Problem in installing Nedcdf with Cygwin

Discussion on computers, ROMS installation and compiling

Moderators: arango, robertson

Post Reply
Message
Author
whcsimon
Posts: 3
Joined: Wed Jun 22, 2011 1:49 pm
Location: Stanford University

Problem in installing Nedcdf with Cygwin

#1 Unread post by whcsimon »

I am a beginner in ROMS (and Linux). I am following the section in wikiROMS - Installing ROMS in Windows XP/Vista (via Cygwin) - to get started. I'm using Windows 7 with Cygwin.

I could not compile Netcdf. I have tried both netcdf 3.6.2 (as described in the wiki) and netcdf 4.1.3 (latest). Essentially, the 'makefile' was not created after I typed:
CC=gcc FC=gfortran-4 F77=gfortran-4 CPPFLAGS=-DpgiFortran ./configure

Apparently, the compilation went well without errors. But the makefile didn't come out. So I couldn't proceed with 'Make Check' and 'Make Install'.

Any prompt help would be very much appreciated!

Perhaps it helps if I paste the configure.log below:


This file contains any messages produced by compilers while
running configure, to aid debugging if configure makes a mistake.

It was created by netCDF configure 3.6.2, which was
generated by GNU Autoconf 2.61. Invocation command line was

$ ./configure

## --------- ##
## Platform. ##
## --------- ##

hostname = simonhcw-pc
uname -m = i686
uname -r = 1.7.9(0.237/5/3)
uname -s = CYGWIN_NT-6.1
uname -v = 2011-03-29 10:10

/usr/bin/uname -p = unknown
/bin/uname -X = unknown

/bin/arch = i686
/usr/bin/arch -k = unknown
/usr/convex/getsysinfo = unknown
/usr/bin/hostinfo = unknown
/bin/machine = unknown
/usr/bin/oslevel = unknown
/bin/universe = unknown

PATH: /usr/local/bin
PATH: /usr/bin
PATH: /cygdrive/c/Program Files/swan
PATH: /cygdrive/c/Program Files/Common Files/Microsoft Shared/Windows Live
PATH: /cygdrive/c/Program Files/MiKTeX 2.7/miktex/bin
PATH: /cygdrive/c/Windows/system32
PATH: /cygdrive/c/Windows
PATH: /cygdrive/c/Windows/System32/Wbem
PATH: /cygdrive/c/Program Files/Common Files/Roxio Shared/10.0/DLLShared
PATH: /cygdrive/c/Program Files/Common Files/Roxio Shared/DLLShared
PATH: /cygdrive/c/Program Files/Softex/OmniPass
PATH: /cygdrive/c/Windows/System32/WindowsPowerShell/v1.0
PATH: /cygdrive/c/Program Files/MATLAB/R2009a Student/bin
PATH: /cygdrive/c/Program Files/MATLAB/R2009a Student/bin/win32
PATH: /cygdrive/c/Program Files/Intel/WiFi/bin
PATH: /cygdrive/c/Program Files/Common Files/Intel/WirelessCommon
PATH: /cygdrive/c/Program Files/Common Files/Thunder Network/KanKan/Codecs
PATH: /cygdrive/c/Program Files/QuickTime/QTSystem
PATH: /cygdrive/c/Program Files/VanDyke Software/Clients
PATH: /cygdrive/c/Program Files/Windows Live/Shared
PATH: /cygdrive/c/strawberry/c/bin
PATH: /cygdrive/c/strawberry/perl/site/bin
PATH: /cygdrive/c/strawberry/perl/bin
PATH: /cygdrive/c/Users/simonhcw/Downloads/g95/bin


## ----------- ##
## Core tests. ##
## ----------- ##

configure:2046: netCDF 3.6.2
configure:2087: checking build system type
configure:2105: result: i686-pc-cygwin
configure:2127: checking host system type
configure:2142: result: i686-pc-cygwin
configure:2187: checking for a BSD-compatible install
configure:2243: result: /usr/bin/install -c
configure:2254: checking whether build environment is sane
configure:2297: result: yes
configure:2362: checking for gawk
configure:2378: found /usr/bin/gawk
configure:2389: result: gawk
configure:2400: checking whether make sets $(MAKE)
configure:2421: result: yes
configure:2609: checking user options
configure:2653: checking whether CXX is set to ''
configure:2657: result: no
configure:2661: checking whether FC is set to ''
configure:2665: result: no
configure:2669: checking whether F90 is set to ''
configure:2673: result: no
configure:2699: checking whether documentation is to be installed
configure:2707: result: no
configure:2723: checking whether Fortran compiler(s) should be tested during configure
configure:2731: result: yes
configure:2736: checking whether configure should try to set compiler flags
configure:2744: result: yes
configure:2748: checking whether FFIO will be used
configure:2756: result: no
configure:2771: checking whether to skip C++, F77, or F90 APIs if compiler is broken
configure:2779: result: yes
configure:2783: checking whether only the C library is desired
configure:2791: result: no
configure:2810: checking whether examples should be built
configure:2818: result: yes
configure:2832: checking whether F77 API is desired
configure:2841: result: yes
configure:2846: checking whether F90 API is desired
configure:2856: result: yes
configure:2860: checking whether fortran type sizes should be checked
configure:2868: result: yes
configure:2874: checking whether C API is desired
configure:2882: result: yes
configure:2889: checking where to get netCDF C-only library for separate fortran libraries
configure:2907: result:
configure:2922: checking whether CXX API is desired
configure:2931: result: yes
configure:2935: checking whether v2 netCDF API should be built
configure:2943: result: yes
configure:2964: checking whether the ncgen/ncdump should be built
configure:2972: result: yes
configure:2986: checking whether large file (> 2GB) tests should be run
configure:2994: result: no
configure:3008: checking whether extreme numbers should be used in tests
configure:3023: result: yes
configure:3037: checking where to put large temp files if large file tests are run
configure:3046: result: .
configure:3057: checking whether a win32 DLL is desired
configure:3065: result: no
configure:3091: checking whether separate fortran libs are desired
configure:3100: result: no
configure:3159: finding C compiler
configure:3279: checking for C compiler version
configure:3286: gcc --version >&5
gcc (GCC) 4.5.0
Copyright (C) 2010 Free Software Foundation, Inc.
This is free software; see the source for copying conditions. There is NO
warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.

configure:3289: $? = 0
configure:3296: gcc -v >&5
Using built-in specs.
COLLECT_GCC=gcc
COLLECT_LTO_WRAPPER=/usr/lib/gcc/i686-pc-cygwin/4.5.0/lto-wrapper.exe
Target: i686-pc-cygwin
Configured with: /gnu/gcc/releases/respins/4.5.0-1/gcc4-4.5.0-1/src/gcc-4.5.0/configure --srcdir=/gnu/gcc/releases/respins/4.5.0-1/gcc4-4.5.0-1/src/gcc-4.5.0 --prefix=/usr --exec-prefix=/usr --bindir=/usr/bin --sbindir=/usr/sbin --libexecdir=/usr/lib --datadir=/usr/share --localstatedir=/var --sysconfdir=/etc --datarootdir=/usr/share --docdir=/usr/share/doc/gcc4 --datadir=/usr/share --infodir=/usr/share/info --mandir=/usr/share/man -v --with-gmp=/usr --with-mpfr=/usr --enable-bootstrap --enable-version-specific-runtime-libs --libexecdir=/usr/lib --enable-static --enable-shared --enable-shared-libgcc --disable-__cxa_atexit --with-gnu-ld --with-gnu-as --with-dwarf2 --disable-sjlj-exceptions --enable-languages=ada,c,c++,fortran,java,lto,objc,obj-c++ --enable-graphite --enable-lto --enable-java-awt=gtk --disable-symvers --enable-libjava --program-suffix=-4 --enable-libgomp --enable-libssp --enable-libada --enable-threads=posix --with-arch=i686 --with-tune=generic --enable-libgcj-sublibs CC=gcc-4 CXX=g++-4 CC_FOR_TARGET=gcc-4 CXX_FOR_TARGET=g++-4 GNATMAKE_FOR_TARGET=gnatmake GNATBIND_FOR_TARGET=gnatbind --with-ecj-jar=/usr/share/java/ecj.jar
Thread model: posix
gcc version 4.5.0 (GCC)
configure:3299: $? = 0
configure:3306: gcc -V >&5
gcc: '-V' option must have argument
configure:3309: $? = 1
configure:3332: checking for C compiler default output file name
configure:3359: gcc -DpgiFortran conftest.c >&5
configure:3362: $? = 0
configure:3400: result: a.exe
configure:3417: checking whether the C compiler works
configure:3427: ./a.exe
configure:3430: $? = 0
configure:3447: result: yes
configure:3454: checking whether we are cross compiling
configure:3456: result: no
configure:3459: checking for suffix of executables
configure:3466: gcc -o conftest.exe -DpgiFortran conftest.c >&5
configure:3469: $? = 0
configure:3493: result: .exe
configure:3499: checking for suffix of object files
configure:3525: gcc -c -DpgiFortran conftest.c >&5
configure:3528: $? = 0
configure:3551: result: o
configure:3555: checking whether we are using the GNU C compiler
configure:3584: gcc -c -DpgiFortran conftest.c >&5
configure:3590: $? = 0
configure:3607: result: yes
configure:3612: checking whether gcc accepts -g
configure:3642: gcc -c -g -DpgiFortran conftest.c >&5
configure:3648: $? = 0
configure:3747: result: yes
configure:3764: checking for gcc option to accept ISO C89
configure:3838: gcc -c -g -O2 -DpgiFortran conftest.c >&5
configure:3844: $? = 0
configure:3867: result: none needed
configure:3896: checking for style of include used by make
configure:3924: result: GNU
configure:3952: checking dependency style of gcc
configure:4042: result: gcc3
configure:4060: checking whether gcc and cc understand -c and -o together
configure:4095: gcc -c conftest.c -o conftest2.o >&5
configure:4098: $? = 0
configure:4104: gcc -c conftest.c -o conftest2.o >&5
configure:4107: $? = 0
configure:4118: cc -c conftest.c >&5
configure:4121: $? = 0
configure:4129: cc -c conftest.c -o conftest2.o >&5
configure:4132: $? = 0
configure:4138: cc -c conftest.c -o conftest2.o >&5
configure:4141: $? = 0
configure:4159: result: yes
configure:4185: checking for an ANSI C-conforming const
configure:4260: gcc -c -g -O2 -DpgiFortran conftest.c >&5
configure:4266: $? = 0
configure:4281: result: yes
configure:4312: finding Fortran compiler (will not be used if Fortran API is not desired)
configure:4702: checking for Fortran compiler version
configure:4709: gfortran-4 --version >&5
GNU Fortran (GCC) 4.3.4 20090804 (release) 1
Copyright (C) 2008 Free Software Foundation, Inc.

GNU Fortran comes with NO WARRANTY, to the extent permitted by law.
You may redistribute copies of GNU Fortran
under the terms of the GNU General Public License.
For more information about these matters, see the file named COPYING

configure:4712: $? = 0
configure:4719: gfortran-4 -v >&5
Using built-in specs.
Target: i686-pc-cygwin
Configured with: /gnu/gcc/releases/respins/4.3.4-4/gcc4-4.3.4-4/src/gcc-4.3.4/configure --srcdir=/gnu/gcc/releases/respins/4.3.4-4/gcc4-4.3.4-4/src/gcc-4.3.4 --prefix=/usr --exec-prefix=/usr --bindir=/usr/bin --sbindir=/usr/sbin --libexecdir=/usr/lib --datadir=/usr/share --localstatedir=/var --sysconfdir=/etc --infodir=/usr/share/info --mandir=/usr/share/man -C --datadir=/usr/share --infodir=/usr/share/info --mandir=/usr/share/man -v --with-gmp=/usr --with-mpfr=/usr --enable-bootstrap --enable-version-specific-runtime-libs --with-slibdir=/usr/bin --libexecdir=/usr/lib --enable-static --enable-shared --enable-shared-libgcc --disable-__cxa_atexit --with-gnu-ld --with-gnu-as --with-dwarf2 --disable-sjlj-exceptions --enable-languages=ada,c,c++,fortran,java,objc,obj-c++ --disable-symvers --enable-libjava --program-suffix=-4 --enable-libgomp --enable-libssp --enable-libada --enable-threads=posix --with-arch=i686 --with-tune=generic --enable-libgcj-sublibs CC=gcc-4 CXX=g++-4 CC_FOR_TARGET=gcc-4 CXX_FOR_TARGET=g++-4 GNATMAKE_FOR_TARGET=gnatmake GNATBIND_FOR_TARGET=gnatbind --with-ecj-jar=/usr/share/java/ecj.jar
Thread model: posix
gcc version 4.3.4 20090804 (release) 1 (GCC)
configure:4722: $? = 0
configure:4729: gfortran-4 -V >&5
gfortran-4: '-V' option must have argument
configure:4732: $? = 1
configure:4740: checking whether we are using the GNU Fortran compiler
configure:4759: gfortran-4 -c conftest.F >&5
gfortran-4: error trying to exec 'cc1': execvp: No such file or directory
configure:4765: $? = 1
configure: failed program was:
| program main
| #ifndef __GNUC__
| choke me
| #endif
|
| end
configure:4782: result: no
configure:4788: checking whether gfortran-4 accepts -g
configure:4805: gfortran-4 -c -g conftest.f >&5
configure:4811: $? = 0
configure:4827: result: yes
configure:4977: checking for Fortran 77 compiler version
configure:4984: gfortran-4 --version >&5
GNU Fortran (GCC) 4.3.4 20090804 (release) 1
Copyright (C) 2008 Free Software Foundation, Inc.

GNU Fortran comes with NO WARRANTY, to the extent permitted by law.
You may redistribute copies of GNU Fortran
under the terms of the GNU General Public License.
For more information about these matters, see the file named COPYING

configure:4987: $? = 0
configure:4994: gfortran-4 -v >&5
Using built-in specs.
Target: i686-pc-cygwin
Configured with: /gnu/gcc/releases/respins/4.3.4-4/gcc4-4.3.4-4/src/gcc-4.3.4/configure --srcdir=/gnu/gcc/releases/respins/4.3.4-4/gcc4-4.3.4-4/src/gcc-4.3.4 --prefix=/usr --exec-prefix=/usr --bindir=/usr/bin --sbindir=/usr/sbin --libexecdir=/usr/lib --datadir=/usr/share --localstatedir=/var --sysconfdir=/etc --infodir=/usr/share/info --mandir=/usr/share/man -C --datadir=/usr/share --infodir=/usr/share/info --mandir=/usr/share/man -v --with-gmp=/usr --with-mpfr=/usr --enable-bootstrap --enable-version-specific-runtime-libs --with-slibdir=/usr/bin --libexecdir=/usr/lib --enable-static --enable-shared --enable-shared-libgcc --disable-__cxa_atexit --with-gnu-ld --with-gnu-as --with-dwarf2 --disable-sjlj-exceptions --enable-languages=ada,c,c++,fortran,java,objc,obj-c++ --disable-symvers --enable-libjava --program-suffix=-4 --enable-libgomp --enable-libssp --enable-libada --enable-threads=posix --with-arch=i686 --with-tune=generic --enable-libgcj-sublibs CC=gcc-4 CXX=g++-4 CC_FOR_TARGET=gcc-4 CXX_FOR_TARGET=g++-4 GNATMAKE_FOR_TARGET=gnatmake GNATBIND_FOR_TARGET=gnatbind --with-ecj-jar=/usr/share/java/ecj.jar
Thread model: posix
gcc version 4.3.4 20090804 (release) 1 (GCC)
configure:4997: $? = 0
configure:5004: gfortran-4 -V >&5
gfortran-4: '-V' option must have argument
configure:5007: $? = 1
configure:5015: checking whether we are using the GNU Fortran 77 compiler
configure:5034: gfortran-4 -c conftest.F >&5
gfortran-4: error trying to exec 'cc1': execvp: No such file or directory
configure:5040: $? = 1
configure: failed program was:
| program main
| #ifndef __GNUC__
| choke me
| #endif
|
| end
configure:5057: result: no
configure:5063: checking whether gfortran-4 accepts -g
configure:5080: gfortran-4 -c -g conftest.f >&5
configure:5086: $? = 0
configure:5102: result: yes
configure:5146: setting up Fortran 90
configure:5165: checking for Fortran flag to compile .f90 files
configure:5187: gfortran-4 -c -g conftest.f90 >&5
configure:5193: $? = 0
configure:5212: result: none
configure:5242: checking fortran 90 modules inclusion flag
configure:5273: gfortran-4 -c -g conftest.f90 >&5
configure:5279: $? = 0
configure:5312: gfortran-4 -c -g -Itmpdir_0 conftest.f90 >&5
configure:5318: $? = 0
configure:5349: result: -I
configure:5361: checking if Fortran compiler can handle Fortran-90
configure:5369: gfortran-4 conftest.f90
/usr/lib/gcc/i686-pc-cygwin/4.3.4/../../../../i686-pc-cygwin/bin/ld: cannot find crtbegin.o: No such file or directory
/usr/lib/gcc/i686-pc-cygwin/4.3.4/../../../../i686-pc-cygwin/bin/ld: cannot find -lgcc_s
/usr/lib/gcc/i686-pc-cygwin/4.3.4/../../../../i686-pc-cygwin/bin/ld: cannot find -lgcc_s
/usr/lib/gcc/i686-pc-cygwin/4.3.4/../../../../i686-pc-cygwin/bin/ld: cannot find -lgcc
/usr/lib/gcc/i686-pc-cygwin/4.3.4/../../../../i686-pc-cygwin/bin/ld: cannot find -lgcc_s
/usr/lib/gcc/i686-pc-cygwin/4.3.4/../../../../i686-pc-cygwin/bin/ld: cannot find -lgcc_s
/usr/lib/gcc/i686-pc-cygwin/4.3.4/../../../../i686-pc-cygwin/bin/ld: cannot find -lgcc
/usr/lib/gcc/i686-pc-cygwin/4.3.4/../../../../i686-pc-cygwin/bin/ld: cannot find crtend.o: No such file or directory
configure:5372: $? = 1
configure:5386: result: no
configure:5389: WARNING: No F90 compiler found. F90 API will not be built.
configure:5395: finding C++ compiler (will not be used if C++ API is not desired)
configure:5462: checking for g++
configure:5478: found /usr/bin/g++
configure:5489: result: g++
configure:5520: checking for C++ compiler version
configure:5527: g++ --version >&5
g++ (GCC) 3.4.4 (cygming special, gdc 0.12, using dmd 0.125)
Copyright (C) 2004 Free Software Foundation, Inc.
This is free software; see the source for copying conditions. There is NO
warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.

configure:5530: $? = 0
configure:5537: g++ -v >&5
Reading specs from /usr/lib/gcc/i686-pc-cygwin/3.4.4/specs
Configured with: /usr/build/package/orig/test.respin/gcc-3.4.4-3/configure --verbose --prefix=/usr --exec-prefix=/usr --sysconfdir=/etc --libdir=/usr/lib --libexecdir=/usr/lib --mandir=/usr/share/man --infodir=/usr/share/info --enable-languages=c,ada,c++,d,f77,pascal,java,objc --enable-nls --without-included-gettext --enable-version-specific-runtime-libs --without-x --enable-libgcj --disable-java-awt --with-system-zlib --enable-interpreter --disable-libgcj-debug --enable-threads=posix --enable-java-gc=boehm --disable-win32-registry --enable-sjlj-exceptions --enable-hash-synchronization --enable-libstdcxx-debug
Thread model: posix
gcc version 3.4.4 (cygming special, gdc 0.12, using dmd 0.125)
configure:5540: $? = 0
configure:5547: g++ -V >&5
g++: `-V' option must have argument
configure:5550: $? = 1
configure:5553: checking whether we are using the GNU C++ compiler
configure:5582: g++ -c -DpgiFortran conftest.cpp >&5
configure:5588: $? = 0
configure:5605: result: yes
configure:5610: checking whether g++ accepts -g
configure:5640: g++ -c -g -DpgiFortran conftest.cpp >&5
configure:5646: $? = 0
configure:5745: result: yes
configure:5770: checking dependency style of g++
configure:5860: result: gcc3
configure:5992: checking for as
configure:6008: found /usr/bin/as
configure:6019: result: as
configure:6088: checking for dlltool
configure:6104: found /usr/bin/dlltool
configure:6115: result: dlltool
configure:6184: checking for objdump
configure:6200: found /usr/bin/objdump
configure:6211: result: objdump
configure:6366: checking for a sed that does not truncate output
configure:6445: result: /usr/bin/sed
configure:6463: checking for grep that handles long lines and -e
configure:6537: result: /usr/bin/grep
configure:6542: checking for egrep
configure:6620: result: /usr/bin/grep -E
configure:6625: checking for fgrep
configure:6703: result: /usr/bin/grep -F
configure:6738: checking for ld used by gcc
configure:6805: result: /usr/i686-pc-cygwin/bin/ld.exe
configure:6814: checking if the linker (/usr/i686-pc-cygwin/bin/ld.exe) is GNU ld
configure:6829: result: yes
configure:6842: checking for BSD- or MS-compatible name lister (nm)
configure:6891: result: /usr/bin/nm -B
configure:7013: checking the name lister (/usr/bin/nm -B) interface
configure:7020: gcc -c -g -O2 -DpgiFortran conftest.c >&5
configure:7023: /usr/bin/nm -B "conftest.o"
configure:7026: output
00000000 b .bss
00000000 d .data
00000000 N .debug_abbrev
00000000 N .debug_info
00000000 N .debug_line
00000000 N .debug_pubnames
00000000 t .text
00000000 B _some_variable
configure:7033: result: BSD nm
configure:7036: checking whether ln -s works
configure:7040: result: yes
configure:7048: checking the maximum length of command line arguments
configure:7162: result: 8192
configure:7180: checking whether the shell understands some XSI constructs
configure:7188: result: yes
configure:7192: checking whether the shell understands "+="
configure:7198: result: yes
configure:7233: checking for /usr/i686-pc-cygwin/bin/ld.exe option to reload object files
configure:7240: result: -r
configure:7267: checking how to recognise dependent libraries
configure:7451: result: file_magic ^x86 archive import|^x86 DLL
configure:7511: checking for ar
configure:7527: found /usr/bin/ar
configure:7538: result: ar
configure:7620: checking for strip
configure:7636: found /usr/bin/strip
configure:7647: result: strip
configure:7723: checking for ranlib
configure:7739: found /usr/bin/ranlib
configure:7750: result: ranlib
configure:7844: checking command to parse /usr/bin/nm -B output from gcc object
configure:7960: gcc -c -g -O2 -DpgiFortran conftest.c >&5
configure:7963: $? = 0
configure:7967: /usr/bin/nm -B conftest.o \| sed -n -e 's/^.*[ ]\([ABCDGIRSTW][ABCDGIRSTW]*\)[ ][ ]*\([_A-Za-z][_A-Za-z0-9]*\)$/\1 \2 \2/p' \> conftest.nm
configure:7970: $? = 0
cannot find nm_test_var in conftest.nm
configure:7960: gcc -c -g -O2 -DpgiFortran conftest.c >&5
configure:7963: $? = 0
configure:7967: /usr/bin/nm -B conftest.o \| sed -n -e 's/^.*[ ]\([ABCDGIRSTW][ABCDGIRSTW]*\)[ ][ ]*_\([_A-Za-z][_A-Za-z0-9]*\)$/\1 _\2 \2/p' \> conftest.nm
configure:7970: $? = 0
configure:8024: gcc -o conftest.exe -g -O2 -DpgiFortran conftest.c conftstm.o >&5
configure:8027: $? = 0
configure:8065: result: ok
configure:8297: checking how to run the C preprocessor
configure:8337: gcc -E -DpgiFortran conftest.c
configure:8343: $? = 0
configure:8374: gcc -E -DpgiFortran conftest.c
conftest.c:12:28: fatal error: ac_nonexistent.h: No such file or directory
compilation terminated.
configure:8380: $? = 1
configure: failed program was:
| /* confdefs.h. */
| #define PACKAGE_NAME "netCDF"
| #define PACKAGE_TARNAME "netcdf"
| #define PACKAGE_VERSION "3.6.2"
| #define PACKAGE_STRING "netCDF 3.6.2"
| #define PACKAGE_BUGREPORT "support@unidata.ucar.edu"
| #define PACKAGE "netcdf"
| #define VERSION "3.6.2"
| #define USE_EXTREME_NUMBERS 1
| #define TEMP_LARGE $TEMP_LARGE
| /* end confdefs.h. */
| #include <ac_nonexistent.h>
configure:8413: result: gcc -E
configure:8442: gcc -E -DpgiFortran conftest.c
configure:8448: $? = 0
configure:8479: gcc -E -DpgiFortran conftest.c
conftest.c:12:28: fatal error: ac_nonexistent.h: No such file or directory
compilation terminated.
configure:8485: $? = 1
configure: failed program was:
| /* confdefs.h. */
| #define PACKAGE_NAME "netCDF"
| #define PACKAGE_TARNAME "netcdf"
| #define PACKAGE_VERSION "3.6.2"
| #define PACKAGE_STRING "netCDF 3.6.2"
| #define PACKAGE_BUGREPORT "support@unidata.ucar.edu"
| #define PACKAGE "netcdf"
| #define VERSION "3.6.2"
| #define USE_EXTREME_NUMBERS 1
| #define TEMP_LARGE $TEMP_LARGE
| /* end confdefs.h. */
| #include <ac_nonexistent.h>
configure:8523: checking for ANSI C header files
configure:8553: gcc -c -g -O2 -DpgiFortran conftest.c >&5
configure:8559: $? = 0
configure:8658: gcc -o conftest.exe -g -O2 -DpgiFortran conftest.c >&5
configure:8661: $? = 0
configure:8667: ./conftest.exe
configure:8670: $? = 0
configure:8687: result: yes
configure:8711: checking for sys/types.h
configure:8732: gcc -c -g -O2 -DpgiFortran conftest.c >&5
configure:8738: $? = 0
configure:8754: result: yes
configure:8711: checking for sys/stat.h
configure:8732: gcc -c -g -O2 -DpgiFortran conftest.c >&5
configure:8738: $? = 0
configure:8754: result: yes
configure:8711: checking for stdlib.h
configure:8732: gcc -c -g -O2 -DpgiFortran conftest.c >&5
configure:8738: $? = 0
configure:8754: result: yes
configure:8711: checking for string.h
configure:8732: gcc -c -g -O2 -DpgiFortran conftest.c >&5
configure:8738: $? = 0
configure:8754: result: yes
configure:8711: checking for memory.h
configure:8732: gcc -c -g -O2 -DpgiFortran conftest.c >&5
configure:8738: $? = 0
configure:8754: result: yes
configure:8711: checking for strings.h
configure:8732: gcc -c -g -O2 -DpgiFortran conftest.c >&5
configure:8738: $? = 0
configure:8754: result: yes
configure:8711: checking for inttypes.h
configure:8732: gcc -c -g -O2 -DpgiFortran conftest.c >&5
configure:8738: $? = 0
configure:8754: result: yes
configure:8711: checking for stdint.h
configure:8732: gcc -c -g -O2 -DpgiFortran conftest.c >&5
configure:8738: $? = 0
configure:8754: result: yes
configure:8711: checking for unistd.h
configure:8732: gcc -c -g -O2 -DpgiFortran conftest.c >&5
configure:8738: $? = 0
configure:8754: result: yes
configure:8770: checking for dlfcn.h
configure:8791: gcc -c -g -O2 -DpgiFortran conftest.c >&5
configure:8797: $? = 0
configure:8813: result: yes
configure:8942: checking for C++ compiler version
configure:8949: g++ --version >&5
g++ (GCC) 3.4.4 (cygming special, gdc 0.12, using dmd 0.125)
Copyright (C) 2004 Free Software Foundation, Inc.
This is free software; see the source for copying conditions. There is NO
warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.

configure:8952: $? = 0
configure:8959: g++ -v >&5
Reading specs from /usr/lib/gcc/i686-pc-cygwin/3.4.4/specs
Configured with: /usr/build/package/orig/test.respin/gcc-3.4.4-3/configure --verbose --prefix=/usr --exec-prefix=/usr --sysconfdir=/etc --libdir=/usr/lib --libexecdir=/usr/lib --mandir=/usr/share/man --infodir=/usr/share/info --enable-languages=c,ada,c++,d,f77,pascal,java,objc --enable-nls --without-included-gettext --enable-version-specific-runtime-libs --without-x --enable-libgcj --disable-java-awt --with-system-zlib --enable-interpreter --disable-libgcj-debug --enable-threads=posix --enable-java-gc=boehm --disable-win32-registry --enable-sjlj-exceptions --enable-hash-synchronization --enable-libstdcxx-debug
Thread model: posix
gcc version 3.4.4 (cygming special, gdc 0.12, using dmd 0.125)
configure:8962: $? = 0
configure:8969: g++ -V >&5
g++: `-V' option must have argument
configure:8972: $? = 1
configure:8975: checking whether we are using the GNU C++ compiler
configure:9027: result: yes
configure:9032: checking whether g++ accepts -g
configure:9167: result: yes
configure:9192: checking dependency style of g++
configure:9282: result: gcc3
configure:9307: checking how to run the C++ preprocessor
configure:9343: g++ -E -DpgiFortran conftest.cpp
configure:9349: $? = 0
configure:9380: g++ -E -DpgiFortran conftest.cpp
conftest.cpp:23:28: ac_nonexistent.h: No such file or directory
configure:9386: $? = 1
configure: failed program was:
| /* confdefs.h. */
| #define PACKAGE_NAME "netCDF"
| #define PACKAGE_TARNAME "netcdf"
| #define PACKAGE_VERSION "3.6.2"
| #define PACKAGE_STRING "netCDF 3.6.2"
| #define PACKAGE_BUGREPORT "support@unidata.ucar.edu"
| #define PACKAGE "netcdf"
| #define VERSION "3.6.2"
| #define USE_EXTREME_NUMBERS 1
| #define TEMP_LARGE $TEMP_LARGE
| #define STDC_HEADERS 1
| #define HAVE_SYS_TYPES_H 1
| #define HAVE_SYS_STAT_H 1
| #define HAVE_STDLIB_H 1
| #define HAVE_STRING_H 1
| #define HAVE_MEMORY_H 1
| #define HAVE_STRINGS_H 1
| #define HAVE_INTTYPES_H 1
| #define HAVE_STDINT_H 1
| #define HAVE_UNISTD_H 1
| #define HAVE_DLFCN_H 1
| /* end confdefs.h. */
| #include <ac_nonexistent.h>
configure:9419: result: g++ -E
configure:9448: g++ -E -DpgiFortran conftest.cpp
configure:9454: $? = 0
configure:9485: g++ -E -DpgiFortran conftest.cpp
conftest.cpp:23:28: ac_nonexistent.h: No such file or directory
configure:9491: $? = 1
configure: failed program was:
| /* confdefs.h. */
| #define PACKAGE_NAME "netCDF"
| #define PACKAGE_TARNAME "netcdf"
| #define PACKAGE_VERSION "3.6.2"
| #define PACKAGE_STRING "netCDF 3.6.2"
| #define PACKAGE_BUGREPORT "support@unidata.ucar.edu"
| #define PACKAGE "netcdf"
| #define VERSION "3.6.2"
| #define USE_EXTREME_NUMBERS 1
| #define TEMP_LARGE $TEMP_LARGE
| #define STDC_HEADERS 1
| #define HAVE_SYS_TYPES_H 1
| #define HAVE_SYS_STAT_H 1
| #define HAVE_STDLIB_H 1
| #define HAVE_STRING_H 1
| #define HAVE_MEMORY_H 1
| #define HAVE_STRINGS_H 1
| #define HAVE_INTTYPES_H 1
| #define HAVE_STDINT_H 1
| #define HAVE_UNISTD_H 1
| #define HAVE_DLFCN_H 1
| /* end confdefs.h. */
| #include <ac_nonexistent.h>
configure:9642: checking for Fortran 77 compiler version
configure:9649: gfortran-4 --version >&5
GNU Fortran (GCC) 4.3.4 20090804 (release) 1
Copyright (C) 2008 Free Software Foundation, Inc.

GNU Fortran comes with NO WARRANTY, to the extent permitted by law.
You may redistribute copies of GNU Fortran
under the terms of the GNU General Public License.
For more information about these matters, see the file named COPYING

configure:9652: $? = 0
configure:9659: gfortran-4 -v >&5
Using built-in specs.
Target: i686-pc-cygwin
Configured with: /gnu/gcc/releases/respins/4.3.4-4/gcc4-4.3.4-4/src/gcc-4.3.4/configure --srcdir=/gnu/gcc/releases/respins/4.3.4-4/gcc4-4.3.4-4/src/gcc-4.3.4 --prefix=/usr --exec-prefix=/usr --bindir=/usr/bin --sbindir=/usr/sbin --libexecdir=/usr/lib --datadir=/usr/share --localstatedir=/var --sysconfdir=/etc --infodir=/usr/share/info --mandir=/usr/share/man -C --datadir=/usr/share --infodir=/usr/share/info --mandir=/usr/share/man -v --with-gmp=/usr --with-mpfr=/usr --enable-bootstrap --enable-version-specific-runtime-libs --with-slibdir=/usr/bin --libexecdir=/usr/lib --enable-static --enable-shared --enable-shared-libgcc --disable-__cxa_atexit --with-gnu-ld --with-gnu-as --with-dwarf2 --disable-sjlj-exceptions --enable-languages=ada,c,c++,fortran,java,objc,obj-c++ --disable-symvers --enable-libjava --program-suffix=-4 --enable-libgomp --enable-libssp --enable-libada --enable-threads=posix --with-arch=i686 --with-tune=generic --enable-libgcj-sublibs CC=gcc-4 CXX=g++-4 CC_FOR_TARGET=gcc-4 CXX_FOR_TARGET=g++-4 GNATMAKE_FOR_TARGET=gnatmake GNATBIND_FOR_TARGET=gnatbind --with-ecj-jar=/usr/share/java/ecj.jar
Thread model: posix
gcc version 4.3.4 20090804 (release) 1 (GCC)
configure:9662: $? = 0
configure:9669: gfortran-4 -V >&5
gfortran-4: '-V' option must have argument
configure:9672: $? = 1
configure:9680: checking whether we are using the GNU Fortran 77 compiler
configure:9722: result: no
configure:9728: checking whether gfortran-4 accepts -g
configure:9767: result: yes
configure:9910: checking for Fortran compiler version
configure:9917: gfortran-4 --version >&5
GNU Fortran (GCC) 4.3.4 20090804 (release) 1
Copyright (C) 2008 Free Software Foundation, Inc.

GNU Fortran comes with NO WARRANTY, to the extent permitted by law.
You may redistribute copies of GNU Fortran
under the terms of the GNU General Public License.
For more information about these matters, see the file named COPYING

configure:9920: $? = 0
configure:9927: gfortran-4 -v >&5
Using built-in specs.
Target: i686-pc-cygwin
Configured with: /gnu/gcc/releases/respins/4.3.4-4/gcc4-4.3.4-4/src/gcc-4.3.4/configure --srcdir=/gnu/gcc/releases/respins/4.3.4-4/gcc4-4.3.4-4/src/gcc-4.3.4 --prefix=/usr --exec-prefix=/usr --bindir=/usr/bin --sbindir=/usr/sbin --libexecdir=/usr/lib --datadir=/usr/share --localstatedir=/var --sysconfdir=/etc --infodir=/usr/share/info --mandir=/usr/share/man -C --datadir=/usr/share --infodir=/usr/share/info --mandir=/usr/share/man -v --with-gmp=/usr --with-mpfr=/usr --enable-bootstrap --enable-version-specific-runtime-libs --with-slibdir=/usr/bin --libexecdir=/usr/lib --enable-static --enable-shared --enable-shared-libgcc --disable-__cxa_atexit --with-gnu-ld --with-gnu-as --with-dwarf2 --disable-sjlj-exceptions --enable-languages=ada,c,c++,fortran,java,objc,obj-c++ --disable-symvers --enable-libjava --program-suffix=-4 --enable-libgomp --enable-libssp --enable-libada --enable-threads=posix --with-arch=i686 --with-tune=generic --enable-libgcj-sublibs CC=gcc-4 CXX=g++-4 CC_FOR_TARGET=gcc-4 CXX_FOR_TARGET=g++-4 GNATMAKE_FOR_TARGET=gnatmake GNATBIND_FOR_TARGET=gnatbind --with-ecj-jar=/usr/share/java/ecj.jar
Thread model: posix
gcc version 4.3.4 20090804 (release) 1 (GCC)
configure:9930: $? = 0
configure:9937: gfortran-4 -V >&5
gfortran-4: '-V' option must have argument
configure:9940: $? = 1
configure:9948: checking whether we are using the GNU Fortran compiler
configure:9990: result: no
configure:9996: checking whether gfortran-4 accepts -g
configure:10035: result: yes
configure:10115: checking for objdir
configure:10130: result: .libs
configure:10422: checking if gcc supports -fno-rtti -fno-exceptions
configure:10440: gcc -c -g -O2 -DpgiFortran -fno-rtti -fno-exceptions conftest.c >&5
cc1: warning: command line option "-fno-rtti" is valid for C++/ObjC++ but not for C
configure:10444: $? = 0
configure:10457: result: no
configure:10477: checking for gcc option to produce PIC
configure:10730: result: -DPIC
configure:10742: checking if gcc PIC flag -DPIC works
configure:10760: gcc -c -g -O2 -DpgiFortran -DPIC -DPIC conftest.c >&5
configure:10764: $? = 0
configure:10777: result: yes
configure:10801: checking if gcc static flag -static works
configure:10829: result: yes
configure:10844: checking if gcc supports -c -o file.o
configure:10865: gcc -c -g -O2 -DpgiFortran -o out/conftest2.o conftest.c >&5
configure:10869: $? = 0
configure:10891: result: yes
configure:10899: checking if gcc supports -c -o file.o
configure:10946: result: yes
configure:10979: checking whether the gcc linker (/usr/i686-pc-cygwin/bin/ld.exe) supports shared libraries
configure:12050: result: yes
configure:12284: checking dynamic linker characteristics
configure:12895: result: Win32 ld.exe
configure:12990: checking how to hardcode library paths into programs
configure:13015: result: immediate
configure:13828: checking whether stripping libraries is possible
configure:13833: result: yes
configure:13868: checking if libtool supports shared libraries
configure:13870: result: yes
configure:13873: checking whether to build shared libraries
configure:13894: result: no
configure:13897: checking whether to build static libraries
configure:13901: result: yes
configure:14050: checking for ld used by g++
configure:14117: result: /usr/i686-pc-cygwin/bin/ld.exe
configure:14126: checking if the linker (/usr/i686-pc-cygwin/bin/ld.exe) is GNU ld
configure:14141: result: yes
configure:14196: checking whether the g++ linker (/usr/i686-pc-cygwin/bin/ld.exe) supports shared libraries
configure:15185: result: yes
configure:15213: g++ -c -g -O2 -DpgiFortran conftest.cpp >&5
configure:15216: $? = 0
configure:15369: checking for g++ option to produce PIC
configure:15672: result: -DPIC
configure:15681: checking if g++ PIC flag -DPIC works
configure:15699: g++ -c -g -O2 -DpgiFortran -DPIC -DPIC conftest.cpp >&5
configure:15703: $? = 0
configure:15716: result: yes
configure:15737: checking if g++ static flag -static works
configure:15765: result: yes
configure:15777: checking if g++ supports -c -o file.o
configure:15798: g++ -c -g -O2 -DpgiFortran -o out/conftest2.o conftest.cpp >&5
configure:15802: $? = 0
configure:15824: result: yes
configure:15829: checking if g++ supports -c -o file.o
configure:15876: result: yes
configure:15906: checking whether the g++ linker (/usr/i686-pc-cygwin/bin/ld.exe) supports shared libraries
configure:15931: result: yes
configure:16066: checking dynamic linker characteristics
configure:16677: result: Win32 ld.exe
configure:16721: checking how to hardcode library paths into programs
configure:16746: result: immediate
configure:16879: checking if libtool supports shared libraries
configure:16881: result: yes
configure:16884: checking whether to build shared libraries
configure:16904: result: no
configure:16907: checking whether to build static libraries
configure:16911: result: yes
configure:16925: checking for gfortran-4 option to produce PIC
configure:17178: result:
configure:17243: checking if gfortran-4 static flag -static works
configure:17271: result: no
configure:17283: checking if gfortran-4 supports -c -o file.o
configure:17304: gfortran-4 -c -g -o out/conftest2.o conftest.f >&5
configure:17308: $? = 0
configure:17330: result: yes
configure:17335: checking if gfortran-4 supports -c -o file.o
configure:17382: result: yes
configure:17412: checking whether the gfortran-4 linker (/usr/i686-pc-cygwin/bin/ld.exe) supports shared libraries
configure:18463: result: yes
configure:18598: checking dynamic linker characteristics
configure:19209: result: Win32 ld.exe
configure:19253: checking how to hardcode library paths into programs
configure:19278: result: immediate
configure:19403: checking if libtool supports shared libraries
configure:19405: result: yes
configure:19408: checking whether to build shared libraries
configure:19428: result: no
configure:19431: checking whether to build static libraries
configure:19435: result: yes
configure:19461: gfortran-4 -c -g conftest.f90 >&5
configure:19464: $? = 0
configure:19573: checking for gfortran-4 option to produce PIC
configure:19826: result:
configure:19891: checking if gfortran-4 static flag -static works
configure:19919: result: no
configure:19931: checking if gfortran-4 supports -c -o file.o
configure:19952: gfortran-4 -c -g -o out/conftest2.o conftest.f90 >&5
configure:19956: $? = 0
configure:19978: result: yes
configure:19983: checking if gfortran-4 supports -c -o file.o
configure:20030: result: yes
configure:20060: checking whether the gfortran-4 linker (/usr/i686-pc-cygwin/bin/ld.exe) supports shared libraries
configure:21111: result: yes
configure:21246: checking dynamic linker characteristics
configure:21857: result: Win32 ld.exe
configure:21901: checking how to hardcode library paths into programs
configure:21926: result: immediate
configure:21973: finding other utilities
configure:21989: checking for a BSD-compatible install
configure:22045: result: /usr/bin/install -c
configure:22058: trying to set fortran flags for this platform
configure:22103: trying to set flags for this platform
configure:22108: checking if _HPUX_SOURCE should be set
configure:22124: result: no
configure:22129: checking if Solaris -Xa option is needed
configure:22142: result: CFLAGS=-g -O2
configure:22168: checking if we need to set _LARGE_FILES despite results of previous tests
configure:22199: result: _LARGE_FILES=
configure:22209: checking for special C compiler options needed for large files
configure:22302: result: no
configure:22308: checking for _FILE_OFFSET_BITS value needed for large files
configure:22343: gcc -c -g -O2 -DpgiFortran conftest.c >&5
configure:22349: $? = 0
configure:22417: result: no
configure:22553: displaying some results
configure:22559: checking CPPFLAGS
configure:22561: result: -DpgiFortran
configure:22563: checking CC CFLAGS
configure:22565: result: gcc -g -O2
configure:22568: checking type gcc
configure:22570: result: gcc is /usr/bin/gcc
configure:22573: checking CXX
configure:22576: result: g++
configure:22578: checking CXXFLAGS
configure:22580: result: -g -O2
configure:22583: checking type g++
configure:22585: result: g++ is /usr/bin/g++
configure:22592: checking FC
configure:22595: result: gfortran-4
configure:22597: checking FFLAGS
configure:22599: result: -g
configure:22602: checking type gfortran-4
configure:22604: result: gfortran-4 is /usr/bin/gfortran-4
configure:22611: checking F90
configure:22626: result: unset
configure:22630: checking AR
configure:22633: result: ar
configure:22635: checking ARFLAGS
configure:22637: result:
configure:22640: checking type ar
configure:22642: result: ar is /usr/bin/ar
configure:22649: checking NM
configure:22652: result: /usr/bin/nm -B
configure:22654: checking NMFLAGS
configure:22656: result:
configure:22723: checking for /usr/bin/nm
configure:22750: result: /usr/bin/nm -B
configure:22763: checking nm flags
configure:22768: result:
configure:22780: checking for C-equivalent to Fortran routine "SUB"
configure:22787: gfortran-4 -c -g conftest.f
configure:22790: $? = 0
configure:22802: result: sub_
configure:22824: checking for Fortran "byte"
configure:22832: gfortran-4 -c -g conftest.f
configure:22835: $? = 0
configure:22837: result: yes
configure:22855: checking for Fortran "integer*2"
configure:22863: gfortran-4 -c -g conftest.f
configure:22866: $? = 0
configure:22868: result: yes
configure:22895: checking if Fortran "byte" is C "signed char"
configure:22905: gcc -c -DpgiFortran -g -O2 conftest.c
conftest.c: In function 'sub_':
conftest.c:4:3: warning: incompatible implicit declaration of built-in function 'exit'
configure:22908: $? = 0
configure:22911: gfortran-4 -g -c conftestf.f
configure:22914: $? = 0
configure:22917: gfortran-4 -o conftest -g conftestf.o conftest.o
/usr/lib/gcc/i686-pc-cygwin/4.3.4/../../../../i686-pc-cygwin/bin/ld: cannot find crtbegin.o: No such file or directory
/usr/lib/gcc/i686-pc-cygwin/4.3.4/../../../../i686-pc-cygwin/bin/ld: cannot find -lgcc_s
/usr/lib/gcc/i686-pc-cygwin/4.3.4/../../../../i686-pc-cygwin/bin/ld: cannot find -lgcc_s
/usr/lib/gcc/i686-pc-cygwin/4.3.4/../../../../i686-pc-cygwin/bin/ld: cannot find -lgcc
/usr/lib/gcc/i686-pc-cygwin/4.3.4/../../../../i686-pc-cygwin/bin/ld: cannot find -lgcc_s
/usr/lib/gcc/i686-pc-cygwin/4.3.4/../../../../i686-pc-cygwin/bin/ld: cannot find -lgcc_s
/usr/lib/gcc/i686-pc-cygwin/4.3.4/../../../../i686-pc-cygwin/bin/ld: cannot find -lgcc
/usr/lib/gcc/i686-pc-cygwin/4.3.4/../../../../i686-pc-cygwin/bin/ld: cannot find crtend.o: No such file or directory
configure:22920: $? = 1
configure:22943: error: Could not link conftestf.o and conftest.o

## ---------------- ##
## Cache variables. ##
## ---------------- ##

ac_cv_build=i686-pc-cygwin
ac_cv_c_compiler_gnu=yes
ac_cv_c_const=yes
ac_cv_cxx_compiler_gnu=yes
ac_cv_env_CCC_set=
ac_cv_env_CCC_value=
ac_cv_env_CC_set=set
ac_cv_env_CC_value=gcc
ac_cv_env_CFLAGS_set=
ac_cv_env_CFLAGS_value=
ac_cv_env_CPPFLAGS_set=set
ac_cv_env_CPPFLAGS_value=-DpgiFortran
ac_cv_env_CPP_set=
ac_cv_env_CPP_value=
ac_cv_env_CXXCPP_set=
ac_cv_env_CXXCPP_value=
ac_cv_env_CXXFLAGS_set=
ac_cv_env_CXXFLAGS_value=
ac_cv_env_CXX_set=
ac_cv_env_CXX_value=
ac_cv_env_F77_set=set
ac_cv_env_F77_value=gfortran-4
ac_cv_env_FCFLAGS_set=
ac_cv_env_FCFLAGS_value=
ac_cv_env_FC_set=set
ac_cv_env_FC_value=gfortran-4
ac_cv_env_FFLAGS_set=
ac_cv_env_FFLAGS_value=
ac_cv_env_LDFLAGS_set=
ac_cv_env_LDFLAGS_value=
ac_cv_env_LIBS_set=
ac_cv_env_LIBS_value=
ac_cv_env_build_alias_set=
ac_cv_env_build_alias_value=
ac_cv_env_host_alias_set=
ac_cv_env_host_alias_value=
ac_cv_env_target_alias_set=
ac_cv_env_target_alias_value=
ac_cv_exeext=.exe
ac_cv_f77_compiler_gnu=no
ac_cv_fc_compiler_gnu=no
ac_cv_fc_srcext_f90=none
ac_cv_header_dlfcn_h=yes
ac_cv_header_inttypes_h=yes
ac_cv_header_memory_h=yes
ac_cv_header_stdc=yes
ac_cv_header_stdint_h=yes
ac_cv_header_stdlib_h=yes
ac_cv_header_string_h=yes
ac_cv_header_strings_h=yes
ac_cv_header_sys_stat_h=yes
ac_cv_header_sys_types_h=yes
ac_cv_header_unistd_h=yes
ac_cv_host=i686-pc-cygwin
ac_cv_objext=o
ac_cv_path_EGREP='/usr/bin/grep -E'
ac_cv_path_FGREP='/usr/bin/grep -F'
ac_cv_path_GREP=/usr/bin/grep
ac_cv_path_SED=/usr/bin/sed
ac_cv_path_install='/usr/bin/install -c'
ac_cv_prog_AWK=gawk
ac_cv_prog_CPP='gcc -E'
ac_cv_prog_CXXCPP='g++ -E'
ac_cv_prog_NM='/usr/bin/nm -B'
ac_cv_prog_ac_ct_AR=ar
ac_cv_prog_ac_ct_AS=as
ac_cv_prog_ac_ct_CXX=g++
ac_cv_prog_ac_ct_DLLTOOL=dlltool
ac_cv_prog_ac_ct_OBJDUMP=objdump
ac_cv_prog_ac_ct_RANLIB=ranlib
ac_cv_prog_ac_ct_STRIP=strip
ac_cv_prog_cc_c89=
ac_cv_prog_cc_g=yes
ac_cv_prog_cc_gcc_c_o=yes
ac_cv_prog_cxx_g=yes
ac_cv_prog_f77_g=yes
ac_cv_prog_f90_uppercase_mod=no
ac_cv_prog_fc_g=yes
ac_cv_prog_make_make_set=yes
ac_cv_sys_file_offset_bits=no
ac_cv_sys_largefile_CC=no
am_cv_CC_dependencies_compiler_type=gcc3
am_cv_CXX_dependencies_compiler_type=gcc3
lt_cv_deplibs_check_method='file_magic ^x86 archive import|^x86 DLL'
lt_cv_file_magic_cmd=func_win32_libid
lt_cv_file_magic_test_file=
lt_cv_ld_reload_flag=-r
lt_cv_nm_interface='BSD nm'
lt_cv_objdir=.libs
lt_cv_path_LD=/usr/i686-pc-cygwin/bin/ld.exe
lt_cv_path_LDCXX=/usr/i686-pc-cygwin/bin/ld.exe
lt_cv_path_NM='/usr/bin/nm -B'
lt_cv_prog_compiler_c_o=yes
lt_cv_prog_compiler_c_o_CXX=yes
lt_cv_prog_compiler_c_o_F77=yes
lt_cv_prog_compiler_c_o_FC=yes
lt_cv_prog_compiler_rtti_exceptions=no
lt_cv_prog_gnu_ld=yes
lt_cv_prog_gnu_ldcxx=yes
lt_cv_sys_global_symbol_pipe='sed -n -e '\''s/^.*[ ]\([ABCDGIRSTW][ABCDGIRSTW]*\)[ ][ ]*_\([_A-Za-z][_A-Za-z0-9]*\)$/\1 _\2 \2/p'\'''
lt_cv_sys_global_symbol_to_c_name_address='sed -n -e '\''s/^: \([^ ]*\) $/ {\"\1\", (void *) 0},/p'\'' -e '\''s/^[ABCDGIRSTW]* \([^ ]*\) \([^ ]*\)$/ {"\2", (void *) \&\2},/p'\'''
lt_cv_sys_global_symbol_to_cdecl='sed -n -e '\''s/^T .* \(.*\)$/extern int \1();/p'\'' -e '\''s/^[ABCDGIRSTW]* .* \(.*\)$/extern char \1;/p'\'''
lt_cv_sys_max_cmd_len=8192

## ----------------- ##
## Output variables. ##
## ----------------- ##

ACLOCAL='${SHELL} /home/simonhcw/software/netcdf-3.6.2/missing --run aclocal-1.9'
ALLOCA=''
AMDEPBACKSLASH='\'
AMDEP_FALSE='#'
AMDEP_TRUE=''
AMTAR='${SHELL} /home/simonhcw/software/netcdf-3.6.2/missing --run tar'
AR='ar'
AS='as'
AUTOCONF='${SHELL} /home/simonhcw/software/netcdf-3.6.2/missing --run autoconf'
AUTOHEADER='${SHELL} /home/simonhcw/software/netcdf-3.6.2/missing --run autoheader'
AUTOMAKE='${SHELL} /home/simonhcw/software/netcdf-3.6.2/missing --run automake-1.9'
AWK='gawk'
BUILD_CXX_FALSE='#'
BUILD_CXX_TRUE=''
BUILD_C_FALSE='#'
BUILD_C_TRUE=''
BUILD_DLL_FALSE=''
BUILD_DLL_TRUE='#'
BUILD_EXAMPLES_FALSE='#'
BUILD_EXAMPLES_TRUE=''
BUILD_F77_FALSE='#'
BUILD_F77_TRUE=''
BUILD_F90_FALSE=''
BUILD_F90_TRUE='#'
BUILD_SEPARATE_FORTRAN_FALSE=''
BUILD_SEPARATE_FORTRAN_TRUE='#'
BUILD_SHARED_FALSE=''
BUILD_SHARED_TRUE='#'
BUILD_UTILITIES_FALSE='#'
BUILD_UTILITIES_TRUE=''
BUILD_V2_FALSE='#'
BUILD_V2_TRUE=''
CC='gcc'
CCDEPMODE='depmode=gcc3'
CFLAGS='-g -O2'
CPP='gcc -E'
CPPFLAGS='-DpgiFortran'
CXX='g++'
CXXCPP='g++ -E'
CXXDEPMODE='depmode=gcc3'
CXXFLAGS='-g -O2'
CYGPATH_W='cygpath -w'
DEFS=''
DEPDIR='.deps'
DLLTOOL='dlltool'
DUMPBIN=''
ECHO_C=''
ECHO_N='-n'
ECHO_T=''
EGREP='/usr/bin/grep -E'
EXEEXT='.exe'
F77='gfortran-4'
FC='gfortran-4'
FCFLAGS='-g'
FCFLAGS_f90=''
FFLAGS='-g'
FGREP='/usr/bin/grep -F'
FTPBINDIR=''
GREP='/usr/bin/grep'
INSTALL_DATA='${INSTALL} -m 644'
INSTALL_DOCS_FALSE=''
INSTALL_DOCS_TRUE='#'
INSTALL_PROGRAM='${INSTALL}'
INSTALL_SCRIPT='${INSTALL}'
INSTALL_STRIP_PROGRAM='${SHELL} $(install_sh) -c -s'
LARGE_FILE_TESTS_FALSE=''
LARGE_FILE_TESTS_TRUE='#'
LD='/usr/i686-pc-cygwin/bin/ld.exe'
LDFLAGS=''
LIBOBJS=''
LIBS=''
LIBTOOL='$(SHELL) $(top_builddir)/libtool'
LN_S='ln -s'
LTLIBOBJS=''
MAKEINFO='${SHELL} /home/simonhcw/software/netcdf-3.6.2/missing --run makeinfo'
MAKEWHATIS_CMD=''
MOD_FLAG='-I'
NETCDF_C_LIB=''
NM='/usr/bin/nm -B'
NMFLAGS=''
OBJDUMP='objdump'
OBJEXT='o'
PACKAGE='netcdf'
PACKAGE_BUGREPORT='support@unidata.ucar.edu'
PACKAGE_NAME='netCDF'
PACKAGE_STRING='netCDF 3.6.2'
PACKAGE_TARNAME='netcdf'
PACKAGE_VERSION='3.6.2'
PATH_SEPARATOR=':'
RANLIB='ranlib'
SED='/usr/bin/sed'
SET_MAKE=''
SHAREEXT_DYLIB_FALSE=''
SHAREEXT_DYLIB_TRUE='#'
SHAREEXT_SL_FALSE=''
SHAREEXT_SL_TRUE='#'
SHELL='/bin/sh'
STRIP='strip'
TEST_F77_FALSE='#'
TEST_F77_TRUE=''
TEST_PARALLEL_FALSE=''
TEST_PARALLEL_TRUE=''
UPPER_CASE_MOD_FALSE=''
UPPER_CASE_MOD_TRUE=''
USE_FFIO_FALSE=''
USE_FFIO_TRUE='#'
USE_HDF5_DIR_FALSE=''
USE_HDF5_DIR_TRUE='#'
USE_NETCDF4_FALSE=''
USE_NETCDF4_TRUE='#'
USE_NETCDF_C_LIB_DIR_FALSE=''
USE_NETCDF_C_LIB_DIR_TRUE='#'
VERSION='3.6.2'
WHATIS=''
ac_ct_CC=''
ac_ct_CXX='g++'
ac_ct_DUMPBIN=''
ac_ct_F77=''
ac_ct_FC=''
am__fastdepCC_FALSE='#'
am__fastdepCC_TRUE=''
am__fastdepCXX_FALSE='#'
am__fastdepCXX_TRUE=''
am__include='include'
am__leading_dot='.'
am__quote=''
am__tar='${AMTAR} chof - "$$tardir"'
am__untar='${AMTAR} xf -'
bindir='${exec_prefix}/bin'
build='i686-pc-cygwin'
build_alias=''
build_cpu='i686'
build_os='cygwin'
build_vendor='pc'
datadir='${datarootdir}'
datarootdir='${prefix}/share'
docdir='${datarootdir}/doc/${PACKAGE_TARNAME}'
dvidir='${docdir}'
exec_prefix='NONE'
host='i686-pc-cygwin'
host_alias=''
host_cpu='i686'
host_os='cygwin'
host_vendor='pc'
htmldir='${docdir}'
includedir='${prefix}/include'
infodir='${datarootdir}/info'
install_sh='/home/simonhcw/software/netcdf-3.6.2/install-sh'
libdir='${exec_prefix}/lib'
libexecdir='${exec_prefix}/libexec'
localedir='${datarootdir}/locale'
localstatedir='${prefix}/var'
lt_ECHO='echo'
mandir='${datarootdir}/man'
mkdir_p='mkdir -p --'
oldincludedir='/usr/include'
pdfdir='${docdir}'
prefix='NONE'
prog=''
program_transform_name='s,x,x,'
psdir='${docdir}'
sbindir='${exec_prefix}/sbin'
sharedstatedir='${prefix}/com'
sysconfdir='${prefix}/etc'
target_alias=''

## ----------- ##
## confdefs.h. ##
## ----------- ##

#define PACKAGE_NAME "netCDF"
#define PACKAGE_TARNAME "netcdf"
#define PACKAGE_VERSION "3.6.2"
#define PACKAGE_STRING "netCDF 3.6.2"
#define PACKAGE_BUGREPORT "support@unidata.ucar.edu"
#define PACKAGE "netcdf"
#define VERSION "3.6.2"
#define USE_EXTREME_NUMBERS 1
#define TEMP_LARGE $TEMP_LARGE
#define STDC_HEADERS 1
#define HAVE_SYS_TYPES_H 1
#define HAVE_SYS_STAT_H 1
#define HAVE_STDLIB_H 1
#define HAVE_STRING_H 1
#define HAVE_MEMORY_H 1
#define HAVE_STRINGS_H 1
#define HAVE_INTTYPES_H 1
#define HAVE_STDINT_H 1
#define HAVE_UNISTD_H 1
#define HAVE_DLFCN_H 1
#define LT_OBJDIR ".libs/"
#define NF_INT1_T byte
#define NF_INT2_T integer*2

configure: exit 1
Top
User avatar
m.hadfield
Posts: 521
Joined: Tue Jul 01, 2003 4:12 am
Location: NIWA

Re: Problem in installing Nedcdf with Cygwin

#2 Unread post by m.hadfield »

This is really a netCDF and/or Cygwin problem rather than a ROMS problem; perhaps you should send it to the netCDF or Cygwin mailing lists.

That said, I have successfully built netCDF 3.6.x and 4.1.x many times without too many problems, so perhaps I can help.

Your configure output suggests you have something pretty basic wrong with your GCC setup, and I'm inclined to think it's related to the transition between GCC versions 3 and 4. When you invoke gcc (the C compiler) do you get version 3.x or 4.x? I suspect 3.x. Gfortran is only available in version 4 and might not play with version 3 of the C compiler and preprocessor. I suggest you read this message

http://cygwin.com/ml/cygwin-announce/20 ... 00045.html

which says that mixed usage between GCC versions 3 and 4 isn't guaranteed to work. It describes the Cygwin alternatives package that you can download and run to specify the default compiler versions. Once you've got everything set up you should be able to configure netCDF 3.6.2 with

Code: Select all

FC=gfortran ./configure
and netCDF 4.1.3 with a little extra stuff to say where the HDF5 library is, eg.

Code: Select all

FC=gfortran CPPFLAGS=-I/usr/local/include LDFLAGS=-L/usr/local/lib ./configure
Caveats:
  • I have no experience on Windows 7.
  • The post I linked to above is a couple of years old and written during the transition from GCC3 to GCC 4. Perhaps it's out of date now
Top
whcsimon
Posts: 3
Joined: Wed Jun 22, 2011 1:49 pm
Location: Stanford University

Re: Problem in installing Nedcdf with Cygwin

#3 Unread post by whcsimon »

Thanks m.hadfield. I resolved my problem after installing GCC 4.0. Perhaps someone can edit the wiki tutorial, which only instructs us to install gcc-g++ (version 3.x).
Top
User avatar
m.hadfield
Posts: 521
Joined: Tue Jul 01, 2003 4:12 am
Location: NIWA

Re: Problem in installing Nedcdf with Cygwin

#4 Unread post by m.hadfield »

I have edited the tutorial as you suggest. The recommended GCC-related packages are now gcc4, gcc4-core and gcc4-fortran. (Not gcc4-g++, as this is the C++ compiler, which shouldn't be necessary.) I hope this is correct.
Top
fereshteh
Posts: 79
Joined: Sun Dec 30, 2012 2:58 pm
Location: inio:Iranian National Institute for Oceanography

cc1

#5 Unread post by fereshteh »

dear all
i use fedora 16 (gcc4.6.2). by applying ./build.bash, after copied netcdf.mod and typesizes.mod in Build folder, this error arise: :?
cpp: error trying to exec 'cc1': execvp: No such file or directory
also it said some thing about permission denied (in detaile /bin/sh: ./ROMS/Bin/sfmakeddepend: permision denied)
would you please help me to sort out reasons of those problem
best regard :wink:
fereshte
Top
Post Reply

Return to “ROMS Installation”