I tried to install freebayes in cygwin, but was not successfully and saw the following. Would you please help me how to fix it?
$ make
wget -q http://hypervolu.me/freebayes/build/v1.0.1-2-g0cb2697 &
cd src && make
make[1]: Entering directory '/home/23227/src/freebayes/src'
DETECTED_VERSION = v1.0.1-2-g0cb2697
CURRENT_VERSION = v1.0.1-2-g0cb2697
cd ../bamtools && mkdir -p build && cd build && cmake .. && make
-- The C compiler identification is GNU 4.9.3
-- The CXX compiler identification is GNU 4.9.3
CMake Warning at /usr/share/cmake-3.3.2/Modules/Platform/CYGWIN.cmake:15 (messag e):
CMake no longer defines WIN32 on Cygwin!
(1) If you are just trying to build this project, ignore this warning or
quiet it by setting CMAKE_LEGACY_CYGWIN_WIN32=0 in your environment or in
the CMake cache. If later configuration or build errors occur then this
project may have been written under the assumption that Cygwin is WIN32.
In that case, set CMAKE_LEGACY_CYGWIN_WIN32=1 instead.
(2) If you are developing this project, add the line
set(CMAKE_LEGACY_CYGWIN_WIN32 0) # Remove when CMake >= 2.8.4 is required
at the top of your top-level CMakeLists.txt file or set the minimum
required version of CMake to 2.8.4 or higher. Then teach your project to
build on Cygwin without WIN32.
Call Stack (most recent call first):
/usr/share/cmake-3.3.2/Modules/CMakeSystemSpecificInformation.cmake:36 (includ e)
CMakeLists.txt:9 (project)
-- Check for working C compiler: /usr/bin/cc
-- Check for working C compiler: /usr/bin/cc -- broken
CMake Error at /usr/share/cmake-3.3.2/Modules/CMakeTestCCompiler.cmake:61 (messa ge):
The C compiler "/usr/bin/cc" is not able to compile a simple test program.
It fails with the following output:
Change Dir: /home/23227/src/freebayes/bamtools/build/CMakeFiles/CMakeTmp
Run Build Command:"/cygdrive/c/strawberry/c/bin/gmake.exe"
"cmTC_95b63/fast"
gmake[2]: Entering directory
`C:/cygwin64/home/23227/src/freebayes/bamtools/build/CMakeFiles/CMakeTmp'
C:/strawberry/c/bin/gmake -f CMakeFiles/cmTC_95b63.dir/build.make
CMakeFiles/cmTC_95b63.dir/build
gmake[3]: Entering directory
`C:/cygwin64/home/23227/src/freebayes/bamtools/build/CMakeFiles/CMakeTmp'
Building C object CMakeFiles/cmTC_95b63.dir/testCCompiler.c.o
/usr/bin/cc -o CMakeFiles/cmTC_95b63.dir/testCCompiler.c.o -c
/home/23227/src/freebayes/bamtools/build/CMakeFiles/CMakeTmp/testCCompiler.c
gmake[3]: Leaving directory
`C:/cygwin64/home/23227/src/freebayes/bamtools/build/CMakeFiles/CMakeTmp'
process_begin: CreateProcess(NULL, /usr/bin/cc -o
CMakeFiles/cmTC_95b63.dir/testCCompiler.c.o -c
/home/23227/src/freebayes/bamtools/build/CMakeFiles/CMakeTmp/testCCompiler.c,
...) failed.
make (e=2): The system cannot find the file specified.
gmake[3]: *** [CMakeFiles/cmTC_95b63.dir/testCCompiler.c.o] Error 2
gmake[2]: Leaving directory
`C:/cygwin64/home/23227/src/freebayes/bamtools/build/CMakeFiles/CMakeTmp'
gmake[2]: *** [cmTC_95b63/fast] Error 2
CMake will not be able to correctly generate this project.
Call Stack (most recent call first):
CMakeLists.txt:9 (project)
-- Configuring incomplete, errors occurred!
See also "/home/23227/src/freebayes/bamtools/build/CMakeFiles/CMakeOutput.log".
See also "/home/23227/src/freebayes/bamtools/build/CMakeFiles/CMakeError.log".
Makefile:39: recipe for target '../bamtools/lib/libbamtools.a' failed
make[1]: *** [../bamtools/lib/libbamtools.a] Error 1
make[1]: Leaving directory '/home/23227/src/freebayes/src'
Makefile:2: recipe for target 'all' failed
make: *** [all] Error 2