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Norman at LOKI /c/tmp/proj-4.6.1
$ ./configure

config.status: executing depfiles commands

Norman at LOKI /c/tmp/proj-4.6.1
$ make
Making all in src
make[1]: Entering directory `/c/tmp/proj-4.6.1/src'
make  all-am
make[2]: Entering directory `/c/tmp/proj-4.6.1/src'

.........................

/bin/sh ../libtool --tag=CC   --mode=link gcc  -g -O2   -o cs2cs.exe cs2cs.o
gen_cheb.o p_series.o libproj.la -lm 
gcc -g -O2 -o cs2cs.exe cs2cs.o gen_cheb.o p_series.o  ./.libs/libproj.a  

Norman at LOKI /c/tmp/proj-4.6.1
$ src/proj
Rel. 4.6.1, 21 August 2008
usage: proj.exe [ -beEfiIlormsStTvVwW [args] ] [ +opts[=arg] ] [ files ]


Here are the tools I used

Norman at LOKI /c/tmp/proj-4.6.1
$ gcc --version
gcc.exe (GCC) 3.4.2 (mingw-special)

Norman at LOKI /c/tmp/proj-4.6.1
$ libtool --version
ltmain.sh (GNU libtool) 1.5.24 Debian 1.5.24-1ubuntu1 (1.1220.2.456
2007/06/24 02:25:32)

Norman at LOKI /c/tmp/proj-4.6.1
$ make --version
GNU Make version 3.79.1, by Richard Stallman and Roland McGrath.
Built for i686-pc-msys