Question: Install freebayes in cygwin
gravatar for wei.shen
5.1 years ago by
wei.shen0 wrote:

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 &
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"

  gmake[2]: Entering directory

  C:/strawberry/c/bin/gmake -f CMakeFiles/cmTC_95b63.dir/build.make

  gmake[3]: Entering directory

  Building C object CMakeFiles/cmTC_95b63.dir/testCCompiler.c.o

  /usr/bin/cc -o CMakeFiles/cmTC_95b63.dir/testCCompiler.c.o -c

  gmake[3]: Leaving directory

  process_begin: CreateProcess(NULL, /usr/bin/cc -o
  CMakeFiles/cmTC_95b63.dir/testCCompiler.c.o -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

  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


next-gen software error • 2.1k views
ADD COMMENTlink written 5.1 years ago by wei.shen0
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