title: tensorflow build fails with "missing dependency" error
body: <p>I'm completely new to bazel and tensorflow so the solution to this may be obvious to someone with some experience. My bazel build of tensorflow fails with a "missing dependency" error message. Here is the relevant sequence of build commands and output:</p>
  
  <pre><code>(tf-gpu)kss@linux-9c32:~/projects&gt; git clone --recurse-submodules https://github.com/tensorflow/tensorflow tensorflow-nogpu
  Cloning into 'tensorflow-nogpu'...
  remote: Counting objects: 16735, done.
  remote: Compressing objects: 100% (152/152), done.
  remote: Total 16735 (delta 73), reused 0 (delta 0), pack-reused 16583
  Receiving objects: 100% (16735/16735), 25.25 MiB | 911.00 KiB/s, done.
  Resolving deltas: 100% (10889/10889), done.
  Checking connectivity... done.
  Submodule 'google/protobuf' (https://github.com/google/protobuf.git) registered for path 'google/protobuf'
  Cloning into 'google/protobuf'...
  remote: Counting objects: 30266, done.
  remote: Compressing objects: 100% (113/113), done.
  remote: Total 30266 (delta 57), reused 0 (delta 0), pack-reused 30151
  Receiving objects: 100% (30266/30266), 28.90 MiB | 1.98 MiB/s, done.
  Resolving deltas: 100% (20225/20225), done.
  Checking connectivity... done.
  Submodule path 'google/protobuf': checked out '0906f5d18a2548024b511eadcbb4cfc0ca56cd67'
  (tf-gpu)kss@linux-9c32:~/projects&gt; cd tensorflow-nogpu/
  (tf-gpu)kss@linux-9c32:~/projects/tensorflow-nogpu&gt; ./configure 
  Please specify the location of python. [Default is /home/kss/.venv/tf-gpu/bin/python]: 
  Do you wish to build TensorFlow with GPU support? [y/N] 
  No GPU support will be enabled for TensorFlow
  Configuration finished
  (tf-gpu)kss@linux-9c32:~/projects/tensorflow-nogpu&gt; bazel build -c opt //tensorflow/tools/pip_package:build_pip_package                                                        
  Sending SIGTERM to previous Bazel server (pid=8491)... done.
  ....
  INFO: Found 1 target...
  ERROR: /home/kss/.cache/bazel/_bazel_kss/b97e0e942a10977a6b42467ea6712cbf/external/re2/BUILD:9:1: undeclared inclusion(s) in rule '@re2//:re2':
  this rule is missing dependency declarations for the following files included by 'external/re2/re2/perl_groups.cc':
    '/usr/lib64/gcc/x86_64-suse-linux/4.8/include/stddef.h'
    '/usr/lib64/gcc/x86_64-suse-linux/4.8/include/stdarg.h'
    '/usr/lib64/gcc/x86_64-suse-linux/4.8/include/stdint.h'
    '/usr/lib64/gcc/x86_64-suse-linux/4.8/include/x86intrin.h'
    '/usr/lib64/gcc/x86_64-suse-linux/4.8/include/ia32intrin.h'
    '/usr/lib64/gcc/x86_64-suse-linux/4.8/include/mmintrin.h'
    '/usr/lib64/gcc/x86_64-suse-linux/4.8/include/xmmintrin.h'
    '/usr/lib64/gcc/x86_64-suse-linux/4.8/include/mm_malloc.h'
    '/usr/lib64/gcc/x86_64-suse-linux/4.8/include/emmintrin.h'
    '/usr/lib64/gcc/x86_64-suse-linux/4.8/include/immintrin.h'
    '/usr/lib64/gcc/x86_64-suse-linux/4.8/include/fxsrintrin.h'
    '/usr/lib64/gcc/x86_64-suse-linux/4.8/include/adxintrin.h'.
  Target //tensorflow/tools/pip_package:build_pip_package failed to build
  Use --verbose_failures to see the command lines of failed build steps.
  INFO: Elapsed time: 144.661s, Critical Path: 1.18s
  (tf-gpu)kss@linux-9c32:~/projects/tensorflow-nogpu&gt; 
  </code></pre>
  
  <p>The version of bazel I'm using is <code>release 0.1.4</code>, I'm running on openSUSE 13.2. I confirmed that the header files do exist which is probably expected:</p>
  
  <pre><code>(tf-gpu)kss@linux-9c32:~/projects/tensorflow-nogpu&gt; ll /usr/lib64/gcc/x86_64-suse-linux/4.8/include/stddef.h
  -rw-r--r-- 1 root root 13619 Oct  6  2014 /usr/lib64/gcc/x86_64-suse-linux/4.8/include/stddef.h
  </code></pre>
  
  <hr>
  
  <p><strong>Note for anyone who finds this question</strong>:</p>
  
  <p>Use Damien's answer below except that you have to use <code>--crosstool_top</code> rather than <code>--crosstool</code>. Also if you are building for GPU acceleration you will also need to modify the <code>CROSSTOOL</code> file in the tensorflow repo like:</p>
  
  <pre><code>(tf-gpu)kss@linux-9c32:~/projects/tensorflow-gpu&gt; git diff third_party/gpus/crosstool/CROSSTOOL | cat
  diff --git a/third_party/gpus/crosstool/CROSSTOOL b/third_party/gpus/crosstool/CROSSTOOL
  index dfde7cd..b63f950 100644
  --- a/third_party/gpus/crosstool/CROSSTOOL
  +++ b/third_party/gpus/crosstool/CROSSTOOL
  @@ -56,6 +56,7 @@ toolchain {
     cxx_builtin_include_directory: "/usr/lib/gcc/"
     cxx_builtin_include_directory: "/usr/local/include"
     cxx_builtin_include_directory: "/usr/include"
  +  cxx_builtin_include_directory: "/usr/lib64/gcc"
     tool_path { name: "gcov" path: "/usr/bin/gcov" }
  
     # C(++) compiles invoke the compiler (as that is the one knowing where
  </code></pre>