Issue 1:
ERROR: /home/wenjian/pkgs/tensorflow/tensorflow/core/kernels/BUILD:2207:1: 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: /home/wenjian/pkgs/tensorflow/tensorflow/core/kernels/BUILD:2207:1: 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: /home/wenjian/pkgs/tensorflow/tensorflow/core/kernels/BUILD:2207:1: 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 /home/wenjian/pkgs/tensorflow/tensorflow/core/BUILD and referenced by '//tensorflow/core/kernels:android_tensorflow_kernels_no_rtti_lite_runtime'.
ERROR: /home/wenjian/pkgs/tensorflow/tensorflow/core/kernels/BUILD:2207:1: 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 /home/wenjian/pkgs/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.

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.