您尝试构建的项目对运行cmake配置的环境有一些限制，并说明了原因：
从OpenMS/contrib/CMakeLists.txt开始

...
  ## check that the console environment has a cl.exe architecture which is identical to the VS Generator
  ## If cl.exe builds 32-bit libs and VS Generator is Win64, we'd end up with mixed 32bit/64bit libraries, depending on how each lib is build (Cmake, bjam, nmake)
  execute_process(COMMAND "cl.exe" OUTPUT_VARIABLE cl_out ERROR_VARIABLE cl_out)
  ##message(STATUS "Cl.exe said: ${cl_out}")
  if (cl_out MATCHES ".*x64.*")
    message(STATUS "Cl.exe produces: 64-bit")
    set(CL_ADDRESSMODEL 64)
  elseif (cl_out MATCHES ".*x86.*")
    message(STATUS "Cl.exe produces: 32-bit")
    set(CL_ADDRESSMODEL 32)
  else()
    message(FATAL_ERROR "Could not determine if cl.exe builds x86 or x64 apps. Make sure cl.exe is available in your environment!")
  endif()
  if (NOT (CL_ADDRESSMODEL EQUAL CONTRIB_ADDRESSMODEL))
    message(FATAL_ERROR "cl.exe (${CL_ADDRESSMODEL}-bit) and Visual Studio Generator (${CONTRIB_ADDRESSMODEL}-bit) do not match. Please fix your PATH environment to find the proper cl.exe or use an appropriate generator by adding -A Win32/x64 to your CMake call.")
  endif()
  ...

CONTRIB_ADDRESSMODEL的设置取决于检测到的CMake（CMAKE_SIZEOF_VOID_P）的编译器属性。
注意，这里cl.exe是从当前进程执行的，以检测所用程序的体系结构。该程序可能与编译器cmake选择使用的不同。
这要求您确保cmake选择的编译和命令提示符中可用的cl.exe都以x64为目标，以设置以x64为目标的cmake项目。在进行cmake配置之前，您需要运行正确的...\vcvarsall.bat x64（或等效程序）。
或者，您需要手动编辑PATH环境变量，以便在列出包含面向不同体系结构得cl.exe得任何其他目录之前列出包含面向x64得cl.exe得目录.
注意：我还没有仔细研究为什么要添加这个CMake逻辑，但听起来这是一个糟糕的选择。当然，有些情况下您希望避免使用意外的编译器进行编译，但有些CMake生成器硬编码到程序的绝对路径，如编译器，使用这些生成器会受到这样的限制的阻碍...