Call Stack (most recent call first):
/usr/local/share/cmake/Modules/FindOpenMP.cmake:324 (_OPENMP_GET_FLAGS)
apps/fiona/CMakeLists.txt:20 (find_package)
This warning is for project developers. Use -Wno-dev to suppress it.
-- Found OpenMP_CXX: -fopenmp (found version "4.5")
-- Boost version: 1.64.0
-- Not building fiona on 32bit architectures.
-- Configuring apps/fx_tools
-- Configuring apps/gustaf
-- Configuring apps/insegt
-- Configuring apps/mason2
-- Found OpenMP_CXX: -fopenmp
-- Configuring apps/micro_razers
-- Configuring apps/ngs_roi
-- Configuring apps/pair_align
-- Configuring apps/param_chooser
-- Configuring apps/rabema
-- Configuring apps/razers
-- Configuring apps/razers3
-- Found BZip2: /usr/lib/libbz2.so (found version "1.0.6")
-- Looking for BZ2_bzCompressInit
-- Looking for BZ2_bzCompressInit - found
-- Configuring apps/rep_sep
-- Configuring apps/sak
-- Configuring apps/sam2matrix
-- Configuring apps/samcat
-- Configuring apps/searchjoin
-- Configuring apps/seqan_tcoffee
-- Configuring apps/seqcons2
-- Configuring apps/sgip
-- Configuring apps/snp_store
-- Boost version: 1.64.0
-- Configuring apps/splazers
-- Not building splazers on 32bit architectures.
-- Configuring apps/stellar
-- Configuring apps/tree_recon
-- Configuring apps/yara
-- Unsupported platform FreeBSD, disabling CTD support.
-- 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_SHARED_LINKER_FLAGS
CMAKE_VERBOSE_MAKEFILE
THREADS_HAVE_PTHREAD_ARG
-- Build files have been written to: /wrkdirs/usr/ports/biology/seqan-apps/work/.build
===========================================================================
=======================<phase: build >============================
===> Building for seqan-apps-2.2.0_6
[1/133] /usr/local/bin/g++6 -DSEQAN_APP_VERSION=\"0.4.4\" -DSEQAN_DATE=\"\" -DSEQAN_HAS_EXECINFO=1 -DSEQAN_REVISION=\"tarball\" -D_FILE_OFFSET_BITS=64 -D_GLIBCXX_USE_C99=1 -D_LARGEFILE_SOURCE -I/wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.2.0/include -O2 -pipe -Wl,-rpath=/usr/local/lib/gcc6 -fno-strict-aliasing -Wl,-rpath=/usr/local/lib/gcc6 -W -Wall -pedantic -fstrict-aliasing -Wstrict-aliasing -O2 -pipe -Wl,-rpath=/usr/local/lib/gcc6 -fno-strict-aliasing -Wl,-rpath=/usr/local/lib/gcc6 -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -MD -MT apps/sak/CMakeFiles/sak.dir/sak.cpp.o -MF apps/sak/CMakeFiles/sak.dir/sak.cpp.o.d -o apps/sak/CMakeFiles/sak.dir/sak.cpp.o -c /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.2.0/apps/sak/sak.cpp
In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.2.0/include/seqan/basic/basic_allocator.h:47:0,
from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.2.0/include/seqan/basic.h:74,
from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.2.0/include/seqan/arg_parse.h:44,
from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.2.0/apps/sak/sak.cpp:42:
/wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.2.0/include/seqan/basic/basic_simd_vector.h:53:3: warning: #warning is a GCC extension
#warning "No supported platform for SIMD vectorization!"
^~~~~~~
/wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.2.0/include/seqan/basic/basic_simd_vector.h:53:3: warning: #warning "No supported platform for SIMD vectorization!" [-Wcpp]
[2/133] : && /usr/local/bin/g++6 -O2 -pipe -Wl,-rpath=/usr/local/lib/gcc6 -fno-strict-aliasing -Wl,-rpath=/usr/local/lib/gcc6 -W -Wall -pedantic -fstrict-aliasing -Wstrict-aliasing -O2 -pipe -Wl,-rpath=/usr/local/lib/gcc6 -fno-strict-aliasing -Wl,-rpath=/usr/local/lib/gcc6 -Wl,-rpath=/usr/local/lib/gcc6 -L/usr/local/lib/gcc6 apps/sak/CMakeFiles/sak.dir/sak.cpp.o -o bin/sak -lpthread -lexecinfo -lelf && :
[3/133] /usr/local/bin/g++6 -DSEQAN_APP_VERSION=\"0.3.4\" -DSEQAN_DATE=\"\" -DSEQAN_HAS_EXECINFO=1 -DSEQAN_REVISION=\"tarball\" -D_FILE_OFFSET_BITS=64 -D_GLIBCXX_USE_C99=1 -D_LARGEFILE_SOURCE -I/wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.2.0/include -O2 -pipe -Wl,-rpath=/usr/local/lib/gcc6 -fno-strict-aliasing -Wl,-rpath=/usr/local/lib/gcc6 -W -Wall -pedantic -fstrict-aliasing -Wstrict-aliasing -O2 -pipe -Wl,-rpath=/usr/local/lib/gcc6 -fno-strict-aliasing -Wl,-rpath=/usr/local/lib/gcc6 -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -MD -MT apps/sam2matrix/CMakeFiles/sam2matrix.dir/sam2matrix.cpp.o -MF apps/sam2matrix/CMakeFiles/sam2matrix.dir/sam2matrix.cpp.o.d -o apps/sam2matrix/CMakeFiles/sam2matrix.dir/sam2matrix.cpp.o -c /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.2.0/apps/sam2matrix/sam2matrix.cpp
In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.2.0/include/seqan/basic/basic_allocator.h:47:0,
from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.2.0/include/seqan/basic.h:74,
from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.2.0/apps/sam2matrix/sam2matrix.cpp:41:
/wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.2.0/include/seqan/basic/basic_simd_vector.h:53:3: warning: #warning is a GCC extension
#warning "No supported platform for SIMD vectorization!"
^~~~~~~
/wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.2.0/include/seqan/basic/basic_simd_vector.h:53:3: warning: #warning "No supported platform for SIMD vectorization!" [-Wcpp]
[4/133] : && /usr/local/bin/g++6 -O2 -pipe -Wl,-rpath=/usr/local/lib/gcc6 -fno-strict-aliasing -Wl,-rpath=/usr/local/lib/gcc6 -W -Wall -pedantic -fstrict-aliasing -Wstrict-aliasing -O2 -pipe -Wl,-rpath=/usr/local/lib/gcc6 -fno-strict-aliasing -Wl,-rpath=/usr/local/lib/gcc6 -Wl,-rpath=/usr/local/lib/gcc6 -L/usr/local/lib/gcc6 apps/sam2matrix/CMakeFiles/sam2matrix.dir/sam2matrix.cpp.o -o bin/sam2matrix -lpthread -lexecinfo -lelf && :
[5/133] /usr/local/bin/g++6 -DSEQAN_APP_VERSION=\"0.3.4\" -DSEQAN_DATE=\"\" -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -DSEQAN_REVISION=\"tarball\" -D_FILE_OFFSET_BITS=64 -D_GLIBCXX_USE_C99=1 -D_LARGEFILE_SOURCE -I/wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.2.0/include -O2 -pipe -Wl,-rpath=/usr/local/lib/gcc6 -fno-strict-aliasing -Wl,-rpath=/usr/local/lib/gcc6 -W -Wall -pedantic -fstrict-aliasing -Wstrict-aliasing -fopenmp -O2 -pipe -Wl,-rpath=/usr/local/lib/gcc6 -fno-strict-aliasing -Wl,-rpath=/usr/local/lib/gcc6 -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -MD -MT apps/samcat/CMakeFiles/samcat.dir/samcat.cpp.o -MF apps/samcat/CMakeFiles/samcat.dir/samcat.cpp.o.d -o apps/samcat/CMakeFiles/samcat.dir/samcat.cpp.o -c /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.2.0/apps/samcat/samcat.cpp
In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.2.0/include/seqan/basic/basic_allocator.h:47:0,
from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.2.0/include/seqan/basic.h:74,
from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.2.0/apps/samcat/samcat.cpp:35:
/wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.2.0/include/seqan/basic/basic_simd_vector.h:53:3: warning: #warning is a GCC extension
#warning "No supported platform for SIMD vectorization!"
^~~~~~~
/wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.2.0/include/seqan/basic/basic_simd_vector.h:53:3: warning: #warning "No supported platform for SIMD vectorization!" [-Wcpp]
[6/133] : && /usr/local/bin/g++6 -O2 -pipe -Wl,-rpath=/usr/local/lib/gcc6 -fno-strict-aliasing -Wl,-rpath=/usr/local/lib/gcc6 -W -Wall -pedantic -fstrict-aliasing -Wstrict-aliasing -fopenmp -O2 -pipe -Wl,-rpath=/usr/local/lib/gcc6 -fno-strict-aliasing -Wl,-rpath=/usr/local/lib/gcc6 -Wl,-rpath=/usr/local/lib/gcc6 -L/usr/local/lib/gcc6 apps/samcat/CMakeFiles/samcat.dir/samcat.cpp.o -o bin/samcat -lpthread -lexecinfo -lelf -lz && :
[7/133] /usr/local/bin/g++6 -DSEARCHJOIN_HUGEDB=TRUE -DSEQAN_APP_VERSION=\"0.5.4\" -DSEQAN_DATE=\"\" -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_REVISION=\"tarball\" -D_FILE_OFFSET_BITS=64 -D_GLIBCXX_USE_C99=1 -D_LARGEFILE_SOURCE -I/wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.2.0/include -O2 -pipe -Wl,-rpath=/usr/local/lib/gcc6 -fno-strict-aliasing -Wl,-rpath=/usr/local/lib/gcc6 -W -Wall -pedantic -fstrict-aliasing -Wstrict-aliasing -fopenmp -O2 -pipe -Wl,-rpath=/usr/local/lib/gcc6 -fno-strict-aliasing -Wl,-rpath=/usr/local/lib/gcc6 -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -MD -MT apps/searchjoin/CMakeFiles/s4_join.dir/join.cpp.o -MF apps/searchjoin/CMakeFiles/s4_join.dir/join.cpp.o.d -o apps/searchjoin/CMakeFiles/s4_join.dir/join.cpp.o -c /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.2.0/apps/searchjoin/join.cpp
FAILED: apps/searchjoin/CMakeFiles/s4_join.dir/join.cpp.o
/usr/local/bin/g++6 -DSEARCHJOIN_HUGEDB=TRUE -DSEQAN_APP_VERSION=\"0.5.4\" -DSEQAN_DATE=\"\" -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_REVISION=\"tarball\" -D_FILE_OFFSET_BITS=64 -D_GLIBCXX_USE_C99=1 -D_LARGEFILE_SOURCE -I/wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.2.0/include -O2 -pipe -Wl,-rpath=/usr/local/lib/gcc6 -fno-strict-aliasing -Wl,-rpath=/usr/local/lib/gcc6 -W -Wall -pedantic -fstrict-aliasing -Wstrict-aliasing -fopenmp -O2 -pipe -Wl,-rpath=/usr/local/lib/gcc6 -fno-strict-aliasing -Wl,-rpath=/usr/local/lib/gcc6 -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -MD -MT apps/searchjoin/CMakeFiles/s4_join.dir/join.cpp.o -MF apps/searchjoin/CMakeFiles/s4_join.dir/join.cpp.o.d -o apps/searchjoin/CMakeFiles/s4_join.dir/join.cpp.o -c /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.2.0/apps/searchjoin/join.cpp
In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.2.0/include/seqan/basic/basic_allocator.h:47:0,
from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.2.0/include/seqan/basic.h:74,
from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.2.0/apps/searchjoin/join.cpp:59:
/wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.2.0/include/seqan/basic/basic_simd_vector.h:53:3: warning: #warning is a GCC extension
#warning "No supported platform for SIMD vectorization!"
^~~~~~~
/wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.2.0/include/seqan/basic/basic_simd_vector.h:53:3: warning: #warning "No supported platform for SIMD vectorization!" [-Wcpp]
{standard input}: Assembler messages:
{standard input}:6335: Error: bad instruction `rep'
{standard input}:6352: Error: bad instruction `rep'
{standard input}:6459: Error: bad instruction `rep'
{standard input}:6476: Error: bad instruction `rep'
{standard input}:6813: Error: bad instruction `rep'
{standard input}:6830: Error: bad instruction `rep'
{standard input}:6944: Error: bad instruction `rep'
{standard input}:6961: Error: bad instruction `rep'
{standard input}:7739: Error: bad instruction `rep'
{standard input}:7756: Error: bad instruction `rep'
{standard input}:7866: Error: bad instruction `rep'
{standard input}:7883: Error: bad instruction `rep'
{standard input}:8220: Error: bad instruction `rep'
{standard input}:8237: Error: bad instruction `rep'
{standard input}:8351: Error: bad instruction `rep'
{standard input}:8368: Error: bad instruction `rep'
{standard input}:9140: Error: bad instruction `rep'
{standard input}:9157: Error: bad instruction `rep'
{standard input}:9264: Error: bad instruction `rep'
{standard input}:9281: Error: bad instruction `rep'
{standard input}:9618: Error: bad instruction `rep'
{standard input}:9635: Error: bad instruction `rep'
{standard input}:9749: Error: bad instruction `rep'
{standard input}:9766: Error: bad instruction `rep'
{standard input}:10544: Error: bad instruction `rep'
{standard input}:10561: Error: bad instruction `rep'
{standard input}:10671: Error: bad instruction `rep'
{standard input}:10688: Error: bad instruction `rep'
{standard input}:11025: Error: bad instruction `rep'
{standard input}:11042: Error: bad instruction `rep'
{standard input}:11156: Error: bad instruction `rep'
{standard input}:11173: Error: bad instruction `rep'
{standard input}:29968: Error: bad instruction `rep'
{standard input}:29984: Error: bad instruction `rep'
{standard input}:30115: Error: bad instruction `rep'
{standard input}:30131: Error: bad instruction `rep'
{standard input}:30288: Error: bad instruction `rep'
{standard input}:30304: Error: bad instruction `rep'
{standard input}:30484: Error: bad instruction `rep'
{standard input}:30500: Error: bad instruction `rep'
ninja: build stopped: subcommand failed.
*** Error code 1
Stop.
make: stopped in /usr/ports/biology/seqan-apps
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