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:     bacon4...@gmail.com
Last committer: m...@freebsd.org
Ident:          $FreeBSD: branches/2016Q3/biology/jellyfish/Makefile 412344 
2016-04-01 13:29:15Z mat $
Log URL:        
http://thunderx1.nyi.freebsd.org/data/110arm64-quarterly/422268/logs/jellyfish-2.2.4.log
Build URL:      
http://thunderx1.nyi.freebsd.org/build.html?mastername=110arm64-quarterly&build=422268
Log:

====>> Building biology/jellyfish
build started at Mon Sep 19 14:40:23 UTC 2016
port directory: /usr/ports/biology/jellyfish
building for: FreeBSD 110arm64-quarterly-job-05 11.0-RC3 FreeBSD 11.0-RC3 
r305786 arm64
maintained by: bacon4...@gmail.com
Makefile ident:      $FreeBSD: branches/2016Q3/biology/jellyfish/Makefile 
412344 2016-04-01 13:29:15Z mat $
Poudriere version: 3.1.14
Host OSVERSION: 1100121
Jail OSVERSION: 1100122




!!! Jail is newer than host. (Jail: 1100122, Host: 1100121) !!!
!!! This is not supported. !!!
!!! Host kernel must be same or newer than jail. !!!
!!! Expect build failures. !!!



---Begin Environment---
SHELL=/bin/csh
UNAME_v=FreeBSD 11.0-RC3 r305786
UNAME_r=11.0-RC3
BLOCKSIZE=K
MAIL=/var/mail/root
STATUS=1
OPSYS=FreeBSD
ARCH=aarch64
SAVED_TERM=
MASTERMNT=/usr/local/poudriere/data/.m/110arm64-quarterly/ref
UID=0
PATH=/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin
_JAVA_VERSION_LIST_REGEXP=1.6\|1.7\|1.8\|1.6+\|1.7+\|1.8+
POUDRIERE_BUILD_TYPE=bulk
PKGNAME=jellyfish-2.2.4
OSREL=11.0
_OSRELEASE=11.0-RC3
PYTHONBASE=/usr/local
OLDPWD=/
_SMP_CPUS=48
PWD=/usr/local/poudriere/data/.m/110arm64-quarterly/ref/.p/pool
MASTERNAME=110arm64-quarterly
SCRIPTPREFIX=/usr/local/share/poudriere
_JAVA_VENDOR_LIST_REGEXP=openjdk\|oracle\|sun
USER=root
HOME=/root
POUDRIERE_VERSION=3.1.14
SCRIPTPATH=/usr/local/share/poudriere/bulk.sh
CONFIGURE_MAX_CMD_LEN=262144
LIBEXECPREFIX=/usr/local/libexec/poudriere
LOCALBASE=/usr/local
PACKAGE_BUILDING=yes
_JAVA_OS_LIST_REGEXP=native\|linux
OSVERSION=1100122
---End Environment---

---Begin OPTIONS List---
---End OPTIONS List---

--CONFIGURE_ARGS--
--without-sse --prefix=/usr/local ${_LATE_CONFIGURE_ARGS}
--End CONFIGURE_ARGS--

--CONFIGURE_ENV--
MAKE=gmake PKG_CONFIG=pkgconf 
XDG_DATA_HOME=/wrkdirs/usr/ports/biology/jellyfish/work  
XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/jellyfish/work  
HOME=/wrkdirs/usr/ports/biology/jellyfish/work TMPDIR="/tmp" SHELL=/bin/sh 
CONFIG_SHELL=/bin/sh CONFIG_SITE=/usr/ports/Templates/config.site 
lt_cv_sys_max_cmd_len=262144
--End CONFIGURE_ENV--

--MAKE_ENV--
XDG_DATA_HOME=/wrkdirs/usr/ports/biology/jellyfish/work  
XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/jellyfish/work  
HOME=/wrkdirs/usr/ports/biology/jellyfish/work TMPDIR="/tmp" NO_PIE=yes 
MK_DEBUG_FILES=no MK_KERNEL_SYMBOLS=no SHELL=/bin/sh NO_LINT=YES 
PREFIX=/usr/local  LOCALBASE=/usr/local  LIBDIR="/usr/lib"  CC="cc" CFLAGS="-O2 
-pipe  -fno-strict-aliasing"  CPP="cpp" CPPFLAGS=""  LDFLAGS="" LIBS=""  
CXX="c++" CXXFLAGS="-O2 -pipe -fno-strict-aliasing "  MANPREFIX="/usr/local" 
BSD_INSTALL_PROGRAM="install  -s -m 555"  BSD_INSTALL_LIB="install  -s -m 444"  
BSD_INSTALL_SCRIPT="install  -m 555"  BSD_INSTALL_DATA="install  -m 0644"  
BSD_INSTALL_MAN="install  -m 444"
--End MAKE_ENV--

--PLIST_SUB--
OSREL=11.0
PREFIX=%D
LOCALBASE=/usr/local
RESETPREFIX=/usr/local
PORTDOCS=""
PORTEXAMPLES=""
LIB32DIR=lib
DOCSDIR="share/doc/jellyfish"
EXAMPLESDIR="share/examples/jellyfish"
DATADIR="share/jellyfish"
WWWDIR="www/jellyfish"
ETCDIR="etc/jellyfish"
--End PLIST_SUB--

--SUB_LIST--
PREFIX=/usr/local
LOCALBASE=/usr/local
DATADIR=/usr/local/share/jellyfish
DOCSDIR=/usr/local/share/doc/jellyfish
EXAMPLESDIR=/usr/local/share/examples/jellyfish
WWWDIR=/usr/local/www/jellyfish
ETCDIR=/usr/local/etc/jellyfish
--End SUB_LIST--

---Begin make.conf---
USE_PACKAGE_DEPENDS=yes
BATCH=yes
WRKDIRPREFIX=/wrkdirs
PORTSDIR=/usr/ports
PACKAGES=/packages
DISTDIR=/distfiles
#### /usr/local/etc/poudriere.d/make.conf ####
# XXX: We really need this but cannot use it while 'make checksum' does not
# try the next mirror on checksum failure.  It currently retries the same
# failed mirror and then fails rather then trying another.  It *does*
# try the next if the size is mismatched though.
#MASTER_SITE_FREEBSD=yes
DISABLE_MAKE_JOBS=poudriere
---End make.conf---
=======================<phase: check-sanity   >============================
===>  License GPLv3+ accepted by the user
===========================================================================
=======================<phase: pkg-depends    >============================
===>   jellyfish-2.2.4 depends on file: /usr/local/sbin/pkg - not found
===>   Installing existing package /packages/All/pkg-1.8.7_1.txz
[110arm64-quarterly-job-05] Installing pkg-1.8.7_1...
[110arm64-quarterly-job-05] Extracting pkg-1.8.7_1: .......... done
===>   jellyfish-2.2.4 depends on file: /usr/local/sbin/pkg - found
===>   Returning to build of jellyfish-2.2.4
===========================================================================
=======================<phase: fetch-depends  >============================
===========================================================================
=======================<phase: fetch          >============================
===>  License GPLv3+ accepted by the user
===> Fetching all distfiles required by jellyfish-2.2.4 for building
===========================================================================
=======================<phase: checksum       >============================
===>  License GPLv3+ accepted by the user
===> Fetching all distfiles required by jellyfish-2.2.4 for building
=> SHA256 Checksum OK for gmarcais-Jellyfish-v2.2.4_GH0.tar.gz.
===========================================================================
=======================<phase: extract-depends>============================
===========================================================================
=======================<phase: extract        >============================
===>  License GPLv3+ accepted by the user
===> Fetching all distfiles required by jellyfish-2.2.4 for building
===>  Extracting for jellyfish-2.2.4
=> SHA256 Checksum OK for gmarcais-Jellyfish-v2.2.4_GH0.tar.gz.
===========================================================================
=======================<phase: patch-depends  >============================
===========================================================================
=======================<phase: patch          >============================
===>  Patching for jellyfish-2.2.4
===>  Applying FreeBSD patches for jellyfish-2.2.4
===========================================================================
=======================<phase: build-depends  >============================
===>   jellyfish-2.2.4 depends on executable: yaggo - not found
===>   Installing existing package /packages/All/yaggo-1.5.9.txz
[110arm64-quarterly-job-05] Installing yaggo-1.5.9...
[110arm64-quarterly-job-05] `-- Installing ruby-2.2.5,1...
[110arm64-quarterly-job-05] |   `-- Installing libffi-3.2.1...
[110arm64-quarterly-job-05] |   | `-- Installing indexinfo-0.2.4...
[110arm64-quarterly-job-05] |   | `-- Extracting indexinfo-0.2.4: .... done
[110arm64-quarterly-job-05] |   `-- Extracting libffi-3.2.1: .......... done
[110arm64-quarterly-job-05] |   `-- Installing libyaml-0.1.6_2...
[110arm64-quarterly-job-05] |   `-- Extracting libyaml-0.1.6_2: ......... done
[110arm64-quarterly-job-05] |   `-- Installing libedit-3.1.20150325_2,1...
[110arm64-quarterly-job-05] |   `-- Extracting libedit-3.1.20150325_2,1: 
.......... done
[110arm64-quarterly-job-05] `-- Extracting ruby-2.2.5,1: .......... done
[110arm64-quarterly-job-05] Extracting yaggo-1.5.9: ...... done
Message from ruby-2.2.5,1:
====
Some of the standard commands are provided as separate ports for ease
of upgrading:

        devel/ruby-gems:        gem - RubyGems package manager
        devel/rubygem-rake:     rake - Ruby Make

And some of the standard libraries are provided as separate ports
since they require extra dependencies:

        databases/ruby-gdbm:    GDBM module

Install them as occasion demands.
====
===>   jellyfish-2.2.4 depends on executable: yaggo - found
===>   Returning to build of jellyfish-2.2.4
===>   jellyfish-2.2.4 depends on executable: autoconf-2.69 - not found
===>   Installing existing package /packages/All/autoconf-2.69_1.txz
[110arm64-quarterly-job-05] Installing autoconf-2.69_1...
[110arm64-quarterly-job-05] `-- Installing autoconf-wrapper-20131203...
[110arm64-quarterly-job-05] `-- Extracting autoconf-wrapper-20131203: ........ 
done
[110arm64-quarterly-job-05] `-- Installing perl5-5.20.3_15...
[110arm64-quarterly-job-05] `-- Extracting perl5-5.20.3_15: .......... done
[110arm64-quarterly-job-05] `-- Installing m4-1.4.17_1,1...
[110arm64-quarterly-job-05] `-- Extracting m4-1.4.17_1,1: .......... done
[110arm64-quarterly-job-05] Extracting autoconf-2.69_1: .......... done
Message from perl5-5.20.3_15:
The /usr/bin/perl symlink has been removed starting with Perl 5.20.
For shebangs, you should either use:

#!/usr/local/bin/perl

or

#!/usr/bin/env perl
<snip>
===>   Returning to build of jellyfish-2.2.4
===>   jellyfish-2.2.4 depends on executable: autoheader-2.69 - found
===>   jellyfish-2.2.4 depends on executable: autoreconf-2.69 - found
===>   jellyfish-2.2.4 depends on executable: aclocal-1.15 - not found
===>   Installing existing package /packages/All/automake-1.15_1.txz
[110arm64-quarterly-job-05] Installing automake-1.15_1...
[110arm64-quarterly-job-05] `-- Installing automake-wrapper-20131203...
[110arm64-quarterly-job-05] `-- Extracting automake-wrapper-20131203: ... done
[110arm64-quarterly-job-05] Extracting automake-1.15_1: .......... done
===>   jellyfish-2.2.4 depends on executable: aclocal-1.15 - found
===>   Returning to build of jellyfish-2.2.4
===>   jellyfish-2.2.4 depends on executable: automake-1.15 - found
===>   jellyfish-2.2.4 depends on executable: libtoolize - not found
===>   Installing existing package /packages/All/libtool-2.4.6.txz
[110arm64-quarterly-job-05] Installing libtool-2.4.6...
[110arm64-quarterly-job-05] Extracting libtool-2.4.6: .......... done
===>   jellyfish-2.2.4 depends on executable: libtoolize - found
===>   Returning to build of jellyfish-2.2.4
===>   jellyfish-2.2.4 depends on executable: gmake - not found
===>   Installing existing package /packages/All/gmake-4.2.1.txz
[110arm64-quarterly-job-05] Installing gmake-4.2.1...
[110arm64-quarterly-job-05] `-- Installing gettext-runtime-0.19.8.1...
[110arm64-quarterly-job-05] `-- Extracting gettext-runtime-0.19.8.1: .......... 
done
[110arm64-quarterly-job-05] Extracting gmake-4.2.1: .......... done
===>   jellyfish-2.2.4 depends on executable: gmake - found
===>   Returning to build of jellyfish-2.2.4
===>   jellyfish-2.2.4 depends on package: pkgconf>=0.9.10 - not found
===>   Installing existing package /packages/All/pkgconf-0.9.12_1.txz
[110arm64-quarterly-job-05] Installing pkgconf-0.9.12_1...
[110arm64-quarterly-job-05] Extracting pkgconf-0.9.12_1: ....... done
===>   jellyfish-2.2.4 depends on package: pkgconf>=0.9.10 - found
===>   Returning to build of jellyfish-2.2.4
===========================================================================
=======================<phase: lib-depends    >============================
===========================================================================
=======================<phase: configure      >============================
===>  Configuring for jellyfish-2.2.4
libtoolize: putting auxiliary files in '.'.
libtoolize: copying file './ltmain.sh'
libtoolize: putting macros in AC_CONFIG_MACRO_DIRS, 'm4'.
libtoolize: copying file 'm4/libtool.m4'
libtoolize: copying file 'm4/ltoptions.m4'
libtoolize: copying file 'm4/ltsugar.m4'
libtoolize: copying file 'm4/ltversion.m4'
libtoolize: copying file 'm4/lt~obsolete.m4'
configure.ac:8: installing './compile'
configure.ac:2: installing './config.guess'
configure.ac:2: installing './config.sub'
configure.ac:4: installing './install-sh'
configure.ac:4: installing './missing'
Makefile.am: installing './depcomp'
parallel-tests: installing './test-driver'
configure: loading site script /usr/ports/Templates/config.site
checking build system type... aarch64-portbld-freebsd11.0
checking host system type... aarch64-portbld-freebsd11.0
checking for a BSD-compatible install... /usr/bin/install -c
checking whether build environment is sane... yes
checking for a thread-safe mkdir -p... (cached) /bin/mkdir -p
checking for gawk... (cached) /usr/bin/awk
checking whether gmake sets $(MAKE)... yes
checking whether gmake supports nested variables... yes
checking whether gmake supports nested variables... (cached) yes
checking how to print strings... printf
checking for style of include used by gmake... GNU
checking for gcc... cc
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
checking for suffix of executables... 
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether cc accepts -g... yes
checking for cc option to accept ISO C89... none needed
checking whether cc understands -c and -o together... yes
checking dependency style of cc... gcc3
checking for a sed that does not truncate output... (cached) /usr/bin/sed
checking for grep that handles long lines and -e... (cached) /usr/bin/grep
checking for egrep... (cached) /usr/bin/egrep
checking for fgrep... (cached) /usr/bin/fgrep
checking for ld used by cc... /usr/bin/ld
checking if the linker (/usr/bin/ld) is GNU ld... yes
checking for BSD- or MS-compatible name lister (nm)... /usr/bin/nm
checking the name lister (/usr/bin/nm) interface... BSD nm
checking whether ln -s works... yes
checking the maximum length of command line arguments... (cached) 262144
checking how to convert aarch64-portbld-freebsd11.0 file names to 
aarch64-portbld-freebsd11.0 format... func_convert_file_noop
checking how to convert aarch64-portbld-freebsd11.0 file names to toolchain 
format... func_convert_file_noop
checking for /usr/bin/ld option to reload object files... -r
checking for objdump... no
checking how to recognize dependent libraries... pass_all
checking for dlltool... no
checking how to associate runtime and link libraries... printf %s\n
checking for ar... ar
checking for archiver @FILE support... no
checking for strip... strip
checking for ranlib... ranlib
checking command to parse /usr/bin/nm output from cc object... ok
checking for sysroot... no
checking for a working dd... /bin/dd
checking how to truncate binary pipes... /bin/dd bs=4096 count=1
checking for mt... mt
checking if mt is a manifest tool... no
checking how to run the C preprocessor... cpp
checking for ANSI C header files... (cached) yes
checking for sys/types.h... (cached) yes
checking for sys/stat.h... (cached) yes
checking for stdlib.h... (cached) yes
checking for string.h... (cached) yes
checking for memory.h... (cached) yes
checking for strings.h... (cached) yes
checking for inttypes.h... (cached) yes
checking for stdint.h... (cached) yes
checking for unistd.h... (cached) yes
checking for dlfcn.h... (cached) yes
checking for objdir... .libs
checking if cc supports -fno-rtti -fno-exceptions... yes
checking for cc option to produce PIC... -fPIC -DPIC
checking if cc PIC flag -fPIC -DPIC works... yes
checking if cc static flag -static works... yes
checking if cc supports -c -o file.o... yes
checking if cc supports -c -o file.o... (cached) yes
checking whether the cc linker (/usr/bin/ld) supports shared libraries... yes
checking whether -lc should be explicitly linked in... no
checking dynamic linker characteristics... freebsd11.0 ld.so
checking how to hardcode library paths into programs... immediate
checking whether stripping libraries is possible... yes
checking if libtool supports shared libraries... yes
checking whether to build shared libraries... yes
checking whether to build static libraries... yes
checking whether we are using the GNU C++ compiler... yes
checking whether c++ accepts -g... yes
checking dependency style of c++... gcc3
checking how to run the C++ preprocessor... c++ -E
checking for ld used by c++... /usr/bin/ld
checking if the linker (/usr/bin/ld) is GNU ld... yes
checking whether the c++ linker (/usr/bin/ld) supports shared libraries... yes
checking for c++ option to produce PIC... -fPIC -DPIC
checking if c++ PIC flag -fPIC -DPIC works... yes
checking if c++ static flag -static works... yes
checking if c++ supports -c -o file.o... yes
checking if c++ supports -c -o file.o... (cached) yes
checking whether the c++ linker (/usr/bin/ld) supports shared libraries... yes
checking dynamic linker characteristics... freebsd11.0 ld.so
checking how to hardcode library paths into programs... immediate
checking for md5sum... no
checking for md5... md5 -r
checking for yaggo... /usr/local/bin/yaggo
checking pkg-config is at least version 0.9.0... yes
checking for __int128... yes
checking for std::numeric_limits<__int128>... yes
checking for _NSGetExecutablePath... no
checking for execinfo.h... yes
checking for ext/stdio_filebuf.h... no
checking for siginfo_t.si_int... no
checking that generated files are newer than configure... done
configure: creating ./config.status
config.status: creating Makefile
config.status: creating tests/compat.sh
config.status: creating jellyfish-2.0.pc
config.status: creating config.h
config.status: executing depfiles commands
config.status: executing libtool commands
===========================================================================
=======================<phase: build          >============================
===>  Building for jellyfish-2.2.4
gmake[1]: Entering directory 
'/wrkdirs/usr/ports/biology/jellyfish/work/Jellyfish-2.2.4'
  YAGGO    sub_commands/count_main_cmdline.hpp
  YAGGO    sub_commands/info_main_cmdline.hpp
  YAGGO    sub_commands/dump_main_cmdline.hpp
  YAGGO    sub_commands/histo_main_cmdline.hpp
  YAGGO    sub_commands/stats_main_cmdline.hpp
  YAGGO    sub_commands/merge_main_cmdline.hpp
  YAGGO    sub_commands/bc_main_cmdline.hpp
  YAGGO    sub_commands/query_main_cmdline.hpp
  YAGGO    sub_commands/cite_main_cmdline.hpp
  YAGGO    sub_commands/mem_main_cmdline.hpp
  YAGGO    jellyfish/generate_sequence_cmdline.hpp
  YAGGO    unit_tests/test_main_cmdline.hpp
gmake  all-am
gmake[2]: Entering directory 
'/wrkdirs/usr/ports/biology/jellyfish/work/Jellyfish-2.2.4'
  CXX      lib/rectangular_binary_matrix.lo
In file included from lib/rectangular_binary_matrix.cc:22:
./include/jellyfish/rectangular_binary_matrix.hpp:348:17: error: variable 'res' 
is uninitialized when used within its own initialization 
[-Werror,-Wuninitialized]
    u128  res = res ^ res;
          ~~~   ^~~
./include/jellyfish/rectangular_binary_matrix.hpp:142:14: note: in 
instantiation of function template specialization 
'jellyfish::RectangularBinaryMatrix::times_128<unsigned long *>' requested here
      return times_128(v);
             ^
lib/rectangular_binary_matrix.cc:83:24: note: in instantiation of function 
template specialization 'jellyfish::RectangularBinaryMatrix::times<unsigned 
long *>' requested here
    res.get(i) = this->times(&v[0]);
                       ^
1 error generated.
gmake[2]: *** [Makefile:1626: lib/rectangular_binary_matrix.lo] Error 1
gmake[2]: Leaving directory 
'/wrkdirs/usr/ports/biology/jellyfish/work/Jellyfish-2.2.4'
gmake[1]: *** [Makefile:943: all] Error 2
gmake[1]: Leaving directory 
'/wrkdirs/usr/ports/biology/jellyfish/work/Jellyfish-2.2.4'
*** Error code 1

Stop.
make: stopped in /usr/ports/biology/jellyfish
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