Using CMake with Eclipse CDT and Cygwin on Windows - cmake

Question

For a new project we want to use CMake. We are using Eclipse CDT as IDE and Cygwin gcc.
We generated the CMakeLists.txt and followed [this tutorial (option 2)][1].
When I try to run the described Make target to generate the Makefiles with CMake, which executes
cmake -E chdir C:/projects/eclipse_ws/MyApp/Build/ cmake -G "Unix Makefiles" ../ Run CMake
I get the error
CMake Error: The source directory "C:/projects/eclipse_ws/MyApp/Build/CMake" does not exist.
If I run the command directly from a Cygwin console it works just fine, however then I have to run make also from the Cygwin console, because the Makefiles are generated with Unix paths.
EDIT:
So I fixed this issue (see my answer below).
But I'm still having problems.
When I try to run CMake as Make target in Eclipse as suggested in the tutorial I get the following errors:
cmake -E chdir Build/ cmake -G 'Unix Makefiles' ../
-- The C compiler identification is unknown
-- The CXX compiler identification is unknown
System is unknown to cmake, create:
Platform/MINGW32_NT-6.1 to use this system, please send your config file to cmake#www.cmake.org so it can be added to cmake
Your CMakeCache.txt file was copied to CopyOfCMakeCache.txt. Please send that file to cmake#www.cmake.org.
-- Check for working C compiler: /usr/bin/gcc.exe
System is unknown to cmake, create:
Platform/MINGW32_NT-6.1 to use this system, please send your config file to cmake#www.cmake.org so it can be added to cmake
-- Check for working C compiler: /usr/bin/gcc.exe -- broken
CMake Error at /usr/share/cmake-2.8.9/Modules/CMakeTestCCompiler.cmake:52 (MESSAGE):
The C compiler "/usr/bin/gcc.exe" is not able to compile a simple test
program.
It fails with the following output:
Change Dir: /cygdrive/c/projects/eclipse_ws/MyApp/Build/CMakeFiles CMakeTmp
Run Build Command:/usr/bin/make.exe "cmTryCompileExec726566634/fast"
/usr/bin/make -f CMakeFiles/cmTryCompileExec726566634.dir/build.make
CMakeFiles/cmTryCompileExec726566634.dir/build
make[1]: Entering directory
'/cygdrive/c/projects/eclipse_ws/MyApp/Build/CMakeFiles/CMakeTmp'
/usr/bin/cmake.exe -E cmake_progress_report
/cygdrive/c/projects/eclipse_ws/MyApp/Build/CMakeFiles/CMakeTmp/CMakeFiles
1
Building C object
CMakeFiles/cmTryCompileExec726566634.dir/testCCompiler.c.obj
/usr/bin/gcc.exe -o
CMakeFiles/cmTryCompileExec726566634.dir/testCCompiler.c.obj -c
/cygdrive/c/projects/eclipse_ws/MyApp/Build/CMakeFiles/CMakeTmp/testCCompiler.c
CMakeFiles/cmTryCompileExec726566634.dir/build.make:60: recipe for target
'CMakeFiles/cmTryCompileExec726566634.dir/testCCompiler.c.obj' failed
make[1]: Leaving directory
'/cygdrive/c/projects/eclipse_ws/MyApp/Build/CMakeFiles/CMakeTmp'
make[1]: *** [CMakeFiles/cmTryCompileExec726566634.dir/testCCompiler.c.obj]
Error 1
Makefile:117: recipe for target 'cmTryCompileExec726566634/fast' failed
make: *** [cmTryCompileExec726566634/fast] Error 2
CMake will not be able to correctly generate this project.
Call Stack (most recent call first):
CMakeLists.txt:3 (project)
-- Configuring incomplete, errors occurred!
Seems like for some reason CMake assumes I have an MinGW environment and not Cygwin.
EDIT2
MinGW system was assumed, because a Git installation was in PATH before Cygwin and Git's uname command was used (which returns MinGW).

Answer 1

If you check "Make Target - Same as the target name" in Eclipse's Make dialog, Eclipse will add a
Run CMake
to the command (see question), which is misinterpreted by CMake.
I just unchecked "Same as the target name".