Opened 15 years ago
Closed 14 years ago
#24582 closed defect (fixed)
nco compile fails
| Reported by: | ohtinsel@… | Owned by: | tenomoto (Takeshi Enomoto) |
|---|---|---|---|
| Priority: | Normal | Milestone: | |
| Component: | ports | Version: | 1.8.2 |
| Keywords: | Cc: | mikejmills@… | |
| Port: | nco |
Description (last modified by jmroot (Joshua Root))
I'm having problems installing NCO. The basic issue is some sort of duplicate symbol problem with netcdf4:
ld: warning: directory '/lib' following -L not found ld: duplicate symbol _nc_get_vara_string in /opt/local/lib/netcdf-devel/lib/libnetcdf.a(nc4var.o) and ./.libs/libnco.a(nco_netcdf.o) collect2: ld returned 1 exit status
I've successfully installed other (non macport) software using the netcdf-devel library so that seems fine. I have not installed the basic netcdf port.
I have attached the debug of the build.
Mike
Attachments (1)
Change History (10)
Changed 15 years ago by ohtinsel@…
| Attachment: | nco_debug.txt added |
|---|
comment:1 Changed 15 years ago by jmroot (Joshua Root)
| Description: | modified (diff) |
|---|---|
| Keywords: | nco removed |
| Owner: | changed from macports-tickets@… to takeshi@… |
comment:3 Changed 15 years ago by mikejmills@…
I have been struggling with this same problem today. I have managed to install NCO with MacPorts on an identical Mac Pro at work, but not at home. I have also just installed successfully on my MacBook Pro. I noticed someone else had a similar problem, reported in Ticket #23645. I tried the commands suggested there, but no luck.
comment:4 Changed 15 years ago by tenomoto (Takeshi Enomoto)
The help on #23645 is out of date. netcdf port is not required for nco; to avoid problems I separated netcdf-4 enabled version as netcdf-devel. I would like to take a look at configure messages. Could you clean nco and configure again? I would like to look at work/nco-4.0.1/config.log.
sudo port -d clean nco sudo port -d configure nco
comment:5 Changed 15 years ago by ohtinsel@…
Okay, here is the debug dump.
Mike
---> Computing dependencies for nco ---> Fetching nco ---> Verifying checksum(s) for nco ---> Checksumming nco-4.0.1.tar.gz ---> Extracting nco ---> Extracting nco-4.0.1.tar.gz ---> Configuring nco checking build system type... i386-apple-darwin10.3.0 checking host system type... i386-apple-darwin10.3.0 checking target system type... i386-apple-darwin10.3.0 checking for grep that handles long lines and -e... /usr/bin/grep checking for egrep... /usr/bin/grep -E checking for a BSD-compatible install... /usr/bin/install -c checking whether build environment is sane... yes checking for a thread-safe mkdir -p... /opt/local/bin/mkdir -p checking for gawk... no checking for mawk... no checking for nawk... no checking for awk... awk checking whether make sets $(MAKE)... yes checking for gcc... /usr/bin/gcc-4.2 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 /usr/bin/gcc-4.2 accepts -g... yes checking for /usr/bin/gcc-4.2 option to accept ISO C89... none needed checking for style of include used by make... GNU checking dependency style of /usr/bin/gcc-4.2... none checking whether we are using the GNU C++ compiler... yes checking whether /usr/bin/g++-4.2 accepts -g... yes checking dependency style of /usr/bin/g++-4.2... none checking how to run the C preprocessor... /usr/bin/gcc-4.2 -E checking how to run the C++ preprocessor... /usr/bin/g++-4.2 -E checking for /usr/bin/gcc-4.2 option to accept ISO C99... -std=gnu99 checking for /usr/bin/gcc-4.2 -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 whether ln -s works... yes checking for a sed that does not truncate output... /usr/bin/sed checking for fgrep... /usr/bin/grep -F checking for ld used by /usr/bin/gcc-4.2 -std=gnu99... /usr/libexec/gcc/i686-apple-darwin10/4.2.1/ld checking if the linker (/usr/libexec/gcc/i686-apple-darwin10/4.2.1/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 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/libexec/gcc/i686-apple-darwin10/4.2.1/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 /usr/bin/gcc-4.2 -std=gnu99 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 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 /usr/bin/g++-4.2 accepts -g... (cached) yes checking dependency style of /usr/bin/g++-4.2... (cached) none checking how to run the C++ preprocessor... /usr/bin/g++-4.2 -E checking for objdir... .libs checking if /usr/bin/gcc-4.2 -std=gnu99 supports -fno-rtti -fno-exceptions... no checking for /usr/bin/gcc-4.2 -std=gnu99 option to produce PIC... -fno-common -DPIC checking if /usr/bin/gcc-4.2 -std=gnu99 PIC flag -fno-common -DPIC works... yes checking if /usr/bin/gcc-4.2 -std=gnu99 static flag -static works... no checking if /usr/bin/gcc-4.2 -std=gnu99 supports -c -o file.o... yes checking if /usr/bin/gcc-4.2 -std=gnu99 supports -c -o file.o... (cached) yes checking whether the /usr/bin/gcc-4.2 -std=gnu99 linker (/usr/libexec/gcc/i686-apple-darwin10/4.2.1/ld) supports shared libraries... yes checking dynamic linker characteristics... darwin10.3.0 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 for ld used by /usr/bin/g++-4.2... /usr/libexec/gcc/i686-apple-darwin10/4.2.1/ld checking if the linker (/usr/libexec/gcc/i686-apple-darwin10/4.2.1/ld) is GNU ld... no checking whether the /usr/bin/g++-4.2 linker (/usr/libexec/gcc/i686-apple-darwin10/4.2.1/ld) supports shared libraries... yes checking for /usr/bin/g++-4.2 option to produce PIC... -fno-common -DPIC checking if /usr/bin/g++-4.2 PIC flag -fno-common -DPIC works... yes checking if /usr/bin/g++-4.2 static flag -static works... no checking if /usr/bin/g++-4.2 supports -c -o file.o... yes checking if /usr/bin/g++-4.2 supports -c -o file.o... (cached) yes checking whether the /usr/bin/g++-4.2 linker (/usr/libexec/gcc/i686-apple-darwin10/4.2.1/ld) supports shared libraries... yes checking dynamic linker characteristics... darwin10.3.0 dyld 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... no checking whether stat accepts an empty string... no checking for working strtod... yes checking for canonicalize_file_name... no checking for floor... yes 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... yes checking for readlink... yes checking for realpath... yes checking for regcomp... yes checking for setlocale... yes checking for sqrt... yes 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 = no Testing for DAP-netCDF support (is DAP in libnetcdf.a?)... checking for nc__opendap in -lnetcdf... yes configure: DAP support enabled 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... no DEBUG: After netCDF4 section LIBS = -lnetcdf DEBUG: After netCDF4 section header_defines_nc_chunked = DEBUG: After netCDF3 section LIBS = -lnetcdf 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... yes checking for res_init in -lresolv... yes checking for main in -lsocket... no checking for main in -lthread... no checking for nco_open in -lnco... no checking for nc_inq_format... no 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... no 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 = 1 DEBUG: After library checks LIBS=-lresolv -lintl -lm -lnetcdf ################################# # Testing for ANTLR support # ################################# checking for runantlr... yes checking antlr/CommonToken.hpp usability... yes checking antlr/CommonToken.hpp presence... yes checking for antlr/CommonToken.hpp... yes INFO: ANTLR development support found---will build nco++ directory and ncap2 DEBUG: enable_mpi = '' ######################################## # 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 /opt/local/include/gsl/gsl_sf_gamma.h... yes configure: GSL support enabled DEBUG: After GSL tests LIBS = -lgsl -L/opt/local/lib -lgsl -lgslcblas -lm -lresolv -lintl -lm -lnetcdf 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 = yes and enable_udunits2 = no checking for tdelete... yes checking for /usr/local/etc/udunits.dat... no configure: WARNING: file /usr/local/etc/udunits.dat was not found but will still attempt to build NCO with UDUnits support. checking for tdelete... (cached) yes configure: NB: Following tests of UDUnits library and header must succeed for UDUnits support: checking for utInit in -ludunits... yes checking udunits.h usability... yes checking udunits.h presence... yes checking for udunits.h... yes configure: UDUnits support enabled DEBUG: After UDUnits tests LIBS = -ludunits -lgsl -L/opt/local/lib -lgsl -lgslcblas -lm -lresolv -lintl -lm -lnetcdf -ludunits DEBUG: After UDUnits2 tests LIBS = -ludunits -lgsl -L/opt/local/lib -lgsl -lgslcblas -lm -lresolv -lintl -lm -lnetcdf -ludunits checking for ncgen... /opt/local/lib/netcdf-devel/bin/ncgen configure: Creating sample netCDF data files for self-tests ############################### # Require Shared Libs? # ############################### DEBUG: enable_shared: no DEBUG: enable_shared: rejected due to netcdf4 requirement DEBUG: enable_ncoxx: yes and NCOXX = nco++ 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 src/nco++/Makefile config.status: creating config.h config.status: executing depfiles commands config.status: executing libtool commands Configuration Parameters: AR_FLAGS............. cru CC................... /usr/bin/gcc-4.2 -std=gnu99 CFLAGS............... -fno-common -O2 -arch x86_64 -std=c99 -D_BSD_SOURCE CPP.................. /usr/bin/gcc-4.2 -E CPPFLAGS............. -I/opt/local/include -I/usr/include/malloc -I/opt/local/lib/netcdf-devel/include -I/opt/local/include -I/opt/local/include CXX.................. /usr/bin/g++-4.2 CXXFLAGS............. -O2 -arch x86_64 ENABLE_DAP_NETCDF.... yes ENABLE_DAP_OPENDAP... no ENABLE_DAP........... yes ENABLE_GSL........... yes ENABLE_MPI........... ENABLE_NETCDF4....... no ENABLE_UDUNITS....... yes ENABLE_UDUNITS2...... no GSL_ROOT............. /opt/local HAVE_NETCDF4_H....... HOST................. host................. i386-apple-darwin10.3.0 HOSTNAME............. boreas.giss.nasa.gov LDFLAGS.............. -L/opt/local/lib/netcdf-devel/lib -L/opt/local/lib -L/opt/local/lib LIBS................. -ludunits -lgsl -L/opt/local/lib -lgsl -lgslcblas -lm -lresolv -lintl -lm -lnetcdf -ludunits 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. *******************************************************************
comment:6 Changed 15 years ago by tenomoto (Takeshi Enomoto)
You have netcdf-4 disabled version of netcdf-devel. netcdf-devel should be netcdf-4 enabled by default. I would like to look the results of the two commands:
port installed netcdf-devel
and
/opt/local/lib/netcdf-devel/bin/nc-config --has-nc4
comment:7 Changed 15 years ago by ohtinsel@…
Okay,
port installed netcdf-devel The following ports are currently installed: netcdf-devel @4.1.1_0 (active)
/opt/local/lib/netcdf-devel/bin/nc-config --has-nc4 yes
Thanks for working on this!
comment:8 Changed 14 years ago by tenomoto (Takeshi Enomoto)
netcdf and netcdf-devel have been merged (r69159). Do you still have a problem?
comment:9 Changed 14 years ago by tenomoto (Takeshi Enomoto)
| Resolution: | → fixed |
|---|---|
| Status: | new → closed |
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