I think the cause of this problem is that LIB_CLOCK_GETTIME in
some files[1] aren't substituted by configure, due to Gcc 4.5.3
that Cygwin updated recently. Here is a part in question in
config.log:
configure:11868: gcc -std=gnu99 -o conftest.exe -g3 -O2 -D_REENTRANT -I/usr/include/librsvg-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/cairo -I/usr/include/libpng15 -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/p11-kit-1 conftest.c @LIB_CLOCK_GETTIME@ -lgnutls -lnettle -lhogweed -lgmp -lintl -liconv -ltasn1 -lp11-kit -lz -lrsvg-2 -lgio-2.0 -lgdk_pixbuf-2.0 -lcairo -lgmodule-2.0 -lgobject-2.0 -lffi -lpixman-1 -lfontconfig -lexpat -lfreetype -lbz2 -lpng15 -lm -lz -lxcb-shm -lxcb-render -lXrender -lXext -lglib-2.0 -lintl -liconv -lpcre -lX11 -lxcb -lXau -lXdmcp -lX11 -lpthread >&5
gcc: @LIB_CLOCK_GETTIME@: No such file or directory
[1]
autogen/Makefile.in:LIB_CLOCK_GETTIME = @LIB_CLOCK_GETTIME@
lib-src/Makefile.in:LIB_CLOCK_GETTIME = @LIB_CLOCK_GETTIME@
lib/Makefile.in:LIB_CLOCK_GETTIME = @LIB_CLOCK_GETTIME@
src/Makefile.in:LIB_CLOCK_GETTIME=@LIB_CLOCK_GETTIME@
However, manually replacing those @LIB_CLOCK_GETTIME@ with -lrt
(after running autogen.sh) didn't help. I'm going to tackle it
again next week.