I isolated the problem, and fixed it. Notice that it wasn't detecting PHP in the output below. Line 1320 of configure was the problem:
if test "yes" = `echo '<?php echo phpversion()>3?"yes":"no"; ?>' | $PHP -q`; then
Apprently, cygwin doesn't support piping fully, as this generates no output at all when I run it independently:
$echo '<?php echo phpversion()>3?"yes":"no"; ?>' | php -q
Owner@Chiara ~/peardoc
$
However, if I save the contents into a small file testphpver.php, and change line 1320 to:
if test "yes" = $PHP -q testphpver.php; then
it works as expected and successfully configures.
This is what we have already done a very long time ago. You are using a *very* old phpdoc checkout. The current configure script first prints debug information, version numbers, environment values and then starts its work. If you update the phpdoc checkout, everything will work well.
Goba