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Gentoo's Bugzilla – Attachment 256342 Details for
Bug 347756
sci-libs/netcdf-4.1.1 +hdf5 fails with "Can't delete temporary "module file 'netcdf.mod0': No such file or directory"
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build log
1291491635-install-sci-libs_netcdf-4.1.1:0::gentoo.out (text/plain), 58.87 KB, created by
Nico Schlömer
on 2010-12-04 19:51:27 UTC
(
hide
)
Description:
build log
Filename:
MIME Type:
Creator:
Nico Schlömer
Created:
2010-12-04 19:51:27 UTC
Size:
58.87 KB
patch
obsolete
>[34m>>>[0m Running ebuild phase killold as root:root... >[34m>>>[0m Starting builtin_killold >[34m>>>[0m Done builtin_killold >[34m>>>[0m Completed ebuild phase killold >[34m>>>[0m Running ebuild phases init saveenv as paludisbuild:paludisbuild... >[34m>>>[0m Starting builtin_init >[34m>>>[0m Done builtin_init >[34m>>>[0m Starting builtin_saveenv >[34m>>>[0m Done builtin_saveenv >[34m>>>[0m Completed ebuild phases init saveenv >[34m>>>[0m Running ebuild phases loadenv setup saveenv as root:root... >[34m>>>[0m Starting builtin_loadenv >[34m>>>[0m Done builtin_loadenv >[34m>>>[0m Starting pkg_setup >[34m>>>[0m Done pkg_setup >[34m>>>[0m Starting builtin_saveenv >[34m>>>[0m Done builtin_saveenv >[34m>>>[0m Completed ebuild phases loadenv setup saveenv >[34m>>>[0m Running ebuild phases loadenv unpack saveenv as paludisbuild:paludisbuild... >[34m>>>[0m Starting builtin_loadenv >[34m>>>[0m Done builtin_loadenv >[34m>>>[0m Starting src_unpack >>>> Unpacking netcdf-4.1.1.tar.gz to /var/tmp/paludis/sci-libs-netcdf-4.1.1/work >tar zxf /usr/portage/distfiles/netcdf-4.1.1.tar.gz --no-same-owner >[34m>>>[0m Done src_unpack >[34m>>>[0m Starting builtin_saveenv >[34m>>>[0m Done builtin_saveenv >[34m>>>[0m Completed ebuild phases loadenv unpack saveenv >[34m>>>[0m Running ebuild phases loadenv prepare saveenv as paludisbuild:paludisbuild... >[34m>>>[0m Starting builtin_loadenv >[34m>>>[0m Done builtin_loadenv >[34m>>>[0m Starting src_prepare >[34m>>>[0m Done src_prepare >[34m>>>[0m Starting builtin_saveenv >[34m>>>[0m Done builtin_saveenv >[34m>>>[0m Completed ebuild phases loadenv prepare saveenv >[34m>>>[0m Running ebuild phases loadenv configure saveenv as paludisbuild:paludisbuild... >[34m>>>[0m Starting builtin_loadenv >[34m>>>[0m Done builtin_loadenv >[34m>>>[0m Starting src_configure >econf: updating /var/tmp/paludis/sci-libs-netcdf-4.1.1/work/netcdf-4.1.1/config.sub with /usr/share/gnuconfig/config.sub >econf: updating /var/tmp/paludis/sci-libs-netcdf-4.1.1/work/netcdf-4.1.1/config.guess with /usr/share/gnuconfig/config.guess >econf: updating /var/tmp/paludis/sci-libs-netcdf-4.1.1/work/netcdf-4.1.1/libcf/config.sub with /usr/share/gnuconfig/config.sub >econf: updating /var/tmp/paludis/sci-libs-netcdf-4.1.1/work/netcdf-4.1.1/libcf/config.guess with /usr/share/gnuconfig/config.guess >econf: updating /var/tmp/paludis/sci-libs-netcdf-4.1.1/work/netcdf-4.1.1/udunits/config.sub with /usr/share/gnuconfig/config.sub >econf: updating /var/tmp/paludis/sci-libs-netcdf-4.1.1/work/netcdf-4.1.1/udunits/config.guess with /usr/share/gnuconfig/config.guess >./configure --prefix=/usr --host=x86_64-pc-linux-gnu --mandir=/usr/share/man --infodir=/usr/share/info --datadir=/usr/share --sysconfdir=/etc --localstatedir=/var/lib --libdir=/usr/lib64 --enable-shared --docdir=/usr/share/doc/netcdf-4.1.1 --disable-dap --disable-static --enable-f77 --enable-f90 --enable-cxx --enable-separate-fortran --enable-netcdf-4 --enable-ncgen4 --disable-docs-install --with-hdf5=/usr --with-zlib=/usr --build=x86_64-pc-linux-gnu >configure: netCDF 4.1.1 >checking build system type... x86_64-pc-linux-gnu >checking host 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 >configure: checking user options >checking whether CXX is set to ''... no >checking whether FC is set to ''... no >checking whether F90 is set to ''... no >checking whether a NCIO_MINBLOCKSIZE was specified... 256 >checking whether udunits is to be built... no >checking if fsync support is enabled... yes >checking whether extra valgrind tests should be run... no >checking whether libcf is to be built... 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 a location for the parallel-netcdf library was specified... no >checking whether new netCDF-4 C++ API is to be built... no >checking whether extra example tests should be run... no >checking whether parallel IO tests should be run... no >checking whether a location for the HDF5 library was specified... /usr >checking whether a location for the ZLIB library was specified... /usr >checking whether a location for the SZLIB library was specified... >checking whether a location for the HDF4 library was specified... >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 a path for curl-config was specified... no >checking whether a location for curl installation was specified... no >configure: checking whether a location for curl-config is in PATH... yes >checking whether DAP client is to be built... no >checking whether dap remote testing should be enabled (default on)... no >checking whether the time-consuming dap tests should be enabled (default off)... no >checking whether a location for liboc was specified... no >checking whether netCDF extra tests should be run (developers only)... no >checking whether Fortran compiler(s) should be tested during configure... yes >checking whether FFIO will be used... no >checking whether to skip C++, F77, or F90 APIs if compiler is broken... yes >checking whether only the C library is desired... no >checking whether examples should be built... yes >checking whether F77 API is desired... yes >checking whether any Fortran API is desired... yes >checking whether F90 API is desired... yes >checking whether fortran type sizes should be checked... yes >checking whether C API is desired... yes >checking where to get netCDF C-only library for separate fortran libraries... >checking whether CXX API is desired... yes >checking whether v2 netCDF API should be built... yes >checking whether the ncgen/ncdump should be built... 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... . >checking whether a win32 DLL is desired... no >checking whether separate fortran libs are desired... yes >configure: finding C compiler >checking for x86_64-pc-linux-gnu-xlc... no >checking for x86_64-pc-linux-gnu-cc... no >checking for x86_64-pc-linux-gnu-c89... no >checking for x86_64-pc-linux-gnu-acc... no >checking for x86_64-pc-linux-gnu-gcc... x86_64-pc-linux-gnu-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 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 for style of include used by make... GNU >checking dependency style of x86_64-pc-linux-gnu-gcc... gcc3 >checking whether x86_64-pc-linux-gnu-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 for x86_64-pc-linux-gnu-xlf90... no >checking for x86_64-pc-linux-gnu-fort... no >checking for x86_64-pc-linux-gnu-xlf95... no >checking for x86_64-pc-linux-gnu-ifort... no >checking for x86_64-pc-linux-gnu-ifc... no >checking for x86_64-pc-linux-gnu-efc... no >checking for x86_64-pc-linux-gnu-pgf95... no >checking for x86_64-pc-linux-gnu-lf95... no >checking for x86_64-pc-linux-gnu-g95... no >checking for x86_64-pc-linux-gnu-gfortran... x86_64-pc-linux-gnu-gfortran >checking whether we are using the GNU Fortran compiler... yes >checking whether x86_64-pc-linux-gnu-gfortran accepts -g... yes >checking for x86_64-pc-linux-gnu-xlf... no >checking for x86_64-pc-linux-gnu-fort... no >checking for x86_64-pc-linux-gnu-xlf95... no >checking for x86_64-pc-linux-gnu-ifort... no >checking for x86_64-pc-linux-gnu-ifc... no >checking for x86_64-pc-linux-gnu-efc... no >checking for x86_64-pc-linux-gnu-pgf77... no >checking for x86_64-pc-linux-gnu-lf95... no >checking for x86_64-pc-linux-gnu-g95... no >checking for x86_64-pc-linux-gnu-gfortran... x86_64-pc-linux-gnu-gfortran >checking whether we are using the GNU Fortran 77 compiler... yes >checking whether x86_64-pc-linux-gnu-gfortran accepts -g... yes >configure: setting up Fortran 90 >checking for Fortran flag to compile .f90 files... none >checking fortran 90 modules inclusion flag... -I >checking if Fortran compiler can handle Fortran-90... yes >configure: finding C++ compiler (will not be used if C++ API is not desired) >checking for x86_64-pc-linux-gnu-cl... no >checking for x86_64-pc-linux-gnu-KCC... no >checking for x86_64-pc-linux-gnu-CC... no >checking for x86_64-pc-linux-gnu-cxx... no >checking for x86_64-pc-linux-gnu-cc++... no >checking for x86_64-pc-linux-gnu-xlC... no >checking for x86_64-pc-linux-gnu-aCC... no >checking for x86_64-pc-linux-gnu-c++... x86_64-pc-linux-gnu-c++ >checking whether we are using the GNU C++ compiler... yes >checking whether x86_64-pc-linux-gnu-c++ accepts -g... yes >checking dependency style of x86_64-pc-linux-gnu-c++... gcc3 >configure: setting up libtool >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/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... 25162752 >checking whether the shell understands some XSI constructs... yes >checking whether the shell understands "+="... yes >checking for /usr/x86_64-pc-linux-gnu/bin/ld option to reload object files... -r >checking how to recognize dependent libraries... pass_all >checking for x86_64-pc-linux-gnu-ar... x86_64-pc-linux-gnu-ar >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/nm -B output from x86_64-pc-linux-gnu-gcc object... ok >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 whether we are using the GNU C++ compiler... (cached) yes >checking whether x86_64-pc-linux-gnu-c++ accepts -g... (cached) yes >checking dependency style of x86_64-pc-linux-gnu-c++... (cached) gcc3 >checking how to run the C++ preprocessor... x86_64-pc-linux-gnu-c++ -E >checking for x86_64-pc-linux-gnu-g77... (cached) x86_64-pc-linux-gnu-gfortran >checking whether we are using the GNU Fortran 77 compiler... (cached) yes >checking whether x86_64-pc-linux-gnu-gfortran accepts -g... (cached) yes >checking for x86_64-pc-linux-gnu-gfortran... (cached) x86_64-pc-linux-gnu-gfortran >checking whether we are using the GNU Fortran compiler... (cached) yes >checking whether x86_64-pc-linux-gnu-gfortran accepts -g... (cached) 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 for ld used by x86_64-pc-linux-gnu-c++... /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-c++ linker (/usr/x86_64-pc-linux-gnu/bin/ld -m elf_x86_64) supports shared libraries... yes >checking for x86_64-pc-linux-gnu-c++ option to produce PIC... -fPIC -DPIC >checking if x86_64-pc-linux-gnu-c++ PIC flag -fPIC -DPIC works... yes >checking if x86_64-pc-linux-gnu-c++ static flag -static works... yes >checking if x86_64-pc-linux-gnu-c++ supports -c -o file.o... yes >checking if x86_64-pc-linux-gnu-c++ supports -c -o file.o... (cached) yes >checking whether the x86_64-pc-linux-gnu-c++ linker (/usr/x86_64-pc-linux-gnu/bin/ld -m elf_x86_64) supports shared libraries... yes >checking dynamic linker characteristics... GNU/Linux ld.so >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... no >checking for x86_64-pc-linux-gnu-gfortran option to produce PIC... -fPIC >checking if x86_64-pc-linux-gnu-gfortran PIC flag -fPIC works... yes >checking if x86_64-pc-linux-gnu-gfortran static flag -static works... yes >checking if x86_64-pc-linux-gnu-gfortran supports -c -o file.o... yes >checking if x86_64-pc-linux-gnu-gfortran supports -c -o file.o... (cached) yes >checking whether the x86_64-pc-linux-gnu-gfortran linker (/usr/x86_64-pc-linux-gnu/bin/ld -m elf_x86_64) supports shared libraries... yes >checking dynamic linker characteristics... GNU/Linux ld.so >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... no >checking for x86_64-pc-linux-gnu-gfortran option to produce PIC... -fPIC >checking if x86_64-pc-linux-gnu-gfortran PIC flag -fPIC works... yes >checking if x86_64-pc-linux-gnu-gfortran static flag -static works... yes >checking if x86_64-pc-linux-gnu-gfortran supports -c -o file.o... yes >checking if x86_64-pc-linux-gnu-gfortran supports -c -o file.o... (cached) yes >checking whether the x86_64-pc-linux-gnu-gfortran linker (/usr/x86_64-pc-linux-gnu/bin/ld -m elf_x86_64) supports shared libraries... yes >checking dynamic linker characteristics... GNU/Linux ld.so >checking how to hardcode library paths into programs... immediate >configure: finding other utilities >configure: trying to set fortran flags for this platform >checking if we need to set _LARGE_FILES despite results of previous tests... _LARGE_FILES= >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... x86_64-pc-linux-gnu-gcc -O2 -march=native -pipe >checking type x86_64-pc-linux-gnu-gcc... x86_64-pc-linux-gnu-gcc is /usr/bin/x86_64-pc-linux-gnu-gcc >checking CXX... x86_64-pc-linux-gnu-c++ >checking CXXFLAGS... -O2 -march=native -pipe >checking type x86_64-pc-linux-gnu-c++... x86_64-pc-linux-gnu-c++ is /usr/bin/x86_64-pc-linux-gnu-c++ >checking FC... x86_64-pc-linux-gnu-gfortran >checking FFLAGS... -g -O2 >checking type x86_64-pc-linux-gnu-gfortran... x86_64-pc-linux-gnu-gfortran is /usr/bin/x86_64-pc-linux-gnu-gfortran >checking F90... x86_64-pc-linux-gnu-gfortran >checking FCFLAGS... -g -O2 >checking type x86_64-pc-linux-gnu-gfortran... x86_64-pc-linux-gnu-gfortran is /usr/bin/x86_64-pc-linux-gnu-gfortran >checking AR... x86_64-pc-linux-gnu-ar >checking AR_FLAGS... cru >checking type x86_64-pc-linux-gnu-ar... x86_64-pc-linux-gnu-ar is /usr/bin/x86_64-pc-linux-gnu-ar >checking NM... /usr/bin/nm -B >checking NMFLAGS... >checking for /usr/bin/nm... /usr/bin/nm -B >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... no >configure: checking types, headers, and functions >checking for stdlib.h... (cached) yes >checking for sys/types.h... (cached) yes >checking locale.h usability... yes >checking locale.h presence... yes >checking for locale.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 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... yes >checking malloc.h presence... yes >checking for malloc.h... yes >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 for vprintf... yes >checking for _doprnt... no >checking for stdbool.h that conforms to C99... yes >checking for _Bool... yes >checking for strlcat... no >checking for strerror... yes >checking for snprintf... yes >checking for strchr... yes >checking for strrchr... yes >checking for mktemp... yes >checking for strcat... yes >checking for strcpy... yes >checking for strdup... yes >checking for strcasecmp... yes >checking for getrlimit... yes >checking for gettimeofday... yes >checking for fsync... yes >checking for MPI_Comm_f2c... no >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... yes >checking for off_t... yes >checking for ssize_t... yes >checking for ptrdiff_t... yes >checking for uchar... 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 float... 4 >checking size of double... 8 >checking size of off_t... 8 >checking size of size_t... 8 >checking for manual-page index command... >checking hdf5.h usability... yes >checking hdf5.h presence... yes >checking for hdf5.h... yes >checking whether we should try to build netCDF-4... yes >checking for H5Fflush in -lhdf5... yes >checking for H5DSis_scale in -lhdf5_hl... yes >checking for H5Pget_fapl_mpiposix in -lhdf5... no >checking for H5Pget_fapl_mpio in -lhdf5... no >checking how to modify netcdf.h to deal with parallel I/O... without parallel >checking whether parallel I/O features are to be included... no >checking for H5Pset_deflate in -lhdf5... yes >checking for H5Z_can_apply_szip in -lhdf5... no >checking if API dispatch is enabled... no >checking for long long int... yes >checking for unsigned long long int... yes >checking what to call the output of the ftpbin target... binary-netcdf-4.1.1_x86_64-pc-linux-gnu-gfortran_x86_64-pc-linux-gnu-gfortran_x86_64-pc-linux-gnu-c++.tar x86_64-pc-linux-gnu-gfortran x86_64-pc-linux-gnu-c++ >checking binary distribution directory... /home/ftp/pub/binary/dummy_system >checking for library containing xdr_void... none required >configure: XDR Functions appear to be in libc. >checking for rpc/types.h... yes >checking for rpc/xdr.h... yes >configure: generating header files and makefiles >configure: creating ./config.status >config.status: creating Makefile >config.status: creating nc-config >config.status: creating netcdf.pc >config.status: creating man4/Makefile >config.status: creating fortran/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 nf_test/Makefile >config.status: creating cxx/Makefile >config.status: creating cxx4/Makefile >config.status: creating f90/Makefile >config.status: creating examples/Makefile >config.status: creating examples/C/Makefile >config.status: creating examples/CDL/Makefile >config.status: creating examples/CXX/Makefile >config.status: creating examples/CXX4/Makefile >config.status: creating examples/F90/Makefile >config.status: creating examples/F77/Makefile >config.status: creating libncdap3/Makefile >config.status: creating libncdap3/oc/Makefile >config.status: creating libncdap4/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 ncdump/cdl4/Makefile >config.status: creating ncdump/expected4/Makefile >config.status: creating config.h >config.status: creating fortran/nfconfig1.inc >config.status: executing depfiles commands >config.status: executing libtool commands >=== configuring in udunits (/var/tmp/paludis/sci-libs-netcdf-4.1.1/work/netcdf-4.1.1/udunits) >configure: running /bin/sh ./configure --disable-option-checking '--prefix=/usr' '--host=x86_64-pc-linux-gnu' '--mandir=/usr/share/man' '--infodir=/usr/share/info' '--datadir=/usr/share' '--sysconfdir=/etc' '--localstatedir=/var/lib' '--libdir=/usr/lib64' '--enable-shared' '--docdir=/usr/share/doc/netcdf-4.1.1' '--disable-dap' '--disable-static' '--enable-f77' '--enable-f90' '--enable-cxx' '--enable-separate-fortran' '--enable-netcdf-4' '--enable-ncgen4' '--disable-docs-install' '--with-hdf5=/usr' '--with-zlib=/usr' '--build=x86_64-pc-linux-gnu' 'build_alias=x86_64-pc-linux-gnu' 'host_alias=x86_64-pc-linux-gnu' 'CFLAGS=-O2 -march=native -pipe' 'LDFLAGS=-Wl,-O1 -Wl,--as-needed' 'CXXFLAGS=-O2 -march=native -pipe' --cache-file=/dev/null --srcdir=. >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 for x86_64-pc-linux-gnu-xlc... no >checking for x86_64-pc-linux-gnu-cc... no >checking for x86_64-pc-linux-gnu-c89... no >checking for x86_64-pc-linux-gnu-acc... no >checking for x86_64-pc-linux-gnu-gcc... x86_64-pc-linux-gnu-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 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 for style of include used by make... GNU >checking dependency style of x86_64-pc-linux-gnu-gcc... gcc3 >checking whether x86_64-pc-linux-gnu-gcc and cc understand -c and -o together... yes >checking how to run the C preprocessor... x86_64-pc-linux-gnu-gcc -E >checking whether ln -s works... yes >checking whether make sets $(MAKE)... (cached) yes >checking for bison... bison -y >checking for flex... flex >checking lex output file root... lex.yy >checking lex library... -lfl >checking whether yytext is a pointer... yes >checking for library containing dirname... none required >checking for library containing log10... -lm >checking for grep that handles long lines and -e... /bin/grep >checking for egrep... /bin/grep -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 float.h usability... yes >checking float.h presence... yes >checking for float.h... yes >checking for inttypes.h... (cached) 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 >configure: CUNIT not found. Disabling unit-tests. >checking for an ANSI C-conforming const... yes >checking for size_t... yes >checking whether byte ordering is bigendian... no >checking for floor... yes >checking for memmove... yes >checking for memset... yes >checking for modf... yes >checking for pow... yes >checking for strcasecmp... yes >checking for strdup... yes >checking for strpbrk... yes >checking build system type... x86_64-pc-linux-gnu >checking host system type... x86_64-pc-linux-gnu >checking for a sed that does not truncate output... /bin/sed >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/nm -B >checking the name lister (/usr/bin/nm -B) interface... BSD nm >checking the maximum length of command line arguments... 25162752 >checking whether the shell understands some XSI constructs... yes >checking whether the shell understands "+="... yes >checking for /usr/x86_64-pc-linux-gnu/bin/ld option to reload object files... -r >checking how to recognize dependent libraries... pass_all >checking for x86_64-pc-linux-gnu-ar... x86_64-pc-linux-gnu-ar >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/nm -B output from x86_64-pc-linux-gnu-gcc object... ok >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 >configure: creating ./config.status >config.status: creating Makefile >config.status: creating expat/Makefile >config.status: creating lib/Makefile >config.status: creating lib/xmlFailures/Makefile >config.status: creating lib/xmlSuccesses/Makefile >config.status: creating prog/Makefile >config.status: creating test/Makefile >config.status: creating config.h >config.status: creating expat/expat_config.h >config.status: executing depfiles commands >config.status: executing libtool commands >=== configuring in libcf (/var/tmp/paludis/sci-libs-netcdf-4.1.1/work/netcdf-4.1.1/libcf) >configure: running /bin/sh ./configure --disable-option-checking '--prefix=/usr' '--host=x86_64-pc-linux-gnu' '--mandir=/usr/share/man' '--infodir=/usr/share/info' '--datadir=/usr/share' '--sysconfdir=/etc' '--localstatedir=/var/lib' '--libdir=/usr/lib64' '--enable-shared' '--docdir=/usr/share/doc/netcdf-4.1.1' '--disable-dap' '--disable-static' '--enable-f77' '--enable-f90' '--enable-cxx' '--enable-separate-fortran' '--enable-netcdf-4' '--enable-ncgen4' '--disable-docs-install' '--with-hdf5=/usr' '--with-zlib=/usr' '--build=x86_64-pc-linux-gnu' 'build_alias=x86_64-pc-linux-gnu' 'host_alias=x86_64-pc-linux-gnu' 'CFLAGS=-O2 -march=native -pipe' 'LDFLAGS=-Wl,-O1 -Wl,--as-needed' 'CXXFLAGS=-O2 -march=native -pipe' --cache-file=/dev/null --srcdir=. >configure: libcf 1.0-alpha5 >checking build system type... x86_64-pc-linux-gnu >checking host 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 >configure: checking user options >checking whether FC is set to ''... no >checking whether documentation is to be built... no >checking whether gridspec tools are to be built... no >checking whether gridspec test data should be fetched from Unidata FTP site... no >checking whether cfcheck is to be built... yes >checking whether logging is enabled (useful to CF developers, mainly... no >checking whether netCDF-4 is to be used... yes >checking whether extra tests on sample data should be performed... no >checking whether a location for the HDF5 library was specified... /usr >checking whether a location for the HDF4 library was specified... >checking whether a location for the ZLIB library was specified... /usr >checking whether a location for the SZLIB library was specified... >checking whether Fortran 90 API is desired... yes >checking whether a location for the netCDF library was specified... no >configure: finding C compiler >checking for x86_64-pc-linux-gnu-mpcc_r... no >checking for x86_64-pc-linux-gnu-xlc... no >checking for x86_64-pc-linux-gnu-cc... no >checking for x86_64-pc-linux-gnu-c89... no >checking for x86_64-pc-linux-gnu-acc... no >checking for x86_64-pc-linux-gnu-gcc... x86_64-pc-linux-gnu-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 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 for style of include used by make... GNU >checking dependency style of x86_64-pc-linux-gnu-gcc... gcc3 >checking whether x86_64-pc-linux-gnu-gcc and cc understand -c and -o together... yes >configure: finding Fortran compiler (required, even if Fortran API is not desired) >checking for x86_64-pc-linux-gnu-xlf90... no >checking for x86_64-pc-linux-gnu-fort... no >checking for x86_64-pc-linux-gnu-xlf95... no >checking for x86_64-pc-linux-gnu-ifort... no >checking for x86_64-pc-linux-gnu-ifc... no >checking for x86_64-pc-linux-gnu-efc... no >checking for x86_64-pc-linux-gnu-pgf95... no >checking for x86_64-pc-linux-gnu-lf95... no >checking for x86_64-pc-linux-gnu-g95... no >checking for x86_64-pc-linux-gnu-gfortran... x86_64-pc-linux-gnu-gfortran >checking whether we are using the GNU Fortran compiler... yes >checking whether x86_64-pc-linux-gnu-gfortran accepts -g... yes >checking for x86_64-pc-linux-gnu-xlf... no >checking for x86_64-pc-linux-gnu-fort... no >checking for x86_64-pc-linux-gnu-xlf95... no >checking for x86_64-pc-linux-gnu-ifort... no >checking for x86_64-pc-linux-gnu-ifc... no >checking for x86_64-pc-linux-gnu-efc... no >checking for x86_64-pc-linux-gnu-pgf77... no >checking for x86_64-pc-linux-gnu-lf95... no >checking for x86_64-pc-linux-gnu-g95... no >checking for x86_64-pc-linux-gnu-gfortran... x86_64-pc-linux-gnu-gfortran >checking whether we are using the GNU Fortran 77 compiler... yes >checking whether x86_64-pc-linux-gnu-gfortran accepts -g... yes >checking for Fortran flag to compile .f90 files... none >checking fortran 90 modules inclusion flag... -I >checking if Fortran 90 compiler capitalizes .mod filenames... no >configure: finding other utilities >configure: setting up libtool >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/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... 25162752 >checking whether the shell understands some XSI constructs... yes >checking whether the shell understands "+="... yes >checking for /usr/x86_64-pc-linux-gnu/bin/ld option to reload object files... -r >checking how to recognize dependent libraries... pass_all >checking for x86_64-pc-linux-gnu-ar... x86_64-pc-linux-gnu-ar >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/nm -B output from x86_64-pc-linux-gnu-gcc object... ok >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 x86_64-pc-linux-gnu-g77... (cached) x86_64-pc-linux-gnu-gfortran >checking whether we are using the GNU Fortran 77 compiler... (cached) yes >checking whether x86_64-pc-linux-gnu-gfortran accepts -g... (cached) yes >checking for x86_64-pc-linux-gnu-gfortran... (cached) x86_64-pc-linux-gnu-gfortran >checking whether we are using the GNU Fortran compiler... (cached) yes >checking whether x86_64-pc-linux-gnu-gfortran accepts -g... (cached) 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 if libtool supports shared libraries... yes >checking whether to build shared libraries... yes >checking whether to build static libraries... no >checking for x86_64-pc-linux-gnu-gfortran option to produce PIC... -fPIC >checking if x86_64-pc-linux-gnu-gfortran PIC flag -fPIC works... yes >checking if x86_64-pc-linux-gnu-gfortran static flag -static works... yes >checking if x86_64-pc-linux-gnu-gfortran supports -c -o file.o... yes >checking if x86_64-pc-linux-gnu-gfortran supports -c -o file.o... (cached) yes >checking whether the x86_64-pc-linux-gnu-gfortran linker (/usr/x86_64-pc-linux-gnu/bin/ld -m elf_x86_64) supports shared libraries... yes >checking dynamic linker characteristics... GNU/Linux ld.so >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... no >checking for x86_64-pc-linux-gnu-gfortran option to produce PIC... -fPIC >checking if x86_64-pc-linux-gnu-gfortran PIC flag -fPIC works... yes >checking if x86_64-pc-linux-gnu-gfortran static flag -static works... yes >checking if x86_64-pc-linux-gnu-gfortran supports -c -o file.o... yes >checking if x86_64-pc-linux-gnu-gfortran supports -c -o file.o... (cached) yes >checking whether the x86_64-pc-linux-gnu-gfortran linker (/usr/x86_64-pc-linux-gnu/bin/ld -m elf_x86_64) supports shared libraries... yes >checking dynamic linker characteristics... GNU/Linux ld.so >checking how to hardcode library paths into programs... immediate >configure: checking for large file support >checking for special C compiler options needed for large files... no >checking for _FILE_OFFSET_BITS value needed for large files... no >configure: checking types, headers, and functions >checking for stdlib.h... (cached) yes >checking for sys/types.h... (cached) yes >checking for unistd.h... (cached) yes >checking for strerror... yes >checking for strlcat... no >checking for working alloca.h... yes >checking for alloca... yes >checking for struct stat.st_blksize... 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 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 float... 4 >checking size of double... 8 >checking size of off_t... 8 >checking size of size_t... 8 >checking for library containing floor... -lm >configure: generating header files and makefiles >configure: creating ./config.status >config.status: creating gridspec/tools/make_hgrid/run_tests >config.status: creating gridspec/tools/make_vgrid/run_tests >config.status: creating gridspec/tools/make_topog/run_tests >config.status: creating Makefile >config.status: creating doc/Makefile >config.status: creating cfcheck/Makefile >config.status: creating src/Makefile >config.status: creating gridspec/Makefile >config.status: creating gridspec/shared/Makefile >config.status: creating gridspec/shared/mosaic/Makefile >config.status: creating gridspec/tools/Makefile >config.status: creating gridspec/tools/shared/Makefile >config.status: creating gridspec/tools/make_hgrid/Makefile >config.status: creating gridspec/tools/make_solo_mosaic/Makefile >config.status: creating gridspec/tools/make_coupler_mosaic/Makefile >config.status: creating gridspec/tools/fregrid/Makefile >config.status: creating gridspec/tools/make_topog/Makefile >config.status: creating gridspec/tools/make_vgrid/Makefile >config.status: creating gridspec/tools/river_regrid/Makefile >config.status: creating gridspec/tools/transfer_to_mosaic_grid/Makefile >config.status: creating config.h >config.status: creating nfconfig.inc >config.status: executing depfiles commands >config.status: executing libtool commands >[34m>>>[0m Done src_configure >[34m>>>[0m Starting builtin_saveenv >[34m>>>[0m Done builtin_saveenv >[34m>>>[0m Completed ebuild phases loadenv configure saveenv >[34m>>>[0m Running ebuild phases loadenv compile saveenv as paludisbuild:paludisbuild... >[34m>>>[0m Starting builtin_loadenv >[34m>>>[0m Done builtin_loadenv >[34m>>>[0m Starting src_compile >make -j3 >make all-recursive >make[1]: Entering directory `/var/tmp/paludis/sci-libs-netcdf-4.1.1/work/netcdf-4.1.1' >Making all in libsrc >make[2]: Entering directory `/var/tmp/paludis/sci-libs-netcdf-4.1.1/work/netcdf-4.1.1/libsrc' >depbase=`echo v2i.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ > /bin/sh ../libtool --tag=CC --mode=compile x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I../fortran -I/usr/include -I/usr/include -O2 -march=native -pipe -MT v2i.lo -MD -MP -MF $depbase.Tpo -c -o v2i.lo v2i.c &&\ > mv -f $depbase.Tpo $depbase.Plo >depbase=`echo attr.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ > /bin/sh ../libtool --tag=CC --mode=compile x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I../fortran -I/usr/include -I/usr/include -O2 -march=native -pipe -MT attr.lo -MD -MP -MF $depbase.Tpo -c -o attr.lo attr.c &&\ > mv -f $depbase.Tpo $depbase.Plo >depbase=`echo ncx.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ > /bin/sh ../libtool --tag=CC --mode=compile x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I../fortran -I/usr/include -I/usr/include -O2 -march=native -pipe -MT ncx.lo -MD -MP -MF $depbase.Tpo -c -o ncx.lo ncx.c &&\ > mv -f $depbase.Tpo $depbase.Plo >libtool: compile: x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I../fortran -I/usr/include -I/usr/include -O2 -march=native -pipe -MT attr.lo -MD -MP -MF .deps/attr.Tpo -c attr.c -fPIC -DPIC -o .libs/attr.o >libtool: compile: x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I../fortran -I/usr/include -I/usr/include -O2 -march=native -pipe -MT v2i.lo -MD -MP -MF .deps/v2i.Tpo -c v2i.c -fPIC -DPIC -o .libs/v2i.o >libtool: compile: x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I../fortran -I/usr/include -I/usr/include -O2 -march=native -pipe -MT ncx.lo -MD -MP -MF .deps/ncx.Tpo -c ncx.c -fPIC -DPIC -o .libs/ncx.o >depbase=`echo dim.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ > /bin/sh ../libtool --tag=CC --mode=compile x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I../fortran -I/usr/include -I/usr/include -O2 -march=native -pipe -MT dim.lo -MD -MP -MF $depbase.Tpo -c -o dim.lo dim.c &&\ > mv -f $depbase.Tpo $depbase.Plo >libtool: compile: x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I../fortran -I/usr/include -I/usr/include -O2 -march=native -pipe -MT dim.lo -MD -MP -MF .deps/dim.Tpo -c dim.c -fPIC -DPIC -o .libs/dim.o >depbase=`echo error.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ > /bin/sh ../libtool --tag=CC --mode=compile x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I../fortran -I/usr/include -I/usr/include -O2 -march=native -pipe -MT error.lo -MD -MP -MF $depbase.Tpo -c -o error.lo error.c &&\ > mv -f $depbase.Tpo $depbase.Plo >depbase=`echo libvers.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ > /bin/sh ../libtool --tag=CC --mode=compile x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I../fortran -I/usr/include -I/usr/include -O2 -march=native -pipe -MT libvers.lo -MD -MP -MF $depbase.Tpo -c -o libvers.lo libvers.c &&\ > mv -f $depbase.Tpo $depbase.Plo >libtool: compile: x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I../fortran -I/usr/include -I/usr/include -O2 -march=native -pipe -MT error.lo -MD -MP -MF .deps/error.Tpo -c error.c -fPIC -DPIC -o .libs/error.o >libtool: compile: x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I../fortran -I/usr/include -I/usr/include -O2 -march=native -pipe -MT libvers.lo -MD -MP -MF .deps/libvers.Tpo -c libvers.c -fPIC -DPIC -o .libs/libvers.o >depbase=`echo nc.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ > /bin/sh ../libtool --tag=CC --mode=compile x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I../fortran -I/usr/include -I/usr/include -O2 -march=native -pipe -MT nc.lo -MD -MP -MF $depbase.Tpo -c -o nc.lo nc.c &&\ > mv -f $depbase.Tpo $depbase.Plo >depbase=`echo string.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ > /bin/sh ../libtool --tag=CC --mode=compile x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I../fortran -I/usr/include -I/usr/include -O2 -march=native -pipe -MT string.lo -MD -MP -MF $depbase.Tpo -c -o string.lo string.c &&\ > mv -f $depbase.Tpo $depbase.Plo >libtool: compile: x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I../fortran -I/usr/include -I/usr/include -O2 -march=native -pipe -MT nc.lo -MD -MP -MF .deps/nc.Tpo -c nc.c -fPIC -DPIC -o .libs/nc.o >libtool: compile: x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I../fortran -I/usr/include -I/usr/include -O2 -march=native -pipe -MT string.lo -MD -MP -MF .deps/string.Tpo -c string.c -fPIC -DPIC -o .libs/string.o >depbase=`echo v1hpg.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ > /bin/sh ../libtool --tag=CC --mode=compile x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I../fortran -I/usr/include -I/usr/include -O2 -march=native -pipe -MT v1hpg.lo -MD -MP -MF $depbase.Tpo -c -o v1hpg.lo v1hpg.c &&\ > mv -f $depbase.Tpo $depbase.Plo >libtool: compile: x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I../fortran -I/usr/include -I/usr/include -O2 -march=native -pipe -MT v1hpg.lo -MD -MP -MF .deps/v1hpg.Tpo -c v1hpg.c -fPIC -DPIC -o .libs/v1hpg.o >depbase=`echo var.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ > /bin/sh ../libtool --tag=CC --mode=compile x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I../fortran -I/usr/include -I/usr/include -O2 -march=native -pipe -MT var.lo -MD -MP -MF $depbase.Tpo -c -o var.lo var.c &&\ > mv -f $depbase.Tpo $depbase.Plo >libtool: compile: x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I../fortran -I/usr/include -I/usr/include -O2 -march=native -pipe -MT var.lo -MD -MP -MF .deps/var.Tpo -c var.c -fPIC -DPIC -o .libs/var.o >depbase=`echo utf8proc.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ > /bin/sh ../libtool --tag=CC --mode=compile x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I../fortran -I/usr/include -I/usr/include -O2 -march=native -pipe -MT utf8proc.lo -MD -MP -MF $depbase.Tpo -c -o utf8proc.lo utf8proc.c &&\ > mv -f $depbase.Tpo $depbase.Plo >depbase=`echo putget.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ > /bin/sh ../libtool --tag=CC --mode=compile x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I../fortran -I/usr/include -I/usr/include -O2 -march=native -pipe -MT putget.lo -MD -MP -MF $depbase.Tpo -c -o putget.lo putget.c &&\ > mv -f $depbase.Tpo $depbase.Plo >libtool: compile: x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I../fortran -I/usr/include -I/usr/include -O2 -march=native -pipe -MT utf8proc.lo -MD -MP -MF .deps/utf8proc.Tpo -c utf8proc.c -fPIC -DPIC -o .libs/utf8proc.o >libtool: compile: x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I../fortran -I/usr/include -I/usr/include -O2 -march=native -pipe -MT putget.lo -MD -MP -MF .deps/putget.Tpo -c putget.c -fPIC -DPIC -o .libs/putget.o >depbase=`echo posixio.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ > /bin/sh ../libtool --tag=CC --mode=compile x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I../fortran -I/usr/include -I/usr/include -O2 -march=native -pipe -MT posixio.lo -MD -MP -MF $depbase.Tpo -c -o posixio.lo posixio.c &&\ > mv -f $depbase.Tpo $depbase.Plo >libtool: compile: x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I../fortran -I/usr/include -I/usr/include -O2 -march=native -pipe -MT posixio.lo -MD -MP -MF .deps/posixio.Tpo -c posixio.c -fPIC -DPIC -o .libs/posixio.o >/bin/sh ../libtool --tag=CC --mode=link x86_64-pc-linux-gnu-gcc -O2 -march=native -pipe -L/usr/lib -L/usr/lib -Wl,-O1 -Wl,--as-needed -o libnetcdf2.la v2i.lo >libtool: link: x86_64-pc-linux-gnu-ar cru .libs/libnetcdf2.a .libs/v2i.o >libtool: link: x86_64-pc-linux-gnu-ranlib .libs/libnetcdf2.a >libtool: link: ( cd ".libs" && rm -f "libnetcdf2.la" && ln -s "../libnetcdf2.la" "libnetcdf2.la" ) >/bin/sh ../libtool --tag=CC --mode=link x86_64-pc-linux-gnu-gcc -O2 -march=native -pipe -L/usr/lib -L/usr/lib -Wl,-O1 -Wl,--as-needed -o libnetcdf3.la attr.lo ncx.lo dim.lo error.lo libvers.lo nc.lo string.lo v1hpg.lo var.lo utf8proc.lo putget.lo posixio.lo >libtool: link: x86_64-pc-linux-gnu-ar cru .libs/libnetcdf3.a .libs/attr.o .libs/ncx.o .libs/dim.o .libs/error.o .libs/libvers.o .libs/nc.o .libs/string.o .libs/v1hpg.o .libs/var.o .libs/utf8proc.o .libs/putget.o .libs/posixio.o >libtool: link: x86_64-pc-linux-gnu-ranlib .libs/libnetcdf3.a >libtool: link: ( cd ".libs" && rm -f "libnetcdf3.la" && ln -s "../libnetcdf3.la" "libnetcdf3.la" ) >make[2]: Leaving directory `/var/tmp/paludis/sci-libs-netcdf-4.1.1/work/netcdf-4.1.1/libsrc' >Making all in libsrc4 >make[2]: Entering directory `/var/tmp/paludis/sci-libs-netcdf-4.1.1/work/netcdf-4.1.1/libsrc4' >depbase=`echo nc4attr.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ > /bin/sh ../libtool --tag=CC --mode=compile x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I../fortran -I../libsrc -I/usr/include -I/usr/include -O2 -march=native -pipe -MT nc4attr.lo -MD -MP -MF $depbase.Tpo -c -o nc4attr.lo nc4attr.c &&\ > mv -f $depbase.Tpo $depbase.Plo >depbase=`echo nc4internal.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ > /bin/sh ../libtool --tag=CC --mode=compile x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I../fortran -I../libsrc -I/usr/include -I/usr/include -O2 -march=native -pipe -MT nc4internal.lo -MD -MP -MF $depbase.Tpo -c -o nc4internal.lo nc4internal.c &&\ > mv -f $depbase.Tpo $depbase.Plo >depbase=`echo nc4var.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ > /bin/sh ../libtool --tag=CC --mode=compile x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I../fortran -I../libsrc -I/usr/include -I/usr/include -O2 -march=native -pipe -MT nc4var.lo -MD -MP -MF $depbase.Tpo -c -o nc4var.lo nc4var.c &&\ > mv -f $depbase.Tpo $depbase.Plo >libtool: compile: x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I../fortran -I../libsrc -I/usr/include -I/usr/include -O2 -march=native -pipe -MT nc4internal.lo -MD -MP -MF .deps/nc4internal.Tpo -c nc4internal.c -fPIC -DPIC -o .libs/nc4internal.o >libtool: compile: x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I../fortran -I../libsrc -I/usr/include -I/usr/include -O2 -march=native -pipe -MT nc4var.lo -MD -MP -MF .deps/nc4var.Tpo -c nc4var.c -fPIC -DPIC -o .libs/nc4var.o >libtool: compile: x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I../fortran -I../libsrc -I/usr/include -I/usr/include -O2 -march=native -pipe -MT nc4attr.lo -MD -MP -MF .deps/nc4attr.Tpo -c nc4attr.c -fPIC -DPIC -o .libs/nc4attr.o >depbase=`echo nc4dim.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ > /bin/sh ../libtool --tag=CC --mode=compile x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I../fortran -I../libsrc -I/usr/include -I/usr/include -O2 -march=native -pipe -MT nc4dim.lo -MD -MP -MF $depbase.Tpo -c -o nc4dim.lo nc4dim.c &&\ > mv -f $depbase.Tpo $depbase.Plo >depbase=`echo ncfunc.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ > /bin/sh ../libtool --tag=CC --mode=compile x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I../fortran -I../libsrc -I/usr/include -I/usr/include -O2 -march=native -pipe -MT ncfunc.lo -MD -MP -MF $depbase.Tpo -c -o ncfunc.lo ncfunc.c &&\ > mv -f $depbase.Tpo $depbase.Plo >libtool: compile: x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I../fortran -I../libsrc -I/usr/include -I/usr/include -O2 -march=native -pipe -MT nc4dim.lo -MD -MP -MF .deps/nc4dim.Tpo -c nc4dim.c -fPIC -DPIC -o .libs/nc4dim.o >libtool: compile: x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I../fortran -I../libsrc -I/usr/include -I/usr/include -O2 -march=native -pipe -MT ncfunc.lo -MD -MP -MF .deps/ncfunc.Tpo -c ncfunc.c -fPIC -DPIC -o .libs/ncfunc.o >depbase=`echo nc4file.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ > /bin/sh ../libtool --tag=CC --mode=compile x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I../fortran -I../libsrc -I/usr/include -I/usr/include -O2 -march=native -pipe -MT nc4file.lo -MD -MP -MF $depbase.Tpo -c -o nc4file.lo nc4file.c &&\ > mv -f $depbase.Tpo $depbase.Plo >depbase=`echo error.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ > /bin/sh ../libtool --tag=CC --mode=compile x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I../fortran -I../libsrc -I/usr/include -I/usr/include -O2 -march=native -pipe -MT error.lo -MD -MP -MF $depbase.Tpo -c -o error.lo error.c &&\ > mv -f $depbase.Tpo $depbase.Plo >libtool: compile: x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I../fortran -I../libsrc -I/usr/include -I/usr/include -O2 -march=native -pipe -MT nc4file.lo -MD -MP -MF .deps/nc4file.Tpo -c nc4file.c -fPIC -DPIC -o .libs/nc4file.o >libtool: compile: x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I../fortran -I../libsrc -I/usr/include -I/usr/include -O2 -march=native -pipe -MT error.lo -MD -MP -MF .deps/error.Tpo -c error.c -fPIC -DPIC -o .libs/error.o >depbase=`echo nc4grp.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ > /bin/sh ../libtool --tag=CC --mode=compile x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I../fortran -I../libsrc -I/usr/include -I/usr/include -O2 -march=native -pipe -MT nc4grp.lo -MD -MP -MF $depbase.Tpo -c -o nc4grp.lo nc4grp.c &&\ > mv -f $depbase.Tpo $depbase.Plo >libtool: compile: x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I../fortran -I../libsrc -I/usr/include -I/usr/include -O2 -march=native -pipe -MT nc4grp.lo -MD -MP -MF .deps/nc4grp.Tpo -c nc4grp.c -fPIC -DPIC -o .libs/nc4grp.o >depbase=`echo nc4type.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ > /bin/sh ../libtool --tag=CC --mode=compile x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I../fortran -I../libsrc -I/usr/include -I/usr/include -O2 -march=native -pipe -MT nc4type.lo -MD -MP -MF $depbase.Tpo -c -o nc4type.lo nc4type.c &&\ > mv -f $depbase.Tpo $depbase.Plo >libtool: compile: x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I../fortran -I../libsrc -I/usr/include -I/usr/include -O2 -march=native -pipe -MT nc4type.lo -MD -MP -MF .deps/nc4type.Tpo -c nc4type.c -fPIC -DPIC -o .libs/nc4type.o >depbase=`echo nc4hdf.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ > /bin/sh ../libtool --tag=CC --mode=compile x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I../fortran -I../libsrc -I/usr/include -I/usr/include -O2 -march=native -pipe -MT nc4hdf.lo -MD -MP -MF $depbase.Tpo -c -o nc4hdf.lo nc4hdf.c &&\ > mv -f $depbase.Tpo $depbase.Plo >libtool: compile: x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I../fortran -I../libsrc -I/usr/include -I/usr/include -O2 -march=native -pipe -MT nc4hdf.lo -MD -MP -MF .deps/nc4hdf.Tpo -c nc4hdf.c -fPIC -DPIC -o .libs/nc4hdf.o >/bin/sh ../libtool --tag=CC --mode=link x86_64-pc-linux-gnu-gcc -O2 -march=native -pipe -version-number 6:0:0 -Wl,-O1 -Wl,--as-needed -o libnetcdf.la -rpath /usr/lib64 nc4attr.lo nc4internal.lo nc4var.lo nc4dim.lo ncfunc.lo nc4file.lo error.lo nc4grp.lo nc4type.lo nc4hdf.lo ../libsrc/libnetcdf3.la ../libsrc/libnetcdf2.la -lhdf5_hl -lhdf5 >libtool: link: x86_64-pc-linux-gnu-gcc -shared .libs/nc4attr.o .libs/nc4internal.o .libs/nc4var.o .libs/nc4dim.o .libs/ncfunc.o .libs/nc4file.o .libs/error.o .libs/nc4grp.o .libs/nc4type.o .libs/nc4hdf.o -Wl,--whole-archive ../libsrc/.libs/libnetcdf3.a ../libsrc/.libs/libnetcdf2.a -Wl,--no-whole-archive -L/usr/lib /usr/lib64/libhdf5_hl.so -L/usr/lib64 /usr/lib64/libhdf5.so -lz -lm -march=native -Wl,-O1 -Wl,--as-needed -Wl,-soname -Wl,libnetcdf.so.6 -o .libs/libnetcdf.so.6.0.0 >libtool: link: (cd ".libs" && rm -f "libnetcdf.so.6" && ln -s "libnetcdf.so.6.0.0" "libnetcdf.so.6") >libtool: link: (cd ".libs" && rm -f "libnetcdf.so" && ln -s "libnetcdf.so.6.0.0" "libnetcdf.so") >libtool: link: ( cd ".libs" && rm -f "libnetcdf.la" && ln -s "../libnetcdf.la" "libnetcdf.la" ) >make[2]: Leaving directory `/var/tmp/paludis/sci-libs-netcdf-4.1.1/work/netcdf-4.1.1/libsrc4' >Making all in f90 >make[2]: Entering directory `/var/tmp/paludis/sci-libs-netcdf-4.1.1/work/netcdf-4.1.1/f90' >x86_64-pc-linux-gnu-gfortran -I/usr/include -I/usr/include -I../libsrc4 -I. -g -O2 -c -o typeSizes.o typeSizes.f90 >make all-am >make[3]: Entering directory `/var/tmp/paludis/sci-libs-netcdf-4.1.1/work/netcdf-4.1.1/f90' >/bin/sh ../libtool --tag=FC --mode=compile x86_64-pc-linux-gnu-gfortran -I/usr/include -I/usr/include -I../libsrc4 -I. -g -O2 -c -o typeSizes.lo typeSizes.f90 >/bin/sh ../libtool --tag=FC --mode=compile x86_64-pc-linux-gnu-gfortran -I/usr/include -I/usr/include -I../libsrc4 -I. -g -O2 -c -o netcdf4.lo netcdf4.f90 >x86_64-pc-linux-gnu-gfortran -I/usr/include -I/usr/include -I../libsrc4 -I. -g -O2 -c -o netcdf4.o netcdf4.f90 >libtool: compile: x86_64-pc-linux-gnu-gfortran -I/usr/include -I/usr/include -I../libsrc4 -I. -g -O2 -c netcdf4.f90 -fPIC -o .libs/netcdf4.o >libtool: compile: x86_64-pc-linux-gnu-gfortran -I/usr/include -I/usr/include -I../libsrc4 -I. -g -O2 -c typeSizes.f90 -fPIC -o .libs/typeSizes.o >Fatal Error: Can't delete temporary module file 'netcdf.mod0': No such file or directory >make[3]: *** [netcdf4.lo] Error 1 >make[3]: *** Waiting for unfinished jobs.... >make[3]: Leaving directory `/var/tmp/paludis/sci-libs-netcdf-4.1.1/work/netcdf-4.1.1/f90' >make[2]: Leaving directory `/var/tmp/paludis/sci-libs-netcdf-4.1.1/work/netcdf-4.1.1/f90' >make[2]: *** [all] Error 2 >make[1]: Leaving directory `/var/tmp/paludis/sci-libs-netcdf-4.1.1/work/netcdf-4.1.1' >make[1]: *** [all-recursive] Error 1 >make: *** [all] Error 2 >/usr/libexec/paludis/utils/emake: emake returned error 2 > >!!! ERROR in sci-libs/netcdf-4.1.1::gentoo: >!!! In src_compile at line 3873 >!!! emake failed > >!!! Call stack: >!!! * src_compile (/var/tmp/paludis/sci-libs-netcdf-4.1.1/temp/loadsaveenv:3873) >!!! * ebuild_f_compile (/usr/libexec/paludis/2/src_compile.bash:56) >!!! * ebuild_main (/usr/libexec/paludis/ebuild.bash:647) >!!! * main (/usr/libexec/paludis/ebuild.bash:675) > >diefunc: making ebuild PID 10636 exit with error >die trap: exiting with error. > >Install error: > * In program paludis -i netcdf: > * When performing install action from command line: > * When executing install task: > * When installing 'sci-libs/netcdf-4.1.1:0::gentoo' replacing { 'sci-libs/netcdf-4.1.1:0::installed' }: > * When running an ebuild command on 'sci-libs/netcdf-4.1.1:0::gentoo': > * Install failed for 'sci-libs/netcdf-4.1.1:0::gentoo' > >
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