Issue 1:
When running ./configure on OS X with CUDA support enabled with bazel 0.3.1-homebrew, these errors occur:

ERROR: /Users/jmhodges/src/github.com/tensorflow/tensorflow/tensorflow/core/BUILD:692:1: no such package 'base': BUILD file not found on package path and referenced by '//tensorflow/core:ios_tensorflow_test_lib'.
ERROR: /Users/jmhodges/src/github.com/tensorflow/tensorflow/tensorflow/core/kernels/BUILD:2211:1: no such package 'base': BUILD file not found on package path and referenced by '//tensorflow/core/kernels:android_tensorflow_kernels_no_rtti_lite_runtime'.
ERROR: /Users/jmhodges/src/github.com/tensorflow/tensorflow/tensorflow/core/kernels/BUILD:2211:1: no such target '//tensorflow/core:android_tensorflow_lib_lite_no_rtti_lite_runtime': target 'android_tensorflow_lib_lite_no_rtti_lite_runtime' not declared in package 'tensorflow/core' defined by /Users/jmhodges/src/github.com/tensorflow/tensorflow/tensorflow/core/BUILD and referenced by '//tensorflow/core/kernels:android_tensorflow_kernels_no_rtti_lite_runtime'.
ERROR: /Users/jmhodges/src/github.com/tensorflow/tensorflow/tensorflow/core/kernels/BUILD:2211:1: no such target '//tensorflow/core:android_proto_lib_no_rtti_lite_runtime': target 'android_proto_lib_no_rtti_lite_runtime' not declared in package 'tensorflow/core' defined by /Users/jmhodges/src/github.com/tensorflow/tensorflow/tensorflow/core/BUILD and referenced by '//tensorflow/core/kernels:android_tensorflow_kernels_no_rtti_lite_runtime'.
ERROR: Evaluation of query "deps((//... union @bazel_tools//tools/jdk:toolchain))" failed: errors were encountered while computing transitive closure.

This seems to be because of targets like "ios_tensorflow_test_lib" and, so on, depending on a //base and //tensorflow/core:android_tensorflow_lib_lite_no_rtti_lite_runtime that do not exist.

Off hand, I'm not able to figure out what this was trying to refer to. Perhaps it used to exist?

Issue 2:
I am having trouble configuring the latest master branch (dbe7ee0). When I run ./configure, I get:

ERROR: [...]/tensorflow/tensorflow/contrib/session_bundle/BUILD:107:1: no such target '//tensorflow/core:android_lib_lite': target 'android_lib_lite' not declared in package 'tensorflow/core' defined by [...]/tensorflow/tensorflow/core/BUILD and referenced by '//tensorflow/contrib/session_bundle:session_bundle'.
ERROR: [...]/tensorflow/tensorflow/contrib/session_bundle/BUILD:213:1: no such target '//tensorflow/core:android_lib_lite': target 'android_lib_lite' not declared in package 'tensorflow/core' defined by [...]/tensorflow/tensorflow/core/BUILD and referenced by '//tensorflow/contrib/session_bundle:signature'.
ERROR: [...]/tensorflow/tensorflow/contrib/session_bundle/BUILD:107:1: no such target '//tensorflow/core:meta_graph_portable_proto': target 'meta_graph_portable_proto' not declared in package 'tensorflow/core' defined by [...]/tensorflow/tensorflow/core/BUILD and referenced by '//tensorflow/contrib/session_bundle:session_bundle'.
ERROR: [...]/tensorflow/tensorflow/contrib/session_bundle/BUILD:213:1: no such target '//tensorflow/core:meta_graph_portable_proto': target 'meta_graph_portable_proto' not declared in package 'tensorflow/core' defined by [...]/tensorflow/tensorflow/core/BUILD and referenced by '//tensorflow/contrib/session_bundle:signature'.
ERROR: [...]/tensorflow/tensorflow/contrib/session_bundle/BUILD:213:1: no such target '//tensorflow/core:meta_graph_portable_proto': target 'meta_graph_portable_proto' not declared in package 'tensorflow/core' defined by [...]/tensorflow/tensorflow/core/BUILD and referenced by '//tensorflow/contrib/session_bundle:signature'.
ERROR: [...]/tensorflow/tensorflow/contrib/session_bundle/BUILD:107:1: no such target '//tensorflow/core:meta_graph_portable_proto': target 'meta_graph_portable_proto' not declared in package 'tensorflow/core' defined by [...]/tensorflow/tensorflow/core/BUILD and referenced by '//tensorflow/contrib/session_bundle:session_bundle'.
ERROR: [...]/tensorflow/tensorflow/contrib/session_bundle/BUILD:107:1: no such target '//tensorflow/core:android_lib_lite': target 'android_lib_lite' not declared in package 'tensorflow/core' defined by [...]/tensorflow/tensorflow/core/BUILD and referenced by '//tensorflow/contrib/session_bundle:session_bundle'.
ERROR: Evaluation of query "deps((//... union @bazel_tools//tools/jdk:toolchain))" failed: errors were encountered while computing transitive closure.
Configuration finished

To summarize, the dependencies that are included inside the if_android and if_ios are not found. They don't exist in the repository, so that is not that surprising. What is more surprising though is that my vanilla installation is not returning empty lists when if_android is called. I haven't looked into how those functions work, so not sure why that is happening.

Environment info

Setup: CentOS, Bazel 0.3.1, CUDA 7.5, CuDNN 5.1, Tensorflow master (dbe7ee0)

I run configure and set it up for GPU support. Actually, I don't think this is criticial, but first I had to open up configure and add --output_base=... on the two calls to bazel, since my setup requires a custom cache directory.

Fix

The if_... lines were added in ed87884, so a fix that I know works is to use its parent commit 7705791.