[netCDF #GOK-784955]: Problem encountered: catastrophic error: cannot open source file "stdarg.h"

Hi,

> I am trying to install GMT (version 4.5.7) with netCDF (version 4.0.1)
> using the install parameters provided by the http://gmt.soest.hawaii.edu in
> a Mac Pro with OS X 10.7.3 using Intel Fortran Composer XE 2011 and C++
> Composer XE 2011. I am encountering an error in the configuration of the
> status of the netCDF, specifically in executing libtool commands. In
> "Making check in libsrc", this error occurs:
> 
> libtool: compile:  icc -DHAVE_CONFIG_H -I. -I.. -I../fortran -g -O2 -MT
> dim.lo -MD -MP -MF .deps/dim.Tpo -c dim.c -o dim.o
> depbase=`echo error.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\
> /bin/sh ../libtool --tag=CC   --mode=compile icc -DHAVE_CONFIG_H -I. -I..
> -I../fortran        -g -O2 -MT error.lo -MD -MP -MF $depbase.Tpo -c -o
> error.lo error.c &&\
> mv -f $depbase.Tpo $depbase.Plo
> libtool: compile:  icc -DHAVE_CONFIG_H -I. -I.. -I../fortran -g -O2 -MT
> error.lo -MD -MP -MF .deps/error.Tpo -c error.c -o error.o
> error.c(11): catastrophic error: cannot open source file "stdarg.h"
> #include <stdarg.h>
> ^
> 
> Pasted below is a copy of the netCDF configuration run. I have also
> attached the log file. I have actually tried several versions of netCDF but
> it seems that 4.0.1 gives the least errors.

I see that the configure script determined that stdarg.h was a problem

> checking stdarg.h usability... no
> checking stdarg.h presence... no
> checking for stdarg.h... no

before the error that "make check" encountered.

I see configure is picking up g++ as the C++ compiler, and I'm not sure it's
compatible with icc that you're using as the C compiler.  If you don't really
need the C++ API for netCDF, you might try rebuilding with the environment
variable CXX='' or the configure option --disable-cxx and see if stdarg.h is
still a problem.  Another possibility is that your XCode Development Tools
for MacOS X need updating for OS X 10.7.3.  Another possibility is that you
overwrote the version of the configure script that came with the netCDF
distribution by running an old version of autoconf or autoreconf before
running configure.

Otherwise, I'm not sure what the problem is.  If this doesn't help, can you
send the information requested here and we'll see if we can see another
problem:

  http://www.unidata.ucar.edu/netcdf/docs/netcdf-install/Reporting-Problems.html

Thanks,

--Russ

> I am not really sure how this could be solved though I have found a quite
> similar problem reported in 2009 in the Intel software support. The
> suggested solution is an upgrade and I'm not sure if the similar approach
> is still applicable today. I have also sent an inquiry to the Intel team.
> Could your team please suggest a solution to this issue?
> 
> Thanks! I would greatly appreciate your help!
> 
> --
> *Cherry May R. Mateo*
> *MS Civil Engineering student, University of Tokyo*
> *President, International Students' Association in Civil Engineering - UT*
> *PRO, Association of Filipino Students in Japan*
> *Finance, Science and Technology Advisory Council - Japan*
> 
> configure: netCDF 4.0.1
> checking build system type... i386-apple-darwin11.3.0
> checking host system type... i386-apple-darwin11.3.0
> checking for a BSD-compatible install... /usr/bin/install -c
> checking whether build environment is sane... yes
> checking for a thread-safe mkdir -p... ./install-sh -c -d
> checking for gawk... no
> checking for mawk... no
> checking for nawk... no
> checking for awk... awk
> checking whether make sets $(MAKE)... yes
> configure: checking user options
> checking whether 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 this is a netCDF-4.x build... yes
> checking whether extra valgrind tests should be run... no
> configure: Processing NetCDF-4 options.
> checking whether netCDF-4 is to be built... no
> checking whether new netCDF-4 C++ API is to be built... no
> checking whether HDF5 should do data conversions... 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...
> checking whether a location for the ZLIB library was specified...
> checking whether a location for the SZLIB library was specified...
> checking whether a default cache size for HDF5 was specified... 32000000
> checking whether a default cache maximum number of elements for HDF5 was
> specified... 1000
> checking whether a default cache preemption for HDF5 was specified... 0.75
> checking whether netCDF-4 logging is enabled... no
> checking whether DAP client is to be built... no
> checking whether dap remote testing should be enabled... no
> checking whether netCDF extra tests should be run (developers only)... no
> checking whether documentation is to be installed... 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... yes
> checking whether examples should be built... no
> checking whether F77 API is desired... no
> checking whether F90 API is desired... no
> 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... no
> checking whether v2 netCDF API should be built... no
> checking whether the ncgen/ncdump should be built... no
> 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 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 icc accepts -g... yes
> checking for icc option to accept ISO C89... unsupported
> checking for style of include used by make... GNU
> checking dependency style of icc... gcc3
> checking whether icc 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 xlf90... no
> checking for fort... no
> checking for xlf95... no
> checking for ifort... ifort
> checking whether we are using the GNU Fortran compiler... no
> checking whether ifort accepts -g... yes
> checking for xlf... no
> checking for fort... no
> checking for xlf95... no
> checking for ifort... ifort
> checking whether we are using the GNU Fortran 77 compiler... no
> checking whether ifort accepts -g... yes
> configure: finding C++ compiler (will not be used if C++ API is not desired)
> checking for g++... g++
> checking whether we are using the GNU C++ compiler... yes
> checking whether g++ accepts -g... yes
> checking dependency style of g++... gcc3
> configure: setting up libtool
> checking for a sed that does not truncate output... /usr/bin/sed
> checking for grep that handles long lines and -e... /usr/bin/grep
> checking for egrep... /usr/bin/grep -E
> checking for fgrep... /usr/bin/grep -F
> checking for ld used by icc... /usr/bin/ld
> checking if the linker (/usr/bin/ld) is GNU ld... no
> checking for BSD- or MS-compatible name lister (nm)... /usr/bin/nm
> checking the name lister (/usr/bin/nm) interface... BSD nm
> checking whether ln -s works... yes
> checking the maximum length of command line arguments... 196608
> checking whether the shell understands some XSI constructs... yes
> checking whether the shell understands "+="... yes
> checking for /usr/bin/ld option to reload object files... -r
> 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 icc 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 how to run the C preprocessor... icc -E
> checking for ANSI C header files... no
> 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 g++ accepts -g... (cached) yes
> checking dependency style of g++... (cached) gcc3
> checking how to run the C++ preprocessor... g++ -E
> checking whether we are using the GNU Fortran 77 compiler... (cached) no
> checking whether ifort accepts -g... (cached) yes
> checking whether we are using the GNU Fortran compiler... (cached) no
> checking whether ifort accepts -g... (cached) yes
> checking for objdir... .libs
> checking if icc supports -fno-rtti -fno-exceptions... yes
> checking for icc option to produce PIC... -fno-common -DPIC
> checking if icc PIC flag -fno-common -DPIC works... yes
> checking if icc static flag -static works... no
> checking if icc supports -c -o file.o... yes
> checking if icc supports -c -o file.o... (cached) yes
> checking whether the icc linker (/usr/bin/ld) supports shared libraries...
> yes
> checking dynamic linker characteristics... darwin11.3.0 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 g++... /usr/bin/ld
> checking if the linker (/usr/bin/ld) is GNU ld... no
> checking whether the g++ linker (/usr/bin/ld) supports shared libraries...
> yes
> checking for g++ option to produce PIC... -fno-common -DPIC
> checking if g++ PIC flag -fno-common -DPIC works... yes
> checking if g++ static flag -static works... no
> checking if g++ supports -c -o file.o... yes
> checking if g++ supports -c -o file.o... (cached) yes
> checking whether the g++ linker (/usr/bin/ld) supports shared libraries...
> yes
> checking dynamic linker characteristics... darwin11.3.0 dyld
> checking how to hardcode library paths into programs... immediate
> checking if libtool supports shared libraries... yes
> checking whether to build shared libraries... yes
> checking whether to build static libraries... yes
> checking for ifort option to produce PIC...
> checking if ifort static flag  works... yes
> checking if ifort supports -c -o file.o... yes
> checking if ifort supports -c -o file.o... (cached) yes
> checking whether the ifort linker (/usr/bin/ld) supports shared
> libraries... no
> checking dynamic linker characteristics... darwin11.3.0 dyld
> checking how to hardcode library paths into programs... immediate
> checking if libtool supports shared libraries... no
> checking whether to build shared libraries... no
> checking whether to build static libraries... yes
> checking for ifort option to produce PIC...
> checking if ifort static flag  works... yes
> checking if ifort supports -c -o file.o... yes
> checking if ifort supports -c -o file.o... (cached) yes
> checking whether the ifort linker (/usr/bin/ld) supports shared
> libraries... no
> checking dynamic linker characteristics... darwin11.3.0 dyld
> checking how to hardcode library paths into programs... immediate
> configure: finding other utilities
> checking for a BSD-compatible install... /usr/bin/install -c
> 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... icc -g -O2
> checking type icc... icc is hashed (/usr/bin/icc)
> checking CXX... g++
> checking CXXFLAGS... -g -O2
> checking type g++... g++ is /usr/bin/g++
> checking FC... ifort
> checking FFLAGS... -g
> checking type ifort... ifort is /usr/bin/ifort
> checking F90... unset
> checking AR... ar
> checking AR_FLAGS... cru
> checking type ar... ar is /usr/bin/ar
> checking NM... /usr/bin/nm
> checking NMFLAGS...
> configure: checking types, headers, and functions
> checking for stdlib.h... (cached) yes
> checking for sys/types.h... (cached) yes
> checking locale.h usability... yes
> checking locale.h presence... yes
> checking for locale.h... yes
> checking for stdbool.h that conforms to C99... yes
> checking for _Bool... yes
> checking for strlcat... yes
> checking for strerror... yes
> checking for snprintf... yes
> checking for 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... no
> checking for uchar... no
> checking whether char is unsigned... no
> checking whether byte ordering is bigendian... universal
> 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 catman... no
> checking for makewhatis... no
> checking for /usr/lib/makewhatis... no
> checking for manual-page index command...
> checking what to call the output of the ftpbin target...
> binary-netcdf-4.0.1_nc3.tar ifort g++
> checking binary distribution directory... /home/ftp/pub/binary/dummy_system
> checking for dirent.h that defines DIR... yes
> checking for library containing opendir... none required
> checking for ANSI C header files... (cached) no
> 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... no
> checking stdarg.h presence... no
> checking for stdarg.h... no
> checking errno.h usability... yes
> checking errno.h presence... yes
> checking for errno.h... yes
> checking ctype.h usability... yes
> checking ctype.h presence... yes
> checking for ctype.h... yes
> checking fcntl.h usability... yes
> checking fcntl.h presence... yes
> checking for fcntl.h... yes
> checking malloc.h usability... no
> checking malloc.h presence... no
> checking for malloc.h... no
> checking for stdlib.h... (cached) yes
> checking for string.h... (cached) yes
> checking for strings.h... (cached) yes
> checking for unistd.h... (cached) yes
> checking for sys/stat.h... (cached) yes
> checking for strchr... yes
> checking for strrchr... yes
> checking for mktemp... yes
> checking for strcat... yes
> checking for strcpy... yes
> checking for vprintf... yes
> checking for _doprnt... no
> checking whether ncgen4 should be built... no
> configure: generating header files and makefiles
> configure: creating ./config.status
> config.status: creating Makefile
> chmod: nc-config: No such file or directory
> 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 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 win32/Makefile
> config.status: creating win32/NET/Makefile
> config.status: creating win32/NET/libsrc/Makefile
> config.status: creating win32/NET/ncdump/Makefile
> config.status: creating win32/NET/ncgen/Makefile
> config.status: creating win32/NET/examples/Makefile
> config.status: creating win32/NET/nctest/Makefile
> config.status: creating win32/NET/nc_test/Makefile
> config.status: creating libncdap3/Makefile
> config.status: creating libncdap3/oc/Makefile
> config.status: creating ncdap_test/Makefile
> config.status: creating ncdap_test/expected3/Makefile
> config.status: creating ncdap_test/testdata3/Makefile
> config.status: creating ncgen4/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
> Making check in libsrc
> depbase=`echo attr.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\
> /bin/sh ../libtool --tag=CC   --mode=compile icc -DHAVE_CONFIG_H -I. -I..
> -I../fortran        -g -O2 -MT attr.lo -MD -MP -MF $depbase.Tpo -c -o
> attr.lo attr.c &&\
> mv -f $depbase.Tpo $depbase.Plo
> libtool: compile:  icc -DHAVE_CONFIG_H -I. -I.. -I../fortran -g -O2 -MT
> attr.lo -MD -MP -MF .deps/attr.Tpo -c attr.c -o attr.o
> depbase=`echo ncx.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\
> /bin/sh ../libtool --tag=CC   --mode=compile icc -DHAVE_CONFIG_H -I. -I..
> -I../fortran        -g -O2 -MT ncx.lo -MD -MP -MF $depbase.Tpo -c -o ncx.lo
> ncx.c &&\
> mv -f $depbase.Tpo $depbase.Plo
> libtool: compile:  icc -DHAVE_CONFIG_H -I. -I.. -I../fortran -g -O2 -MT
> ncx.lo -MD -MP -MF .deps/ncx.Tpo -c ncx.c -o ncx.o
> depbase=`echo putget.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\
> /bin/sh ../libtool --tag=CC   --mode=compile icc -DHAVE_CONFIG_H -I. -I..
> -I../fortran        -g -O2 -MT putget.lo -MD -MP -MF $depbase.Tpo -c -o
> putget.lo putget.c &&\
> mv -f $depbase.Tpo $depbase.Plo
> libtool: compile:  icc -DHAVE_CONFIG_H -I. -I.. -I../fortran -g -O2 -MT
> putget.lo -MD -MP -MF .deps/putget.Tpo -c putget.c -o putget.o
> depbase=`echo dim.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\
> /bin/sh ../libtool --tag=CC   --mode=compile icc -DHAVE_CONFIG_H -I. -I..
> -I../fortran        -g -O2 -MT dim.lo -MD -MP -MF $depbase.Tpo -c -o dim.lo
> dim.c &&\
> mv -f $depbase.Tpo $depbase.Plo
> libtool: compile:  icc -DHAVE_CONFIG_H -I. -I.. -I../fortran -g -O2 -MT
> dim.lo -MD -MP -MF .deps/dim.Tpo -c dim.c -o dim.o
> depbase=`echo error.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\
> /bin/sh ../libtool --tag=CC   --mode=compile icc -DHAVE_CONFIG_H -I. -I..
> -I../fortran        -g -O2 -MT error.lo -MD -MP -MF $depbase.Tpo -c -o
> error.lo error.c &&\
> mv -f $depbase.Tpo $depbase.Plo
> libtool: compile:  icc -DHAVE_CONFIG_H -I. -I.. -I../fortran -g -O2 -MT
> error.lo -MD -MP -MF .deps/error.Tpo -c error.c -o error.o
> error.c(11): catastrophic error: cannot open source file "stdarg.h"
> #include <stdarg.h>
> ^
> 
> compilation aborted for error.c (code 4)
> make[1]: *** [error.lo] Error 1
> make: *** [check-recursive] Error 1
> 
> 
Russ Rew                                         UCAR Unidata Program
address@hidden                      http://www.unidata.ucar.edu



Ticket Details
===================
Ticket ID: GOK-784955
Department: Support netCDF
Priority: Normal
Status: Closed