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Re: 20010419: netCDF3.5 test failure with Cygwin GNU gcc

>From: "Forsberg, Carl Fredrik" <address@hidden>
>Subject: netCDF3.5 test failure with Cygwin GNU gcc
>Organization: Norwegian Polar Institute
>Keywords: 200104191239.f3JCd8L09299 netCDF make test

Hi Carl,

> Compilation with Cygwin GNU gcc was without error messages, however running
> "make test" produced an error.
> 
> This message contains commands and responses, and includes the files
> configure.log, config.log, make.log and test.log.
> 
> Thanks for any help you may be able to give.

Thanks for reporting the problem.  We didn't test netCDF 3.5.0 on
Cygwin, but I just found someone close by that has Cygwin on his
Windows 2000 machine, so I'll try to duplicate the problem and figure
out what's going on sometime when he's not using it.  It may be a few
days.

Alternatively, there's another Cygwin fan and netCDF user on our
mailing list, Arlindo da Silva, who may be able to see what's wrong
quickly.

I'm CC:ing him on this response (Hi Arlindo!), just in case he's
already run into the problem and knows the fix ...

--Russ

> ************** Commands and response *********************
> 
> $ configure >configure.log
> configure: warning: Could not find working Fortran-90 compiler
> configure: warning: The Fortran-90 interface will not be built
> 
> $ make > make.log
> Not making `f90/all' because no FORTRAN-90 compiler
> 
> $ make test > test.log
> make[2]: *** [test] Error 1
> make[1]: *** [subdir_target] Error 1
> make: *** [libsrc/test] Error 2
> 
> **********   configure.log   *****************
> creating cache ./config.cache
> checking for top-level source-directory
> /cygdrive/c/gmt-3.4/netcdf-3.5.0/src
> checking for m4 preprocessor
> checking for m4... m4
> checking m4 flags... -B10000
> checking for xlc... no
> checking for c89... no
> checking for acc... no
> checking for cc... no
> checking for gcc... gcc
> checking C compiler "gcc"... works
> checking how to make dependencies... false
> checking for CC... no
> checking for cxx... no
> checking for c++... c++
> checking C++ compiler "c++"... works
> checking how to run the C preprocessor... gcc -E
> checking for xlf... no
> checking for fort77... no
> checking for ghf77... no
> checking for f77... no
> checking for cf77... no
> checking for g77... g77
> checking for Fortran .F compiler... 
> checking if Fortran-77 compiler handles *.F files... yes
> checking "g77" as Fortran-90 compiler... failed to build test program
> checking for xlf90... no
> checking for f90... no
> checking for nm utility
> checking for nm... nm
> checking nm flags... 
> checking for C-equivalent to Fortran routine "SUB"... sub_
> checking for Fortran "byte"... yes
> checking for Fortran "integer*2"... yes
> checking if Fortran "byte" is C "signed char"... yes
> checking if Fortran "byte" is C "short"... no
> checking if Fortran "byte" is C "int"... no
> checking if Fortran "byte" is C "long"... no
> checking if Fortran "integer*2" is C "short"... yes
> checking if Fortran "integer*2" is C "int"... no
> checking if Fortran "integer*2" is C "long"... no
> checking if Fortran "integer" is C "int"... yes
> checking if Fortran "real" is C "float"... yes
> checking if Fortran "doubleprecision" is C "double"... yes
> checking for Fortran-equivalent to netCDF "byte"... byte
> checking for Fortran-equivalent to netCDF "short"... integer*2
> checking for math library
> checking for tanh in -lc... yes
> checking for ar utility
> checking for ar... ar
> checking ar flags... cru
> checking for nm utility
> checking for nm... (cached) nm
> checking nm flags... 
> checking for ranlib... ranlib
> checking for stdlib.h... yes
> checking for sys/types.h... yes
> checking for strerror... yes
> checking for working ftruncate()... yes
> checking for working alloca.h... no
> checking for alloca... yes
> checking for st_blksize in struct stat... yes
> checking for IEEE floating point format... yes
> checking for ANSI C header files... yes
> checking for size_t... yes
> checking for off_t... yes
> checking for ssize_t... yes
> checking for ptrdiff_t... yes
> checking for uchar... no
> checking whether char is unsigned... no
> checking whether byte ordering is bigendian... no
> checking size of short... 2
> checking size of int... 4
> checking size of long... 4
> checking size of float... 4
> checking size of double... 8
> checking size of off_t... 4
> checking size of size_t... 4
> checking for catman... no
> checking for makewhatis... no
> checking for /usr/lib/makewhatis... no
> checking for manual-page index command... 
> checking binary distribution directory... /home/ftp/pub/binary/dummy_system
> updating cache ./config.cache
> creating ./config.status
> creating macros.make
> udcreating fortran/nfconfig.inc
> creating libsrc/ncconfig.h
> 
> ********************* config.log ********************************
> This file contains any messages produced by compilers while
> running configure, to aid debugging if configure makes a mistake.
> 
> configure:928: checking for top-level source-directory
> configure:938: checking for m4 preprocessor
> configure:945: checking for m4
> configure:1012: checking m4 flags
> configure:1040: checking for xlc
> configure:1040: checking for c89
> configure:1040: checking for acc
> configure:1040: checking for cc
> configure:1040: checking for gcc
> configure:1085: checking C compiler "gcc"
> configure:1094: gcc -c -O -DNDEBUG conftest.c 1>&5
> configure:1121: checking how to make dependencies
> configure:1189: checking for CC
> configure:1189: checking for cxx
> configure:1189: checking for c++
> configure:1225: checking C++ compiler "c++"
> configure:1243: c++ -o conftest  -DNDEBUG  conftest.C  1>&5
> configure:1294: checking how to run the C preprocessor
> configure:1315: gcc -E -DNDEBUG conftest.c >/dev/null 2>conftest.out
> configure:1475: checking for xlf
> configure:1475: checking for fort77
> configure:1475: checking for ghf77
> configure:1475: checking for f77
> configure:1475: checking for cf77
> configure:1475: checking for g77
> configure:1516: g77 -c  conftest.f
> configure:1548: checking for Fortran .F compiler
> configure:1558: checking if Fortran-77 compiler handles *.F files
> configure:1569: g77 -o conftest  conftest.F 
> configure:1638: checking "g77" as Fortran-90 compiler
> configure:1640: g77 -o conftest  conftest.f90 
> /usr/lib/gcc-lib/i686-pc-cygwin/2.95.2-6/../../../../i686-pc-cygwin/bin/ld:c
> onftest.f90: file format not recognized; treating as linker script
> /usr/lib/gcc-lib/i686-pc-cygwin/2.95.2-6/../../../../i686-pc-cygwin/bin/ld:c
> onftest.f90:1: syntax error
> collect2: ld returned 1 exit status
> configure:1669: checking for xlf90
> configure:1669: checking for f90
> configure:1751: checking for nm utility
> configure:1758: checking for nm
> configure:1825: checking nm flags
> configure:1841: checking for C-equivalent to Fortran routine "SUB"
> configure:1847: g77 -c  conftest.f
> configure:1876: checking for Fortran "byte"
> configure:1883: g77 -c  conftest.f
> configure:1900: checking for Fortran "integer*2"
> configure:1907: g77 -c  conftest.f
> configure:1933: checking if Fortran "byte" is C "signed char"
> configure:1942: gcc -c -DNDEBUG -O conftest.c
> configure:1944: g77  -c conftestf.f
> configure:1946: g77 -o conftest   conftestf.o conftest.o 
> configure:1948: ./conftest
> configure:1981: checking if Fortran "byte" is C "short"
> configure:1990: gcc -c -DNDEBUG -O conftest.c
> configure:1992: g77  -c conftestf.f
> configure:1994: g77 -o conftest   conftestf.o conftest.o 
> configure:1996: ./conftest
> configure:2029: checking if Fortran "byte" is C "int"
> configure:2038: gcc -c -DNDEBUG -O conftest.c
> configure:2040: g77  -c conftestf.f
> configure:2042: g77 -o conftest   conftestf.o conftest.o 
> configure:2044: ./conftest
> configure:2077: checking if Fortran "byte" is C "long"
> configure:2086: gcc -c -DNDEBUG -O conftest.c
> configure:2088: g77  -c conftestf.f
> configure:2090: g77 -o conftest   conftestf.o conftest.o 
> configure:2092: ./conftest
> configure:2129: checking if Fortran "integer*2" is C "short"
> configure:2138: gcc -c -DNDEBUG -O conftest.c
> configure:2140: g77  -c conftestf.f
> configure:2142: g77 -o conftest   conftestf.o conftest.o 
> configure:2144: ./conftest
> configure:2177: checking if Fortran "integer*2" is C "int"
> configure:2186: gcc -c -DNDEBUG -O conftest.c
> configure:2188: g77  -c conftestf.f
> configure:2190: g77 -o conftest   conftestf.o conftest.o 
> configure:2192: ./conftest
> configure:2225: checking if Fortran "integer*2" is C "long"
> configure:2234: gcc -c -DNDEBUG -O conftest.c
> configure:2236: g77  -c conftestf.f
> configure:2238: g77 -o conftest   conftestf.o conftest.o 
> configure:2240: ./conftest
> configure:2275: checking if Fortran "integer" is C "int"
> configure:2284: gcc -c -DNDEBUG -O conftest.c
> configure:2286: g77  -c conftestf.f
> configure:2288: g77 -o conftest   conftestf.o conftest.o 
> configure:2290: ./conftest
> configure:2323: checking if Fortran "real" is C "float"
> configure:2332: gcc -c -DNDEBUG -O conftest.c
> configure:2334: g77  -c conftestf.f
> configure:2336: g77 -o conftest   conftestf.o conftest.o 
> configure:2338: ./conftest
> configure:2371: checking if Fortran "doubleprecision" is C "double"
> configure:2380: gcc -c -DNDEBUG -O conftest.c
> configure:2382: g77  -c conftestf.f
> configure:2384: g77 -o conftest   conftestf.o conftest.o 
> configure:2386: ./conftest
> configure:2413: checking for Fortran-equivalent to netCDF "byte"
> configure:2420: g77 -c  conftest.f
> configure:2435: checking for Fortran-equivalent to netCDF "short"
> configure:2442: g77 -c  conftest.f
> configure:2462: checking for math library
> configure:2466: checking for tanh in -lc
> configure:2485: gcc -o conftest -O -DNDEBUG  conftest.c -lc   1>&5
> configure:2555: checking for ar utility
> configure:2562: checking for ar
> configure:2629: checking ar flags
> configure:2638: checking for nm utility
> configure:2680: checking for nm
> configure:2712: checking nm flags
> configure:2722: checking for ranlib
> configure:2751: checking for stdlib.h
> configure:2761: gcc -E -DNDEBUG conftest.c >/dev/null 2>conftest.out
> configure:2788: checking for sys/types.h
> configure:2798: gcc -E -DNDEBUG conftest.c >/dev/null 2>conftest.out
> configure:2824: checking for strerror
> configure:2852: gcc -o conftest -O -DNDEBUG  conftest.c  1>&5
> configure:2877: checking for working ftruncate()
> configure:2930: gcc -o conftest -O -DNDEBUG  conftest.c  1>&5
> configure:2952: checking for working alloca.h
> configure:2964: gcc -o conftest -O -DNDEBUG  conftest.c  1>&5
> configure:2958: alloca.h: No such file or directory
> configure: failed program was:
> #line 2957 "configure"
> #include "confdefs.h"
> #include <alloca.h>
> int main() {
> char *p = alloca(2 * sizeof(int));
> ; return 0; }
> configure:2985: checking for alloca
> configure:3018: gcc -o conftest -O -DNDEBUG  conftest.c  1>&5
> configure:3184: checking for st_blksize in struct stat
> configure:3197: gcc -c -O -DNDEBUG conftest.c 1>&5
> configure:3219: checking for IEEE floating point format
> configure:3257: gcc -o conftest -O -DNDEBUG  conftest.c  1>&5
> configure:3278: checking for ANSI C header files
> configure:3291: gcc -E -DNDEBUG conftest.c >/dev/null 2>conftest.out
> configure:3358: gcc -o conftest -O -DNDEBUG  conftest.c  1>&5
> configure:3382: checking for size_t
> configure:3415: checking for off_t
> configure:3448: checking for ssize_t
> configure:3481: checking for ptrdiff_t
> configure:3514: checking for uchar
> configure:3547: checking whether char is unsigned
> configure:3610: checking whether byte ordering is bigendian
> configure:3628: gcc -c -O -DNDEBUG conftest.c 1>&5
> configure:3643: gcc -c -O -DNDEBUG conftest.c 1>&5
> configure: In function `main':
> configure:3638: `not' undeclared (first use in this function)
> configure:3638: (Each undeclared identifier is reported only once
> configure:3638: for each function it appears in.)
> configure:3638: parse error before `big'
> configure: failed program was:
> #line 3632 "configure"
> #include "confdefs.h"
> #include <sys/types.h>
> #include <sys/param.h>
> int main() {
> 
> #if BYTE_ORDER != BIG_ENDIAN
>  not big endian
> #endif
> ; return 0; }
> configure:3700: checking size of short
> configure:3719: gcc -o conftest -O -DNDEBUG  conftest.c  1>&5
> configure:3739: checking size of int
> configure:3758: gcc -o conftest -O -DNDEBUG  conftest.c  1>&5
> configure:3778: checking size of long
> configure:3797: gcc -o conftest -O -DNDEBUG  conftest.c  1>&5
> configure:3817: checking size of float
> configure:3836: gcc -o conftest -O -DNDEBUG  conftest.c  1>&5
> configure:3856: checking size of double
> configure:3875: gcc -o conftest -O -DNDEBUG  conftest.c  1>&5
> configure:3895: checking size of off_t
> configure:3918: gcc -o conftest -O -DNDEBUG  conftest.c  1>&5
> configure:3938: checking size of size_t
> configure:3961: gcc -o conftest -O -DNDEBUG  conftest.c  1>&5
> configure:4020: checking for catman
> configure:4020: checking for makewhatis
> configure:4020: checking for /usr/lib/makewhatis
> configure:4062: checking for manual-page index command
> configure:4066: checking binary distribution directory
> 
> *************************** make.log
> *********************************************
> make[1]: Entering directory `/cygdrive/c/gmt-3.4/netcdf-3.5.0/src'
> 
> Making `all' in directory /cygdrive/c/gmt-3.4/netcdf-3.5.0/src/libsrc
> 
> make[2]: Entering directory `/cygdrive/c/gmt-3.4/netcdf-3.5.0/src/libsrc'
> gcc -c -O -I.  -DNDEBUG attr.c
> gcc -c -O -I.  -DNDEBUG dim.c
> gcc -c -O -I.  -DNDEBUG error.c
> gcc -c -O -I.  -DNDEBUG -DVERSION=`cat ../VERSION` libvers.c
> gcc -c -O -I.  -DNDEBUG nc.c
> gcc -c -O -I.  -DNDEBUG ncio.c
> gcc -c -O -I.  -DNDEBUG ncx.c
> gcc -c -O -I.  -DNDEBUG putget.c
> gcc -c -O -I.  -DNDEBUG string.c
> gcc -c -O -I.  -DNDEBUG v1hpg.c
> gcc -c -O -I.  -DNDEBUG v2i.c
> gcc -c -O -I.  -DNDEBUG var.c
> ar cru libnetcdf.a attr.o dim.o error.o libvers.o nc.o ncio.o ncx.o putget.o
> string.o v1hpg.o v2i.o var.o
> ranlib libnetcdf.a
> make[2]: Leaving directory `/cygdrive/c/gmt-3.4/netcdf-3.5.0/src/libsrc'
> 
> Returning to directory /cygdrive/c/gmt-3.4/netcdf-3.5.0/src
> 
> make[1]: Leaving directory `/cygdrive/c/gmt-3.4/netcdf-3.5.0/src'
> make[1]: Entering directory `/cygdrive/c/gmt-3.4/netcdf-3.5.0/src'
> 
> Making `all' in directory /cygdrive/c/gmt-3.4/netcdf-3.5.0/src/fortran
> 
> make[2]: Entering directory `/cygdrive/c/gmt-3.4/netcdf-3.5.0/src/fortran'
> gcc -c -O -I../libsrc  -DNDEBUG fort-attio.c
> gcc -c -O -I../libsrc  -DNDEBUG fort-control.c
> gcc -c -O -I../libsrc  -DNDEBUG fort-dim.c
> gcc -c -O -I../libsrc  -DNDEBUG fort-genatt.c
> gcc -c -O -I../libsrc  -DNDEBUG fort-geninq.c
> gcc -c -O -I../libsrc  -DNDEBUG fort-genvar.c
> gcc -c -O -I../libsrc  -DNDEBUG fort-lib.c
> gcc -c -O -I../libsrc  -DNDEBUG fort-misc.c
> gcc -c -O -I../libsrc  -DNDEBUG fort-v2compat.c
> gcc -c -O -I../libsrc  -DNDEBUG fort-vario.c
> gcc -c -O -I../libsrc  -DNDEBUG fort-var1io.c
> gcc -c -O -I../libsrc  -DNDEBUG fort-varaio.c
> gcc -c -O -I../libsrc  -DNDEBUG fort-varmio.c
> gcc -c -O -I../libsrc  -DNDEBUG fort-varsio.c
> ar cru ../libsrc/libnetcdf.a fort-attio.o fort-control.o fort-dim.o
> fort-genatt.o fort-geninq.o fort-genvar.o fort-lib.o fort-misc.o
> fort-v2compat.o fort-vario.o fort-var1io.o fort-varaio.o fort-varmio.o
> fort-varsio.o
> ranlib ../libsrc/libnetcdf.a
> make[2]: Leaving directory `/cygdrive/c/gmt-3.4/netcdf-3.5.0/src/fortran'
> 
> Returning to directory /cygdrive/c/gmt-3.4/netcdf-3.5.0/src
> 
> make[1]: Leaving directory `/cygdrive/c/gmt-3.4/netcdf-3.5.0/src'
> make[1]: Entering directory `/cygdrive/c/gmt-3.4/netcdf-3.5.0/src'
> 
> Making `all' in directory /cygdrive/c/gmt-3.4/netcdf-3.5.0/src/ncdump
> 
> make[2]: Entering directory `/cygdrive/c/gmt-3.4/netcdf-3.5.0/src/ncdump'
> gcc -c -O -I../libsrc  -DNDEBUG ncdump.c
> gcc -c -O -I../libsrc  -DNDEBUG vardata.c
> gcc -c -O -I../libsrc  -DNDEBUG dumplib.c
> gcc -o ncdump -O  ncdump.o vardata.o dumplib.o ../libsrc/libnetcdf.a  
> make[2]: Leaving directory `/cygdrive/c/gmt-3.4/netcdf-3.5.0/src/ncdump'
> 
> Returning to directory /cygdrive/c/gmt-3.4/netcdf-3.5.0/src
> 
> make[1]: Leaving directory `/cygdrive/c/gmt-3.4/netcdf-3.5.0/src'
> make[1]: Entering directory `/cygdrive/c/gmt-3.4/netcdf-3.5.0/src'
> 
> Making `all' in directory /cygdrive/c/gmt-3.4/netcdf-3.5.0/src/ncgen
> 
> make[2]: Entering directory `/cygdrive/c/gmt-3.4/netcdf-3.5.0/src/ncgen'
> gcc -c -O -I../libsrc -I.  -DNDEBUG main.c
> gcc -c -O -I../libsrc -I.  -DNDEBUG load.c
> gcc -c -O -I../libsrc -I.  -DNDEBUG ncgentab.c
> gcc -c -O -I../libsrc -I.  -DNDEBUG escapes.c
> gcc -c -O -I../libsrc -I.  -DNDEBUG getfill.c
> gcc -c -O -I../libsrc -I.  -DNDEBUG init.c
> gcc -c -O -I../libsrc -I.  -DNDEBUG genlib.c
> gcc -o ncgen -O  main.o load.o ncgentab.o escapes.o getfill.o init.o
> genlib.o ../libsrc/libnetcdf.a  
> make[2]: Leaving directory `/cygdrive/c/gmt-3.4/netcdf-3.5.0/src/ncgen'
> 
> Returning to directory /cygdrive/c/gmt-3.4/netcdf-3.5.0/src
> 
> make[1]: Leaving directory `/cygdrive/c/gmt-3.4/netcdf-3.5.0/src'
> make[1]: Entering directory `/cygdrive/c/gmt-3.4/netcdf-3.5.0/src'
> 
> Making `all' in directory /cygdrive/c/gmt-3.4/netcdf-3.5.0/src/cxx
> 
> make[2]: Entering directory `/cygdrive/c/gmt-3.4/netcdf-3.5.0/src/cxx'
> c++ -c  -I../libsrc -I.  -DNDEBUG netcdf.cpp
> c++ -c  -I../libsrc -I.  -DNDEBUG ncvalues.cpp
> ar cru libnetcdf_c++.a netcdf.o ncvalues.o
> ranlib libnetcdf_c++.a
> c++ -c  -I../libsrc -I.  -DNDEBUG nctst.cpp
> c++ -o nctst   nctst.o libnetcdf_c++.a -L../libsrc -lnetcdf 
> make[2]: Leaving directory `/cygdrive/c/gmt-3.4/netcdf-3.5.0/src/cxx'
> 
> Returning to directory /cygdrive/c/gmt-3.4/netcdf-3.5.0/src
> 
> make[1]: Leaving directory `/cygdrive/c/gmt-3.4/netcdf-3.5.0/src'
> 
> *************************** test.log *************************************
> make[1]: Entering directory `/cygdrive/c/gmt-3.4/netcdf-3.5.0/src'
> 
> Making `test' in directory /cygdrive/c/gmt-3.4/netcdf-3.5.0/src/libsrc
> 
> make[2]: Entering directory `/cygdrive/c/gmt-3.4/netcdf-3.5.0/src/libsrc'
> gcc -c -O -I.  -DNDEBUG t_nc.c
> ar cru libnetcdf.a attr.o dim.o error.o libvers.o nc.o ncio.o ncx.o putget.o
> string.o v1hpg.o v2i.o var.o
> ranlib libnetcdf.a
> gcc -o t_nc -O  t_nc.o -L. -lnetcdf 
> ./t_nc
> dimrename: IXX
> nc_close ret = 0
> 
> reopen id = 3 for filename test.nc
> NC done
> GATTR VAR VATTR
> VATTR
> VATTR
> VATTR
> VATTR
> VATTR
> fill_seq indices       1 2 3  75.000000 != 2.718282
> Done
> got val = 3.250000
> got val = 0.000000
> got val = 2.718282
> got val = 82555
> got val = 97
> got NC_CHAR val = A (0x41) 
> got NC_CHAR val = B (0x42) 
> got NC_CHAR val = "The red death had long devastated the country."
> got val = A (0x41) 
> got val = B (0x42) 
> got val = "The red death had long devastated the country."
> got vals = 0.000000 ... 447.000000
> re nc_close ret = 0
> cmp test.nc test_nc.sav
> test.nc test_nc.sav differ: char 1545, line 5
> make[2]: Leaving directory `/cygdrive/c/gmt-3.4/netcdf-3.5.0/src/libsrc'
> make[1]: Leaving directory `/cygdrive/c/gmt-3.4/netcdf-3.5.0/src'