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ARROW-3366: [R] Dockerfile for docker-compose setup #2770

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ARROW-3366: [R] Dockerfile for docker-compose setup #2770

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210a774
ARROW-3366: [R] Dockerfile for docker-compose setup
jameslamb Oct 16, 2018
d8e55d7
removed todo about R containers in docker-compose
jameslamb Oct 16, 2018
4a7112b
Fixed comment text in R Dockerfile
jameslamb Oct 16, 2018
94242b3
Add explict cpp build in usage for R docker-compose
jameslamb Oct 17, 2018
4d7f02c
fixed a few issues in R container
jameslamb Oct 17, 2018
64ea840
Updated LD_LIBRARY_PATH in R container
jameslamb Oct 27, 2018
8a8376d
Put R build steps into a separate CI script
jameslamb Oct 27, 2018
db9ee5b
pass CXXFLAGS
kszucs Oct 28, 2018
f7c050e
R_CHECK_FORCE_SUGGESTS
kszucs Oct 28, 2018
0db3369
added bit64 dependency to R package
jameslamb Nov 1, 2018
343456a
more changes
jameslamb Nov 14, 2018
dd26d4b
fixed failing test in the R package
jameslamb Nov 17, 2018
9fcebe5
removed failing test in the R package
jameslamb Nov 17, 2018
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fixed failing test in the R package
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@jameslamb
jameslamb committed Nov 17, 2018
commit dd26d4b972717f202e9c32dd1a4ab748e6764f93
2 changes: 1 addition & 1 deletion ci/docker_build_r.sh
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Expand Up @@ -34,6 +34,6 @@ R CMD build --keep-empty-dirs .
R CMD INSTALL $(ls | grep arrow_*.tar.gz)

export _R_CHECK_FORCE_SUGGESTS_=false
R CMD check $(ls | grep arrow_*.tar.gz) --as-cran
R CMD check $(ls | grep arrow_*.tar.gz) --as-cran --no-manual

popd
1 change: 1 addition & 0 deletions r/.Rbuildignore
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Expand Up @@ -6,3 +6,4 @@ LICENSE.md
^data-raw$
lint.sh
Dockerfile
.*\.tar\.gz
9 changes: 5 additions & 4 deletions r/Dockerfile
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Expand Up @@ -41,10 +41,13 @@ RUN apt update && \
libgit2-dev \
libssl-dev && \
# install clang to mirror what was done on Travis
apt install -y\
apt install -y \
clang \
clang-format \
clang-tidy && \
# R CMD CHECK --as-cran needs pdflatex to build the package manual
apt install -y \
texlive-latex-base && \
# Install vctrs from Github
Rscript -e "install.packages('devtools', repos = 'http://cran.rstudio.com')" && \
Rscript -e "devtools::install_github('romainfrancois/vctrs@bit64')" && \
Expand All @@ -67,9 +70,7 @@ RUN apt update && \
# Tell R where it can find the source code for arrow
ENV PKG_CONFIG_PATH=${PKG_CONFIG_PATH}:/build/cpp/src/arrow
ENV LD_LIBRARY_PATH=/opt/conda/lib/:/build/cpp/src/arrow:/arrow/r/src
env CXXFLAGS="-D_GLIBCXX_USE_CXX11_ABI=0"

#export BUILD_DIR=/build/cpp-install
ENV CXXFLAGS="-D_GLIBCXX_USE_CXX11_ABI=0"

# build, install, test R package
CMD /arrow/ci/docker_build_cpp.sh && \
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2 changes: 1 addition & 1 deletion r/tests/testthat/test-RecordBatch.R
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Expand Up @@ -137,7 +137,7 @@ test_that("read_record_batch handles various streams (ARROW-3450, ARROW-3505)",
batch4 <- read_record_batch(mmap_file)
batch5 <- read_record_batch(bytes)
batch6 <- read_record_batch(buf_reader)
expect_error(read_record_batch(buf_reader))
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@romainfrancois I believe this PR is now working! However, I want to talk about this test.

I had to remove this to get R CMD CHECK or devtools::test() to complete. I think the issue is that expect_error cannot trap C++ exceptions. When running with this test restored, testing immediately stops with error:

terminate called after throwing an instance of 'std::bad_alloc'
    what():  std::bad_alloc
  Aborted

Have you ever seen that issue with expect_error() before? I tried googling around and nothing obvious jumped out to me. I have no idea how this could be working on Travis but not in my setup on docker :/.

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Created issue for it: https://issues.apache.org/jira/browse/ARROW-3833

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Another question is why an exception is being thrown at all

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That’s what Rcpp::stop does, but this is supposed to be caught by the generated code.

#expect_error(read_record_batch(buf_reader))

stream_reader <- record_batch_stream_reader(bytes)
batch7 <- read_record_batch(stream_reader)
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