[MacPorts] #29189: Gromacs 4.5.1 installation error
MacPorts
noreply at macports.org
Sun Apr 17 15:22:40 PDT 2011
#29189: Gromacs 4.5.1 installation error
---------------------------------+------------------------------------------
Reporter: jimmymisc@… | Owner: macports-tickets@…
Type: defect | Status: new
Priority: High | Milestone:
Component: ports | Version: 1.9.2
Keywords: | Port:
---------------------------------+------------------------------------------
Hello all,
I have installed all the dependencies, but when I executed :
sudo port install gromacs, I obtained this error (log attached). Can
someone help please ?
Thank you
version:1
:debug:main epoch: in tree: 0 installed: 0
:debug:main pkgconfig 0.25_2 exists in the ports tree
:debug:main pkgconfig 0.25_2 is the latest installed
:debug:main pkgconfig 0.25_2 is active
:debug:main Merging existing variants '' into variants
:debug:main new fully merged portvariants:
:debug:main Changing to port directory:
/opt/local/var/macports/sources/rsync.macports.org/release/ports/devel/pkgconfig
:debug:main OS darwin/10.6.0 (Mac OS X 10.6) arch i386
:debug:main org.macports.load registered provides 'load', a pre-existing
procedure. Target override will not be provided
:debug:main org.macports.unload registered provides 'unload', a pre-
existing procedure. Target override will not be provided
:debug:main org.macports.distfiles registered provides 'distfiles', a pre-
existing procedure. Target override will not be provided
:debug:main adding the default universal variant
:debug:main Reading variant descriptions from
/opt/local/var/macports/sources/rsync.macports.org/release/ports/_resources/port1.0/variant_descriptions.conf
:debug:main No need to upgrade! pkgconfig 0.25_2 >= pkgconfig 0.25_2
:debug:main epoch: in tree: 1 installed: 1
:debug:main gcc44 4.4.5_0 exists in the ports tree
:debug:main gcc44 4.4.5_0 is the latest installed
:debug:main gcc44 4.4.5_0 is active
:debug:main Merging existing variants '' into variants
:debug:main new fully merged portvariants:
:debug:main Changing to port directory:
/opt/local/var/macports/sources/rsync.macports.org/release/ports/lang/gcc44
:debug:main OS darwin/10.6.0 (Mac OS X 10.6) arch i386
:debug:main org.macports.load registered provides 'load', a pre-existing
procedure. Target override will not be provided
:debug:main org.macports.unload registered provides 'unload', a pre-
existing procedure. Target override will not be provided
:debug:main org.macports.distfiles registered provides 'distfiles', a pre-
existing procedure. Target override will not be provided
:debug:main Reading variant descriptions from
/opt/local/var/macports/sources/rsync.macports.org/release/ports/_resources/port1.0/variant_descriptions.conf
:debug:main universal variant already exists, so not adding the default
one
:debug:main No need to upgrade! gcc44 4.4.5_0 >= gcc44 4.4.5_0
:debug:main epoch: in tree: 0 installed: 0
:debug:main gmp 5.0.1_1 exists in the ports tree
:debug:main gmp 5.0.1_1 is the latest installed
:debug:main gmp 5.0.1_1 is active
:debug:main Merging existing variants '' into variants
:debug:main new fully merged portvariants:
:debug:main Changing to port directory:
/opt/local/var/macports/sources/rsync.macports.org/release/ports/devel/gmp
:debug:main OS darwin/10.6.0 (Mac OS X 10.6) arch i386
:debug:main org.macports.load registered provides 'load', a pre-existing
procedure. Target override will not be provided
:debug:main org.macports.unload registered provides 'unload', a pre-
existing procedure. Target override will not be provided
:debug:main org.macports.distfiles registered provides 'distfiles', a pre-
existing procedure. Target override will not be provided
:debug:main Using group file
/opt/local/var/macports/sources/rsync.macports.org/release/ports/_resources/port1.0/group/muniversal-1.0.tcl
:debug:main Reading variant descriptions from
/opt/local/var/macports/sources/rsync.macports.org/release/ports/_resources/port1.0/variant_descriptions.conf
:debug:main universal variant already exists, so not adding the default
one
:debug:main No need to upgrade! gmp 5.0.1_1 >= gmp 5.0.1_1
:debug:main epoch: in tree: 0 installed: 0
:debug:main mpfr 3.0.1_0 exists in the ports tree
:debug:main mpfr 3.0.1_0 is the latest installed
:debug:main mpfr 3.0.1_0 is active
:debug:main Merging existing variants '' into variants
:debug:main new fully merged portvariants:
:debug:main Changing to port directory:
/opt/local/var/macports/sources/rsync.macports.org/release/ports/devel/mpfr
:debug:main OS darwin/10.6.0 (Mac OS X 10.6) arch i386
:debug:main org.macports.load registered provides 'load', a pre-existing
procedure. Target override will not be provided
:debug:main org.macports.unload registered provides 'unload', a pre-
existing procedure. Target override will not be provided
:debug:main org.macports.distfiles registered provides 'distfiles', a pre-
existing procedure. Target override will not be provided
:debug:main Using group file
/opt/local/var/macports/sources/rsync.macports.org/release/ports/_resources/port1.0/group/muniversal-1.0.tcl
:debug:main Reading variant descriptions from
/opt/local/var/macports/sources/rsync.macports.org/release/ports/_resources/port1.0/variant_descriptions.conf
:debug:main universal variant already exists, so not adding the default
one
:debug:main No need to upgrade! mpfr 3.0.1_0 >= mpfr 3.0.1_0
:debug:main epoch: in tree: 0 installed: 0
:debug:main libiconv 1.13.1_0 exists in the ports tree
:debug:main libiconv 1.13.1_0 is the latest installed
:debug:main libiconv 1.13.1_0 is active
:debug:main Merging existing variants '' into variants
:debug:main new fully merged portvariants:
:debug:main Changing to port directory:
/opt/local/var/macports/sources/rsync.macports.org/release/ports/textproc/libiconv
:debug:main OS darwin/10.6.0 (Mac OS X 10.6) arch i386
:debug:main org.macports.load registered provides 'load', a pre-existing
procedure. Target override will not be provided
:debug:main org.macports.unload registered provides 'unload', a pre-
existing procedure. Target override will not be provided
:debug:main org.macports.distfiles registered provides 'distfiles', a pre-
existing procedure. Target override will not be provided
:debug:main Using group file
/opt/local/var/macports/sources/rsync.macports.org/release/ports/_resources/port1.0/group/muniversal-1.0.tcl
:debug:main Reading variant descriptions from
/opt/local/var/macports/sources/rsync.macports.org/release/ports/_resources/port1.0/variant_descriptions.conf
:debug:main universal variant already exists, so not adding the default
one
:debug:main No need to upgrade! libiconv 1.13.1_0 >= libiconv 1.13.1_0
:msg:main ---> Computing dependencies for gromacs:info:main .:debug:main
Searching for dependency: pkgconfig
:debug:main Found Dependency: receipt exists for pkgconfig
:debug:main Searching for dependency: gcc44
:debug:main Found Dependency: receipt exists for gcc44
:msg:main
:debug:main Executing org.macports.main (gromacs)
:debug:main Skipping completed org.macports.fetch (gromacs)
:debug:main Skipping completed org.macports.checksum (gromacs)
:debug:main Skipping completed org.macports.extract (gromacs)
:debug:main Skipping completed org.macports.patch (gromacs)
:msg:main ---> Configuring gromacs
:debug:main Using compiler 'MacPorts gcc 4.4'
:debug:configure configure phase started at Sun Apr 17 18:17:12 EDT 2011
:debug:configure Executing org.macports.configure (gromacs)
:debug:configure Environment: CPATH='/opt/local/include' CFLAGS='-pipe -O2
-m64' CPPFLAGS='-I/opt/local/include' CXXFLAGS='-pipe -O2 -m64'
LIBRARY_PATH='/opt/local/lib' MACOSX_DEPLOYMENT_TARGET='10.6'
CXX='/opt/local/bin/g++-mp-4.4'
CC_PRINT_OPTIONS_FILE='/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_ports_science_gromacs/work/.CC_PRINT_OPTIONS'
F90FLAGS='-pipe -O2 -m64' LDFLAGS='-L/opt/local/lib' FCFLAGS='-pipe -O2
-m64' OBJC='/opt/local/bin/gcc-mp-4.4' INSTALL='/usr/bin/install -c'
F90='/opt/local/bin/gfortran-mp-4.4' FC='/opt/local/bin/gfortran-mp-4.4'
FFLAGS='-pipe -O2 -m64' OBJCFLAGS='-pipe -O2 -m64' F77='/opt/local/bin
/gfortran-mp-4.4' CC_PRINT_OPTIONS='YES' CC='/opt/local/bin/gcc-mp-4.4'
:debug:configure Assembled command: 'cd
"/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_ports_science_gromacs/work/gromacs-4.5.1"
&& ./configure --prefix=/opt/local --bindir=/opt/local/lib/gromacs/bin
--enable-shared --with-x'
:info:configure checking build system type... x86_64-apple-darwin10.6.0
:info:configure checking host system type... x86_64-apple-darwin10.6.0
:info:configure checking for a BSD-compatible install... /usr/bin/install
-c
:info:configure checking whether build environment is sane... yes
:info:configure checking for a thread-safe mkdir -p... config/install-sh
-c -d
:info:configure checking for gawk... no
:info:configure checking for mawk... no
:info:configure checking for nawk... no
:info:configure checking for awk... awk
:info:configure checking whether make sets $(MAKE)... yes
:info:configure checking how to create a ustar tar archive... gnutar
:info:configure checking for C compiler default output file name... a.out
:info:configure checking whether the C compiler works... yes
:info:configure checking whether we are cross compiling... no
:info:configure checking for suffix of executables...
:info:configure checking for suffix of object files... o
:info:configure checking whether we are using the GNU C compiler... yes
:info:configure checking whether /opt/local/bin/gcc-mp-4.4 accepts -g...
yes
:info:configure checking for /opt/local/bin/gcc-mp-4.4 option to accept
ISO C89... none needed
:info:configure checking for style of include used by make... GNU
:info:configure checking dependency style of /opt/local/bin/gcc-mp-4.4...
gcc3
:info:configure checking dependency style of /opt/local/bin/gcc-mp-4.4...
gcc3
:info:configure checking how to run the C preprocessor... /opt/local/bin
/gcc-mp-4.4 -E
:info:configure checking for grep that handles long lines and -e...
/usr/bin/grep
:info:configure checking for egrep... /usr/bin/grep -E
:info:configure checking whether ln -s works... yes
:info:configure checking whether /opt/local/bin/gcc-mp-4.4 accepts -O3...
yes
:info:configure checking whether /opt/local/bin/gcc-mp-4.4 accepts
-msse2... yes
:info:configure checking whether /opt/local/bin/gcc-mp-4.4 accepts
-funroll-all-loops... yes
:info:configure checking whether /opt/local/bin/gcc-mp-4.4 accepts
-std=gnu99... yes
:info:configure checking whether /opt/local/bin/gcc-mp-4.4 accepts
-fexcess-precision=fast... no
:info:configure ******************************************
:info:configure * Using CFLAGS from environment variable *
:info:configure ******************************************
:info:configure checking for ANSI C header files... yes
:info:configure checking for sys/types.h... yes
:info:configure checking for sys/stat.h... yes
:info:configure checking for stdlib.h... yes
:info:configure checking for string.h... yes
:info:configure checking for memory.h... yes
:info:configure checking for strings.h... yes
:info:configure checking for inttypes.h... yes
:info:configure checking for stdint.h... yes
:info:configure checking for unistd.h... yes
:info:configure checking for unistd.h... (cached) yes
:info:configure checking sys/time.h usability... yes
:info:configure checking sys/time.h presence... yes
:info:configure checking for sys/time.h... yes
:info:configure checking sched.h usability... yes
:info:configure checking sched.h presence... yes
:info:configure checking for sched.h... yes
:info:configure checking for sysconf... yes
:info:configure checking for the pthreads library -lpthreads... no
:info:configure checking whether pthreads work without any flags... yes
:info:configure checking for joinable pthread attribute...
PTHREAD_CREATE_JOINABLE
:info:configure checking if more special flags are required for
pthreads... no
:info:configure checking for cc_r... /opt/local/bin/gcc-mp-4.4
:info:configure checking if atomic operations are supported... yes
:info:configure checking whether byte ordering is bigendian... no
:info:configure checking that size_t can hold pointers... yes
:info:configure checking for SIGUSR1... yes
:info:configure checking for pipes... yes
:info:configure checking floating-point format... IEEE754 (little-endian
byte and word order)
:info:configure checking whether ln -s works... yes
:info:configure checking whether make sets $(MAKE)... (cached) yes
:info:configure checking for a sed that does not truncate output...
/usr/bin/sed
:info:configure checking for ld used by /opt/local/bin/gcc-mp-4.4 ...
/usr/bin/ld
:info:configure checking if the linker (/usr/bin/ld) is GNU ld... no
:info:configure checking for /usr/bin/ld option to reload object files...
-r
:info:configure checking for BSD-compatible nm... /usr/bin/nm
:info:configure checking how to recognise dependent libraries... pass_all
:info:configure checking dlfcn.h usability... yes
:info:configure checking dlfcn.h presence... yes
:info:configure checking for dlfcn.h... yes
:info:configure checking whether we are using the GNU C++ compiler... yes
:info:configure checking whether /opt/local/bin/g++-mp-4.4 accepts -g...
yes
:info:configure checking dependency style of /opt/local/bin/g++-mp-4.4...
gcc3
:info:configure checking how to run the C++ preprocessor...
/opt/local/bin/g++-mp-4.4 -E
:info:configure checking the maximum length of command line arguments...
196608
:info:configure checking command to parse /usr/bin/nm output from
/opt/local/bin/gcc-mp-4.4 object... ok
:info:configure checking for objdir... .libs
:info:configure checking for ar... ar
:info:configure checking for ranlib... ranlib
:info:configure checking for strip... strip
:info:configure checking if /opt/local/bin/gcc-mp-4.4 supports -fno-rtti
-fno-exceptions... no
:info:configure checking for /opt/local/bin/gcc-mp-4.4 option to produce
PIC... -fno-common
:info:configure checking if /opt/local/bin/gcc-mp-4.4 PIC flag -fno-
common works... yes
:info:configure checking if /opt/local/bin/gcc-mp-4.4 static flag -static
works... no
:info:configure checking if /opt/local/bin/gcc-mp-4.4 supports -c -o
file.o... yes
:info:configure checking whether the /opt/local/bin/gcc-mp-4.4 linker
(/usr/bin/ld) supports shared libraries... yes
:info:configure checking dynamic linker characteristics... darwin10.6.0
dyld
:info:configure checking how to hardcode library paths into programs...
immediate
:info:configure checking whether stripping libraries is possible... yes
:info:configure checking if libtool supports shared libraries... yes
:info:configure checking whether to build shared libraries... yes
:info:configure checking whether to build static libraries... yes
:info:configure configure: creating libtool
:info:configure appending configuration tag "CXX" to libtool
:info:configure checking for ld used by /opt/local/bin/g++-mp-4.4...
/usr/bin/ld
:info:configure checking if the linker (/usr/bin/ld) is GNU ld... no
:info:configure checking whether the /opt/local/bin/g++-mp-4.4 linker
(/usr/bin/ld) supports shared libraries... yes
:info:configure checking for /opt/local/bin/g++-mp-4.4 option to produce
PIC... -fno-common
:info:configure checking if /opt/local/bin/g++-mp-4.4 PIC flag -fno-common
works... yes
:info:configure checking if /opt/local/bin/g++-mp-4.4 static flag -static
works... no
:info:configure checking if /opt/local/bin/g++-mp-4.4 supports -c -o
file.o... yes
:info:configure checking whether the /opt/local/bin/g++-mp-4.4 linker
(/usr/bin/ld) supports shared libraries... yes
:info:configure checking dynamic linker characteristics... darwin10.6.0
dyld
:info:configure checking how to hardcode library paths into programs...
immediate
:info:configure appending configuration tag "F77" to libtool
:info:configure checking if libtool supports shared libraries... yes
:info:configure checking whether to build shared libraries... yes
:info:configure checking whether to build static libraries... yes
:info:configure checking for /opt/local/bin/gfortran-mp-4.4 option to
produce PIC... -fno-common
:info:configure checking if /opt/local/bin/gfortran-mp-4.4 PIC flag -fno-
common works... yes
:info:configure checking if /opt/local/bin/gfortran-mp-4.4 static flag
-static works... no
:info:configure checking if /opt/local/bin/gfortran-mp-4.4 supports -c -o
file.o... yes
:info:configure checking whether the /opt/local/bin/gfortran-mp-4.4 linker
(/usr/bin/ld) supports shared libraries... yes
:info:configure checking dynamic linker characteristics... darwin10.6.0
dyld
:info:configure checking how to hardcode library paths into programs...
immediate
:info:configure checking for special C compiler options needed for large
files... no
:info:configure checking for _FILE_OFFSET_BITS value needed for large
files... no
:info:configure checking for _LARGEFILE_SOURCE value needed for large
files... no
:info:configure checking for sqrt in -lm... yes
:info:configure checking for fftw3.h... configure: error: Cannot find the
default external FFT library (fftw3).
:info:configure Other alternatives are 'fftw2', or 'mkl' for Intel MKL.
:info:configure You are STRONGLY recommended to use one of these - fftw is
free.
:info:configure
:info:configure Use CPPFLAGS and LDFLAGS if the library is installed in a
:info:configure non-standard location. (see FAQ at http://www.gromacs.org)
:info:configure
:info:configure If you dont care about performance you can also specify
'fftpack'
:info:configure to use a slower set of FFTs built into Gromacs.
:info:configure (Just install FFTW3 unless you really know what you are
doing).
:info:configure
:info:configure shell command " cd
"/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_ports_science_gromacs/work/gromacs-4.5.1"
&& ./configure --prefix=/opt/local --bindir=/opt/local/lib/gromacs/bin
--enable-shared --with-x " returned error 1
:error:configure Target org.macports.configure returned: configure
failure: shell command failed (see log for details)
:debug:configure Backtrace: configure failure: shell command failed (see
log for details)
while executing
"$procedure $targetname"
:info:configure Warning: the following items did not execute (for
gromacs): org.macports.activate org.macports.configure org.macports.build
org.macports.destroot org.macports.install
:notice:configure Log for gromacs is at:
/opt/local/var/macports/logs/_opt_local_var_macports_sources_rsync.macports.org_release_ports_science_gromacs/main.log
--
Ticket URL: <https://trac.macports.org/ticket/29189>
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