[package - head-armv6-default][biology/seqan-apps] Failed for seqan-apps-2.2.0 in build

pkg-fallout at FreeBSD.org pkg-fallout at FreeBSD.org
Sat Oct 15 21:28:23 UTC 2016


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: pawel at FreeBSD.org
Ident:          $FreeBSD: head/biology/seqan-apps/Makefile 422156 2016-09-14 19:38:58Z pawel $
Log URL:        http://beefy8.nyi.freebsd.org/data/head-armv6-default/p423739_s307008/logs/seqan-apps-2.2.0.log
Build URL:      http://beefy8.nyi.freebsd.org/build.html?mastername=head-armv6-default&build=p423739_s307008
Log:

====>> Building biology/seqan-apps
build started at Sat Oct 15 21:12:15 UTC 2016
port directory: /usr/ports/biology/seqan-apps
building for: FreeBSD head-armv6-default-job-24 12.0-CURRENT FreeBSD 12.0-CURRENT r307008 arm
maintained by: h2+fbsdports at fsfe.org
Makefile ident:      $FreeBSD: head/biology/seqan-apps/Makefile 422156 2016-09-14 19:38:58Z pawel $
Poudriere version: 3.1.14
Host OSVERSION: 1200005
Jail OSVERSION: 1200012




!!! Jail is newer than host. (Jail: 1200012, Host: 1200005) !!!
!!! This is not supported. !!!
!!! Host kernel must be same or newer than jail. !!!
!!! Expect build failures. !!!



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---End Environment---

---Begin OPTIONS List---
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--CONFIGURE_ARGS--

--End CONFIGURE_ARGS--

--CONFIGURE_ENV--
XDG_DATA_HOME=/wrkdirs/usr/ports/biology/seqan-apps/work  XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/seqan-apps/work  HOME=/wrkdirs/usr/ports/biology/seqan-apps/work TMPDIR="/tmp" SHELL=/bin/sh CONFIG_SHELL=/bin/sh
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PREFIX=%D
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DATADIR="share/seqan-apps"
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---Begin make.conf---
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CXX=/nxb-bin/usr/bin/c++
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MAKE=/nxb-bin/usr/bin/make
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<snip>
Assessment and verification of trust is the complete responsibility of the
system administrator.

*********************************** NOTE **********************************

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

***************************************************************************
===>   seqan-apps-2.2.0 depends on file: /usr/local/bin/cmake - found
===>   Returning to build of seqan-apps-2.2.0
===>   seqan-apps-2.2.0 depends on executable: gcc49 - not found
===>   Installing existing package /packages/All/gcc49-4.9.4.txz
[head-armv6-default-job-24] Installing gcc49-4.9.4...
[head-armv6-default-job-24] `-- Installing indexinfo-0.2.5...
[head-armv6-default-job-24] `-- Extracting indexinfo-0.2.5: .... done
[head-armv6-default-job-24] `-- Installing mpc-1.0.3...
[head-armv6-default-job-24] |   `-- Installing gmp-5.1.3_3...
[head-armv6-default-job-24] |   `-- Extracting gmp-5.1.3_3: .......... done
[head-armv6-default-job-24] |   `-- Installing mpfr-3.1.5...
[head-armv6-default-job-24] |   `-- Extracting mpfr-3.1.5: .......... done
[head-armv6-default-job-24] `-- Extracting mpc-1.0.3: ...... done
[head-armv6-default-job-24] `-- Installing binutils-2.27_4,1...
[head-armv6-default-job-24] |   `-- Installing gettext-runtime-0.19.8.1...
[head-armv6-default-job-24] |   `-- Extracting gettext-runtime-0.19.8.1: .......... done
[head-armv6-default-job-24] `-- Extracting binutils-2.27_4,1: .......... done
[head-armv6-default-job-24] Extracting gcc49-4.9.4: .......... done
Message from gcc49-4.9.4:
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/gcc49

For ports leveraging USE_GCC, USES=compiler, or USES=fortran this happens
transparently.
===>   seqan-apps-2.2.0 depends on executable: gcc49 - found
===>   Returning to build of seqan-apps-2.2.0
===>   seqan-apps-2.2.0 depends on file: /usr/local/bin/as - found
===========================================================================
=======================<phase: lib-depends    >============================
===========================================================================
=======================<phase: configure      >============================
===>  Configuring for seqan-apps-2.2.0
===>  Performing out-of-source build
/bin/mkdir -p /wrkdirs/usr/ports/biology/seqan-apps/work/.build
-- The CXX compiler identification is GNU 4.9.4
-- Check for working CXX compiler: /usr/local/bin/g++49
-- Check for working CXX compiler: /usr/local/bin/g++49 -- 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 - Failed
-- Performing Test CXX14_FLAG
-- Performing Test CXX14_FLAG - 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 "1.2.8") 
-- Boost version: 1.55.0
-- Could NOT find PythonInterp (missing:  PYTHON_EXECUTABLE) 
-- Configuring apps/dfi
-- Could NOT find PythonInterp (missing:  PYTHON_EXECUTABLE) 
-- Configuring apps/fiona
-- Try OpenMP CXX flag = [-fopenmp]
-- Performing Test OpenMP_FLAG_DETECTED
-- Performing Test OpenMP_FLAG_DETECTED - Success
-- Found OpenMP: -fopenmp  
-- Boost version: 1.55.0
--   Not building fiona on 32bit architectures.
-- Configuring apps/fx_tools
-- Configuring apps/gustaf
-- Could NOT find PythonInterp (missing:  PYTHON_EXECUTABLE) 
-- Configuring apps/insegt
-- Could NOT find PythonInterp (missing:  PYTHON_EXECUTABLE) 
-- Configuring apps/mason2
-- Could NOT find PythonInterp (missing:  PYTHON_EXECUTABLE) 
-- Configuring apps/micro_razers
-- Could NOT find PythonInterp (missing:  PYTHON_EXECUTABLE) 
-- Configuring apps/ngs_roi
-- Could NOT find PythonInterp (missing:  PYTHON_EXECUTABLE) 
-- Configuring apps/pair_align
-- Could NOT find PythonInterp (missing:  PYTHON_EXECUTABLE) 
-- Configuring apps/param_chooser
-- Configuring apps/rabema
-- Could NOT find PythonInterp (missing:  PYTHON_EXECUTABLE) 
-- Configuring apps/razers
-- Could NOT find PythonInterp (missing:  PYTHON_EXECUTABLE) 
-- Configuring apps/razers3
-- Found BZip2: /usr/lib/libbz2.so (found version "1.0.6") 
-- Looking for BZ2_bzCompressInit
-- Looking for BZ2_bzCompressInit - found
-- Could NOT find PythonInterp (missing:  PYTHON_EXECUTABLE) 
-- Could NOT find PythonInterp (missing:  PYTHON_EXECUTABLE) 
-- Configuring apps/rep_sep
-- Configuring apps/sak
-- Could NOT find PythonInterp (missing:  PYTHON_EXECUTABLE) 
-- Configuring apps/sam2matrix
-- Could NOT find PythonInterp (missing:  PYTHON_EXECUTABLE) 
-- Configuring apps/samcat
-- Could NOT find PythonInterp (missing:  PYTHON_EXECUTABLE) 
-- Configuring apps/searchjoin
-- Could NOT find PythonInterp (missing:  PYTHON_EXECUTABLE) 
-- Configuring apps/seqan_tcoffee
-- Could NOT find PythonInterp (missing:  PYTHON_EXECUTABLE) 
-- Configuring apps/seqcons2
-- Could NOT find PythonInterp (missing:  PYTHON_EXECUTABLE) 
-- Configuring apps/sgip
-- Could NOT find PythonInterp (missing:  PYTHON_EXECUTABLE) 
-- Configuring apps/snp_store
-- Boost version: 1.55.0
-- Could NOT find PythonInterp (missing:  PYTHON_EXECUTABLE) 
-- Configuring apps/splazers
--   Not building splazers on 32bit architectures.
-- Configuring apps/stellar
-- Could NOT find PythonInterp (missing:  PYTHON_EXECUTABLE) 
-- Configuring apps/tree_recon
-- Could NOT find PythonInterp (missing:  PYTHON_EXECUTABLE) 
-- Configuring apps/yara
-- Could NOT find PythonInterp (missing:  PYTHON_EXECUTABLE) 
-- Unsupported platform FreeBSD, disabling CTD support.
-- Configuring done
-- Generating done
CMake Warning:
  Manually-specified variables were not used by the project:

    CMAKE_C_COMPILER
    CMAKE_C_FLAGS
    CMAKE_C_FLAGS_DEBUG
    CMAKE_C_FLAGS_RELEASE
    CMAKE_MODULE_LINKER_FLAGS
    CMAKE_SHARED_LINKER_FLAGS
    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
/usr/local/bin/cmake -H/wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.2.0 -B/wrkdirs/usr/ports/biology/seqan-apps/work/.build --check-build-system CMakeFiles/Makefile.cmake 0
/usr/local/bin/cmake -E cmake_progress_start /wrkdirs/usr/ports/biology/seqan-apps/work/.build/CMakeFiles /wrkdirs/usr/ports/biology/seqan-apps/work/.build/CMakeFiles/progress.marks
/nxb-bin/usr/bin/make -f CMakeFiles/Makefile2 all
/nxb-bin/usr/bin/make -f CMakeFiles/seqan_library.dir/build.make CMakeFiles/seqan_library.dir/depend
cd /wrkdirs/usr/ports/biology/seqan-apps/work/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.2.0 /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.2.0 /wrkdirs/usr/ports/biology/seqan-apps/work/.build /wrkdirs/usr/ports/biology/seqan-apps/work/.build /wrkdirs/usr/ports/biology/seqan-apps/work/.build/CMakeFiles/seqan_library.dir/DependInfo.cmake
Scanning dependencies of target seqan_library
/nxb-bin/usr/bin/make -f CMakeFiles/seqan_library.dir/build.make CMakeFiles/seqan_library.dir/build
[  0%] Built target seqan_library
/nxb-bin/usr/bin/make -f apps/alf/CMakeFiles/alf.dir/build.make apps/alf/CMakeFiles/alf.dir/depend
cd /wrkdirs/usr/ports/biology/seqan-apps/work/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.2.0 /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.2.0/apps/alf /wrkdirs/usr/ports/biology/seqan-apps/work/.build /wrkdirs/usr/ports/biology/seqan-apps/work/.build/apps/alf /wrkdirs/usr/ports/biology/seqan-apps/work/.build/apps/alf/CMakeFiles/alf.dir/DependInfo.cmake
Scanning dependencies of target alf
/nxb-bin/usr/bin/make -f apps/alf/CMakeFiles/alf.dir/build.make apps/alf/CMakeFiles/alf.dir/build
[  0%] Building CXX object apps/alf/CMakeFiles/alf.dir/alf.cpp.o
cd /wrkdirs/usr/ports/biology/seqan-apps/work/.build/apps/alf && /usr/local/bin/g++49   -DSEQAN_APP_VERSION=\"1.1.6\" -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/gcc49 -fno-strict-aliasing  -Wl,-rpath=/usr/local/lib/gcc49 -std=c++14  -W -Wall -pedantic -fstrict-aliasing -Wstrict-aliasing -O2 -pipe -Wl,-rpath=/usr/local/lib/gcc49 -fno-strict-aliasing  -Wl,-rpath=/usr/local/lib/gcc49    -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/alf.dir/alf.cpp.o -c /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.2.0/apps/alf/alf.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/alf/alf.cpp:44:
/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]
[  1%] Linking CXX executable ../../bin/alf
cd /wrkdirs/usr/ports/biology/seqan-apps/work/.build/apps/alf && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/alf.dir/link.txt --verbose=1
/usr/local/bin/g++49   -O2 -pipe -Wl,-rpath=/usr/local/lib/gcc49 -fno-strict-aliasing  -Wl,-rpath=/usr/local/lib/gcc49 -std=c++14  -W -Wall -pedantic -fstrict-aliasing -Wstrict-aliasing -O2 -pipe -Wl,-rpath=/usr/local/lib/gcc49 -fno-strict-aliasing  -Wl,-rpath=/usr/local/lib/gcc49   -Wl,-rpath=/usr/local/lib/gcc49 -L/usr/local/lib/gcc49 CMakeFiles/alf.dir/alf.cpp.o  -o ../../bin/alf  -lpthread -lexecinfo -lelf 
//usr/lib/libexecinfo.so: undefined reference to `_Unwind_GetIP at GCC_3.0'
//usr/lib/libexecinfo.so: undefined reference to `_Unwind_Backtrace at GCC_3.3'
collect2: error: ld returned 1 exit status
*** Error code 1

Stop.
make[3]: stopped in /wrkdirs/usr/ports/biology/seqan-apps/work/.build
*** Error code 1

Stop.
make[2]: stopped in /wrkdirs/usr/ports/biology/seqan-apps/work/.build
*** Error code 1

Stop.
make[1]: stopped in /wrkdirs/usr/ports/biology/seqan-apps/work/.build
*** Error code 1

Stop.
make: stopped in /usr/ports/biology/seqan-apps


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