sci-misc:nco-3.9.9:20160405-224602.log

sci-misc:nco-3.9.9:20160405-224602.log (text/plain), 16.41 KB, created by Toralf Förster on 2016-04-06 14:15:14 UTC

 * Package:    sci-misc/nco-3.9.9
 * Repository: gentoo
 * Maintainer: [e-mail]
 * USE:        abi_x86_64 amd64 elibc_glibc kernel_linux policykit userland_GNU
 * FEATURES:   preserve-libs sandbox userpriv usersandbox
>>> Unpacking source...
>>> Unpacking nco-3.9.9.tar.gz to /var/tmp/portage/sci-misc/nco-3.9.9/work
>>> Source unpacked in /var/tmp/portage/sci-misc/nco-3.9.9/work
>>> Preparing source in /var/tmp/portage/sci-misc/nco-3.9.9/work/nco-3.9.9 ...
>>> Source prepared.
>>> Configuring source in /var/tmp/portage/sci-misc/nco-3.9.9/work/nco-3.9.9 ...
 * econf: updating nco-3.9.9/autobld/config.guess with /usr/share/gnuconfig/config.guess
 * econf: updating nco-3.9.9/autobld/config.sub with /usr/share/gnuconfig/config.sub
./configure --prefix=/usr --build=x86_64-pc-linux-gnu --host=x86_64-pc-linux-gnu --mandir=/usr/share/man --infodir=/usr/share/info --datadir=/usr/share --sysconfdir=/etc --localstatedir=/var/lib --libdir=/usr/lib64 --enable-netcdf4 --disable-udunits --disable-ncap2 --disable-udunits2 --disable-mpi
checking build system type... x86_64-pc-linux-gnu
checking host system type... x86_64-pc-linux-gnu
checking target system type... x86_64-pc-linux-gnu
checking for grep that handles long lines and -e... /bin/grep
checking for egrep... /bin/grep -E
checking for a BSD-compatible install... /usr/lib/portage/python3.4/ebuild-helpers/xattr/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-gcc... x86_64-pc-linux-gnu-gcc
checking for C compiler default output file name... a.out
checking whether the C compiler works... yes
checking whether we are cross compiling... no
checking for suffix of executables... 
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 for x86_64-pc-linux-gnu-g++... x86_64-pc-linux-gnu-g++
checking whether we are using the GNU C++ compiler... yes
checking whether x86_64-pc-linux-gnu-g++ accepts -g... yes
checking dependency style of x86_64-pc-linux-gnu-g++... gcc3
checking how to run the C preprocessor... x86_64-pc-linux-gnu-gcc -E
checking how to run the C++ preprocessor... x86_64-pc-linux-gnu-g++ -E
checking for x86_64-pc-linux-gnu-gcc option to accept ISO C99... -std=gnu99
checking for x86_64-pc-linux-gnu-gcc -std=gnu99 option to accept ISO Standard C... (cached) -std=gnu99
checking for flex... flex
checking lex output file root... lex.yy
checking lex library... -lfl
checking whether yytext is a pointer... yes
checking for bison... bison -y
checking for a BSD-compatible install... /usr/lib/portage/python3.4/ebuild-helpers/xattr/install -c
checking whether ln -s works... yes
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 -std=gnu99... /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... 1572864
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 for x86_64-pc-linux-gnu-objdump... x86_64-pc-linux-gnu-objdump
checking how to recognize dependent libraries... pass_all
checking for x86_64-pc-linux-gnu-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 -std=gnu99 object... ok
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-g++ accepts -g... (cached) yes
checking dependency style of x86_64-pc-linux-gnu-g++... (cached) gcc3
checking how to run the C++ preprocessor... x86_64-pc-linux-gnu-g++ -E
checking for objdir... .libs
checking if x86_64-pc-linux-gnu-gcc -std=gnu99 supports -fno-rtti -fno-exceptions... no
checking for x86_64-pc-linux-gnu-gcc -std=gnu99 option to produce PIC... -fPIC -DPIC
checking if x86_64-pc-linux-gnu-gcc -std=gnu99 PIC flag -fPIC -DPIC works... yes
checking if x86_64-pc-linux-gnu-gcc -std=gnu99 static flag -static works... yes
checking if x86_64-pc-linux-gnu-gcc -std=gnu99 supports -c -o file.o... yes
checking if x86_64-pc-linux-gnu-gcc -std=gnu99 supports -c -o file.o... (cached) yes
checking whether the x86_64-pc-linux-gnu-gcc -std=gnu99 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... yes
checking for ld used by x86_64-pc-linux-gnu-g++... /usr/x86_64-pc-linux-gnu/bin/ld -m elf_x86_64
checking if the linker (/usr/x86_64-pc-linux-gnu/bin/ld -m elf_x86_64) is GNU ld... yes
checking whether the x86_64-pc-linux-gnu-g++ linker (/usr/x86_64-pc-linux-gnu/bin/ld -m elf_x86_64) supports shared libraries... yes
checking for x86_64-pc-linux-gnu-g++ option to produce PIC... -fPIC -DPIC
checking if x86_64-pc-linux-gnu-g++ PIC flag -fPIC -DPIC works... yes
checking if x86_64-pc-linux-gnu-g++ static flag -static works... yes
checking if x86_64-pc-linux-gnu-g++ supports -c -o file.o... yes
checking if x86_64-pc-linux-gnu-g++ supports -c -o file.o... (cached) yes
checking whether the x86_64-pc-linux-gnu-g++ linker (/usr/x86_64-pc-linux-gnu/bin/ld -m elf_x86_64) supports shared libraries... yes
checking dynamic linker characteristics... GNU/Linux ld.so
checking how to hardcode library paths into programs... immediate
checking whether to enable maintainer-specific portions of Makefiles... no
checking for working memcmp... yes
checking whether lstat dereferences a symlink specified with a trailing slash... yes
checking whether stat accepts an empty string... no
checking for working strtod... yes
checking for canonicalize_file_name... yes
checking for floor... no
checking for gethostname... yes
checking for getpagesize... yes
checking for getrusage... yes
checking for memchr... yes
checking for memmove... yes
checking for memset... yes
checking for mkstemp... yes
checking for pow... no
checking for readlink... yes
checking for realpath... yes
checking for regcomp... yes
checking for setlocale... yes
checking for sqrt... no
checking for strchr... yes
checking for strerror... yes
checking for strpbrk... yes
checking for strrchr... yes
checking for strstr... yes
checking for strtol... yes
checking for ANSI C header files... (cached) yes
checking getopt.h usability... yes
checking getopt.h presence... yes
checking for getopt.h... yes
checking libintl.h usability... yes
checking libintl.h presence... yes
checking for libintl.h... yes
checking limits.h usability... yes
checking limits.h presence... yes
checking for limits.h... yes
checking locale.h usability... yes
checking locale.h presence... yes
checking for locale.h... yes
checking netinet/in.h usability... yes
checking netinet/in.h presence... yes
checking for netinet/in.h... yes
checking for stdlib.h... (cached) yes
checking for string.h... (cached) yes
checking for unistd.h... (cached) yes
checking cstdlib usability... yes
checking cstdlib presence... yes
checking for cstdlib... yes
checking for an ANSI C-conforming const... yes
checking for inline... inline
checking for pid_t... yes
checking for size_t... yes
checking whether struct tm is in sys/time.h or time.h... time.h
checking for uid_t in sys/types.h... yes
checking for ptrdiff_t... yes
checking size of int*... 8
checking whether C++ compiler implements namespaces... yes
checking whether C++ compiler has working valarray<T>... yes
checking for special C compiler options needed for large files... no
checking for _FILE_OFFSET_BITS value needed for large files... no
Beginning generic tests for DAP support
DEBUG: enable_dap_netcdf = yes and enable_dap_opendap = yes
WARNING: Requested both DAP-netCDF and DAP-OPeNDAP support---overriding OPeNDAP
Will attempt to build NCO with DAP support from netCDF4, not from OPeNDAP
Testing for DAP-netCDF support (is DAP in libnetcdf.a?)...
checking for nc__opendap in -lnetcdf... no
configure: WARNING: DAP-netCDF support through libnetCDF disabled (missing DAP library)
checking netcdf.h usability... yes
checking netcdf.h presence... yes
checking for netcdf.h... yes
#################################
#  Test for netCDF4 support     #
#################################
User set '--enable-netcdf4' but did not set NETCDF4_ROOT
Assuming netCDF4 is on standard path...
checking for nc4_enddef_netcdf4_file in -lnetcdf... yes
DEBUG: After netCDF4 section LIBS = -lnetcdf -lhdf5_hl -lhdf5 -lz 
configure: netcdf.h contains netCDF4 definitions
DEBUG: After netCDF4 section header_defines_nc_chunked = 
DEBUG: After netCDF3 section LIBS = -lnetcdf -lhdf5_hl -lhdf5 -lz 
checking for getopt_long... yes
checking for _g95_ac_array in -lf95... no
checking for sin in -lm... yes
checking for sinf in -lsunmath... no
checking for gettext in -lintl... no
checking for res_init in -lresolv... no
checking for main in -lsocket... no
checking for main in -lthread... no
checking for nco_open in -lnco... no
checking for nc_inq_format... yes
checking for getopt... yes
checking for getopt_long... (cached) yes
checking for atan2... yes
checking for acosf... yes
checking for asinf... yes
checking for atanf... yes
checking for atan2f... yes
checking for cosf... yes
checking for expf... yes
checking for fabsf... yes
checking for fmodf... yes
checking for log10f... yes
checking for logf... yes
checking for powf... yes
checking for sinf... yes
checking for sqrtf... yes
checking for tanf... yes
checking for erff... yes
checking for erfcf... yes
checking for gammaf... yes
checking for acoshf... yes
checking for asinhf... yes
checking for atanhf... yes
checking for coshf... yes
checking for sinhf... yes
checking for tanhf... yes
checking for ceilf... yes
checking for floorf... yes
checking for nearbyintf... yes
checking for rintf... yes
checking for roundf... yes
checking for truncf... yes
checking for getopt_long... (cached) yes
checking for strdup... yes
checking for strcasecmp... yes
##########################################################
#     Sorting out MacOSX build parameters                #
##########################################################
DEBUG: enable_libnco =  and MACOSX = 
DEBUG: After library checks LIBS=-lm -lnetcdf -lhdf5_hl -lhdf5 -lz 
#################################
#  Testing for ANTLR support    #
#################################
INFO: ANTLR support not found. To build ncap2, please install ANTLR and its C++ development package, e.g., 'sudo aptitude install antlr libantlr-dev' or 'sudo yum install antlr antlr-c++-devel'
DEBUG: enable_mpi = 'no'
########################################
#     Testing for GSL support          #
########################################
configure: These GSL library and header tests must succeed for GSL support:
checking for gsl_sf_gamma_inc in -lgsl... yes
checking for /usr/include/gsl/gsl_sf_gamma.h... yes
configure: GSL support enabled
DEBUG: After GSL tests LIBS = -lgsl -L/usr/lib64 -lgsl -lgslcblas -lm -lm -lnetcdf -lhdf5_hl -lhdf5 -lz 
checking regex.h usability... yes
checking regex.h presence... yes
checking for regex.h... yes
checking for sys/types.h... (cached) yes
checking for regexec... yes
checking for regcomp... (cached) yes
checking for regfree... yes
########################################
#     Testing for UDUNITS support      #
########################################
Beginning generic tests for UDUnits
DEBUG: enable_udunits = no and enable_udunits2 = no
checking for tdelete... yes
DEBUG: After UDUnits tests LIBS = -lgsl -L/usr/lib64 -lgsl -lgslcblas -lm -lm -lnetcdf -lhdf5_hl -lhdf5 -lz 
DEBUG: After UDUnits2 tests LIBS = -lgsl -L/usr/lib64 -lgsl -lgslcblas -lm -lm -lnetcdf -lhdf5_hl -lhdf5 -lz 
checking for ncgen... /usr/bin/ncgen
configure: Creating sample netCDF data files for self-tests
Bad octal constant: \b\n\0"
###############################
#    Require Shared Libs?     #
###############################
DEBUG: enable_shared: yes 
DEBUG: enable_shared: rejected due to netcdf4 requirement
DEBUG: enable_ncoxx: no and NCOXX = 
configure: creating ./config.status
config.status: creating Makefile
config.status: creating data/Makefile
config.status: creating src/Makefile
config.status: creating src/nco/Makefile
config.status: creating man/Makefile
config.status: creating doc/Makefile
config.status: creating src/nco_c++/Makefile
config.status: creating config.h
config.status: executing depfiles commands
config.status: executing libtool commands

Configuration Parameters:
AR_FLAGS............. cru
CC................... x86_64-pc-linux-gnu-gcc -std=gnu99
CFLAGS............... -march=native -O2 -pipe -std=c99 -D_BSD_SOURCE -D_POSIX_SOURCE
CPP.................. x86_64-pc-linux-gnu-gcc -E
CPPFLAGS............. -I/usr/include  -DHAVE_NETCDF4_H
CXX.................. x86_64-pc-linux-gnu-g++
CXXFLAGS............. -march=native -O2 -pipe
ENABLE_DAP_NETCDF.... no
ENABLE_DAP_OPENDAP... no
ENABLE_DAP........... no
ENABLE_GSL........... yes
ENABLE_MPI........... no
ENABLE_NETCDF4....... yes
ENABLE_UDUNITS....... no
ENABLE_UDUNITS2...... no
GSL_ROOT............. /usr
HAVE_NETCDF4_H....... 
HOST................. 
host................. x86_64-pc-linux-gnu
HOSTNAME............. ms-magpie
LDFLAGS.............. -Wl,-O1 -Wl,--as-needed
LIBS................. -lgsl -L/usr/lib64 -lgsl -lgslcblas -lm -lm -lnetcdf -lhdf5_hl -lhdf5 -lz 
NETCDF4_ROOT......... 
*******************************************************************
Configuration complete. You are now ready to run 'make'.
Ensure 'make' points to GNU Make (AT&T Make chokes on GNU syntax).
If the build fails, please examine the file 'configure.eg'
in the top-level NCO directory.  It contains examples known to
build NCO for various platforms and compilers.
*******************************************************************
>>> Source configured.
>>> Compiling source in /var/tmp/portage/sci-misc/nco-3.9.9/work/nco-3.9.9 ...
make -j1 
make  all-recursive
make[1]: Entering directory '/var/tmp/portage/sci-misc/nco-3.9.9/work/nco-3.9.9'
Making all in data
make[2]: Entering directory '/var/tmp/portage/sci-misc/nco-3.9.9/work/nco-3.9.9/data'
/usr/bin/ncgen -o big.nc big.cdl 
/usr/bin/ncgen -o in.nc in.cdl 
Bad octal constant: \b\n\0"
Makefile:374: recipe for target 'in.nc' failed
make[2]: *** [in.nc] Error 1
make[2]: Leaving directory '/var/tmp/portage/sci-misc/nco-3.9.9/work/nco-3.9.9/data'
Makefile:299: recipe for target 'all-recursive' failed
make[1]: *** [all-recursive] Error 1
make[1]: Leaving directory '/var/tmp/portage/sci-misc/nco-3.9.9/work/nco-3.9.9'
Makefile:229: recipe for target 'all' failed
make: *** [all] Error 2
emake failed
 * ERROR: sci-misc/nco-3.9.9::gentoo failed (compile phase):
 *   emake failed
 * 
 * Call stack:
 *     ebuild.sh, line 133:  Called src_compile
 *   environment, line 2255:  Called die
 * The specific snippet of code:
 *       emake || die "emake failed";
 * 
 * If you need support, post the output of `emerge --info '=sci-misc/nco-3.9.9::gentoo'`,
 * the complete build log and the output of `emerge -pqv '=sci-misc/nco-3.9.9::gentoo'`.
 * The complete build log is located at '/var/log/portage/sci-misc:nco-3.9.9:20160405-224602.log'.
 * For convenience, a symlink to the build log is located at '/var/tmp/portage/sci-misc/nco-3.9.9/temp/build.log'.
 * The ebuild environment file is located at '/var/tmp/portage/sci-misc/nco-3.9.9/temp/environment'.
 * Working directory: '/var/tmp/portage/sci-misc/nco-3.9.9/work/nco-3.9.9'
 * S: '/var/tmp/portage/sci-misc/nco-3.9.9/work/nco-3.9.9'