Try to fix broken file by just deleting it.

gyp/gpu.gypi

 # Copyright 2015 Google Inc.
 #
 # Use of this source code is governed by a BSD-style license that can be
 # found in the LICENSE file.
 # Include this gypi to include all 'gpu' files
 # The parent gyp/gypi file must define
 #       'skia_src_path'     e.g. skia/trunk/src
 #       'skia_include_path' e.g. skia/trunk/include
 #
 # The skia build defines these in common_variables.gypi
@@ skipping 444 matching lines @@
       '<(skia_src_path)/gpu/vk/GrVkIndexBuffer.h',
       '<(skia_src_path)/gpu/vk/GrVkInterface.cpp',
       '<(skia_src_path)/gpu/vk/GrVkMemory.cpp',
       '<(skia_src_path)/gpu/vk/GrVkMemory.h',
       '<(skia_src_path)/gpu/vk/GrVkPipeline.cpp',
       '<(skia_src_path)/gpu/vk/GrVkPipeline.h',
       '<(skia_src_path)/gpu/vk/GrVkProgram.cpp',
       '<(skia_src_path)/gpu/vk/GrVkProgram.h',
       '<(skia_src_path)/gpu/vk/GrVkProgramBuilder.cpp',
       '<(skia_src_path)/gpu/vk/GrVkProgramBuilder.h',
-      '<(skia_src_path)/gpu/vk/GrVkProgramDataManager.cpp',
+    #  '<(skia_src_path)/gpu/vk/GrVkProgramDataManager.cpp',
       '<(skia_src_path)/gpu/vk/GrVkProgramDataManager.h',
       '<(skia_src_path)/gpu/vk/GrVkProgramDesc.cpp',
       '<(skia_src_path)/gpu/vk/GrVkProgramDesc.h',
       '<(skia_src_path)/gpu/vk/GrVkRenderPass.cpp',
       '<(skia_src_path)/gpu/vk/GrVkRenderPass.h',
       '<(skia_src_path)/gpu/vk/GrVkRenderTarget.cpp',
       '<(skia_src_path)/gpu/vk/GrVkRenderTarget.h',
       '<(skia_src_path)/gpu/vk/GrVkResource.h',
       '<(skia_src_path)/gpu/vk/GrVkResourceProvider.cpp',
       '<(skia_src_path)/gpu/vk/GrVkResourceProvider.h',
@@ skipping 78 matching lines @@
       '<(skia_src_path)/gpu/gl/debug/SkDebugGLContext.cpp',
       '<(skia_src_path)/gpu/gl/debug/SkDebugGLContext.h',
     ],
     'skgpu_null_gl_sources': [
       '<(skia_src_path)/gpu/gl/GrGLCreateNullInterface.cpp',
       '<(skia_src_path)/gpu/gl/SkNullGLContext.cpp',
       '<(skia_include_path)/gpu/gl/SkNullGLContext.h',
     ],
   },
 }