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Gentoo's Bugzilla – Attachment 398792 Details for
Bug 543136
sci-physics/espresso-3.3.0 - error compiling Cython file:
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emerge log
sci-physics-espresso-3.3.0-20150313-051116.log (text/plain), 232.25 KB, created by
Toralf Förster
on 2015-03-13 11:47:42 UTC
(
hide
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Description:
emerge log
Filename:
MIME Type:
Creator:
Toralf Förster
Created:
2015-03-13 11:47:42 UTC
Size:
232.25 KB
patch
obsolete
> * Package: sci-physics/espresso-3.3.0 > * Repository: gentoo > * Maintainer: ottxor@gentoo.org sci-physics@gentoo.org > * USE: X abi_x86_64 amd64 elibc_glibc fftw kernel_linux python python_targets_python2_7 tk userland_GNU > * FEATURES: preserve-libs sandbox userpriv usersandbox >>>> Unpacking source... >>>> Unpacking espresso-3.3.0.tar.gz to /var/tmp/portage/sci-physics/espresso-3.3.0/work >>>> Source unpacked in /var/tmp/portage/sci-physics/espresso-3.3.0/work >>>> Preparing source in /var/tmp/portage/sci-physics/espresso-3.3.0/work/espresso-3.3.0 ... > * Running elibtoolize in: espresso-3.3.0/ > * Applying target-nm/2.4.2 patch ... > * Running elibtoolize in: espresso-3.3.0/config/ > * Applying portage/1.2.0 patch ... > * Applying sed/1.5.6 patch ... > * Applying as-needed/2.4.2 patch ... >>>> Source prepared. >>>> Configuring source in /var/tmp/portage/sci-physics/espresso-3.3.0/work/espresso-3.3.0 ... >>>> Working in BUILD_DIR: "/var/tmp/portage/sci-physics/espresso-3.3.0/work/espresso-3.3.0_build" > * econf: updating espresso-3.3.0/config/config.guess with /usr/share/gnuconfig/config.guess > * econf: updating espresso-3.3.0/config/config.sub with /usr/share/gnuconfig/config.sub >/var/tmp/portage/sci-physics/espresso-3.3.0/work/espresso-3.3.0/configure --prefix=/usr --build=x86_64-pc-linux-gnu --host=x86_64-pc-linux-gnu --mandir=/usr/share/man --infodir=/usr/share/info --datadir=/usr/share --sysconfdir=/etc --localstatedir=/var/lib --disable-dependency-tracking --disable-silent-rules --libdir=/usr/lib64 --docdir=/usr/share/doc/espresso-3.3.0 --with-fftw --without-cuda --with-python-interface --without-mpi --with-tk --with-x >checking build system type... x86_64-pc-linux-gnu >checking host system type... x86_64-pc-linux-gnu >checking target system type... x86_64-pc-linux-gnu >checking for a BSD-compatible install... /usr/bin/install -c >checking whether build environment is sane... yes >checking for a thread-safe mkdir -p... /bin/mkdir -p >checking for gawk... gawk >checking whether make sets $(MAKE)... yes >checking how to create a ustar tar archive... gnutar >checking whether to enable maintainer-specific portions of Makefiles... no >checking whether make supports nested variables... yes >checking whether we are using development sources... no >**************************************************************** >* Checking compiler characteristics and MPI support * >**************************************************************** >checking for style of include used by make... GNU >checking whether to compile using MPI... no >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 dependency style of x86_64-pc-linux-gnu-g++... none >configure: WARNING: No MPI c++ compiler found, will use fake implementation! >checking whether x86_64-pc-linux-gnu-g++ understands -c and -o together... yes >**************************************************************** >* Checking for programs * >**************************************************************** >checking how to print strings... printf >checking for x86_64-pc-linux-gnu-gcc... x86_64-pc-linux-gnu-gcc >checking whether we are using the GNU C compiler... yes >checking whether x86_64-pc-linux-gnu-gcc accepts -g... yes >checking for x86_64-pc-linux-gnu-gcc option to accept ISO C89... none needed >checking dependency style of x86_64-pc-linux-gnu-gcc... none >checking for a sed that does not truncate output... /bin/sed >checking for grep that handles long lines and -e... /bin/grep >checking for egrep... /bin/grep -E >checking for fgrep... /bin/grep -F >checking for ld used by x86_64-pc-linux-gnu-gcc... /usr/x86_64-pc-linux-gnu/bin/ld >checking if the linker (/usr/x86_64-pc-linux-gnu/bin/ld) is GNU ld... yes >checking for BSD- or MS-compatible name lister (nm)... /usr/bin/x86_64-pc-linux-gnu-nm -B >checking the name lister (/usr/bin/x86_64-pc-linux-gnu-nm -B) interface... BSD nm >checking whether ln -s works... yes >checking the maximum length of command line arguments... 1572864 >checking whether the shell understands some XSI constructs... yes >checking whether the shell understands "+="... yes >checking how to convert x86_64-pc-linux-gnu file names to x86_64-pc-linux-gnu format... func_convert_file_noop >checking how to convert x86_64-pc-linux-gnu file names to toolchain format... func_convert_file_noop >checking for /usr/x86_64-pc-linux-gnu/bin/ld option to reload object files... -r >checking for x86_64-pc-linux-gnu-objdump... x86_64-pc-linux-gnu-objdump >checking how to recognize dependent libraries... pass_all >checking for x86_64-pc-linux-gnu-dlltool... no >checking for dlltool... no >checking how to associate runtime and link libraries... printf %s\n >checking for x86_64-pc-linux-gnu-ar... x86_64-pc-linux-gnu-ar >checking for archiver @FILE support... @ >checking for x86_64-pc-linux-gnu-strip... x86_64-pc-linux-gnu-strip >checking for x86_64-pc-linux-gnu-ranlib... x86_64-pc-linux-gnu-ranlib >checking command to parse /usr/bin/x86_64-pc-linux-gnu-nm -B output from x86_64-pc-linux-gnu-gcc object... ok >checking for sysroot... no >checking for x86_64-pc-linux-gnu-mt... no >checking for mt... no >checking if : is a manifest tool... no >checking how to run the C preprocessor... x86_64-pc-linux-gnu-gcc -E >checking for ANSI C header files... yes >checking for sys/types.h... yes >checking for sys/stat.h... yes >checking for stdlib.h... yes >checking for string.h... yes >checking for memory.h... yes >checking for strings.h... yes >checking for inttypes.h... yes >checking for stdint.h... yes >checking for unistd.h... yes >checking for dlfcn.h... yes >checking for objdir... .libs >checking if x86_64-pc-linux-gnu-gcc supports -fno-rtti -fno-exceptions... no >checking for x86_64-pc-linux-gnu-gcc option to produce PIC... -fPIC -DPIC >checking if x86_64-pc-linux-gnu-gcc PIC flag -fPIC -DPIC works... yes >checking if x86_64-pc-linux-gnu-gcc static flag -static works... yes >checking if x86_64-pc-linux-gnu-gcc supports -c -o file.o... yes >checking if x86_64-pc-linux-gnu-gcc supports -c -o file.o... (cached) yes >checking whether the x86_64-pc-linux-gnu-gcc linker (/usr/x86_64-pc-linux-gnu/bin/ld -m elf_x86_64) supports shared libraries... yes >checking whether -lc should be explicitly linked in... no >checking dynamic linker characteristics... GNU/Linux 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... no >checking how to run the C++ preprocessor... x86_64-pc-linux-gnu-g++ -E >checking for ld used by x86_64-pc-linux-gnu-g++... /usr/x86_64-pc-linux-gnu/bin/ld -m elf_x86_64 >checking if the linker (/usr/x86_64-pc-linux-gnu/bin/ld -m elf_x86_64) is GNU ld... yes >checking whether the x86_64-pc-linux-gnu-g++ linker (/usr/x86_64-pc-linux-gnu/bin/ld -m elf_x86_64) supports shared libraries... yes >checking for x86_64-pc-linux-gnu-g++ option to produce PIC... -fPIC -DPIC >checking if x86_64-pc-linux-gnu-g++ PIC flag -fPIC -DPIC works... yes >checking if x86_64-pc-linux-gnu-g++ static flag -static works... yes >checking if x86_64-pc-linux-gnu-g++ supports -c -o file.o... yes >checking if x86_64-pc-linux-gnu-g++ supports -c -o file.o... (cached) yes >checking whether the x86_64-pc-linux-gnu-g++ linker (/usr/x86_64-pc-linux-gnu/bin/ld -m elf_x86_64) supports shared libraries... yes >checking dynamic linker characteristics... (cached) GNU/Linux ld.so >checking how to hardcode library paths into programs... immediate >checking for gawk... (cached) gawk >checking for egrep... (cached) /bin/grep -E >checking whether ln -s works... yes >checking for doxygen... no >checking for dot... /usr/bin/dot >checking for pdflatex... no >checking for makeindex... no >checking for bibtex... no >**************************************************************** >* Checking for standard headers * >**************************************************************** >checking for ANSI C header files... (cached) yes >checking arpa/inet.h usability... yes >checking arpa/inet.h presence... yes >checking for arpa/inet.h... yes >checking fcntl.h usability... yes >checking fcntl.h presence... yes >checking for fcntl.h... yes >checking float.h usability... yes >checking float.h presence... yes >checking for float.h... yes >checking for inttypes.h... (cached) yes >checking limits.h usability... yes >checking limits.h presence... yes >checking for limits.h... yes >checking netdb.h usability... yes >checking netdb.h presence... yes >checking for netdb.h... yes >checking netinet/in.h usability... yes >checking netinet/in.h presence... yes >checking for netinet/in.h... yes >checking stddef.h usability... yes >checking stddef.h presence... yes >checking for stddef.h... yes >checking for stdlib.h... (cached) yes >checking for string.h... (cached) yes >checking for strings.h... (cached) yes >checking sys/file.h usability... yes >checking sys/file.h presence... yes >checking for sys/file.h... yes >checking sys/socket.h usability... yes >checking sys/socket.h presence... yes >checking for sys/socket.h... yes >checking sys/time.h usability... yes >checking sys/time.h presence... yes >checking for sys/time.h... yes >checking for unistd.h... (cached) yes >**************************************************************** >* Checking for standard functions * >**************************************************************** >checking for stdlib.h... (cached) yes >checking for GNU libc compatible malloc... yes >checking for working memcmp... yes >checking for stdlib.h... (cached) yes >checking for GNU libc compatible realloc... yes >checking sys/select.h usability... yes >checking sys/select.h presence... yes >checking for sys/select.h... yes >checking for sys/socket.h... (cached) yes >checking types of arguments for select... int,fd_set *,struct timeval * >checking for size_t... yes >checking for working strtod... yes >checking for atexit... yes >checking for floor... yes >checking for getcwd... yes >checking for gethostbyname... yes >checking for memset... yes >checking for pow... yes >checking for rint... yes >checking for select... yes >checking for socket... yes >checking for sqrt... yes >**************************************************************** >* Checking for required tools and libraries * >**************************************************************** >checking whether to use FFTW... yes >checking for library containing fftw_plan_many_dft... -lfftw3 >checking fftw3.h usability... yes >checking fftw3.h presence... yes >checking for fftw3.h... yes >checking whether to use CUDA... no >checking for nvcc... no >**************************************************************** >* Checking for Python * >**************************************************************** >checking whether /usr/bin/python2.7 version is >= 2.5... yes >checking for /usr/bin/python2.7 version... 2.7 >checking for /usr/bin/python2.7 platform... linux2 >checking for /usr/bin/python2.7 script directory... ${prefix}/lib64/python2.7/site-packages >checking for /usr/bin/python2.7 extension module directory... ${exec_prefix}/lib64/python2.7/site-packages >checking whether python -B works... yes >checking whether the python interface is wanted... yes >checking for python2.7... /usr/bin/python2.7 -B >checking for a version of Python >= '2.5'... yes >checking for python2.7-config... /usr/bin/python2.7-config >checking consistency of all components of python development environment... yes >checking for cython... /usr/bin/cython >/var/tmp/portage/sci-physics/espresso-3.3.0/work/espresso-3.3.0/configure: line 19821: test: /usr/bin/python2.7: binary operator expected >checking python2.7 module: numpy... yes >checking for numpy include path... /usr/lib64/python2.7/site-packages/numpy/core/include >**************************************************************** >* Checking for Tcl/Tk * >**************************************************************** >checking whether to build the Tcl interface... yes >checking for libtcl8.6... yes >checking for tcl.h... yes >checking whether to use Tk... yes >checking for X... libraries , headers >checking for gethostbyname... (cached) yes >checking for connect... yes >checking for remove... yes >checking for shmat... yes >checking for IceConnectionNumber in -lICE... yes >checking for libtk8.5... no >checking for libtk8.4... no >checking for libtk8.3... no >checking for libtk8.2... no >checking for libtk... yes >configure: WARNING: You are using a generic Tk version, but a defined Tcl version. This may cause problems. >Try --with-tcl=tcl to also use a generic Tcl version, which may fit better. >checking for tk.h... yes >**************************************************************** >* Other settings * >**************************************************************** >checking whether to use efence... no >checking whether the variable MYCONFIG is set... no >checking the number of available CPUs... 8 >**************************************************************** >* Creating output files * >**************************************************************** >checking that generated files are newer than configure... done >configure: creating ./config.status >config.status: creating Makefile >config.status: creating config/Makefile >config.status: creating config/myconfig-sample-header.hpp >config.status: creating src/Makefile >config.status: creating src/core/Makefile >config.status: creating src/tcl/Makefile >config.status: creating src/python/espressomd/Makefile >config.status: creating tools/Makefile >config.status: creating scripts/Makefile >config.status: creating testsuite/Makefile >config.status: creating doc/Makefile >config.status: creating doc/logo/Makefile >config.status: creating doc/ug/Makefile >config.status: creating doc/dg/Makefile >config.status: creating doc/doxygen/Makefile >config.status: creating doc/tutorials/Makefile >config.status: creating doc/tutorials/01-lennard_jones/Makefile >config.status: creating doc/tutorials/02-charged_system/Makefile >config.status: creating doc/tutorials/03-object_in_fluid/Makefile >config.status: creating doc/latexit.sh >config.status: creating testsuite/runtest.sh >config.status: creating tools/es_mpiexec >config.status: creating src/python/pypresso >config.status: creating src/acconfig.hpp >config.status: executing depfiles commands >config.status: executing libtool commands >config.status: executing myconfig-sample.hpp commands >**************************************************************** >* Configuration summary * >**************************************************************** >platform detected = x86_64-pc-linux-gnu >package version = 3.3.0 >development sources = no > >Compiler >-------- >compiler = x86_64-pc-linux-gnu-g++ >linker = /usr/x86_64-pc-linux-gnu/bin/ld -m elf_x86_64 >c++ compiler flags = -march=native -O2 -pipe >c++ preprocessor flags = >linker flags = -Wl,-O1 -Wl,--as-needed >libraries = -ltk -ltcl8.6 -lfftw3 -lm -lSM -lICE -lX11 >using debug flags = >using profiling flags = > >Libraries >--------- >FFTW = yes >efence = no > > >Tcl/Tk >------ >Tcl version = tcl8.6 >Tk version = tk > >Python >------ >python = /usr/bin/python2.7 -B >build python interface = yes >preprocessor flags = -I/usr/include/python2.7 -I/usr/include/python2.7 -fno-strict-aliasing -march=native -O2 -pipe -fwrapv -DNDEBUG -I/usr/lib64/python2.7/site-packages/numpy/core/include >linker flags = -lpython2.7 -lpthread -ldl -lutil -lm -Xlinker -export-dynamic >extra flags = -lpython2.7 -lpthread -ldl -lutil -lm >extra linker flags = > >Other settings >-------------- >config = myconfig.hpp >installation prefix = /usr >number of test tasks = 8 >mympiexec = >mpiexec = >pdflatex = no >makeindex = no >bibtex = no >doxygen = no >dot = /usr/bin/dot > >CUDA disabled or not supported. >WARNING: MPI disabled or not supported! Parallelization turned off. >>>> Source configured. >>>> Compiling source in /var/tmp/portage/sci-physics/espresso-3.3.0/work/espresso-3.3.0 ... >>>> Working in BUILD_DIR: "/var/tmp/portage/sci-physics/espresso-3.3.0/work/espresso-3.3.0_build" >make -j1 >Making all in config >make[1]: Entering directory '/var/tmp/portage/sci-physics/espresso-3.3.0/work/espresso-3.3.0_build/config' >make[1]: Nothing to be done for 'all'. >make[1]: Leaving directory '/var/tmp/portage/sci-physics/espresso-3.3.0/work/espresso-3.3.0_build/config' >Making all in src >make[1]: Entering directory '/var/tmp/portage/sci-physics/espresso-3.3.0/work/espresso-3.3.0_build/src' >make all-recursive >make[2]: Entering directory '/var/tmp/portage/sci-physics/espresso-3.3.0/work/espresso-3.3.0_build/src' >Making all in core >make[3]: Entering directory '/var/tmp/portage/sci-physics/espresso-3.3.0/work/espresso-3.3.0_build/src/core' > GEN myconfig-final.hpp <= /var/tmp/portage/sci-physics/espresso-3.3.0/work/espresso-3.3.0/src/core/myconfig-default.hpp >make all-am >make[4]: Entering directory '/var/tmp/portage/sci-physics/espresso-3.3.0/work/espresso-3.3.0_build/src/core' >/bin/sh ../../libtool --tag=CXX --mode=compile x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I/var/tmp/portage/sci-physics/espresso-3.3.0/work/espresso-3.3.0/src/core -I../../src -I/var/tmp/portage/sci-physics/espresso-3.3.0/work/espresso-3.3.0/src/core/mpifake -march=native -O2 -pipe -c -o config-features.lo /var/tmp/portage/sci-physics/espresso-3.3.0/work/espresso-3.3.0/src/core/config-features.cpp >libtool: compile: x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I/var/tmp/portage/sci-physics/espresso-3.3.0/work/espresso-3.3.0/src/core -I../../src -I/var/tmp/portage/sci-physics/espresso-3.3.0/work/espresso-3.3.0/src/core/mpifake -march=native -O2 -pipe -c /var/tmp/portage/sci-physics/espresso-3.3.0/work/espresso-3.3.0/src/core/config-features.cpp -fPIC -DPIC -o .libs/config-features.o >/bin/sh ../../libtool --tag=CXX --mode=compile x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I/var/tmp/portage/sci-physics/espresso-3.3.0/work/espresso-3.3.0/src/core -I../../src -I/var/tmp/portage/sci-physics/espresso-3.3.0/work/espresso-3.3.0/src/core/mpifake -march=native -O2 -pipe -c -o cells.lo /var/tmp/portage/sci-physics/espresso-3.3.0/work/espresso-3.3.0/src/core/cells.cpp >libtool: compile: x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I/var/tmp/portage/sci-physics/espresso-3.3.0/work/espresso-3.3.0/src/core -I../../src -I/var/tmp/portage/sci-physics/espresso-3.3.0/work/espresso-3.3.0/src/core/mpifake -march=native -O2 -pipe -c /var/tmp/portage/sci-physics/espresso-3.3.0/work/espresso-3.3.0/src/core/cells.cpp -fPIC -DPIC -o .libs/cells.o >/bin/sh ../../libtool --tag=CXX --mode=compile x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I/var/tmp/portage/sci-physics/espresso-3.3.0/work/espresso-3.3.0/src/core -I../../src -I/var/tmp/portage/sci-physics/espresso-3.3.0/work/espresso-3.3.0/src/core/mpifake -march=native -O2 -pipe -c -o collision.lo /var/tmp/portage/sci-physics/espresso-3.3.0/work/espresso-3.3.0/src/core/collision.cpp >libtool: compile: x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I/var/tmp/portage/sci-physics/espresso-3.3.0/work/espresso-3.3.0/src/core -I../../src -I/var/tmp/portage/sci-physics/espresso-3.3.0/work/espresso-3.3.0/src/core/mpifake -march=native -O2 -pipe -c /var/tmp/portage/sci-physics/espresso-3.3.0/work/espresso-3.3.0/src/core/collision.cpp -fPIC -DPIC -o .libs/collision.o >/bin/sh ../../libtool --tag=CXX --mode=compile x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I/var/tmp/portage/sci-physics/espresso-3.3.0/work/espresso-3.3.0/src/core -I../../src -I/var/tmp/portage/sci-physics/espresso-3.3.0/work/espresso-3.3.0/src/core/mpifake -march=native -O2 -pipe -c -o communication.lo /var/tmp/portage/sci-physics/espresso-3.3.0/work/espresso-3.3.0/src/core/communication.cpp >libtool: compile: x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I/var/tmp/portage/sci-physics/espresso-3.3.0/work/espresso-3.3.0/src/core -I../../src -I/var/tmp/portage/sci-physics/espresso-3.3.0/work/espresso-3.3.0/src/core/mpifake -march=native -O2 -pipe -c /var/tmp/portage/sci-physics/espresso-3.3.0/work/espresso-3.3.0/src/core/communication.cpp -fPIC -DPIC -o .libs/communication.o >/bin/sh ../../libtool --tag=CXX --mode=compile x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I/var/tmp/portage/sci-physics/espresso-3.3.0/work/espresso-3.3.0/src/core -I../../src -I/var/tmp/portage/sci-physics/espresso-3.3.0/work/espresso-3.3.0/src/core/mpifake -march=native -O2 -pipe -c -o comfixed.lo /var/tmp/portage/sci-physics/espresso-3.3.0/work/espresso-3.3.0/src/core/comfixed.cpp >libtool: compile: x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I/var/tmp/portage/sci-physics/espresso-3.3.0/work/espresso-3.3.0/src/core -I../../src 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>/bin/sh ../../libtool --tag=CXX --mode=compile x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I/var/tmp/portage/sci-physics/espresso-3.3.0/work/espresso-3.3.0/src/core -I../../src -I/var/tmp/portage/sci-physics/espresso-3.3.0/work/espresso-3.3.0/src/core/mpifake -march=native -O2 -pipe -c -o constraint.lo /var/tmp/portage/sci-physics/espresso-3.3.0/work/espresso-3.3.0/src/core/constraint.cpp >libtool: compile: x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I/var/tmp/portage/sci-physics/espresso-3.3.0/work/espresso-3.3.0/src/core -I../../src -I/var/tmp/portage/sci-physics/espresso-3.3.0/work/espresso-3.3.0/src/core/mpifake -march=native -O2 -pipe -c /var/tmp/portage/sci-physics/espresso-3.3.0/work/espresso-3.3.0/src/core/constraint.cpp -fPIC -DPIC -o .libs/constraint.o >/bin/sh ../../libtool --tag=CXX --mode=compile x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I/var/tmp/portage/sci-physics/espresso-3.3.0/work/espresso-3.3.0/src/core -I../../src 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-fPIC -DPIC -o mpifake/.libs/mpi.o >/bin/sh ../../libtool --tag=CXX --mode=link x86_64-pc-linux-gnu-g++ -march=native -O2 -pipe -Wl,-O1 -Wl,--as-needed -o libEspresso.la config-features.lo cells.lo collision.lo communication.lo comfixed.lo comforce.lo constraint.lo cuda_interface.lo debug.lo domain_decomposition.lo electrokinetics_pdb_parse.lo energy.lo external_potential.lo errorhandling.lo fft.lo fft-common.lo fft-dipolar.lo forcecap.lo forces.lo galilei.lo ghosts.lo global.lo grid.lo halo.lo iccp3m.lo imd.lo initialize.lo integrate.lo interaction_data.lo lattice.lo layered.lo lb.lo lb-boundaries.lo lbgpu.lo metadynamics.lo modes.lo molforces.lo mol_cut.lo nemd.lo nsquare.lo particle_data.lo polymer.lo pressure.lo random.lo rattle.lo reaction.lo rotation.lo specfunc.lo statistics.lo statistics_chain.lo statistics_cluster.lo statistics_correlation.lo statistics_fluid.lo statistics_molecule.lo statistics_observable.lo statistics_wallstuff.lo thermostat.lo topology.lo tuning.lo uwerr.lo verlet.lo virtual_sites.lo virtual_sites_com.lo virtual_sites_relative.lo vmdsock.lo ghmc.lo EspressoSystemInterface.lo bmhtf-nacl.lo buckingham.lo dpd.lo gaussian.lo gb.lo hat.lo hertzian.lo lj.lo ljangle.lo ljcos.lo ljcos2.lo ljgen.lo morse.lo soft_sphere.lo steppot.lo tab.lo tunable_slip.lo angle.lo angle_harmonic.lo angle_cosine.lo angle_cossquare.lo angledist.lo dihedral.lo endangledist.lo fene.lo harmonic.lo overlap.lo subt_lj.lo object-in-fluid/area_force_local.lo object-in-fluid/area_force_global.lo object-in-fluid/bending_force.lo object-in-fluid/stretching_force.lo object-in-fluid/stretchlin_force.lo object-in-fluid/volume_force.lo debye_hueckel.lo elc.lo magnetic_non_p3m_methods.lo mdlc_correction.lo maggs.lo mmm1d.lo mmm2d.lo mmm-common.lo p3m.lo p3m-common.lo p3m-dipolar.lo reaction_field.lo actor/ActorList.lo actor/HarmonicWell.lo actor/Mmm1dgpuForce.lo config-version.lo mpifake/mpi.lo -ltk -ltcl8.6 -lfftw3 -lm -lSM -lICE -lX11 >libtool: link: x86_64-pc-linux-gnu-ar cru 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.libs/statistics_molecule.o .libs/statistics_observable.o .libs/statistics_wallstuff.o .libs/thermostat.o .libs/topology.o .libs/tuning.o .libs/uwerr.o .libs/verlet.o .libs/virtual_sites.o .libs/virtual_sites_com.o .libs/virtual_sites_relative.o .libs/vmdsock.o .libs/ghmc.o .libs/EspressoSystemInterface.o .libs/bmhtf-nacl.o .libs/buckingham.o .libs/dpd.o .libs/gaussian.o .libs/gb.o .libs/hat.o .libs/hertzian.o .libs/lj.o .libs/ljangle.o .libs/ljcos.o .libs/ljcos2.o .libs/ljgen.o .libs/morse.o .libs/soft_sphere.o .libs/steppot.o .libs/tab.o .libs/tunable_slip.o .libs/angle.o .libs/angle_harmonic.o .libs/angle_cosine.o .libs/angle_cossquare.o .libs/angledist.o .libs/dihedral.o .libs/endangledist.o .libs/fene.o .libs/harmonic.o .libs/overlap.o .libs/subt_lj.o object-in-fluid/.libs/area_force_local.o object-in-fluid/.libs/area_force_global.o object-in-fluid/.libs/bending_force.o object-in-fluid/.libs/stretching_force.o object-in-fluid/.libs/stretchlin_force.o object-in-fluid/.libs/volume_force.o .libs/debye_hueckel.o .libs/elc.o .libs/magnetic_non_p3m_methods.o .libs/mdlc_correction.o .libs/maggs.o .libs/mmm1d.o .libs/mmm2d.o .libs/mmm-common.o .libs/p3m.o .libs/p3m-common.o .libs/p3m-dipolar.o .libs/reaction_field.o actor/.libs/ActorList.o actor/.libs/HarmonicWell.o actor/.libs/Mmm1dgpuForce.o .libs/config-version.o mpifake/.libs/mpi.o >libtool: link: x86_64-pc-linux-gnu-ranlib .libs/libEspresso.a >libtool: link: ( cd ".libs" && rm -f "libEspresso.la" && ln -s "../libEspresso.la" "libEspresso.la" ) >make[4]: Leaving directory '/var/tmp/portage/sci-physics/espresso-3.3.0/work/espresso-3.3.0_build/src/core' >make[3]: Leaving directory '/var/tmp/portage/sci-physics/espresso-3.3.0/work/espresso-3.3.0_build/src/core' >Making all in tcl >make[3]: Entering directory '/var/tmp/portage/sci-physics/espresso-3.3.0/work/espresso-3.3.0_build/src/tcl' >/bin/sh ../../libtool --tag=CXX --mode=compile x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. 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-I/var/tmp/portage/sci-physics/espresso-3.3.0/work/espresso-3.3.0/src -I./../core -I/var/tmp/portage/sci-physics/espresso-3.3.0/work/espresso-3.3.0/src/core/mpifake -march=native -O2 -pipe -c /var/tmp/portage/sci-physics/espresso-3.3.0/work/espresso-3.3.0/src/tcl/actor/HarmonicWell_tcl.cpp -fPIC -DPIC -o actor/.libs/HarmonicWell_tcl.o >/bin/sh ../../libtool --tag=CXX --mode=link x86_64-pc-linux-gnu-g++ -march=native -O2 -pipe -Wl,-O1 -Wl,--as-needed -o libEspressoTcl.la bin_tcl.lo binary_file_tcl.lo blockfile_tcl.lo cells_tcl.lo channels_tcl.lo collision_tcl.lo comfixed_tcl.lo comforce_tcl.lo config_tcl.lo constraint_tcl.lo domain_decomposition_tcl.lo electrokinetics_tcl.lo external_potential_tcl.lo energy_tcl.lo galilei_tcl.lo global_tcl.lo grid_tcl.lo iccp3m_tcl.lo imd_tcl.lo initialize_interpreter.lo integrate_tcl.lo interaction_data_tcl.lo lb-boundaries_tcl.lo lb_tcl.lo metadynamics_tcl.lo nemd_tcl.lo mol_cut_tcl.lo parser.lo particle_data_tcl.lo polymer_tcl.lo pressure_tcl.lo random_tcl.lo reaction_tcl.lo rattle_tcl.lo statistics_chain_tcl.lo statistics_cluster_tcl.lo statistics_correlation_tcl.lo statistics_fluid_tcl.lo statistics_observable_tcl.lo statistics_wallstuff_tcl.lo statistics_tcl.lo thermostat_tcl.lo topology_tcl.lo tuning_tcl.lo uwerr_tcl.lo virtual_sites_com_tcl.lo ghmc_tcl.lo bmhtf-nacl_tcl.lo buckingham_tcl.lo dpd_tcl.lo forcecap_tcl.lo gaussian_tcl.lo gb_tcl.lo hat_tcl.lo hertzian_tcl.lo lj_tcl.lo ljangle_tcl.lo ljcos2_tcl.lo ljcos_tcl.lo ljgen_tcl.lo morse_tcl.lo soft_sphere_tcl.lo steppot_tcl.lo tab_tcl.lo tunable_slip_tcl.lo angle_tcl.lo angle_harmonic_tcl.lo angle_cosine_tcl.lo angle_cossquare_tcl.lo angledist_tcl.lo dihedral_tcl.lo endangledist_tcl.lo fene_tcl.lo harmonic_tcl.lo overlap_tcl.lo subt_lj_tcl.lo object-in-fluid/area_force_local_tcl.lo object-in-fluid/area_force_global_tcl.lo object-in-fluid/bending_force_tcl.lo object-in-fluid/stretching_force_tcl.lo object-in-fluid/stretchlin_force_tcl.lo object-in-fluid/volume_force_tcl.lo debye_hueckel_tcl.lo elc_tcl.lo magnetic_non_p3m_methods_tcl.lo maggs_tcl.lo mmm1d_tcl.lo mmm2d_tcl.lo p3m-dipolar_tcl.lo p3m_tcl.lo reaction_field_tcl.lo mdlc_correction_tcl.lo actor/Mmm1dgpu_tcl.lo actor/HarmonicWell_tcl.lo -ltk -ltcl8.6 -lfftw3 -lm -lSM -lICE -lX11 >libtool: link: x86_64-pc-linux-gnu-ar cru .libs/libEspressoTcl.a .libs/bin_tcl.o .libs/binary_file_tcl.o .libs/blockfile_tcl.o .libs/cells_tcl.o .libs/channels_tcl.o .libs/collision_tcl.o .libs/comfixed_tcl.o .libs/comforce_tcl.o .libs/config_tcl.o .libs/constraint_tcl.o .libs/domain_decomposition_tcl.o .libs/electrokinetics_tcl.o .libs/external_potential_tcl.o .libs/energy_tcl.o .libs/galilei_tcl.o .libs/global_tcl.o .libs/grid_tcl.o .libs/iccp3m_tcl.o .libs/imd_tcl.o .libs/initialize_interpreter.o .libs/integrate_tcl.o .libs/interaction_data_tcl.o .libs/lb-boundaries_tcl.o .libs/lb_tcl.o .libs/metadynamics_tcl.o .libs/nemd_tcl.o .libs/mol_cut_tcl.o .libs/parser.o .libs/particle_data_tcl.o .libs/polymer_tcl.o .libs/pressure_tcl.o .libs/random_tcl.o .libs/reaction_tcl.o .libs/rattle_tcl.o .libs/statistics_chain_tcl.o .libs/statistics_cluster_tcl.o .libs/statistics_correlation_tcl.o .libs/statistics_fluid_tcl.o .libs/statistics_observable_tcl.o .libs/statistics_wallstuff_tcl.o .libs/statistics_tcl.o .libs/thermostat_tcl.o .libs/topology_tcl.o .libs/tuning_tcl.o .libs/uwerr_tcl.o .libs/virtual_sites_com_tcl.o .libs/ghmc_tcl.o .libs/bmhtf-nacl_tcl.o .libs/buckingham_tcl.o .libs/dpd_tcl.o .libs/forcecap_tcl.o .libs/gaussian_tcl.o .libs/gb_tcl.o .libs/hat_tcl.o .libs/hertzian_tcl.o .libs/lj_tcl.o .libs/ljangle_tcl.o .libs/ljcos2_tcl.o .libs/ljcos_tcl.o .libs/ljgen_tcl.o .libs/morse_tcl.o .libs/soft_sphere_tcl.o .libs/steppot_tcl.o .libs/tab_tcl.o .libs/tunable_slip_tcl.o .libs/angle_tcl.o .libs/angle_harmonic_tcl.o .libs/angle_cosine_tcl.o .libs/angle_cossquare_tcl.o .libs/angledist_tcl.o .libs/dihedral_tcl.o .libs/endangledist_tcl.o .libs/fene_tcl.o .libs/harmonic_tcl.o .libs/overlap_tcl.o .libs/subt_lj_tcl.o object-in-fluid/.libs/area_force_local_tcl.o object-in-fluid/.libs/area_force_global_tcl.o object-in-fluid/.libs/bending_force_tcl.o object-in-fluid/.libs/stretching_force_tcl.o object-in-fluid/.libs/stretchlin_force_tcl.o object-in-fluid/.libs/volume_force_tcl.o .libs/debye_hueckel_tcl.o .libs/elc_tcl.o .libs/magnetic_non_p3m_methods_tcl.o .libs/maggs_tcl.o .libs/mmm1d_tcl.o .libs/mmm2d_tcl.o .libs/p3m-dipolar_tcl.o .libs/p3m_tcl.o .libs/reaction_field_tcl.o .libs/mdlc_correction_tcl.o actor/.libs/Mmm1dgpu_tcl.o actor/.libs/HarmonicWell_tcl.o >libtool: link: x86_64-pc-linux-gnu-ranlib .libs/libEspressoTcl.a >libtool: link: ( cd ".libs" && rm -f "libEspressoTcl.la" && ln -s "../libEspressoTcl.la" "libEspressoTcl.la" ) >x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I/var/tmp/portage/sci-physics/espresso-3.3.0/work/espresso-3.3.0/src/tcl -I../../src -D ESPRESSO_SCRIPTS_DEFAULT=\"/usr/share/espresso/scripts\" -I/var/tmp/portage/sci-physics/espresso-3.3.0/work/espresso-3.3.0/src/core -I/var/tmp/portage/sci-physics/espresso-3.3.0/work/espresso-3.3.0/src -I./../core -I/var/tmp/portage/sci-physics/espresso-3.3.0/work/espresso-3.3.0/src/core/mpifake -march=native -O2 -pipe -c -o Espresso_install-scriptsdir.o `test -f 'scriptsdir.cpp' || echo '/var/tmp/portage/sci-physics/espresso-3.3.0/work/espresso-3.3.0/src/tcl/'`scriptsdir.cpp >x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I/var/tmp/portage/sci-physics/espresso-3.3.0/work/espresso-3.3.0/src/tcl -I../../src -D ESPRESSO_SCRIPTS_DEFAULT=\"/usr/share/espresso/scripts\" -I/var/tmp/portage/sci-physics/espresso-3.3.0/work/espresso-3.3.0/src/core -I/var/tmp/portage/sci-physics/espresso-3.3.0/work/espresso-3.3.0/src -I./../core -I/var/tmp/portage/sci-physics/espresso-3.3.0/work/espresso-3.3.0/src/core/mpifake -march=native -O2 -pipe -c -o Espresso_install-main.o `test -f 'main.cpp' || echo '/var/tmp/portage/sci-physics/espresso-3.3.0/work/espresso-3.3.0/src/tcl/'`main.cpp >/bin/sh ../../libtool --tag=CXX --mode=link x86_64-pc-linux-gnu-g++ -march=native -O2 -pipe -Wl,-O1 -Wl,--as-needed -o Espresso.install Espresso_install-scriptsdir.o Espresso_install-main.o libEspressoTcl.la ../core/libEspresso.la -ltk -ltcl8.6 -lfftw3 -lm -lSM -lICE -lX11 >libtool: link: x86_64-pc-linux-gnu-g++ -march=native -O2 -pipe -Wl,-O1 -o Espresso.install Espresso_install-scriptsdir.o Espresso_install-main.o -Wl,--as-needed ./.libs/libEspressoTcl.a ../core/.libs/libEspresso.a -ltk -ltcl8.6 -lfftw3 -lm -lSM -lICE -lX11 >x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I/var/tmp/portage/sci-physics/espresso-3.3.0/work/espresso-3.3.0/src/tcl -I../../src -D ESPRESSO_SCRIPTS_DEFAULT=\"/var/tmp/portage/sci-physics/espresso-3.3.0/work/espresso-3.3.0_build/scripts\" -I/var/tmp/portage/sci-physics/espresso-3.3.0/work/espresso-3.3.0/src/core -I/var/tmp/portage/sci-physics/espresso-3.3.0/work/espresso-3.3.0/src -I./../core -I/var/tmp/portage/sci-physics/espresso-3.3.0/work/espresso-3.3.0/src/core/mpifake -march=native -O2 -pipe -c -o Espresso-scriptsdir.o `test -f 'scriptsdir.cpp' || echo '/var/tmp/portage/sci-physics/espresso-3.3.0/work/espresso-3.3.0/src/tcl/'`scriptsdir.cpp >x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I/var/tmp/portage/sci-physics/espresso-3.3.0/work/espresso-3.3.0/src/tcl -I../../src -D ESPRESSO_SCRIPTS_DEFAULT=\"/var/tmp/portage/sci-physics/espresso-3.3.0/work/espresso-3.3.0_build/scripts\" -I/var/tmp/portage/sci-physics/espresso-3.3.0/work/espresso-3.3.0/src/core -I/var/tmp/portage/sci-physics/espresso-3.3.0/work/espresso-3.3.0/src -I./../core -I/var/tmp/portage/sci-physics/espresso-3.3.0/work/espresso-3.3.0/src/core/mpifake -march=native -O2 -pipe -c -o Espresso-main.o `test -f 'main.cpp' || echo '/var/tmp/portage/sci-physics/espresso-3.3.0/work/espresso-3.3.0/src/tcl/'`main.cpp >/bin/sh ../../libtool --tag=CXX --mode=link x86_64-pc-linux-gnu-g++ -march=native -O2 -pipe -Wl,-O1 -Wl,--as-needed -o Espresso Espresso-scriptsdir.o Espresso-main.o libEspressoTcl.la ../core/libEspresso.la -ltk -ltcl8.6 -lfftw3 -lm -lSM -lICE -lX11 >libtool: link: x86_64-pc-linux-gnu-g++ -march=native -O2 -pipe -Wl,-O1 -o Espresso Espresso-scriptsdir.o Espresso-main.o -Wl,--as-needed ./.libs/libEspressoTcl.a ../core/.libs/libEspresso.a -ltk -ltcl8.6 -lfftw3 -lm -lSM -lICE -lX11 >make[3]: Leaving directory '/var/tmp/portage/sci-physics/espresso-3.3.0/work/espresso-3.3.0_build/src/tcl' >Making all in python/espressomd >make[3]: Entering directory '/var/tmp/portage/sci-physics/espresso-3.3.0/work/espresso-3.3.0_build/src/python/espressomd' >/usr/bin/python2.7 -B /var/tmp/portage/sci-physics/espresso-3.3.0/work/espresso-3.3.0/src/python/espressomd/gen_pxiconfig.py \ > /var/tmp/portage/sci-physics/espresso-3.3.0/work/espresso-3.3.0/src/features.def gen_pxiconfig.cpp >Reading definitions from /var/tmp/portage/sci-physics/espresso-3.3.0/work/espresso-3.3.0/src/features.def... >Done. >Writing gen_pxiconfig.cpp... >Done. >/bin/sh ../../../libtool --tag=CXX --mode=link x86_64-pc-linux-gnu-g++ -march=native -O2 -pipe -lpython2.7 -lpthread -ldl -lutil -lm -Xlinker -export-dynamic -module -avoid-version -no-undefined -Wl,-O1 -Wl,--as-needed -o gen_pxiconfig -I/var/tmp/portage/sci-physics/espresso-3.3.0/work/espresso-3.3.0/src/core -I../../../src/core -I../../../src gen_pxiconfig.cpp >libtool: link: x86_64-pc-linux-gnu-g++ -march=native -O2 -pipe -Wl,-export-dynamic -Wl,-O1 -o gen_pxiconfig -I/var/tmp/portage/sci-physics/espresso-3.3.0/work/espresso-3.3.0/src/core -I../../../src/core -I../../../src gen_pxiconfig.cpp -lpython2.7 -lpthread -ldl -lutil -lm -Wl,--as-needed >./gen_pxiconfig > myconfig.pxi >make all-am >make[4]: Entering directory '/var/tmp/portage/sci-physics/espresso-3.3.0/work/espresso-3.3.0_build/src/python/espressomd' >x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I/var/tmp/portage/sci-physics/espresso-3.3.0/work/espresso-3.3.0/src/python/espressomd -I../../../src -I/usr/include/python2.7 -I/usr/include/python2.7 -fno-strict-aliasing -march=native -O2 -pipe -fwrapv -DNDEBUG -I/usr/lib64/python2.7/site-packages/numpy/core/include -I/var/tmp/portage/sci-physics/espresso-3.3.0/work/espresso-3.3.0/src -I/var/tmp/portage/sci-physics/espresso-3.3.0/work/espresso-3.3.0/src/core -I../../../src/core -I/var/tmp/portage/sci-physics/espresso-3.3.0/work/espresso-3.3.0/src/core/mpifake -march=native -O2 -pipe -c -o dummy.o /var/tmp/portage/sci-physics/espresso-3.3.0/work/espresso-3.3.0/src/python/espressomd/dummy.cpp >/bin/sh ../../../libtool --tag=CXX --mode=link x86_64-pc-linux-gnu-g++ -march=native -O2 -pipe -lpython2.7 -lpthread -ldl -lutil -lm -Xlinker -export-dynamic -module -avoid-version -no-undefined -Wl,-O1 -Wl,--as-needed -o dummy dummy.o ../../../src/core/libEspresso.la -ltk -ltcl8.6 -lfftw3 -lm -lSM -lICE -lX11 >libtool: link: x86_64-pc-linux-gnu-g++ -march=native -O2 -pipe -Wl,-export-dynamic -Wl,-O1 -o dummy dummy.o -lpython2.7 -lpthread -ldl -lutil -Wl,--as-needed ../../../src/core/.libs/libEspresso.a -ltk -ltcl8.6 -lfftw3 -lm -lSM -lICE -lX11 >for f in __init__.py; do \ > if test ! -f $f || test /var/tmp/portage/sci-physics/espresso-3.3.0/work/espresso-3.3.0/src/python/espressomd/$f -nt $f; then \ > /usr/bin/install -c -D /var/tmp/portage/sci-physics/espresso-3.3.0/work/espresso-3.3.0/src/python/espressomd/$f $f; \ > fi ; \ > done >cython -I . /var/tmp/portage/sci-physics/espresso-3.3.0/work/espresso-3.3.0/src/python/espressomd/System.pyx -o System.cpp >/bin/sh ../../../libtool --tag=CXX --mode=compile x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I/var/tmp/portage/sci-physics/espresso-3.3.0/work/espresso-3.3.0/src/python/espressomd -I../../../src -I/usr/include/python2.7 -I/usr/include/python2.7 -fno-strict-aliasing -march=native -O2 -pipe -fwrapv -DNDEBUG -I/usr/lib64/python2.7/site-packages/numpy/core/include -I/var/tmp/portage/sci-physics/espresso-3.3.0/work/espresso-3.3.0/src -I/var/tmp/portage/sci-physics/espresso-3.3.0/work/espresso-3.3.0/src/core -I../../../src/core -I/var/tmp/portage/sci-physics/espresso-3.3.0/work/espresso-3.3.0/src/core/mpifake -march=native -O2 -pipe -c -o System.lo System.cpp >libtool: compile: x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I/var/tmp/portage/sci-physics/espresso-3.3.0/work/espresso-3.3.0/src/python/espressomd -I../../../src -I/usr/include/python2.7 -I/usr/include/python2.7 -fno-strict-aliasing -march=native -O2 -pipe -fwrapv -DNDEBUG -I/usr/lib64/python2.7/site-packages/numpy/core/include -I/var/tmp/portage/sci-physics/espresso-3.3.0/work/espresso-3.3.0/src -I/var/tmp/portage/sci-physics/espresso-3.3.0/work/espresso-3.3.0/src/core -I../../../src/core -I/var/tmp/portage/sci-physics/espresso-3.3.0/work/espresso-3.3.0/src/core/mpifake -march=native -O2 -pipe -c System.cpp -fPIC -DPIC -o .libs/System.o >In file included from /usr/lib64/python2.7/site-packages/numpy/core/include/numpy/ndarraytypes.h:1804:0, > from /usr/lib64/python2.7/site-packages/numpy/core/include/numpy/ndarrayobject.h:17, > from /usr/lib64/python2.7/site-packages/numpy/core/include/numpy/arrayobject.h:4, > from System.cpp:250: >/usr/lib64/python2.7/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:15:2: warning: #warning "Using deprecated NumPy API, disable it by " "#defining NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp] > #warning "Using deprecated NumPy API, disable it by " \ > ^ >/bin/sh ../../../libtool --tag=CXX --mode=link x86_64-pc-linux-gnu-g++ -march=native -O2 -pipe -lpython2.7 -lpthread -ldl -lutil -lm -Xlinker -export-dynamic -module -avoid-version -no-undefined -Wl,-O1 -Wl,--as-needed -o System.la -rpath /usr/lib64/python2.7/site-packages System.lo ../../../src/core/libEspresso.la -ltk -ltcl8.6 -lfftw3 -lm -lSM -lICE -lX11 >libtool: link: x86_64-pc-linux-gnu-g++ -fPIC -DPIC -shared -nostdlib /usr/lib/gcc/x86_64-pc-linux-gnu/4.8.3/../../../../lib64/crti.o /usr/lib/gcc/x86_64-pc-linux-gnu/4.8.3/crtbeginS.o .libs/System.o -Wl,--whole-archive ../../../src/core/.libs/libEspresso.a -Wl,--no-whole-archive -lpython2.7 -lpthread -ldl -lutil -Wl,--as-needed -ltk -ltcl8.6 -lfftw3 -lSM -lICE -lX11 -L/usr/lib/gcc/x86_64-pc-linux-gnu/4.8.3 -L/usr/lib/gcc/x86_64-pc-linux-gnu/4.8.3/../../../../lib64 -L/lib/../lib64 -L/usr/lib/../lib64 -L/usr/lib/gcc/x86_64-pc-linux-gnu/4.8.3/../../../../x86_64-pc-linux-gnu/lib -L/usr/lib/gcc/x86_64-pc-linux-gnu/4.8.3/../../.. -lstdc++ -lm -lc -lgcc_s /usr/lib/gcc/x86_64-pc-linux-gnu/4.8.3/crtendS.o /usr/lib/gcc/x86_64-pc-linux-gnu/4.8.3/../../../../lib64/crtn.o -march=native -O2 -Wl,-export-dynamic -Wl,-O1 -Wl,-soname -Wl,System.so -o .libs/System.so >libtool: link: ( cd ".libs" && rm -f "System.la" && ln -s "../System.la" "System.la" ) >test -L System.so || ln -s .libs/System.so System.so >cython -I . /var/tmp/portage/sci-physics/espresso-3.3.0/work/espresso-3.3.0/src/python/espressomd/particle_data.pyx -o particle_data.cpp > >Error compiling Cython file: >------------------------------------------------------------ >... > def __cinit__(self, _id): ># utils.init_intlist(self.particleData.el) > utils.init_intlist(&(self.particleData.bl)) > self.id=_id > > cdef int updateParticleData(self) except -1: > ^ >------------------------------------------------------------ > >/var/tmp/portage/sci-physics/espresso-3.3.0/work/espresso-3.3.0/src/python/espressomd/particle_data.pyx:32:7: Signature not compatible with previous declaration > >Error compiling Cython file: >------------------------------------------------------------ >... > >cdef class ParticleHandle(object): > cdef public int id > cdef bint valid > cdef Particle particleData > cdef int updateParticleData(self) > ^ >------------------------------------------------------------ > >/var/tmp/portage/sci-physics/espresso-3.3.0/work/espresso-3.3.0/src/python/espressomd/particle_data.pxd:186:29: Previous declaration is here >warning: /var/tmp/portage/sci-physics/espresso-3.3.0/work/espresso-3.3.0/src/python/espressomd/particle_data.pyx:164:47: local variable 'x' referenced before assignment >warning: /var/tmp/portage/sci-physics/espresso-3.3.0/work/espresso-3.3.0/src/python/espressomd/particle_data.pyx:165:16: local variable 'x' referenced before assignment >warning: /var/tmp/portage/sci-physics/espresso-3.3.0/work/espresso-3.3.0/src/python/espressomd/particle_data.pyx:264:43: local variable 'x' referenced before assignment >warning: /var/tmp/portage/sci-physics/espresso-3.3.0/work/espresso-3.3.0/src/python/espressomd/particle_data.pyx:265:16: local variable 'x' referenced before assignment >Makefile:694: recipe for target 'particle_data.cpp' failed >make[4]: *** [particle_data.cpp] Error 1 >make[4]: Leaving directory '/var/tmp/portage/sci-physics/espresso-3.3.0/work/espresso-3.3.0_build/src/python/espressomd' >Makefile:370: recipe for target 'all' failed >make[3]: *** [all] Error 2 >make[3]: Leaving directory '/var/tmp/portage/sci-physics/espresso-3.3.0/work/espresso-3.3.0_build/src/python/espressomd' >Makefile:384: recipe for target 'all-recursive' failed >make[2]: *** [all-recursive] Error 1 >make[2]: Leaving directory '/var/tmp/portage/sci-physics/espresso-3.3.0/work/espresso-3.3.0_build/src' >Makefile:322: recipe for target 'all' failed >make[1]: *** [all] Error 2 >make[1]: Leaving directory '/var/tmp/portage/sci-physics/espresso-3.3.0/work/espresso-3.3.0_build/src' >Makefile:410: recipe for target 'all-recursive' failed >make: *** [all-recursive] Error 1 > * ERROR: sci-physics/espresso-3.3.0::gentoo failed (compile phase): > * emake failed > * > * If you need support, post the output of `emerge --info '=sci-physics/espresso-3.3.0::gentoo'`, > * the complete build log and the output of `emerge -pqv '=sci-physics/espresso-3.3.0::gentoo'`. > * The complete build log is located at '/var/log/portage/sci-physics:espresso-3.3.0:20150313-051116.log'. > * For convenience, a symlink to the build log is located at '/var/tmp/portage/sci-physics/espresso-3.3.0/temp/build.log'. > * The ebuild environment file is located at '/var/tmp/portage/sci-physics/espresso-3.3.0/temp/environment'. > * Working directory: '/var/tmp/portage/sci-physics/espresso-3.3.0/work/espresso-3.3.0_build' > * S: '/var/tmp/portage/sci-physics/espresso-3.3.0/work/espresso-3.3.0'
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