[package - head-armv6-default][science/gromacs] Failed for gromacs-5.0.6 in configure
pkg-fallout at FreeBSD.org
pkg-fallout at FreeBSD.org
Tue Sep 8 07:37:11 UTC 2015
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: freebsd at skysmurf.nl
Last committer: amdmi3 at 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/p396164_s287479/logs/gromacs-5.0.6.log
Build URL: http://beefy8.nyi.freebsd.org/build.html?mastername=head-armv6-default&build=p396164_s287479
Log:
====>> Building science/gromacs
build started at Tue Sep 8 07:27:20 UTC 2015
port directory: /usr/ports/science/gromacs
building for: FreeBSD head-armv6-default-job-20 11.0-CURRENT FreeBSD 11.0-CURRENT r287479 arm
maintained by: freebsd at skysmurf.nl
Makefile ident: $FreeBSD: head/science/gromacs/Makefile 394419 2015-08-16 21:31:41Z amdmi3 $
Poudriere version: 3.1.7
Host OSVERSION: 1100077
Jail OSVERSION: 1100079
!!! Jail is newer than host. (Jail: 1100079, Host: 1100077) !!!
!!! 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
OSVERSION=1100079
UNAME_v=FreeBSD 11.0-CURRENT r287479
UNAME_r=11.0-CURRENT
LC_COLLATE=C
BLOCKSIZE=K
MAIL=/var/mail/root
STATUS=1
SAVED_TERM=screen
MASTERMNT=/usr/local/poudriere/data/.m/head-armv6-default/ref
PATH=/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin
POUDRIERE_BUILD_TYPE=bulk
PKGNAME=gromacs-5.0.6
OLDPWD=/
PWD=/usr/local/poudriere/data/.m/head-armv6-default/ref/.p/pool
MASTERNAME=head-armv6-default
SCRIPTPREFIX=/usr/local/share/poudriere
USER=root
HOME=/root
POUDRIERE_VERSION=3.1.7
SCRIPTPATH=/usr/local/share/poudriere/bulk.sh
LIBEXECPREFIX=/usr/local/libexec/poudriere
LOCALBASE=/usr/local
PACKAGE_BUILDING=yes
---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 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"
OSREL=11.0
PREFIX=%D
LOCALBASE=/usr/local
RESETPREFIX=/usr/local
PORTDOCS=""
PORTEXAMPLES=""
LIB32DIR=lib
GTK2_VERSION="2.10.0"
GTK3_VERSION="3.0.0"
PERL_VERSION=5.20.2
PERL_VER=5.20
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
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
<snip>
-- Check for working C compiler: /usr/local/bin/gcc48 -- works
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Detecting C compile features
-- Detecting C compile features - done
-- Check for working CXX compiler: /usr/local/bin/g++48
-- Check for working CXX compiler: /usr/local/bin/g++48 -- works
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Detecting CXX compile features
-- Detecting CXX compile features - done
-- Looking for NVIDIA GPUs present in the system
-- Could not detect NVIDIA GPUs
-- No compatible CUDA toolkit found (v4.0+), disabling native GPU acceleration
-- Try OpenMP C flag = [-fopenmp]
-- Performing Test OpenMP_FLAG_DETECTED
-- Performing Test OpenMP_FLAG_DETECTED - Success
-- Try OpenMP CXX flag = [-fopenmp]
-- Performing Test OpenMP_FLAG_DETECTED
-- Performing Test OpenMP_FLAG_DETECTED - Success
-- Found OpenMP: -fopenmp
-- Performing Test CFLAGS_WARN
-- Performing Test CFLAGS_WARN - Success
-- Performing Test CFLAGS_WARN_EXTRA
-- Performing Test CFLAGS_WARN_EXTRA - Success
-- Performing Test CFLAGS_WARN_REL
-- Performing Test CFLAGS_WARN_REL - Success
-- Performing Test CFLAGS_WARN_UNINIT
-- Performing Test CFLAGS_WARN_UNINIT - Success
-- Performing Test CFLAGS_EXCESS_PREC
-- Performing Test CFLAGS_EXCESS_PREC - Success
-- Performing Test CFLAGS_COPT
-- Performing Test CFLAGS_COPT - Success
-- Performing Test CFLAGS_NOINLINE
-- Performing Test CFLAGS_NOINLINE - Success
-- 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
CMake Error: Generator: execution of make failed. Make command was: "/usr/bin/make" "cmTryCompileExec3541826762/fast"
-- Looking for include file sched.h - not 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 "2.9.2")
-- 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 include file pthread.h
-- Looking for include file 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_
-- Performing Test _callconv_ - Success
-- checking for module 'fftw3f'
-- found fftw3f, version 3.3.3
-- Looking for fftwf_plan_r2r_1d in /usr/local/lib/libfftw3f.so
CMake Error: Generator: execution of make failed. Make command was: "/usr/bin/make" "cmTryCompileExec2410214199/fast"
-- Looking for fftwf_plan_r2r_1d in /usr/local/lib/libfftw3f.so - not found
CMake Error at cmake/FindFFTW.cmake:100 (message):
Could not find fftwf_plan_r2r_1d in /usr/local/lib/libfftw3f.so, take a
look at the error message in
/wrkdirs/usr/ports/science/gromacs/work/gromacs-5.0.6/CMakeFiles/CMakeError.log
to find out what went wrong. If you are using a static lib (.a) make sure
you have specified all dependencies of fftw3f in FFTWF_LIBRARY by hand
(e.g. -DFFTWF_LIBRARY='/path/to/libfftw3f.so;/path/to/libm.so') !
Call Stack (most recent call first):
cmake/gmxManageFFTLibraries.cmake:77 (find_package)
CMakeLists.txt:751 (include)
-- 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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