Nobody else appears to have run into this problem, but here's what it was:

When autoconf (2.57) processed this section of configure.in

dnl output the Makefiles
AC_OUTPUT([Makefile \
util/Makefile \
util/Transcoders/Cygwin/Makefile \
util/Transcoders/ICU/Makefile \
util/Transcoders/Iconv/Makefile \
util/Transcoders/Iconv390/Makefile \
util/Transcoders/Uniconv390/Makefile \
util/Transcoders/Iconv400/Makefile \
util/Transcoders/IconvFBSD/Makefile \
util/Transcoders/IconvGNU/Makefile \
... etc...

For some reason the "\" at the end of the line was causing autconf to create the 
following output

for ac_config_target in $ac_config_targets
do
  case "$ac_config_target" in
  # Handling of arguments.
  "Makefile" ) CONFIG_FILES="$CONFIG_FILES Makefile" ;;
  "\^M
" ) CONFIG_FILES="$CONFIG_FILES \^M
" ;;
  "util/Makefile" ) CONFIG_FILES="$CONFIG_FILES util/Makefile" ;;
  "\^M
" ) CONFIG_FILES="$CONFIG_FILES \^M
" ;;
  "util/Transcoders/Cygwin/Makefile" ) CONFIG_FILES="$CONFIG_FILES 
util/Transcoders/Cygwin/Makefile" ;;
  "\^M
" ) CONFIG_FILES="$CONFIG_FILES \^M
" ;;
... etc.

Where the \^M was screwing up the configure process. I guess these are DOS LF 
characters (or CR, I can't remember which is different from UNIX....). Seems like 
autoconf wasn't recognizing the line continuation character. I verified that I'm 
running autoconf 2.57. Oh well.

When I edited the configure.in to put the Makefiles all on one line and ran autoconf 
again, I was able to run configure successfully.

If anybody knows of environment variables or other configuration that affects autoconf 
in this area, I would love to hear about it.

- DAP

>  -----Original Message-----
> From:         David Parker  
> Sent: Friday, September 26, 2003 3:00 PM
> To:   '[EMAIL PROTECTED]'
> Subject:      resend: runConfigure under cygwin
> 
> Apologies for re-posting this, if in fact I am: When I sent 
> it the first time I wasn't subscribed, so I thought it might 
> have gone into the bit-bucket....
> 
> I'm trying to get the xercesc 2.3 source to build using 
> cygwin. I tried the following:
> 
> $ runConfigure -pcygwin -cgcc -xg++
> Generating makefiles with the following options ...
> Platform: cygwin
> C Compiler: gcc
> C++ Compiler: g++
> Message Loader: inmem
> Net Accessor: socket
> Transcoder: native
> Thread option: pthread
> bitsToBuild option: 32
> Extra compile options:
> Extra link options:
> Extra configure options:
> Debug is OFF
> 
> checking for gcc... gcc
> checking for C compiler default output... a.exe
> checking whether the C compiler works... yes
> checking whether we are cross compiling... no
> checking for suffix of executables... .exe
> checking for suffix of object files... o
> checking whether we are using the GNU C compiler... yes
> checking whether gcc accepts -g... yes
> checking for gcc option to accept ANSI C... none needed
> checking whether we are using the GNU C++ compiler... yes
> checking whether g++ accepts -g... yes
> checking for a BSD-compatible install... /usr/bin/install -c
> checking for autoconf... autoconf
> checking how to run the C preprocessor... gcc -E
> checking for egrep... grep -E
> 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 XMLByte... no
> checking build system type... i686-pc-cygwin
> checking host system type... i686-pc-cygwin
> configure: creating ./config.status
> config.status: creating Makefile
> config.status: creating \
> .infig.status: error: cannot find input file: \
> 
> It looks like I'm missing an environment variable or a 
> configure switch. My $XERCESCROOT appears to be set properly. 
> Any hints would be appreciated!
> 
> 
> - DAP
> --------------------------------------------------------------
> ------------
> David Parker   
> Rocket Software
> (617) 614-2128
> 


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