netcdf_config.log

configure: netCDF 4.3.0
checking build system type... x86_64-apple-darwin12.5.0
checking host system type... x86_64-apple-darwin12.5.0
checking target system type... x86_64-apple-darwin12.5.0
checking for a BSD-compatible install... /usr/bin/install -c
checking whether build environment is sane... yes
checking for a thread-safe mkdir -p... ./install-sh -c -d
checking for gawk... no
checking for mawk... no
checking for nawk... no
checking for awk... awk
checking whether make sets $(MAKE)... yes
checking whether make supports nested variables... yes
configure: checking user options
checking whether a win32 DLL is desired... no
checking whether a NCIO_MINBLOCKSIZE was specified... 256
checking if fsync support is enabled... no
checking whether extra valgrind tests should be run... no
checking whether we should try to build netCDF-4... no
checking whether reading of HDF4 SD files is to be enabled... no
checking whether to fetch some sample HDF4 files from Unidata ftp site to test HDF4 reading (requires wget)... no
checking whether parallel I/O for classic and 64-bit offset files using parallel-netcdf is to be enabled... no
checking whether extra example tests should be run... no
checking whether parallel IO tests should be run... no
checking whether a default chunk size in bytes was specified... 4194304
checking whether a maximum per-variable cache size for HDF5 was specified... 67108864
checking whether a number of chunks for the default per-variable cache was specified... 10
checking whether a default file cache size for HDF5 was specified... 4194304
checking whether a default file cache maximum number of elements for HDF5 was specified... 1009
checking whether a default cache preemption for HDF5 was specified... 0.75
checking whether netCDF-4 logging is enabled... no
checking whether cdmremote client is to be built... no
checking whether DAP client is to be built... no
checking for style of include used by make... GNU
checking for 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 curl_easy_setopt in -lcurl... yes
checking whether dap remote testing should be enabled (default on)... no
checking whether netcdf4 group names should be enabled (default on)... configure: dap groups disabled because dap disabled or netcdf-4 disabled
no
checking whether the time-consuming dap tests should be enabled (default off)... no
checking whether netCDF extra tests should be run (developers only)... no
checking whether FFIO will be used... no
checking whether examples should be built... yes
checking whether v2 netCDF API should be built... yes
checking whether the ncgen/ncdump/nccopy should be built... yes
checking whether test should be built and run... yes
checking whether large file (> 2GB) tests should be run... no
checking whether benchmaks should be run (experimental)... no
checking whether extreme numbers should be used in tests... yes
checking where to put large temp files if large file tests are run... .
configure: finding C compiler
checking for 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 an ANSI C-conforming const... yes
checking whether a CURLOPT_KEYPASSWD is defined... yes
configure: setting up libtool
checking how to print strings... printf
checking for a sed that does not truncate output... /usr/local/Library/ENV/4.3/sed
checking for grep that handles long lines and -e... /usr/bin/grep
checking for egrep... /usr/bin/grep -E
checking for fgrep... /usr/bin/grep -F
checking for ld used by gcc... /usr/local/Library/ENV/4.3/ld
checking if the linker (/usr/local/Library/ENV/4.3/ld) is GNU ld... no
checking for BSD- or MS-compatible name lister (nm)... /usr/bin/nm
checking the name lister (/usr/bin/nm) 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 "+="... yes
checking how to convert x86_64-apple-darwin12.5.0 file names to x86_64-apple-darwin12.5.0 format... func_convert_file_noop
checking how to convert x86_64-apple-darwin12.5.0 file names to toolchain format... func_convert_file_noop
checking for /usr/local/Library/ENV/4.3/ld option to reload object files... -r
checking for objdump... no
checking how to recognize dependent libraries... pass_all
checking for dlltool... no
checking how to associate runtime and link libraries... printf %s\n
checking for ar... ar
checking for archiver @FILE support... no
checking for strip... strip
checking for ranlib... ranlib
checking command to parse /usr/bin/nm output from gcc object... ok
checking for sysroot... no
checking for mt... no
checking if : is a manifest tool... no
checking for dsymutil... dsymutil
checking for nmedit... nmedit
checking for lipo... lipo
checking for otool... otool
checking for otool64... no
checking for -single_module linker flag... yes
checking for -exported_symbols_list linker flag... yes
checking for -force_load linker flag... yes
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... -fno-common -DPIC
checking if gcc PIC flag -fno-common -DPIC works... yes
checking if gcc static flag -static works... no
checking if gcc supports -c -o file.o... yes
checking if gcc supports -c -o file.o... (cached) yes
checking whether the gcc linker (/usr/local/Library/ENV/4.3/ld) supports shared libraries... yes
checking dynamic linker characteristics... darwin12.5.0 dyld
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
configure: finding other utilities
checking for doxygen... no
configure: WARNING: Doxygen not found - documentation will not be built
checking for special C compiler options needed for large files... no
checking for _FILE_OFFSET_BITS value needed for large files... no
configure: displaying some results
checking CPPFLAGS... 
checking CC CFLAGS... gcc  -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -DBINTRAJ 
checking type gcc... gcc is hashed (/usr/local/Library/ENV/4.3/gcc)
checking CXX... g++-4.8
checking CXXFLAGS... 
checking type g++-4.8... g++-4.8 is /usr/local/Library/ENV/4.3/g++-4.8
checking FC... /usr/local/bin/gfortran
checking FFLAGS... 
checking type /usr/local/bin/gfortran... /usr/local/bin/gfortran is /usr/local/bin/gfortran
checking F90... unset
checking AR... ar
checking AR_FLAGS... cru
checking type ar... ar is hashed (/usr/bin/ar)
checking NM... /usr/bin/nm
checking NMFLAGS... 
configure: checking types, headers, and functions
checking for stdlib.h... (cached) yes
checking for sys/types.h... (cached) yes
checking sys/param.h usability... yes
checking sys/param.h presence... yes
checking for sys/param.h... yes
checking for dirent.h that defines DIR... yes
checking for library containing opendir... none required
checking for ANSI C header files... (cached) yes
checking for sys/wait.h that is POSIX.1 compatible... yes
checking whether time.h and sys/time.h may both be included... yes
checking locale.h usability... yes
checking locale.h presence... yes
checking for locale.h... yes
checking stdio.h usability... yes
checking stdio.h presence... yes
checking for stdio.h... yes
checking stdarg.h usability... yes
checking stdarg.h presence... yes
checking for stdarg.h... yes
checking errno.h usability... yes
checking errno.h presence... yes
checking for errno.h... yes
checking ctype.h usability... yes
checking ctype.h presence... yes
checking for ctype.h... yes
checking fcntl.h usability... yes
checking fcntl.h presence... yes
checking for fcntl.h... yes
checking malloc.h usability... no
checking malloc.h presence... no
checking for malloc.h... no
checking for stdlib.h... (cached) yes
checking for string.h... (cached) yes
checking for strings.h... (cached) yes
checking for unistd.h... (cached) yes
checking for sys/stat.h... (cached) yes
checking getopt.h usability... yes
checking getopt.h presence... yes
checking for getopt.h... yes
checking sys/time.h usability... yes
checking sys/time.h presence... yes
checking for sys/time.h... yes
checking for vprintf... yes
checking for _doprnt... no
checking sys/resource.h usability... yes
checking sys/resource.h presence... yes
checking for sys/resource.h... yes
checking for stdbool.h that conforms to C99... yes
checking for _Bool... yes
checking for strlcat... yes
checking for strerror... yes
checking for snprintf... yes
checking for strchr... yes
checking for strrchr... yes
checking for strcat... yes
checking for strcpy... yes
checking for strdup... yes
checking for strcasecmp... yes
checking for strtod... yes
checking for strtoll... yes
checking for strtoull... yes
checking for strstr... yes
checking for mkstemp... yes
checking for rand... yes
checking for getrlimit... yes
checking for gettimeofday... yes
checking for fsync... yes
checking for MPI_Comm_f2c... no
checking whether in-memory files are enabled... yes
checking for memmove... yes
checking for getpagesize... yes
checking for sysconf... yes
checking whether mmap is enabled for in-memory files... no
checking for stdlib.h... (cached) yes
checking for unistd.h... (cached) yes
checking for sys/param.h... (cached) yes
checking for getpagesize... (cached) yes
checking for working mmap... yes
checking for mremap... no
mmap function or mremap function is not available: disabling mmap
checking for size_t... yes
checking for working alloca.h... yes
checking for alloca... yes
checking whether isnan is declared... yes
checking whether isinf is declared... yes
checking whether isfinite is declared... yes
checking whether signbit is declared... yes
checking for struct stat.st_blksize... yes
checking for IEEE floating point format... yes
checking for size_t... (cached) yes
checking for off_t... yes
checking for ssize_t... yes
checking for ptrdiff_t... yes
checking for uchar... no
checking for longlong... no
checking whether char is unsigned... no
checking whether byte ordering is bigendian... no
checking size of short... 2
checking size of int... 4
checking size of long... 8
checking size of long long... 8
checking size of float... 4
checking size of double... 8
checking size of off_t... 8
checking size of size_t... 8
checking for floor in -lm... yes
checking what to call the output of the ftpbin target... binary-netcdf-4.3.0_nc3.tar /usr/local/bin/gfortran g++-4.8
checking value of LIBS... -lm 
configure: generating header files and makefiles
checking that generated files are newer than configure... done
configure: creating ./config.status
config.status: creating Makefile
config.status: creating nc-config
config.status: creating netcdf.pc
config.status: creating include/Makefile
config.status: creating h5_test/Makefile
config.status: creating man4/Makefile
config.status: creating man4/images/Makefile
config.status: creating libsrc/Makefile
config.status: creating libsrc4/Makefile
config.status: creating nctest/Makefile
config.status: creating nc_test4/Makefile
config.status: creating nc_test/Makefile
config.status: creating ncdump/Makefile
config.status: creating ncgen3/Makefile
config.status: creating ncgen/Makefile
config.status: creating examples/Makefile
config.status: creating examples/C/Makefile
config.status: creating examples/CDL/Makefile
config.status: creating oc2/Makefile
config.status: creating libdap2/Makefile
config.status: creating libcdmr/Makefile
config.status: creating librpc/Makefile
config.status: creating libdispatch/Makefile
config.status: creating liblib/Makefile
config.status: creating ncdump/cdl4/Makefile
config.status: creating ncdump/expected4/Makefile
config.status: creating ncdap_test/Makefile
config.status: creating ncdap_test/testdata3/Makefile
config.status: creating ncdap_test/expected3/Makefile
config.status: creating ncdap_test/expected4/Makefile
config.status: creating ncdap_test/expectremote3/Makefile
config.status: creating ncdap_test/expectremote4/Makefile
config.status: creating config.h
config.status: executing depfiles commands
config.status: executing libtool commands
configure: netCDF-Fortran 4.2
checking build system type... x86_64-apple-darwin12.5.0
checking host system type... x86_64-apple-darwin12.5.0
checking target system type... x86_64-apple-darwin12.5.0
checking for a BSD-compatible install... /usr/bin/install -c
checking whether build environment is sane... yes
checking for a thread-safe mkdir -p... ./install-sh -c -d
checking for gawk... no
checking for mawk... no
checking for nawk... no
checking for awk... awk
checking whether make sets $(MAKE)... yes
configure: checking user options
checking whether extra valgrind tests should be run... no
checking whether parallel IO tests should be run... no
checking whether netCDF extra tests should be run (developers only)... no
checking whether F90 API is desired... yes
checking whether fortran type sizes should be checked... yes
checking whether large file (> 2GB) tests should be run... no
checking whether benchmaks should be run (experimental)... no
checking where to put large temp files if large file tests are run... .
configure: finding C compiler
checking for 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 gcc and cc understand -c and -o together... yes
checking for an ANSI C-conforming const... yes
configure: finding Fortran compiler (will not be used if Fortran API is not desired)
checking whether we are using the GNU Fortran compiler... yes
checking whether gfortran accepts -g... yes
checking whether we are using the GNU Fortran 77 compiler... yes
checking whether gfortran accepts -g... yes
configure: setting up Fortran 90
checking what FC is set to... gfortran
checking for Fortran flag to compile .f90 files... none
checking fortran 90 modules inclusion flag... -I
configure: setting up libtool
checking how to print strings... printf
checking for a sed that does not truncate output... /usr/local/Library/ENV/4.3/sed
checking for grep that handles long lines and -e... /usr/bin/grep
checking for egrep... /usr/bin/grep -E
checking for fgrep... /usr/bin/grep -F
checking for ld used by gcc... /usr/local/Library/ENV/4.3/ld
checking if the linker (/usr/local/Library/ENV/4.3/ld) is GNU ld... no
checking for BSD- or MS-compatible name lister (nm)... /usr/bin/nm
checking the name lister (/usr/bin/nm) 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 "+="... yes
checking for /usr/local/Library/ENV/4.3/ld option to reload object files... -r
checking for objdump... no
checking how to recognize dependent libraries... pass_all
checking for ar... ar
checking for strip... strip
checking for ranlib... ranlib
checking command to parse /usr/bin/nm output from gcc object... ok
checking for dsymutil... dsymutil
checking for nmedit... nmedit
checking for lipo... lipo
checking for otool... otool
checking for otool64... no
checking for -single_module linker flag... yes
checking for -exported_symbols_list linker flag... yes
checking for -force_load linker flag... yes
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... -fno-common -DPIC
checking if gcc PIC flag -fno-common -DPIC works... yes
checking if gcc static flag -static works... no
checking if gcc supports -c -o file.o... yes
checking if gcc supports -c -o file.o... (cached) yes
checking whether the gcc linker (/usr/local/Library/ENV/4.3/ld) supports shared libraries... yes
checking dynamic linker characteristics... darwin12.5.0 dyld
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 if libtool supports shared libraries... yes
checking whether to build shared libraries... yes
checking whether to build static libraries... yes
checking for gfortran option to produce PIC... -fno-common
checking if gfortran PIC flag -fno-common works... yes
checking if gfortran static flag -static works... no
checking if gfortran supports -c -o file.o... yes
checking if gfortran supports -c -o file.o... (cached) yes
checking whether the gfortran linker (/usr/local/Library/ENV/4.3/ld) supports shared libraries... yes
checking dynamic linker characteristics... darwin12.5.0 dyld
checking how to hardcode library paths into programs... immediate
checking if libtool supports shared libraries... yes
checking whether to build shared libraries... yes
checking whether to build static libraries... yes
checking for gfortran option to produce PIC... -fno-common
checking if gfortran PIC flag -fno-common works... yes
checking if gfortran static flag -static works... no
checking if gfortran supports -c -o file.o... yes
checking if gfortran supports -c -o file.o... (cached) yes
checking whether the gfortran linker (/usr/local/Library/ENV/4.3/ld) supports shared libraries... yes
checking dynamic linker characteristics... darwin12.5.0 dyld
checking how to hardcode library paths into programs... immediate
configure: finding other utilities
configure: trying to set fortran flags for this platform
checking what FC is set to... gfortran
checking for special C compiler options needed for large files... no
checking for _FILE_OFFSET_BITS value needed for large files... no
configure: displaying some results
checking for /usr/bin/nm... /usr/bin/nm
checking nm flags... 
checking for C-equivalent to Fortran routine "SUB"... sub_
checking for Fortran "byte"... yes
checking for Fortran "integer*2"... yes
checking if Fortran "byte" is C "signed char"... yes
checking if Fortran "byte" is C "short"... no
checking if Fortran "byte" is C "int"... no
checking if Fortran "byte" is C "long"... no
checking if Fortran "integer*2" is C "short"... yes
checking if Fortran "integer*2" is C "int"... no
checking if Fortran "integer*2" is C "long"... no
checking if Fortran "integer" is C "int"... yes
checking if Fortran "real" is C "float"... yes
checking if Fortran "doubleprecision" is C "double"... yes
checking for Fortran-equivalent to netCDF "byte"... byte
checking for Fortran-equivalent to netCDF "short"... integer*2
checking if Fortran 90 compiler capitalizes .mod filenames... yes
checking whether extra example tests should be run... no
checking whether a win32 DLL is desired... no
configure: checking types, headers, and functions
checking netcdf.h usability... yes
checking netcdf.h presence... yes
checking for netcdf.h... yes
checking for library containing nc_open... -lnetcdf
checking for nc_def_opaque... yes
checking for nccreate... yes
checking for nc_set_log_level... no
checking for oc_open... yes
checking for nc_use_parallel_enabled... yes
checking netCDF v2 API present... yes
checking netCDF-4 present... yes
checking for stdlib.h... (cached) yes
checking for sys/types.h... (cached) yes
checking sys/param.h usability... yes
checking sys/param.h presence... yes
checking for sys/param.h... yes
checking for dirent.h that defines DIR... yes
checking for library containing opendir... none required
checking for ANSI C header files... (cached) yes
checking for sys/wait.h that is POSIX.1 compatible... yes
checking whether time.h and sys/time.h may both be included... yes
checking locale.h usability... yes
checking locale.h presence... yes
checking for locale.h... yes
checking stdio.h usability... yes
checking stdio.h presence... yes
checking for stdio.h... yes
checking stdarg.h usability... yes
checking stdarg.h presence... yes
checking for stdarg.h... yes
checking errno.h usability... yes
checking errno.h presence... yes
checking for errno.h... yes
checking ctype.h usability... yes
checking ctype.h presence... yes
checking for ctype.h... yes
checking fcntl.h usability... yes
checking fcntl.h presence... yes
checking for fcntl.h... yes
checking malloc.h usability... no
checking malloc.h presence... no
checking for malloc.h... no
checking for stdlib.h... (cached) yes
checking for string.h... (cached) yes
checking for strings.h... (cached) yes
checking for unistd.h... (cached) yes
checking for sys/stat.h... (cached) yes
checking getopt.h usability... yes
checking getopt.h presence... yes
checking for getopt.h... yes
checking sys/time.h usability... yes
checking sys/time.h presence... yes
checking for sys/time.h... yes
checking sys/resource.h usability... yes
checking sys/resource.h presence... yes
checking for sys/resource.h... yes
checking for vprintf... yes
checking for _doprnt... no
checking for stdbool.h that conforms to C99... yes
checking for _Bool... yes
checking for working alloca.h... yes
checking for alloca... yes
checking for size_t... yes
checking for off_t... yes
checking for ssize_t... yes
checking for ptrdiff_t... yes
checking for uchar... no
checking for longlong... no
checking whether char is unsigned... no
checking size of short... 0
checking size of int... 0
checking size of long... 0
checking size of float... 0
checking size of double... 0
checking size of off_t... configure: error: in `/private/tmp/ambertools-hcr1/amber14/AmberTools/src/netcdf-fortran-4.2':
configure: error: cannot compute sizeof (off_t)
See `config.log' for more details