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Please investigate the failure and submit a PR to fix
build.

Maintainer:     free...@skysmurf.nl
Last committer: amd...@freebsd.org
Ident:          $FreeBSD: head/science/gromacs/Makefile 394419 2015-08-16 
21:31:41Z amdmi3 $
Log URL:        
http://beefy8.nyi.freebsd.org/data/head-armv6-default/p410528_s296455/logs/gromacs-5.0.6.log
Build URL:      
http://beefy8.nyi.freebsd.org/build.html?mastername=head-armv6-default&build=p410528_s296455
Log:

====>> Building science/gromacs
build started at Fri Mar 11 06:27:47 UTC 2016
port directory: /usr/ports/science/gromacs
building for: FreeBSD head-armv6-default-job-11 11.0-CURRENT FreeBSD 
11.0-CURRENT r296455 arm
maintained by: free...@skysmurf.nl
Makefile ident:      $FreeBSD: head/science/gromacs/Makefile 394419 2015-08-16 
21:31:41Z amdmi3 $
Poudriere version: 3.1.12
Host OSVERSION: 1100100
Jail OSVERSION: 1100101




!!! Jail is newer than host. (Jail: 1100101, Host: 1100100) !!!
!!! This is not supported. !!!
!!! Host kernel must be same or newer than jail. !!!
!!! Expect build failures. !!!



---Begin Environment---
SHELL=/bin/csh
UNAME_p=armv6
UNAME_m=arm
ABI_FILE=/usr/lib/crt1.o
UNAME_v=FreeBSD 11.0-CURRENT r296455
UNAME_r=11.0-CURRENT
BLOCKSIZE=K
MAIL=/var/mail/root
STATUS=1
OPSYS=FreeBSD
ARCH=armv6
LINUX_OSRELEASE=2.6.32
SAVED_TERM=screen
QEMU_EMULATING=1
MASTERMNT=/usr/local/poudriere/data/.m/head-armv6-default/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=gromacs-5.0.6
OSREL=11.0
_OSRELEASE=11.0-CURRENT
PYTHONBASE=/usr/local
OLDPWD=/
_SMP_CPUS=24
PWD=/usr/local/poudriere/data/.m/head-armv6-default/ref/.p/pool
MASTERNAME=head-armv6-default
SCRIPTPREFIX=/usr/local/share/poudriere
_JAVA_VENDOR_LIST_REGEXP=openjdk\|oracle\|sun
USER=root
HOME=/root
POUDRIERE_VERSION=3.1.12
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=1100101
---End Environment---

---Begin OPTIONS List---
===> The following configuration options are available for gromacs-5.0.6:
     ATLAS=off: Use ATLAS for BLAS and LAPACK
     FLOAT=on: Use single instead of double precision
     OPENMP=on: Parallel processing support via OpenMP
     SIMD=off: Use CPU-specific optimizations
     X11=on: X11 (graphics) support
====> MPI (Message Passing Interface) support: you can only select none or one 
of them
     MPICH2=off: Parallel processing support via MPICH2
     OPENMPI=off: Parallel processing support via Open MPI
===> Use 'make config' to modify these settings
---End OPTIONS List---

--CONFIGURE_ARGS--

--End CONFIGURE_ARGS--

--CONFIGURE_ENV--
F77="gfortran48" FC="gfortran48" FFLAGS="-O -Wl,-rpath=/usr/local/lib/gcc48" 
FCFLAGS="-Wl,-rpath=/usr/local/lib/gcc48" ac_cv_path_PERL=/usr/local/bin/perl 
ac_cv_path_PERL_PATH=/usr/local/bin/perl PKG_CONFIG=pkgconf 
XDG_DATA_HOME=/wrkdirs/usr/ports/science/gromacs/work  
XDG_CONFIG_HOME=/wrkdirs/usr/ports/science/gromacs/work  
HOME=/wrkdirs/usr/ports/science/gromacs/work TMPDIR="/tmp" SHELL=/bin/sh 
CONFIG_SHELL=/bin/sh
--End CONFIGURE_ENV--

--MAKE_ENV--
F77="gfortran48" FC="gfortran48" FFLAGS="-O -Wl,-rpath=/usr/local/lib/gcc48" 
FCFLAGS="-Wl,-rpath=/usr/local/lib/gcc48" 
XDG_DATA_HOME=/wrkdirs/usr/ports/science/gromacs/work  
XDG_CONFIG_HOME=/wrkdirs/usr/ports/science/gromacs/work  
HOME=/wrkdirs/usr/ports/science/gromacs/work TMPDIR="/tmp" NO_PIE=yes 
WITHOUT_DEBUG_FILES=yes WITHOUT_KERNEL_SYMBOLS=yes 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" PREFIX=/usr/local  
LOCALBASE=/usr/local  LIBDIR="/usr/lib"  CC="gcc48" CFLAGS="-O2 -pipe 
-mfloat-abi=softfp  -Wl,-rpath=/usr/local/lib/gcc48 -fno-strict-aliasing"  
CPP="cpp48" CPPFLAGS=""  LDFLAGS=" -Wl,-rpath=/usr/local/lib/gcc48  -L/usr/
 local/lib/gcc48 -B/usr/local/bin -L/usr/local/lib 
-Wl,-rpath=/usr/local/lib/gcc48 -L/usr/local/lib/gcc48" LIBS=""  CXX="g++48" 
CXXFLAGS="-O2 -pipe -mfloat-abi=softfp -Wl,-rpath=/usr/local/lib/gcc48 
-fno-strict-aliasing  -Wl,-rpath=/usr/local/lib/gcc48"  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--
ATLAS="@comment
"
NO_ATLAS=""
FLOAT=""
NO_FLOAT="@comment
"
OPENMP=""
NO_OPENMP="@comment
"
SIMD="@comment
"
NO_SIMD=""
X11=""
NO_X11="@comment
"
MPICH2="@comment
"
NO_MPICH2=""
OPENMPI="@comment
"
NO_OPENMPI=""
SUFFIX_D=""
SUFFIX_MPI=""
CMAKE_BUILD_TYPE="release"
GTK2_VERSION="2.10.0"
GTK3_VERSION="3.0.0"
OSREL=11.0
PREFIX=%D
LOCALBASE=/usr/local
RESETPREFIX=/usr/local
PORTDOCS=""
PORTEXAMPLES=""
LIB32DIR=lib
PERL_VERSION=5.20.3
PERL_VER=5.20
PERL5_MAN1=lib/perl5/site_perl/man/man1
PERL5_MAN3=lib/perl5/site_perl/man/man3
SITE_PERL=lib/perl5/site_perl
SITE_ARCH=lib/perl5/site_perl/mach/5.20
DOCSDIR="share/doc/gromacs"
EXAMPLESDIR="share/examples/gromacs"
DATADIR="share/gromacs"
WWWDIR="www/gromacs"
ETCDIR="etc/gromacs"
--End PLIST_SUB--

--SUB_LIST--
ATLAS="@comment
"
NO_ATLAS=""
FLOAT=""
NO_FLOAT="@comment
"
OPENMP=""
NO_OPENMP="@comment
"
SIMD="@comment
"
NO_SIMD=""
X11=""
NO_X11="@comment
"
MPICH2="@comment
"
NO_MPICH2=""
OPENMPI="@comment
"
NO_OPENMPI=""
PREFIX=/usr/local
LOCALBASE=/usr/local
DATADIR=/usr/local/share/gromacs
DOCSDIR=/usr/local/share/doc/gromacs
EXAMPLESDIR=/usr/local/share/examples/gromacs
WWWDIR=/usr/local/www/gromacs
ETCDIR=/usr/local/etc/gromacs
--End SUB_LIST--

---Begin make.conf---
CC=/nxb-bin/usr/bin/cc
CPP=/nxb-bin/usr/bin/cpp
CXX=/nxb-bin/usr/bin/c++
AS=/nxb-bin/usr/bin/as
NM=/nxb-bin/usr/bin/nm
LD=/nxb-bin/usr/bin/ld
OBJCOPY=/nxb-bin/usr/bin/objcopy
SIZE=/nxb-bin/usr/bin/size
STRIPBIN=/nxb-bin/usr/bin/strip
SED=/nxb-bin/usr/bin/sed
READELF=/nxb-bin/usr/bin/readelf
RANLIB=/nxb-bin/usr/bin/ranlib
YACC=/nxb-bin/usr/bin/yacc
NM=/nxb-bin/usr/bin/nm
MAKE=/nxb-bin/usr/bin/make
STRINGS=/nxb-bin/usr/bin/strings
AWK=/nxb-bin/usr/bin/awk
FLEX=/nxb-bin/usr/bin/flex
CC=/nxb-bin/usr/bin/cc
CPP=/nxb-bin/usr/bin/cpp
CXX=/nxb-bin/usr/bin/c++
AS=/nxb-bin/usr/bin/as
NM=/nxb-bin/usr/bin/nm
LD=/nxb-bin/usr/bin/ld
OBJCOPY=/nxb-bin/usr/bin/objcopy
SIZE=/nxb-bin/usr/bin/size
STRIPBIN=/nxb-bin/usr/bin/strip
SED=/nxb-bin/usr/bin/sed
READELF=/nxb-bin/usr/bin/readelf
RANLIB=/nxb-bin/usr/bin/ranlib
YACC=/nxb-bin/usr/bin/yacc
NM=/nxb-bin/usr/bin/nm
MAKE=/nxb-bin/usr/bin/make
<snip>
-- Performing Test CXXFLAGS_WARN
-- Performing Test CXXFLAGS_WARN - Success
-- Performing Test CXXFLAGS_WARN_EXTRA
-- Performing Test CXXFLAGS_WARN_EXTRA - Success
-- Performing Test CXXFLAGS_WARN_REL
-- Performing Test CXXFLAGS_WARN_REL - Success
-- Performing Test CXXFLAGS_EXCESS_PREC
-- Performing Test CXXFLAGS_EXCESS_PREC - Success
-- Performing Test CXXFLAGS_COPT
-- Performing Test CXXFLAGS_COPT - Success
-- Performing Test CXXFLAGS_NOINLINE
-- Performing Test CXXFLAGS_NOINLINE - Success
-- Looking for include file unistd.h
-- Looking for include file unistd.h - found
-- Looking for include file pwd.h
-- Looking for include file pwd.h - found
-- Looking for include file dirent.h
-- Looking for include file dirent.h - found
-- Looking for include file time.h
-- Looking for include file time.h - found
-- Looking for include file sys/time.h
-- Looking for include file sys/time.h - found
-- Looking for include file io.h
-- Looking for include file io.h - not found
-- Looking for include file sched.h
-- Looking for include file sched.h - found
-- Looking for include file regex.h
-- Looking for include file regex.h - found
-- Looking for posix_memalign
-- Looking for posix_memalign - found
-- Looking for memalign
-- Looking for memalign - not found
-- Looking for _aligned_malloc
-- Looking for _aligned_malloc - not found
-- Looking for gettimeofday
-- Looking for gettimeofday - found
-- Looking for fsync
-- Looking for fsync - found
-- Looking for _fileno
-- Looking for _fileno - not found
-- Looking for fileno
-- Looking for fileno - found
-- Looking for _commit
-- Looking for _commit - not found
-- Looking for sigaction
-- Looking for sigaction - found
-- Looking for sysconf
-- Looking for sysconf - found
-- Looking for rsqrt
-- Looking for rsqrt - not found
-- Looking for rsqrtf
-- Looking for rsqrtf - not found
-- Looking for sqrtf
-- Looking for sqrtf - not found
-- Looking for sqrt in m
-- Looking for sqrt in m - found
-- Looking for clock_gettime in rt
-- Looking for clock_gettime in rt - found
-- Checking for sched.h GNU affinity API
-- Performing Test sched_affinity_compile
-- Performing Test sched_affinity_compile - Failed
-- Check if the system is big endian
-- Searching 16 bit integer
-- Looking for sys/types.h
-- Looking for sys/types.h - found
-- Looking for stdint.h
-- Looking for stdint.h - found
-- Looking for stddef.h
-- Looking for stddef.h - found
-- Check size of unsigned short
-- Check size of unsigned short - done
-- Using unsigned short
-- Check if the system is big endian - little endian
-- Looking for zlibVersion in /usr/lib/libz.so
-- Looking for zlibVersion in /usr/lib/libz.so - found
-- Found LibXml2: /usr/local/lib/libxml2.so (found version "2.9.3") 
-- Looking for xmlTextWriterEndAttribute in /usr/local/lib/libxml2.so
-- Looking for xmlTextWriterEndAttribute in /usr/local/lib/libxml2.so - found
-- Looking for include file libxml/parser.h
-- Looking for include file libxml/parser.h - found
-- Looking for XOpenDisplay in 
/usr/local/lib/libX11.so;/usr/local/lib/libXext.so
-- Looking for XOpenDisplay in 
/usr/local/lib/libX11.so;/usr/local/lib/libXext.so - found
-- Looking for gethostbyname
-- Looking for gethostbyname - found
-- Looking for connect
-- Looking for connect - found
-- Looking for remove
-- Looking for remove - found
-- Looking for shmat
-- Looking for shmat - found
-- Found X11: /usr/local/lib/libX11.so
-- Looking for pthread.h
-- Looking for pthread.h - found
-- Found Threads: TRUE  
-- Looking for include file pthread.h
-- Looking for include file pthread.h - found
-- Atomic operations found
-- Performing Test PTHREAD_SETAFFINITY
-- Performing Test PTHREAD_SETAFFINITY - Failed
-- Boost version: 1.55.0
-- Checking for GCC x86 inline asm
-- Checking for GCC x86 inline asm - not supported
-- Setting build user/date/host/cpu information
-- Setting build user & time - OK
-- Checking floating point format
-- Checking floating point format - IEEE754 (LE byte, LE word)
-- Checking for 64-bit off_t
-- Checking for 64-bit off_t - present
-- Checking for fseeko/ftello
-- Checking for fseeko/ftello - present
-- Checking for SIGUSR1
-- Checking for SIGUSR1 - found
-- Checking for pipe support
-- Checking for isfinite
-- Performing Test isfinite_compile_ok
-- Performing Test isfinite_compile_ok - Success
-- Checking for isfinite - yes
-- Checking for _isfinite
-- Performing Test _isfinite_compile_ok
-- Performing Test _isfinite_compile_ok - Failed
-- Checking for _isfinite - no
-- Checking for _finite
-- Performing Test _finite_compile_ok
-- Performing Test _finite_compile_ok - Failed
-- Checking for _finite - no
-- Performing Test CXXFLAG_STD_CXX0X
-- Performing Test CXXFLAG_STD_CXX0X - Success
-- Performing Test GMX_CXX11_SUPPORTED
-- Performing Test GMX_CXX11_SUPPORTED - Success
-- Looking for C++ include regex
-- Looking for C++ include regex - not found
-- Checking for system XDR support
-- Checking for system XDR support - present
-- SIMD instructions disabled
-- Performing Test _callconv___vectorcall
-- Performing Test _callconv___vectorcall - Failed
-- Performing Test _callconv___regcall
-- Performing Test _callconv___regcall - Failed
-- Performing Test _callconv_
CMake Error: Generator: execution of make failed. Make command was: 
"/usr/bin/make" "cmTC_b3722/fast"
-- Performing Test _callconv_ - Failed
-- Checking for module 'fftw3f'
--   Found fftw3f, version 3.3.3
-- Looking for fftwf_plan_r2r_1d in /usr/local/lib/libfftw3f.so
-- Looking for fftwf_plan_r2r_1d in /usr/local/lib/libfftw3f.so - found
-- Looking for fftwf_have_simd_sse in /usr/local/lib/libfftw3f.so
-- Looking for fftwf_have_simd_sse in /usr/local/lib/libfftw3f.so - not found
-- Looking for fftwf_have_simd_sse2 in /usr/local/lib/libfftw3f.so
-- Looking for fftwf_have_simd_sse2 in /usr/local/lib/libfftw3f.so - not found
-- Looking for fftwf_have_simd_avx_128 in /usr/local/lib/libfftw3f.so
-- Looking for fftwf_have_simd_avx_128 in /usr/local/lib/libfftw3f.so - not 
found
-- Looking for fftwf_have_simd_avx2_128 in /usr/local/lib/libfftw3f.so
-- Looking for fftwf_have_simd_avx2_128 in /usr/local/lib/libfftw3f.so - not 
found
-- Looking for fftwf_have_simd_sse2 in /usr/local/lib/libfftw3f.so
-- Looking for fftwf_have_simd_sse2 in /usr/local/lib/libfftw3f.so - not found
-- Looking for fftwf_have_simd_avx in /usr/local/lib/libfftw3f.so
-- Looking for fftwf_have_simd_avx in /usr/local/lib/libfftw3f.so - not found
-- Looking for fftwf_have_simd_altivec in /usr/local/lib/libfftw3f.so
-- Looking for fftwf_have_simd_altivec in /usr/local/lib/libfftw3f.so - not 
found
-- Looking for fftwf_have_simd_neon in /usr/local/lib/libfftw3f.so
-- Looking for fftwf_have_simd_neon in /usr/local/lib/libfftw3f.so - not found
-- Looking for fftwf_have_sse2 in /usr/local/lib/libfftw3f.so
-- Looking for fftwf_have_sse2 in /usr/local/lib/libfftw3f.so - not found
-- Looking for fftwf_have_sse in /usr/local/lib/libfftw3f.so
-- Looking for fftwf_have_sse in /usr/local/lib/libfftw3f.so - not found
-- Looking for fftwf_have_altivec in /usr/local/lib/libfftw3f.so
-- Looking for fftwf_have_altivec in /usr/local/lib/libfftw3f.so - not found
-- Using external FFT library - FFTW3
-- A library with BLAS API found.
-- A library with LAPACK API found.
-- Checking for dlopen
-- Performing Test HAVE_DLOPEN
-- Performing Test HAVE_DLOPEN - Success
-- Checking for dlopen - found
-- Using dynamic plugins (e.g VMD-supported file formats)
-- Checking for suitable VMD version
-- VMD plugins not found. Path to VMD can be set with VMDDIR.
-- Using default binary suffix: ""
-- Using default library suffix: ""
-- Could NOT find Pandoc (missing:  PANDOC_EXECUTABLE) 
-- Could NOT find PythonInterp (missing:  PYTHON_EXECUTABLE) 
-- Performing Test HAS_NO_UNUSED_VARIABLE
-- Performing Test HAS_NO_UNUSED_VARIABLE - Success
-- Check if the system is big endian
-- Searching 16 bit integer
-- Using unsigned short
-- Check if the system is big endian - little endian
-- Looking for inttypes.h
-- Looking for inttypes.h - found
-- Performing Test HAS_NO_UNUSED_PARAMETER
-- Performing Test HAS_NO_UNUSED_PARAMETER - Success
-- Performing Test HAS_NO_DEPRECATED_REGISTER
-- Performing Test HAS_NO_DEPRECATED_REGISTER - Success
-- Configuring incomplete, errors occurred!
See also 
"/wrkdirs/usr/ports/science/gromacs/work/gromacs-5.0.6/CMakeFiles/CMakeOutput.log".
See also 
"/wrkdirs/usr/ports/science/gromacs/work/gromacs-5.0.6/CMakeFiles/CMakeError.log".
*** Error code 1

Stop.
make: stopped in /usr/ports/science/gromacs
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