=> Bootstrap dependency digest>=20010302: found digest-20121220 => Checksum SHA1 OK for bigdft-1.6.0.tar.gz => Checksum RMD160 OK for bigdft-1.6.0.tar.gz ===> Installing dependencies for bigdft-1.6.0 ========================================================================== The following variables will affect the build process of this package, bigdft-1.6.0. Their current value is shown below: * PYTHON_VERSION_DEFAULT = 27 Based on these variables, the following variables have been set: * PYPACKAGE = python27 You may want to abort the process now with CTRL-C and change their value before continuing. Be sure to run `/usr/bin/make clean' after the changes. ========================================================================== => Tool dependency bash-[0-9]*: found bash-4.2nb2 => Tool dependency gmake>=3.81: found gmake-3.82nb7 => Tool dependency pkg-config>=0.25: found pkg-config-0.28 => Tool dependency checkperms>=1.1: found checkperms-1.11 => Full dependency blas>=1.0nb3: found blas-1.1nb2 => Full dependency lapack>=3.1.1: found lapack-3.1.1nb4 => Full dependency python27>=2.7.1nb2: found python27-2.7.5 => Full dependency g95>=0.91: found g95-0.93nb2 ===> Overriding tools for bigdft-1.6.0 ===> Extracting for bigdft-1.6.0 ===> Patching for bigdft-1.6.0 ===> Creating toolchain wrappers for bigdft-1.6.0 ===> Configuring for bigdft-1.6.0 => Modifying GNU configure scripts to avoid --recheck => Replacing config-guess with pkgsrc versions => Replacing config-sub with pkgsrc versions => Replacing install-sh with pkgsrc version => Adding run-time search paths to pkg-config files. => Checking for portability problems in extracted files checking for a BSD-compatible install... /usr/bin/install -c -o kristerw -g wheel checking whether build environment is sane... yes checking for a thread-safe mkdir -p... config/install-sh -c -d checking for gawk... /usr/bin/awk checking whether make sets $(MAKE)... yes checking for x86_64--netbsd-gcc... gcc checking whether the C compiler works... yes checking for C compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether we are using the GNU C compiler... yes checking whether gcc accepts -g... yes checking for gcc option to accept ISO C89... none needed checking for style of include used by make... GNU checking dependency style of gcc... gcc3 checking whether we are using the GNU C++ compiler... yes checking whether c++ accepts -g... yes checking dependency style of c++... gcc3 checking whether gcc and cc understand -c and -o together... yes checking for x86_64--netbsd-xlf90... g95 checking whether we are using the GNU Fortran compiler... yes checking whether g95 accepts -g... yes checking for x86_64--netbsd-g77... g95 checking whether we are using the GNU Fortran 77 compiler... yes checking whether g95 accepts -g... yes checking for Fortran flag to compile .f90 files... none checking how to get verbose linking output from g95... -v checking for Fortran libraries of g95... -L/scratch/wip/bigdft/work/.buildlink/lib -L/usr/pkg/bin/../lib/gcc-lib/x86_64--netbsd/4.1.2/ -L/usr/pkg/bin/../lib/gcc-lib/x86_64--netbsd/4.1.2 -L/usr/pkg/lib/gcc-lib/x86_64--netbsd/4.1.2/ -L/lib// -L/usr/pkg/bin/../lib/gcc-lib/x86_64--netbsd/4.1.2/// -L/usr/pkg/lib/gcc-lib/x86_64--netbsd/4.1.2/// -L/usr/lib// -R/usr/pkg/lib -lf95 -lm checking for dummy main to link with Fortran libraries... none checking for Fortran name-mangling scheme... lower case, underscore, extra underscore checking for flush(6) in Fortran.... test: ==: unexpected operator test: ==: unexpected operator test: ==: unexpected operator test: ==: unexpected operator yes checking for preprocessor option flag.... test: ==: unexpected operator -D checking for get_command_argument() in Fortran.... test: ==: unexpected operator test: ==: unexpected operator yes checking for 1D pointer structure in Fortran... 1 7 checking for 2D pointer structure in Fortran... 1 10 checking for 3D pointer structure in Fortran... 1 13 checking for 4D pointer structure in Fortran... 1 16 checking for 5D pointer structure in Fortran... 1 19 checking for module output in Fortran... module.mod checking for x86_64--netbsd-ranlib... no checking for ranlib... ranlib checking for x86_64--netbsd-ar... no checking for ar... ar checking for debugging options... no checking for memory limit in GB... undefined checking for convolution optimisation... yes checking for minima hopping... no checking for pseudo generation... no checking for GPU computing with CUDA libraries... no checking for OpenCL support... no test: ==: unexpected operator checking for archive_read_data_block in -larchive... yes checking for strndup... yes checking for config_init in -lconfig++... no checking for BigDFT library build... yes checking for BigDFT binaries build... yes checking for dcopy in -lblas... yes checking for dsysv in -llapack... yes checking for LIBXC... no checking time.h usability... yes checking time.h presence... no configure: WARNING: time.h: accepted by the compiler, rejected by the preprocessor! configure: WARNING: time.h: proceeding with the compiler's result checking for time.h... yes checking for clock_gettime in -lrt... yes checking for clock_gettime... yes checking for pdflatex... no checking for doxygen... no configure: creating ./config.status config.status: creating Makefile config.status: creating bigdft.pc config.status: creating libABINIT/src/Makefile config.status: creating config/Doxyfile config.status: creating src/bigdft-tool config.status: creating src/Makefile config.status: creating src/modules/Makefile config.status: creating src/modules/bigdft_cst.h config.status: creating src/modules/configure.inc config.status: creating src/PSolver/Makefile config.status: creating src/CUDA/Makefile config.status: creating src/OpenCL/Makefile config.status: creating src/convolutions-c/Makefile config.status: creating src/art/Makefile config.status: creating src/tools/Makefile config.status: creating src/tools/bader/Makefile config.status: creating utils/Makefile config.status: creating utils/PSPfiles/Makefile config.status: creating pseudo/Makefile config.status: creating pseudo/src/Makefile config.status: creating pseudo/tests/Makefile config.status: creating doc/Makefile config.status: creating tests/Makefile config.status: creating tests/libs/Makefile config.status: creating tests/libs/fft/Makefile config.status: creating tests/libs/PSolver/Makefile config.status: creating tests/libs/OP2P/Makefile config.status: creating tests/libs/xc/Makefile config.status: creating tests/libs/OpenCL/Makefile config.status: creating tests/libs/CUDA/Makefile config.status: creating tests/libs/IO-wf/Makefile config.status: creating tests/libs/ftypes/Makefile config.status: creating tests/libs/psp/Makefile config.status: creating tests/DFT/Makefile config.status: creating tests/overDFT/Makefile config.status: creating tests/tutorials/Makefile config.status: creating config.h config.status: executing depfiles commands === configuring in libxc-1.1.0 (/scratch/wip/bigdft/work/bigdft-1.6.0/libxc-1.1.0) configure: running /bin/sh ./configure --disable-option-checking '--prefix=/usr/pkg' '--disable-mpi' '--disable-internal-libxc' '--with-archives' '--with-blas' '--with-lapack' '--build=x86_64--netbsd' '--host=x86_64--netbsd' '--mandir=/usr/pkg/man' 'build_alias=x86_64--netbsd' 'host_alias=x86_64--netbsd' 'CC=gcc' 'CFLAGS=-O2 -I/usr/include -I/usr/pkg/include' 'LDFLAGS=-L/usr/lib -Wl,-R/usr/lib -L/usr/pkg/lib -Wl,-R/usr/pkg/lib' 'LIBS=' 'CPPFLAGS=-I/usr/include -I/usr/pkg/include' 'CXX=c++' 'CXXFLAGS=-O2 -I/usr/include -I/usr/pkg/include' 'FC=g95' 'F77=g95' 'FFLAGS=-O' 'PKG_CONFIG=/scratch/wip/bigdft/work/.tools/bin/pkg-config' --cache-file=/dev/null --srcdir=. checking for a BSD-compatible install... /usr/bin/install -c -o kristerw -g wheel checking whether build environment is sane... yes checking for a thread-safe mkdir -p... ./install-sh -c -d checking for gawk... /usr/bin/awk checking whether make sets $(MAKE)... yes checking build system type... x86_64--netbsd checking host system type... x86_64--netbsd checking for style of include used by make... GNU checking for x86_64--netbsd-gcc... gcc checking whether the C compiler works... yes checking for C compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether we are using the GNU C compiler... yes checking whether gcc accepts -g... yes checking for gcc option to accept ISO C89... none needed checking dependency style of gcc... gcc3 checking for a sed that does not truncate output... /usr/bin/sed checking for grep that handles long lines and -e... (cached) /usr/bin/grep checking for egrep... (cached) /usr/bin/egrep checking for fgrep... /usr/bin/grep -F checking for ld used by gcc... /scratch/wip/bigdft/work/.wrapper/bin/ld checking if the linker (/scratch/wip/bigdft/work/.wrapper/bin/ld) is GNU ld... yes checking for BSD- or MS-compatible name lister (nm)... /usr/bin/nm -B checking the name lister (/usr/bin/nm -B) interface... BSD nm checking whether ln -s works... yes checking the maximum length of command line arguments... 196608 checking whether the shell understands some XSI constructs... yes checking whether the shell understands "+="... no checking for /scratch/wip/bigdft/work/.wrapper/bin/ld option to reload object files... -r checking for x86_64--netbsd-objdump... no checking for objdump... objdump checking how to recognize dependent libraries... match_pattern /lib[^/]+(\.so|_pic\.a)$ checking for x86_64--netbsd-ar... no checking for ar... ar checking for x86_64--netbsd-strip... no checking for strip... strip checking for x86_64--netbsd-ranlib... no checking for ranlib... ranlib checking command to parse /usr/bin/nm -B output from gcc object... ok checking how to run the C preprocessor... 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 gcc supports -fno-rtti -fno-exceptions... no checking for gcc option to produce PIC... -fPIC -DPIC checking if gcc PIC flag -fPIC -DPIC works... yes checking if gcc static flag -static works... yes checking if gcc supports -c -o file.o... rm: conftest*: No such file or directory yes checking if gcc supports -c -o file.o... (cached) yes checking whether the gcc linker (/scratch/wip/bigdft/work/.wrapper/bin/ld) supports shared libraries... yes checking dynamic linker characteristics... NetBSD ld.elf_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... no checking whether to build static libraries... yes checking for x86_64--netbsd-gcc... (cached) gcc checking whether we are using the GNU C compiler... (cached) yes checking whether gcc accepts -g... (cached) yes checking for gcc option to accept ISO C89... (cached) none needed checking dependency style of gcc... (cached) gcc3 checking whether gcc and cc understand -c and -o together... yes checking for inline... inline checking for ANSI C header files... (cached) yes checking for working alloca.h... no checking for alloca... yes checking size of void*... 8 checking for sqrtf in -lm... yes checking for cbrt in -lm... yes checking for cbrtf in -lm... yes checking for x86_64--netbsd-xlf90... g95 checking whether we are using the GNU Fortran compiler... yes checking whether g95 accepts -g... yes checking for x86_64--netbsd-gfortran... (cached) g95 checking whether we are using the GNU Fortran compiler... (cached) yes checking whether g95 accepts -g... (cached) yes checking if libtool supports shared libraries... yes checking whether to build shared libraries... no checking whether to build static libraries... yes checking for g95 option to produce PIC... -fPIC checking if g95 PIC flag -fPIC works... yes checking if g95 static flag -static works... yes checking if g95 supports -c -o file.o... rm: conftest*: No such file or directory yes checking if g95 supports -c -o file.o... (cached) yes checking whether the g95 linker (/scratch/wip/bigdft/work/.wrapper/bin/ld) supports shared libraries... Warning (116): Reading file as free form yes checking dynamic linker characteristics... Warning (116): Reading file as free form NetBSD (a.out) ld.so checking how to hardcode library paths into programs... immediate checking for Fortran flag to compile .f90 files... none configure: Using FCFLAGS="-pipe -O3 -funroll-loops -ffast-math" checking how to get verbose linking output from g95... -v checking for Fortran libraries of g95... -L/scratch/wip/bigdft/work/.buildlink/lib -L/usr/pkg/bin/../lib/gcc-lib/x86_64--netbsd/4.1.2/ -L/usr/pkg/bin/../lib/gcc-lib/x86_64--netbsd/4.1.2 -L/usr/pkg/lib/gcc-lib/x86_64--netbsd/4.1.2/ -L/lib// -L/usr/pkg/bin/../lib/gcc-lib/x86_64--netbsd/4.1.2/// -L/usr/pkg/lib/gcc-lib/x86_64--netbsd/4.1.2/// -L/usr/lib// -R/usr/pkg/lib -lf95 -lm checking for dummy main to link with Fortran libraries... none checking for Fortran name-mangling scheme... lower case, underscore, extra underscore checking whether the compiler accepts very long lines... no checking whether the compiler accepts "line-number" lines cast by the preprocessor... no checking fortran 90 modules extension... mod checking for the size of a Fortran integer... 4 bytes checking for which C type corresponds to Fortran integer... int configure: creating ./config.status config.status: creating Makefile config.status: creating src/Makefile config.status: creating testsuite/Makefile config.status: creating build/Makefile config.status: creating build/libxc.pc config.status: creating build/libxc.spec config.status: creating config.h config.status: executing depfiles commands config.status: executing libtool commands rm: libtoolT: No such file or directory === configuring in S_GPU (/scratch/wip/bigdft/work/bigdft-1.6.0/S_GPU) configure: running /bin/sh ./configure --disable-option-checking '--prefix=/usr/pkg' '--disable-mpi' '--disable-internal-libxc' '--with-archives' '--with-blas' '--with-lapack' '--build=x86_64--netbsd' '--host=x86_64--netbsd' '--mandir=/usr/pkg/man' 'build_alias=x86_64--netbsd' 'host_alias=x86_64--netbsd' 'CC=gcc' 'CFLAGS=-O2 -I/usr/include -I/usr/pkg/include' 'LDFLAGS=-L/usr/lib -Wl,-R/usr/lib -L/usr/pkg/lib -Wl,-R/usr/pkg/lib' 'LIBS=' 'CPPFLAGS=-I/usr/include -I/usr/pkg/include' 'CXX=c++' 'CXXFLAGS=-O2 -I/usr/include -I/usr/pkg/include' 'FC=g95' 'F77=g95' 'FFLAGS=-O' 'PKG_CONFIG=/scratch/wip/bigdft/work/.tools/bin/pkg-config' --cache-file=/dev/null --srcdir=. checking whether the C++ compiler works... yes checking for C++ compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether we are using the GNU C++ compiler... yes checking whether c++ accepts -g... yes checking for x86_64--netbsd-gcc... gcc checking whether we are using the GNU C compiler... yes checking whether gcc accepts -g... yes checking for gcc option to accept ISO C89... none needed checking for a BSD-compatible install... /usr/bin/install -c -o kristerw -g wheel checking build system type... x86_64--netbsd checking host system type... x86_64--netbsd checking for a sed that does not truncate output... /usr/bin/sed checking for grep that handles long lines and -e... (cached) /usr/bin/grep checking for egrep... (cached) /usr/bin/egrep checking for fgrep... /usr/bin/grep -F checking for ld used by gcc... /scratch/wip/bigdft/work/.wrapper/bin/ld checking if the linker (/scratch/wip/bigdft/work/.wrapper/bin/ld) is GNU ld... yes checking for BSD- or MS-compatible name lister (nm)... /usr/bin/nm -B checking the name lister (/usr/bin/nm -B) interface... BSD nm checking whether ln -s works... yes checking the maximum length of command line arguments... 196608 checking whether the shell understands some XSI constructs... yes checking whether the shell understands "+="... no checking for /scratch/wip/bigdft/work/.wrapper/bin/ld option to reload object files... -r checking for x86_64--netbsd-objdump... no checking for objdump... objdump checking how to recognize dependent libraries... match_pattern /lib[^/]+(\.so|_pic\.a)$ checking for x86_64--netbsd-ar... no checking for ar... ar checking for x86_64--netbsd-strip... no checking for strip... strip checking for x86_64--netbsd-ranlib... no checking for ranlib... ranlib checking command to parse /usr/bin/nm -B output from gcc object... ok checking how to run the C preprocessor... 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 whether we are using the GNU C++ compiler... (cached) yes checking whether c++ accepts -g... (cached) yes checking how to run the C++ preprocessor... c++ -E checking for objdir... .libs checking if gcc supports -fno-rtti -fno-exceptions... no checking for gcc option to produce PIC... -fPIC -DPIC checking if gcc PIC flag -fPIC -DPIC works... yes checking if gcc static flag -static works... yes checking if gcc supports -c -o file.o... rm: conftest*: No such file or directory yes checking if gcc supports -c -o file.o... (cached) yes checking whether the gcc linker (/scratch/wip/bigdft/work/.wrapper/bin/ld) supports shared libraries... yes checking whether -lc should be explicitly linked in... rm: conftest*: No such file or directory no checking dynamic linker characteristics... NetBSD ld.elf_so checking how to hardcode library paths into programs... immediate checking whether stripping libraries is possible... yes checking if libtool supports shared libraries... yes checking whether to build shared libraries... yes checking whether to build static libraries... yes checking for ld used by c++... /scratch/wip/bigdft/work/.wrapper/bin/ld checking if the linker (/scratch/wip/bigdft/work/.wrapper/bin/ld) is GNU ld... yes checking whether the c++ linker (/scratch/wip/bigdft/work/.wrapper/bin/ld) supports shared libraries... yes checking for c++ option to produce PIC... -fPIC -DPIC checking if c++ PIC flag -fPIC -DPIC works... yes checking if c++ static flag -static works... yes checking if c++ supports -c -o file.o... rm: conftest*: No such file or directory yes checking if c++ supports -c -o file.o... (cached) yes checking whether the c++ linker (/scratch/wip/bigdft/work/.wrapper/bin/ld) supports shared libraries... yes checking dynamic linker characteristics... NetBSD ld.elf_so checking how to hardcode library paths into programs... immediate 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 sys/socket.h usability... yes checking sys/socket.h presence... yes checking for sys/socket.h... yes checking for unistd.h... (cached) yes checking for stdbool.h that conforms to C99... yes checking for _Bool... yes checking for inline... inline checking for size_t... yes checking for stdlib.h... (cached) yes checking for GNU libc compatible malloc... yes checking whether strerror_r is declared... yes checking for strerror_r... yes checking whether strerror_r returns char *... no checking for bzero... yes checking for gethostname... yes checking for socket... yes checking for python... /usr/pkg/bin/python2.7 checking python2.7 module: os... yes checking python2.7 module: sys... yes checking whether build environment is sane... yes checking for a thread-safe mkdir -p... ./install-sh -c -d checking for gawk... /usr/bin/awk checking whether make sets $(MAKE)... yes checking for style of include used by make... GNU checking dependency style of gcc... gcc3 checking dependency style of c++... gcc3 checking for nvcc... no configure: WARNING: CUDA compiler not found. Use --with-cuda-path or --with-cuda-path-bin or check your CUDA installation. checking whether to build documentation for this library... no checking if trace is enabled or not... no checking if verbose is enabled or not... no configure: creating ./config.status config.status: creating Makefile config.status: creating src/Makefile config.status: creating src/CUDA/Makefile config.status: creating examples/Makefile config.status: creating examples/c/Makefile config.status: creating examples/c/simple/Makefile config.status: creating examples/c/add_array/Makefile config.status: creating examples/fortran/Makefile config.status: creating examples/fortran/add_array/Makefile config.status: creating examples/c/simple/Makefile.standalone config.status: creating examples/c/add_array/Makefile.standalone config.status: creating examples/fortran/add_array/Makefile.standalone config.status: creating config.h config.status: executing libtool commands rm: libtoolT: No such file or directory config.status: executing depfiles commands Basics: C compiler: gcc C flags: CXX compiler: c++ CXX flags: -O2 -I/usr/include -I/usr/pkg/include Linker flags: -L/usr/lib -Wl,-R/usr/lib -L/usr/pkg/lib -Wl,-R/usr/pkg/lib Linked libraries: NVidia Cuda Compiler: NVCC flags: -g -O3 -DHAVE_CONFIG_H -I. -I.. -arch sm_13 NVCC C Compiler: Cuda emulation: no Trace functions: no Verbose: no Installation paths: Source code location: . Prefix: /usr/pkg Exec prefix: ${prefix} Binaries: ${exec_prefix}/bin Static libraries: ${exec_prefix}/lib BigDFT configure summary: ======================== Basics: Fortran90 compiler: g95 Fortran90 compiler name: Fortran90 flags: -g -O2 Fortran77 compiler: g95 Fortran77 flags: -O Linker flags: -L/usr/lib -Wl,-R/usr/lib -L/usr/pkg/lib -Wl,-R/usr/pkg/lib -L$(top_builddir)/libABINIT/src Linked libraries: $(top_builddir)/src/libbigdft.a -labinit $(top_builddir)/src/libdft_common.a -llapack -lblas -L/lib -larchive -lrt Build: Library ABINIT: yes Library BigDFT: yes Main binaries (cluster...):yes Minima hopping binary: no atom and pseudo binaries: no User documentation: no Devel. documentation: no / no Options: Debug version: no With MPI: no | include dir.: -I$(top_builddir)/src/modules | linker flags: | linked libraries: | MPI_INIT_THREAD avail: | MPI2 support: With optimised conv.: yes With Cuda GPU conv.: no | NVidia Cuda Compiler: | Cuda flags: With OpenCL support: no With dgemmsy support: no With libXC: no | internal built: no | include dir.: -I/usr/include With libABINIT: yes | internal built: yes | include dir.: -I$(top_builddir)/libABINIT/src With libS_GPU: no | internal built: no | include dir.: With ETSF_IO: no | include dir.: With libarchive: yes | C flags: -I/include | linked libraries: -L/lib -larchive Installation paths: Source code location: . Prefix: /usr/pkg Exec prefix: ${prefix} Binaries: ${exec_prefix}/bin Static libraries: ${exec_prefix}/lib Fortran modules: ${prefix}/include/ Documentation: ${datarootdir}/doc/${PACKAGE_TARNAME}