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Date:      Sat, 11 Nov 2017 03:05:03 GMT
From:      pkg-fallout@FreeBSD.org
To:        pkg-fallout@FreeBSD.org
Subject:   [package - 110armv6-quarterly][biology/seqan-apps] Failed for seqan-apps-2.2.0_8 in build
Message-ID:  <201711110305.vAB353kI094745@beefy15.nyi.freebsd.org>

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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@fsfe.org
Last committer: jbeich@FreeBSD.org
Ident:          $FreeBSD: branches/2017Q4/biology/seqan-apps/Makefile 450560 2017-09-25 00:08:16Z jbeich $
Log URL:        http://beefy15.nyi.freebsd.org/data/110armv6-quarterly/453948/logs/seqan-apps-2.2.0_8.log
Build URL:      http://beefy15.nyi.freebsd.org/build.html?mastername=110armv6-quarterly&build=453948
Log:

====>> Building biology/seqan-apps
build started at Sat Nov 11 03:02:02 UTC 2017
port directory: /usr/ports/biology/seqan-apps
building for: FreeBSD 110armv6-quarterly-job-18 11.0-RELEASE-p14 FreeBSD 11.0-RELEASE-p14 1100122 arm
maintained by: h2+fbsdports@fsfe.org
Makefile ident:      $FreeBSD: branches/2017Q4/biology/seqan-apps/Makefile 450560 2017-09-25 00:08:16Z jbeich $
Poudriere version: 3.1.22
Host OSVERSION: 1200050
Jail OSVERSION: 1100122
Job Id: 18

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USER=root
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MASTERNAME=110armv6-quarterly
PWD=/usr/local/poudriere/data/.m/110armv6-quarterly/ref/.p/pool
OLDPWD=/
PKGNAME=seqan-apps-2.2.0_8
POUDRIERE_BUILD_TYPE=bulk
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--CONFIGURE_ARGS--

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--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
--End CONFIGURE_ENV--

--MAKE_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" NO_PIE=yes MK_DEBUG_FILES=no MK_KERNEL_SYMBOLS=no SHELL=/bin/sh NO_LINT=YES ADDR2LINE="/usr/local/bin/addr2line" AR="/usr/local/bin/ar" AS="/usr/local/bin/as" CPPFILT="/usr/local/bin/c++filt" GPROF="/usr/local/bin/gprof" LD="/usr/local/bin/ld" NM="/usr/local/bin/nm" OBJCOPY="/usr/local/bin/objcopy" OBJDUMP="/usr/local/bin/objdump" RANLIB="/usr/local/bin/ranlib" READELF="/usr/local/bin/readelf" SIZE="/usr/local/bin/size" STRINGS="/usr/local/bin/strings" DESTDIR=/wrkdirs/usr/ports/biology/seqan-apps/work/stage PREFIX=/usr/local  LOCALBASE=/usr/local  LIBDIR="/usr/lib"  CC="gcc6" CFLAGS="-O2 -pipe  -Wl,-rpath=/usr/local/lib/gcc6 -fno-strict-aliasing"  CPP="cpp6" CPPFLAGS=""  LDFLAGS=" -Wl,-rpath=/usr/local/lib/gcc6 -L/usr/local/lib/gcc6" LIBS=""  CXX="g++6" CXXFLAGS="-O2 -pipe -Wl,-rpath=/usr/local/lib/gcc6 -f
 no-strict-aliasing  -Wl,-rpath=/usr/local/lib/gcc6"  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"
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RM_I386=""
OSREL=11.0
PREFIX=%D
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RESETPREFIX=/usr/local
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PORTEXAMPLES=""
LIB32DIR=lib
DOCSDIR="share/doc/seqan-apps"
EXAMPLESDIR="share/examples/seqan-apps"
DATADIR="share/seqan-apps"
WWWDIR="www/seqan-apps"
ETCDIR="etc/seqan-apps"
--End PLIST_SUB--

--SUB_LIST--
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ETCDIR=/usr/local/etc/seqan-apps
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---Begin make.conf---
.sinclude "/etc/make.nxb.conf"
USE_PACKAGE_DEPENDS=yes
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PORTSDIR=/usr/ports
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MACHINE=arm
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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
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# 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=armv6
CONFIGURE_MAX_CMD_LEN=262144
OPSYS=FreeBSD
OSREL=11.0
OSVERSION=1100122
PYTHONBASE=/usr/local
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#### Misc Poudriere ####
GID=0
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--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
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umtx shared locks               (-o)  unlimited
--End resource limits--
=======================<phase: check-sanity   >============================
===>  License BSD3CLAUSE LGPL3 GPLv3 accepted by the user
===========================================================================
=======================<phase: pkg-depends    >============================
===>   seqan-apps-2.2.0_8 depends on file: /usr/local/sbin/pkg - not found
===>   Installing existing package /packages/All/pkg-1.10.1.txz
[110armv6-quarterly-job-18] Installing pkg-1.10.1...
[110armv6-quarterly-job-18] Extracting pkg-1.10.1: .......... done
===>   seqan-apps-2.2.0_8 depends on file: /usr/local/sbin/pkg - found
===>   Returning to build of seqan-apps-2.2.0_8
===========================================================================
=======================<phase: fetch-depends  >============================
===========================================================================
=======================<phase: fetch          >============================
===>  License BSD3CLAUSE LGPL3 GPLv3 accepted by the user
===> Fetching all distfiles required by seqan-apps-2.2.0_8 for building
===========================================================================
=======================<phase: checksum       >============================
===>  License BSD3CLAUSE LGPL3 GPLv3 accepted by the user
===> Fetching all distfiles required by seqan-apps-2.2.0_8 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_8 for building
===>  Extracting for seqan-apps-2.2.0_8
=> SHA256 Checksum OK for seqan-seqan-seqan-v2.2.0_GH0.tar.gz.
===========================================================================
=======================<phase: patch-depends  >============================
===========================================================================
=======================<phase: patch          >============================
===>  Patching for seqan-apps-2.2.0_8
===========================================================================
=======================<phase: build-depends  >============================
===>   seqan-apps-2.2.0_8 depends on package: boost-libs>0 - not found
===>   Installing existing package /packages/All/boost-libs-1.65.1.txz
[110armv6-quarterly-job-18] Installing boost-libs-1.65.1...
[110armv6-quarterly-job-18] `-- Installing icu-59.1,1...
<snip>
[110armv6-quarterly-job-18] `-- Extracting libarchive-3.3.1,1: .......... done
[110armv6-quarterly-job-18] `-- Installing libuv-1.14.1...
[110armv6-quarterly-job-18] `-- Extracting libuv-1.14.1: .......... done
[110armv6-quarterly-job-18] `-- Installing rhash-1.3.4...
[110armv6-quarterly-job-18] `-- Extracting rhash-1.3.4: .......... done
[110armv6-quarterly-job-18] Extracting cmake-3.9.3: .......... done
Message from ca_root_nss-3.32.1:
********************************* WARNING *********************************

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.

*********************************** 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_8 depends on file: /usr/local/bin/cmake - found
===>   Returning to build of seqan-apps-2.2.0_8
===>   seqan-apps-2.2.0_8 depends on executable: ninja - not found
===>   Installing existing package /packages/All/ninja-1.7.2,2.txz
[110armv6-quarterly-job-18] Installing ninja-1.7.2,2...
[110armv6-quarterly-job-18] `-- Installing python27-2.7.14...
[110armv6-quarterly-job-18] |   `-- Installing gettext-runtime-0.19.8.1_1...
[110armv6-quarterly-job-18] |   | `-- Installing indexinfo-0.2.6...
[110armv6-quarterly-job-18] |   | `-- Extracting indexinfo-0.2.6: .... done
[110armv6-quarterly-job-18] |   `-- Extracting gettext-runtime-0.19.8.1_1: .......... done
[110armv6-quarterly-job-18] |   `-- Installing libffi-3.2.1_1...
[110armv6-quarterly-job-18] |   `-- Extracting libffi-3.2.1_1: .......... done
[110armv6-quarterly-job-18] |   `-- Installing readline-7.0.3...
[110armv6-quarterly-job-18] |   `-- Extracting readline-7.0.3: .......... done
[110armv6-quarterly-job-18] `-- Extracting python27-2.7.14: .......... done
[110armv6-quarterly-job-18] Extracting ninja-1.7.2,2: ....... done
Message from python27-2.7.14:
===========================================================================

Note that some standard Python modules are provided as separate ports
as they require additional dependencies. They are available as:

bsddb           databases/py-bsddb
gdbm            databases/py-gdbm
sqlite3         databases/py-sqlite3
tkinter         x11-toolkits/py-tkinter

===========================================================================
===>   seqan-apps-2.2.0_8 depends on executable: ninja - found
===>   Returning to build of seqan-apps-2.2.0_8
===>   seqan-apps-2.2.0_8 depends on executable: gcc6 - not found
===>   Installing existing package /packages/All/gcc6-6.4.0_2.txz
[110armv6-quarterly-job-18] Installing gcc6-6.4.0_2...
[110armv6-quarterly-job-18] `-- Installing binutils-2.28,1...
[110armv6-quarterly-job-18] `-- Extracting binutils-2.28,1: .......... done
[110armv6-quarterly-job-18] `-- Installing gmp-6.1.2...
[110armv6-quarterly-job-18] `-- Extracting gmp-6.1.2: .......... done
[110armv6-quarterly-job-18] `-- Installing mpc-1.0.3...
[110armv6-quarterly-job-18] |   `-- Installing mpfr-3.1.6...
[110armv6-quarterly-job-18] |   `-- Extracting mpfr-3.1.6: .......... done
[110armv6-quarterly-job-18] `-- Extracting mpc-1.0.3: ...... done
[110armv6-quarterly-job-18] Extracting gcc6-6.4.0_2: .......... done
Message from gcc6-6.4.0_2:
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_8 depends on executable: gcc6 - found
===>   Returning to build of seqan-apps-2.2.0_8
===>   seqan-apps-2.2.0_8 depends on file: /usr/local/bin/as - found
===========================================================================
=======================<phase: lib-depends    >============================
===========================================================================
=======================<phase: configure      >============================
===>  Configuring for seqan-apps-2.2.0_8
===>  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 "1.2.8") 
-- Boost version: 1.65.1
-- Found PythonInterp: /usr/local/bin/python2.7 (found version "2.7.14") 
-- 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: 1.65.1
--   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: 1.65.1
-- 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_8
[1/133] /usr/local/bin/g++6  -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/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/alf/CMakeFiles/alf.dir/alf.cpp.o -MF apps/alf/CMakeFiles/alf.dir/alf.cpp.o.d -o apps/alf/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]
[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/alf/CMakeFiles/alf.dir/alf.cpp.o  -o bin/alf  -lpthread -lexecinfo -lelf && :
FAILED: bin/alf 
: && /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/alf/CMakeFiles/alf.dir/alf.cpp.o  -o bin/alf  -lpthread -lexecinfo -lelf && :
//usr/lib/libexecinfo.so: undefined reference to `_Unwind_Backtrace@GCC_3.3'
collect2: error: ld returned 1 exit status
ninja: build stopped: subcommand failed.
*** Error code 1

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



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