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release v0.4.1 failing to compile on ubuntu 16.04 #19

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david-wb opened this issue Dec 21, 2017 · 8 comments
Closed

release v0.4.1 failing to compile on ubuntu 16.04 #19

david-wb opened this issue Dec 21, 2017 · 8 comments

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@david-wb
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david-wb commented Dec 21, 2017

Hi,

This is more of a support question, but I wasn't sure where else to get help. I'm trying to build and test deepvariant inside of a docker image. I know that there is already an image published to google cloud, but for my purposes I prefer to build my own image. My docker file looks like this.

FROM ubuntu:16.04

RUN set -ex \
  && buildDependencies=' \
    ca-certificates \
    curl \
    wget \
    git \
    apt-transport-https \
    xz-utils \
    bzip2 \
    make \
  ' \
  && apt-get update \
  && apt-get install -y --no-install-recommends $buildDependencies \
  # gsutil
  && wget https://storage.googleapis.com/pub/gsutil.tar.gz \
  && tar xfz gsutil.tar.gz -C $HOME && rm gsutil.tar.gz \
  && export PATH=$PATH:$HOME/gsutil \
  # deepvariant
  && git clone https://github.com/google/deepvariant.git \
  && cd deepvariant \
  && git checkout v0.4.1 \
  && ./build-prereq.sh \
  && ./build_and_test.sh

The build_and_test.sh script fails with these errors:

+ ./build_and_test.sh
+ source settings.sh
++ export TF_CUDA_CLANG=0
++ TF_CUDA_CLANG=0
++ export TF_ENABLE_XLA=0
++ TF_ENABLE_XLA=0
++ export TF_NEED_CUDA=0
++ TF_NEED_CUDA=0
++ export TF_NEED_GCP=1
++ TF_NEED_GCP=1
++ export TF_NEED_GDR=0
++ TF_NEED_GDR=0
++ export TF_NEED_HDFS=0
++ TF_NEED_HDFS=0
++ export TF_NEED_JEMALLOC=0
++ TF_NEED_JEMALLOC=0
++ export TF_NEED_MKL=0
++ TF_NEED_MKL=0
++ export TF_NEED_MPI=0
++ TF_NEED_MPI=0
++ export TF_NEED_OPENCL=0
++ TF_NEED_OPENCL=0
++ export TF_NEED_OPENCL_SYCL=0
++ TF_NEED_OPENCL_SYCL=0
++ export TF_NEED_S3=0
++ TF_NEED_S3=0
++ export TF_NEED_VERBS=0
++ TF_NEED_VERBS=0
++ export TF_CUDA_VERSION=8.0
++ TF_CUDA_VERSION=8.0
++ export CUDA_TOOLKIT_PATH=/usr/local/cuda
++ CUDA_TOOLKIT_PATH=/usr/local/cuda
++ export TF_CUDNN_VERSION=6
++ TF_CUDNN_VERSION=6
++ export CUDNN_INSTALL_PATH=/usr/lib/x86_64-linux-gnu
++ CUDNN_INSTALL_PATH=/usr/lib/x86_64-linux-gnu
++ export DEEPVARIANT_BUCKET=gs://deepvariant
++ DEEPVARIANT_BUCKET=gs://deepvariant
++ export DV_PACKAGE_BUCKET_PATH=gs://deepvariant/packages
++ DV_PACKAGE_BUCKET_PATH=gs://deepvariant/packages
++ export DV_GPU_BUILD=0
++ DV_GPU_BUILD=0
++ export DV_USE_GCP_OPTIMIZED_TF_WHL=1
++ DV_USE_GCP_OPTIMIZED_TF_WHL=1
++ export GCP_OPTIMIZED_TF_WHL_FILENAME=tensorflow-1.4.1.deepvariant_gcp-cp27-none-linux_x86_64.whl
++ GCP_OPTIMIZED_TF_WHL_FILENAME=tensorflow-1.4.1.deepvariant_gcp-cp27-none-linux_x86_64.whl
++ export GCP_OPTIMIZED_TF_WHL_PATH=gs://deepvariant/packages/tensorflow
++ GCP_OPTIMIZED_TF_WHL_PATH=gs://deepvariant/packages/tensorflow
++ export DV_TF_NIGHTLY_BUILD=0
++ DV_TF_NIGHTLY_BUILD=0
++ export DV_INSTALL_GPU_DRIVERS=0
++ DV_INSTALL_GPU_DRIVERS=0
+++ which python
++ export PYTHON_BIN_PATH=/usr/bin/python
++ PYTHON_BIN_PATH=/usr/bin/python
++ export USE_DEFAULT_PYTHON_LIB_PATH=1
++ USE_DEFAULT_PYTHON_LIB_PATH=1
++ export 'DV_COPT_FLAGS=--copt=-msse4.1 --copt=-msse4.2 --copt=-mavx --copt=-O3'
++ DV_COPT_FLAGS='--copt=-msse4.1 --copt=-msse4.2 --copt=-mavx --copt=-O3'
++ export DV_TENSORFLOW_GIT_SHA=ab0fcaceda001825654424bf18e8a8e0f8d39df2
++ DV_TENSORFLOW_GIT_SHA=ab0fcaceda001825654424bf18e8a8e0f8d39df2
+ [[ 0 = \1 ]]
+ bazel test -c opt --copt=-msse4.1 --copt=-msse4.2 --copt=-mavx --copt=-O3 deepvariant/...
..................
(09:27:04) INFO: Current date is 2017-12-21
(09:27:04) Loading: 
(09:27:04) Loading: 0 packages loaded
(09:27:05) Loading: 0 packages loaded
(09:27:06) Loading: 7 packages loaded
    currently loading: deepvariant/core/genomics ... (6 packages)
(09:27:07) Loading: 10 packages loaded
    currently loading: deepvariant/core/genomics ... (3 packages)
(09:27:08) Loading: 10 packages loaded
    currently loading: deepvariant/core/genomics ... (3 packages)
(09:27:09) Analyzing: 242 targets (15 packages loaded)
(09:27:11) Analyzing: 242 targets (16 packages loaded)
(09:27:12) Analyzing: 242 targets (18 packages loaded)
(09:27:14) Analyzing: 242 targets (31 packages loaded)
(09:27:14) ERROR: /opt/app/.cache/bazel/_bazel_root/501e9c7e600bb5ec9e98458625ea98f0/external/com_googlesource_code_re2/BUILD:96:1: First argument of 'load' must be a label and start with either '//', ':', or '@'. Use --incompatible_load_argument_is_label=false to temporarily disable this check.
(09:27:14) ERROR: /opt/app/.cache/bazel/_bazel_root/501e9c7e600bb5ec9e98458625ea98f0/external/com_googlesource_code_re2/BUILD:98:1: name 're2_test' is not defined (did you mean 'ios_test'?)
(09:27:14) ERROR: /opt/app/.cache/bazel/_bazel_root/501e9c7e600bb5ec9e98458625ea98f0/external/com_googlesource_code_re2/BUILD:100:1: name 're2_test' is not defined (did you mean 'ios_test'?)
(09:27:14) ERROR: /opt/app/.cache/bazel/_bazel_root/501e9c7e600bb5ec9e98458625ea98f0/external/com_googlesource_code_re2/BUILD:102:1: name 're2_test' is not defined (did you mean 'ios_test'?)
(09:27:14) ERROR: /opt/app/.cache/bazel/_bazel_root/501e9c7e600bb5ec9e98458625ea98f0/external/com_googlesource_code_re2/BUILD:104:1: name 're2_test' is not defined (did you mean 'ios_test'?)
(09:27:14) ERROR: /opt/app/.cache/bazel/_bazel_root/501e9c7e600bb5ec9e98458625ea98f0/external/com_googlesource_code_re2/BUILD:106:1: name 're2_test' is not defined (did you mean 'ios_test'?)
(09:27:14) ERROR: /opt/app/.cache/bazel/_bazel_root/501e9c7e600bb5ec9e98458625ea98f0/external/com_googlesource_code_re2/BUILD:108:1: name 're2_test' is not defined (did you mean 'ios_test'?)
(09:27:14) ERROR: /opt/app/.cache/bazel/_bazel_root/501e9c7e600bb5ec9e98458625ea98f0/external/com_googlesource_code_re2/BUILD:110:1: name 're2_test' is not defined (did you mean 'ios_test'?)
(09:27:14) ERROR: /opt/app/.cache/bazel/_bazel_root/501e9c7e600bb5ec9e98458625ea98f0/external/com_googlesource_code_re2/BUILD:112:1: name 're2_test' is not defined (did you mean 'ios_test'?)
(09:27:14) ERROR: /opt/app/.cache/bazel/_bazel_root/501e9c7e600bb5ec9e98458625ea98f0/external/com_googlesource_code_re2/BUILD:114:1: name 're2_test' is not defined (did you mean 'ios_test'?)
(09:27:14) ERROR: /opt/app/.cache/bazel/_bazel_root/501e9c7e600bb5ec9e98458625ea98f0/external/com_googlesource_code_re2/BUILD:116:1: name 're2_test' is not defined (did you mean 'ios_test'?)
(09:27:14) ERROR: /opt/app/.cache/bazel/_bazel_root/501e9c7e600bb5ec9e98458625ea98f0/external/com_googlesource_code_re2/BUILD:118:1: name 're2_test' is not defined (did you mean 'ios_test'?)
(09:27:14) ERROR: /opt/app/.cache/bazel/_bazel_root/501e9c7e600bb5ec9e98458625ea98f0/external/com_googlesource_code_re2/BUILD:120:1: name 're2_test' is not defined (did you mean 'ios_test'?)
(09:27:14) ERROR: /opt/app/.cache/bazel/_bazel_root/501e9c7e600bb5ec9e98458625ea98f0/external/com_googlesource_code_re2/BUILD:122:1: name 're2_test' is not defined (did you mean 'ios_test'?)
(09:27:14) ERROR: /opt/app/.cache/bazel/_bazel_root/501e9c7e600bb5ec9e98458625ea98f0/external/com_googlesource_code_re2/BUILD:124:1: name 're2_test' is not defined (did you mean 'ios_test'?)
(09:27:14) ERROR: /opt/app/.cache/bazel/_bazel_root/501e9c7e600bb5ec9e98458625ea98f0/external/com_googlesource_code_re2/BUILD:126:1: name 're2_test' is not defined (did you mean 'ios_test'?)
(09:27:14) ERROR: /opt/app/.cache/bazel/_bazel_root/501e9c7e600bb5ec9e98458625ea98f0/external/com_googlesource_code_re2/BUILD:131:1: name 're2_test' is not defined (did you mean 'ios_test'?)
(09:27:14) ERROR: /opt/app/.cache/bazel/_bazel_root/501e9c7e600bb5ec9e98458625ea98f0/external/com_googlesource_code_re2/BUILD:136:1: name 're2_test' is not defined (did you mean 'ios_test'?)
(09:27:14) ERROR: /opt/app/.cache/bazel/_bazel_root/501e9c7e600bb5ec9e98458625ea98f0/external/com_googlesource_code_re2/BUILD:141:1: name 're2_test' is not defined (did you mean 'ios_test'?)
(09:27:14) ERROR: /opt/app/.cache/bazel/_bazel_root/501e9c7e600bb5ec9e98458625ea98f0/external/com_googlesource_code_re2/BUILD:146:1: name 're2_test' is not defined (did you mean 'ios_test'?)
(09:27:14) ERROR: /opt/app/.cache/bazel/_bazel_root/501e9c7e600bb5ec9e98458625ea98f0/external/com_googlesource_code_re2/BUILD:151:1: name 're2_test' is not defined (did you mean 'ios_test'?)
(09:27:15) Analyzing: 242 targets (37 packages loaded)
(09:27:17) Analyzing: 242 targets (45 packages loaded)
(09:27:18) ERROR: /opt/app/.cache/bazel/_bazel_root/501e9c7e600bb5ec9e98458625ea98f0/external/com_googlesource_code_re2/BUILD:11:1: Target '@com_googlesource_code_re2//:re2/bitmap256.h' contains an error and its package is in error and referenced by '@com_googlesource_code_re2//:re2'
(09:27:18) ERROR: /opt/app/.cache/bazel/_bazel_root/501e9c7e600bb5ec9e98458625ea98f0/external/com_googlesource_code_re2/BUILD:11:1: Target '@com_googlesource_code_re2//:re2/bitstate.cc' contains an error and its package is in error and referenced by '@com_googlesource_code_re2//:re2'
(09:27:18) ERROR: /opt/app/.cache/bazel/_bazel_root/501e9c7e600bb5ec9e98458625ea98f0/external/com_googlesource_code_re2/BUILD:11:1: Target '@com_googlesource_code_re2//:re2/compile.cc' contains an error and its package is in error and referenced by '@com_googlesource_code_re2//:re2'
(09:27:18) ERROR: /opt/app/.cache/bazel/_bazel_root/501e9c7e600bb5ec9e98458625ea98f0/external/com_googlesource_code_re2/BUILD:11:1: Target '@com_googlesource_code_re2//:re2/dfa.cc' contains an error and its package is in error and referenced by '@com_googlesource_code_re2//:re2'
(09:27:18) ERROR: /opt/app/.cache/bazel/_bazel_root/501e9c7e600bb5ec9e98458625ea98f0/external/com_googlesource_code_re2/BUILD:11:1: Target '@com_googlesource_code_re2//:re2/filtered_re2.cc' contains an error and its package is in error and referenced by '@com_googlesource_code_re2//:re2'
(09:27:18) ERROR: /opt/app/.cache/bazel/_bazel_root/501e9c7e600bb5ec9e98458625ea98f0/external/com_googlesource_code_re2/BUILD:11:1: Target '@com_googlesource_code_re2//:re2/mimics_pcre.cc' contains an error and its package is in error and referenced by '@com_googlesource_code_re2//:re2'
(09:27:18) ERROR: /opt/app/.cache/bazel/_bazel_root/501e9c7e600bb5ec9e98458625ea98f0/external/com_googlesource_code_re2/BUILD:11:1: Target '@com_googlesource_code_re2//:re2/nfa.cc' contains an error and its package is in error and referenced by '@com_googlesource_code_re2//:re2'
(09:27:18) ERROR: /opt/app/.cache/bazel/_bazel_root/501e9c7e600bb5ec9e98458625ea98f0/external/com_googlesource_code_re2/BUILD:11:1: Target '@com_googlesource_code_re2//:re2/onepass.cc' contains an error and its package is in error and referenced by '@com_googlesource_code_re2//:re2'
(09:27:18) ERROR: /opt/app/.cache/bazel/_bazel_root/501e9c7e600bb5ec9e98458625ea98f0/external/com_googlesource_code_re2/BUILD:11:1: Target '@com_googlesource_code_re2//:re2/parse.cc' contains an error and its package is in error and referenced by '@com_googlesource_code_re2//:re2'
(09:27:18) ERROR: /opt/app/.cache/bazel/_bazel_root/501e9c7e600bb5ec9e98458625ea98f0/external/com_googlesource_code_re2/BUILD:11:1: Target '@com_googlesource_code_re2//:re2/perl_groups.cc' contains an error and its package is in error and referenced by '@com_googlesource_code_re2//:re2'
(09:27:18) ERROR: /opt/app/.cache/bazel/_bazel_root/501e9c7e600bb5ec9e98458625ea98f0/external/com_googlesource_code_re2/BUILD:11:1: Target '@com_googlesource_code_re2//:re2/prefilter.cc' contains an error and its package is in error and referenced by '@com_googlesource_code_re2//:re2'
(09:27:18) ERROR: /opt/app/.cache/bazel/_bazel_root/501e9c7e600bb5ec9e98458625ea98f0/external/com_googlesource_code_re2/BUILD:11:1: Target '@com_googlesource_code_re2//:re2/prefilter.h' contains an error and its package is in error and referenced by '@com_googlesource_code_re2//:re2'
(09:27:18) ERROR: /opt/app/.cache/bazel/_bazel_root/501e9c7e600bb5ec9e98458625ea98f0/external/com_googlesource_code_re2/BUILD:11:1: Target '@com_googlesource_code_re2//:re2/prefilter_tree.cc' contains an error and its package is in error and referenced by '@com_googlesource_code_re2//:re2'
(09:27:18) ERROR: /opt/app/.cache/bazel/_bazel_root/501e9c7e600bb5ec9e98458625ea98f0/external/com_googlesource_code_re2/BUILD:11:1: Target '@com_googlesource_code_re2//:re2/prefilter_tree.h' contains an error and its package is in error and referenced by '@com_googlesource_code_re2//:re2'
(09:27:18) ERROR: /opt/app/.cache/bazel/_bazel_root/501e9c7e600bb5ec9e98458625ea98f0/external/com_googlesource_code_re2/BUILD:11:1: Target '@com_googlesource_code_re2//:re2/prog.cc' contains an error and its package is in error and referenced by '@com_googlesource_code_re2//:re2'
(09:27:18) ERROR: /opt/app/.cache/bazel/_bazel_root/501e9c7e600bb5ec9e98458625ea98f0/external/com_googlesource_code_re2/BUILD:11:1: Target '@com_googlesource_code_re2//:re2/prog.h' contains an error and its package is in error and referenced by '@com_googlesource_code_re2//:re2'
(09:27:18) ERROR: /opt/app/.cache/bazel/_bazel_root/501e9c7e600bb5ec9e98458625ea98f0/external/com_googlesource_code_re2/BUILD:11:1: Target '@com_googlesource_code_re2//:re2/re2.cc' contains an error and its package is in error and referenced by '@com_googlesource_code_re2//:re2'
(09:27:18) ERROR: /opt/app/.cache/bazel/_bazel_root/501e9c7e600bb5ec9e98458625ea98f0/external/com_googlesource_code_re2/BUILD:11:1: Target '@com_googlesource_code_re2//:re2/regexp.cc' contains an error and its package is in error and referenced by '@com_googlesource_code_re2//:re2'
(09:27:18) ERROR: /opt/app/.cache/bazel/_bazel_root/501e9c7e600bb5ec9e98458625ea98f0/external/com_googlesource_code_re2/BUILD:11:1: Target '@com_googlesource_code_re2//:re2/regexp.h' contains an error and its package is in error and referenced by '@com_googlesource_code_re2//:re2'
(09:27:18) ERROR: /opt/app/.cache/bazel/_bazel_root/501e9c7e600bb5ec9e98458625ea98f0/external/com_googlesource_code_re2/BUILD:11:1: Target '@com_googlesource_code_re2//:re2/set.cc' contains an error and its package is in error and referenced by '@com_googlesource_code_re2//:re2'
(09:27:18) ERROR: /opt/app/.cache/bazel/_bazel_root/501e9c7e600bb5ec9e98458625ea98f0/external/com_googlesource_code_re2/BUILD:11:1: Target '@com_googlesource_code_re2//:re2/simplify.cc' contains an error and its package is in error and referenced by '@com_googlesource_code_re2//:re2'
(09:27:18) ERROR: /opt/app/.cache/bazel/_bazel_root/501e9c7e600bb5ec9e98458625ea98f0/external/com_googlesource_code_re2/BUILD:11:1: Target '@com_googlesource_code_re2//:re2/stringpiece.cc' contains an error and its package is in error and referenced by '@com_googlesource_code_re2//:re2'
(09:27:18) ERROR: /opt/app/.cache/bazel/_bazel_root/501e9c7e600bb5ec9e98458625ea98f0/external/com_googlesource_code_re2/BUILD:11:1: Target '@com_googlesource_code_re2//:re2/tostring.cc' contains an error and its package is in error and referenced by '@com_googlesource_code_re2//:re2'
(09:27:18) ERROR: /opt/app/.cache/bazel/_bazel_root/501e9c7e600bb5ec9e98458625ea98f0/external/com_googlesource_code_re2/BUILD:11:1: Target '@com_googlesource_code_re2//:re2/unicode_casefold.cc' contains an error and its package is in error and referenced by '@com_googlesource_code_re2//:re2'
(09:27:18) ERROR: /opt/app/.cache/bazel/_bazel_root/501e9c7e600bb5ec9e98458625ea98f0/external/com_googlesource_code_re2/BUILD:11:1: Target '@com_googlesource_code_re2//:re2/unicode_casefold.h' contains an error and its package is in error and referenced by '@com_googlesource_code_re2//:re2'
(09:27:18) ERROR: /opt/app/.cache/bazel/_bazel_root/501e9c7e600bb5ec9e98458625ea98f0/external/com_googlesource_code_re2/BUILD:11:1: Target '@com_googlesource_code_re2//:re2/unicode_groups.cc' contains an error and its package is in error and referenced by '@com_googlesource_code_re2//:re2'
(09:27:18) ERROR: /opt/app/.cache/bazel/_bazel_root/501e9c7e600bb5ec9e98458625ea98f0/external/com_googlesource_code_re2/BUILD:11:1: Target '@com_googlesource_code_re2//:re2/unicode_groups.h' contains an error and its package is in error and referenced by '@com_googlesource_code_re2//:re2'
(09:27:18) ERROR: /opt/app/.cache/bazel/_bazel_root/501e9c7e600bb5ec9e98458625ea98f0/external/com_googlesource_code_re2/BUILD:11:1: Target '@com_googlesource_code_re2//:re2/walker-inl.h' contains an error and its package is in error and referenced by '@com_googlesource_code_re2//:re2'
(09:27:18) ERROR: /opt/app/.cache/bazel/_bazel_root/501e9c7e600bb5ec9e98458625ea98f0/external/com_googlesource_code_re2/BUILD:11:1: Target '@com_googlesource_code_re2//:util/flags.h' contains an error and its package is in error and referenced by '@com_googlesource_code_re2//:re2'
(09:27:18) ERROR: /opt/app/.cache/bazel/_bazel_root/501e9c7e600bb5ec9e98458625ea98f0/external/com_googlesource_code_re2/BUILD:11:1: Target '@com_googlesource_code_re2//:util/logging.h' contains an error and its package is in error and referenced by '@com_googlesource_code_re2//:re2'
(09:27:18) ERROR: /opt/app/.cache/bazel/_bazel_root/501e9c7e600bb5ec9e98458625ea98f0/external/com_googlesource_code_re2/BUILD:11:1: Target '@com_googlesource_code_re2//:util/mix.h' contains an error and its package is in error and referenced by '@com_googlesource_code_re2//:re2'
(09:27:18) ERROR: /opt/app/.cache/bazel/_bazel_root/501e9c7e600bb5ec9e98458625ea98f0/external/com_googlesource_code_re2/BUILD:11:1: Target '@com_googlesource_code_re2//:util/mutex.h' contains an error and its package is in error and referenced by '@com_googlesource_code_re2//:re2'
(09:27:18) ERROR: /opt/app/.cache/bazel/_bazel_root/501e9c7e600bb5ec9e98458625ea98f0/external/com_googlesource_code_re2/BUILD:11:1: Target '@com_googlesource_code_re2//:util/rune.cc' contains an error and its package is in error and referenced by '@com_googlesource_code_re2//:re2'
(09:27:18) ERROR: /opt/app/.cache/bazel/_bazel_root/501e9c7e600bb5ec9e98458625ea98f0/external/com_googlesource_code_re2/BUILD:11:1: Target '@com_googlesource_code_re2//:util/sparse_array.h' contains an error and its package is in error and referenced by '@com_googlesource_code_re2//:re2'
(09:27:18) ERROR: /opt/app/.cache/bazel/_bazel_root/501e9c7e600bb5ec9e98458625ea98f0/external/com_googlesource_code_re2/BUILD:11:1: Target '@com_googlesource_code_re2//:util/sparse_set.h' contains an error and its package is in error and referenced by '@com_googlesource_code_re2//:re2'
(09:27:18) ERROR: /opt/app/.cache/bazel/_bazel_root/501e9c7e600bb5ec9e98458625ea98f0/external/com_googlesource_code_re2/BUILD:11:1: Target '@com_googlesource_code_re2//:util/strutil.cc' contains an error and its package is in error and referenced by '@com_googlesource_code_re2//:re2'
(09:27:18) ERROR: /opt/app/.cache/bazel/_bazel_root/501e9c7e600bb5ec9e98458625ea98f0/external/com_googlesource_code_re2/BUILD:11:1: Target '@com_googlesource_code_re2//:util/strutil.h' contains an error and its package is in error and referenced by '@com_googlesource_code_re2//:re2'
(09:27:18) ERROR: /opt/app/.cache/bazel/_bazel_root/501e9c7e600bb5ec9e98458625ea98f0/external/com_googlesource_code_re2/BUILD:11:1: Target '@com_googlesource_code_re2//:util/utf.h' contains an error and its package is in error and referenced by '@com_googlesource_code_re2//:re2'
(09:27:18) ERROR: /opt/app/.cache/bazel/_bazel_root/501e9c7e600bb5ec9e98458625ea98f0/external/com_googlesource_code_re2/BUILD:11:1: Target '@com_googlesource_code_re2//:util/util.h' contains an error and its package is in error and referenced by '@com_googlesource_code_re2//:re2'
(09:27:18) ERROR: /opt/app/.cache/bazel/_bazel_root/501e9c7e600bb5ec9e98458625ea98f0/external/com_googlesource_code_re2/BUILD:11:1: Target '@com_googlesource_code_re2//:re2/filtered_re2.h' contains an error and its package is in error and referenced by '@com_googlesource_code_re2//:re2'
(09:27:18) ERROR: /opt/app/.cache/bazel/_bazel_root/501e9c7e600bb5ec9e98458625ea98f0/external/com_googlesource_code_re2/BUILD:11:1: Target '@com_googlesource_code_re2//:re2/re2.h' contains an error and its package is in error and referenced by '@com_googlesource_code_re2//:re2'
(09:27:18) ERROR: /opt/app/.cache/bazel/_bazel_root/501e9c7e600bb5ec9e98458625ea98f0/external/com_googlesource_code_re2/BUILD:11:1: Target '@com_googlesource_code_re2//:re2/set.h' contains an error and its package is in error and referenced by '@com_googlesource_code_re2//:re2'
(09:27:18) ERROR: /opt/app/.cache/bazel/_bazel_root/501e9c7e600bb5ec9e98458625ea98f0/external/com_googlesource_code_re2/BUILD:11:1: Target '@com_googlesource_code_re2//:re2/stringpiece.h' contains an error and its package is in error and referenced by '@com_googlesource_code_re2//:re2'
(09:27:18) ERROR: /opt/app/deepvariant/deepvariant/testing/BUILD:19:1: Target '@com_googlesource_code_re2//:re2' contains an error and its package is in error and referenced by '//deepvariant/testing:gunit_extras'
(09:27:18) ERROR: Analysis of target '//deepvariant/testing:gunit_extras_test' failed; build aborted: Loading failed
(09:27:18) INFO: Elapsed time: 14.618s
(09:27:18) FAILED: Build did NOT complete successfully (48 packages loaded)
(09:27:18) ERROR: Couldn't start the build. Unable to run tests

Could anyone shed some light on this issue? Interestingly this was working a few days ago but possibly on a different host. Could it be hardware dependent?

@pichuan
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pichuan commented Dec 21, 2017

I tried it and I'm seeing it as well.
I wonder if this could be something outside DeepVariant. We'll take a closer look and get back to you later.

@pichuan
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pichuan commented Dec 21, 2017

This could be relevant. I'll give it a try and see.
tensorflow/tensorflow#15492 (comment)

@pichuan
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pichuan commented Dec 21, 2017

I can confirm that downgrading bazel to 0.8.1 as suggested in that comment worked for me.
Here's what I did to install an older version of bazel:

BAZEL_VERSION=0.8.1
wget https://github.com/bazelbuild/bazel/releases/download/"${BAZEL_VERSION}"/bazel-"${BAZEL_VERSION}"-installer-linux-x86_64.sh
chmod +x bazel-*.sh
./bazel-"${BAZEL_VERSION}"-installer-linux-x86_64.sh --user

Give this temporary solution a try and let me know if it works. We'll still need to fix this in a more principled way.

@pgrosu
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pgrosu commented Dec 21, 2017

It might not hurt to install a Jenkins server - similar how the protobuf team does it - for continuous integration, as it also plays well with Github PRs and alleviates these simple headaches.

@david-wb
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Installing bazel 0.8.1 fixed the issue for me. It might be worth updating build-prereq.sh to install a specific version for bazel. Thanks a lot for the help

@scott7z
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scott7z commented Dec 21, 2017

The root cause here is that we are cloning a specific version of Tensorflow, while it (and other things) evolved to deal with the Bazel change. Normally, though, we don't want to just clone from TF HEAD because that can break us in other ways.

So a fix is to change settings.sh to use a more recent commit, like
export DV_TENSORFLOW_GIT_SHA="97a4c226e8a9e7c5c36fc38e2b9f8459c77abd5a"
(That compiles, but is otherwise untested.)

@pgrosu
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pgrosu commented Dec 22, 2017

@scott7z Well, my feeling is that would be too much work, which could be fostered elsewhere. Unless there is a defined criteria for working off a specific revision, it is usually less of a benefit to be tied to a specific release. It'll also make the cost of supporting it too much of a headache, as the other dependencies will continue to evolve. I always prefer to simplify and feel it's more practical to push compliance of dependencies to their maintainers, while expanding on the fun part of adding community-driven features. For example, there over 1000 commits between the two SHAs, and it would be hard to keep track of so many contributions:

$ git log | grep commit | cat -n | grep '97a4c226e8a9e7c5c36fc38e2b9f8459c77abd5a\|ab0fcaceda001825654424bf18e8a8e0f8d39df2'
     1  commit 97a4c226e8a9e7c5c36fc38e2b9f8459c77abd5a
  1244  commit ab0fcaceda001825654424bf18e8a8e0f8d39df2
$

Usually more contributions to a dependency might provide us with more opportunities :)

@scott7z
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scott7z commented Jan 5, 2018

We pushed a change that pins bazel to 0.8.1. That should take care of things for now.

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