GH-35140: [R] Rewrite configure script and ensure we don't use mismatched libarrow by nealrichardson · Pull Request #35147 · apache/arrow

nealrichardson · 2023-04-14T21:14:26Z

I've significantly rewritten r/configure to make it easier to reason about and harder for issues like #34229 and #35140 to happen. I've also added a version check to make sure that we don't obviously try to use a system C++ library that doesn't match the R package version. Making sure this was applied in all of the right places and handling what to do if the versions didn't match was the impetus for the whole refactor.

configure has been broken up into some functions, and the flow of the script is, as is documented at the top of the file:

# * Find libarrow on the system. If it is present, make sure
#   that its version is compatible with the R package.
# * If no suitable libarrow is found, download it (where allowed)
#   or build it from source.
# * Determine what features this libarrow has and what other
#   flags it requires, and set them in src/Makevars for use when
#   compiling the bindings.
# * Run a test program to confirm that arrow headers are found

All of the detection of CFLAGS and -L dirs etc. happen in one place now, and they all prefer using pkg-config to read from the libarrow build what libraries and flags it requires, rather than hard-coding. (autobrew is the only remaining exception, but I didn't feel like messing with that today.) This should make the builds more future proof, should make it so more build configurations work (e.g. I suspect that a static build in ARROW_HOME wouldn't have gotten picked up correctly because it didn't add -larrow_bundled_dependencies to the libs, but now it will), and it may eliminate the redundant -l and -D setting I've observed in some builds (not harmful but definitely sloppy).

Version checking has been added in an R script for ease of testing (and for easier handling of arithmetic), and there is an accompanying test-check-versions.R added. These are run on all the builds that use ci/scripts/r_test.sh.

Behavior changes

If libarrow is found on the system (via ARROW_HOME, pkg-config, or brew), but the version does not match, it will not be used, and we will try a bundled build. This should mean that users installing a released version will never have libarrow version problems.
If both the found C++ library and R package are on matching dev versions (i.e. not identical given the x.y.z.9000 vs x+1.y.z-SNAPSHOT difference), it will proceed with a warning that you may need to rebuild if there are issues. This means that regular developers will see an extra message in the build output.
autobrew is only used on a release version unless you set FORCE_AUTOBREW=true. This eliminates another source of version mismatches (C++ release version, R dev version).
The path where you could set LIB_DIR and INCLUDE_DIR env vars has been removed. Use ARROW_HOME instead.
Closes: [R] configure script for R fails to set PKG_CFLAGS #35140
Closes: [R] Improve package installation (on Fedora 36) with arrow system packages #31989

github-actions · 2023-04-14T21:14:49Z

Closes: [R] configure script for R fails to set PKG_CFLAGS #35140

github-actions · 2023-04-14T21:14:53Z

⚠️ GitHub issue #35140 has been automatically assigned in GitHub to PR creator.

github-actions · 2023-04-14T21:14:55Z

⚠️ GitHub issue #35140 has no components, please add labels for components.

nealrichardson · 2023-04-23T13:11:33Z

If this is in fact the fix for the conda package issues (conda-forge/r-arrow-feedstock#56 (comment), conda-forge/r-arrow-feedstock#62), then we would have a way to test this in the nightly conda packaging jobs. We currently build the packages but don't install them and assert anything about their capabilities.

Perhaps we can add something to https://github.com/apache/arrow/blob/main/dev/tasks/conda-recipes/r-arrow/build.sh to load the installed package and test that it has parquet, dataset, etc.

nealrichardson · 2023-04-23T13:52:26Z

@github-actions crossbow submit conda-linux--r4 conda-osx--r4

github-actions · 2023-04-23T13:54:50Z

Revision: 1bc1a0132178aff5ce942a18f7a62bda4a689454

Submitted crossbow builds: ursacomputing/crossbow @ actions-02dfd6461d

Task	Status
conda-linux-aarch64-cpu-r42
conda-linux-x64-cpu-r42
conda-osx-arm64-cpu-r42
conda-osx-x64-cpu-r42

kou · 2023-04-24T05:33:05Z

I think that the following approach (we must set LIB_DIR when PKG_* are set) is better than this approach:

diff --git a/r/configure b/r/configure index 65528bdc3..f452fffb1 100755 --- a/r/configure +++ b/r/configure @@ -126,10 +126,11 @@ else if [ "$UNAME" = "Darwin" ] && [ "$FORCE_BUNDLED_BUILD" != "true" ]; then if [ "$FORCE_AUTOBREW" != "true" ] && [ "`command -v brew`" ] && [ "`brew ls --versions ${PKG_BREW_NAME}`" != "" ]; then echo "*** Using Homebrew ${PKG_BREW_NAME}" - BREWDIR=`brew --prefix` + BREWDIR=`brew --prefix ${PKG_BREW_NAME}` + LIB_DIR="$BREWDIR/lib" PKG_LIBS="-larrow -larrow_bundled_dependencies" - PKG_DIRS="-L$BREWDIR/opt/$PKG_BREW_NAME/lib $PKG_DIRS" - PKG_CFLAGS="-I$BREWDIR/opt/$PKG_BREW_NAME/include $PKG_CFLAGS" + PKG_DIRS="-L$LIB_DIR $PKG_DIRS" + PKG_CFLAGS="-I$BREWDIR/include $PKG_CFLAGS" else echo "*** Downloading ${PKG_BREW_NAME}" if [ -f "autobrew" ]; then @@ -144,7 +145,9 @@ else if [ $? -ne 0 ]; then echo "Failed to retrieve binary for ${PKG_BREW_NAME}" fi - # autobrew sets `PKG_LIBS`, `PKG_DIRS`, and `PKG_CFLAGS` + # autobrew sets `PKG_LIBS`, `PKG_DIRS`, `PKG_CFLAGS`, and `BREWDIR` + # but `LIB_DIR` isn't set. + LIB_DIR="$BREWDIR/lib" fi else if [ "${NOT_CRAN}" = "true" ]; then

The main reason I didn't take this approach is that r/configure has gotten so complex that I didn't think I could reason about all of the different branches of the code to know that I had found them all (see also #35049). Other, more concrete issues:

I did confirm what @paleolimbot suggested, which is that if you have pkg-config available and have installed apache-arrow via brew, you won't get to this *** Using Homebrew block, you'll see that you're using arrow found by pkg-config. So at a minimum, we (also) need LIB_DIR set in the pkg-config section above this.

Likewise, there have been similar reports, like the conda-forge one and [R] Improve package installation (on Fedora 36) with arrow system packages #31989, not on macOS/brew, so a brew-only fix wouldn't be sufficient.

We actually don't need the autobrew one because (for "historical reasons", I assume) we explicitly set all of the feature flags in the autobrew script https://github.com/apache/arrow/blob/apache-arrow-11.0.0/r/tools/autobrew#L77

@kou is this possibly relevant? PKG_LIBS and PKG_DIRS seem to be set correctly but for some reason LIB_DIR isn't.

diff --git a/r/configure b/r/configure index 65528bdc38..8e130c53b4 100755 --- a/r/configure +++ b/r/configure @@ -110,7 +110,7 @@ else PKG_CFLAGS="$PKGCONFIG_CFLAGS $PKG_CFLAGS" PKG_LIBS="${PKGCONFIG_LIBS}" PKG_DIRS="${PKGCONFIG_DIRS}" - LIB_DIR=${FOUND_LIB_DIR} + LIB_DIR="${FOUND_LIB_DIR}" # Check for version mismatch PC_LIB_VERSION=`pkg-config --modversion arrow`

Sorry. Could you explain more the context for it? Can I see a build log for the case? This case #35140 ? Or other case?

If this is for #35140, I think that the isn't related because FOUND_LIB_DIR doesn't have any space:

*** Arrow C++ libraries found via pkg-config at /opt/homebrew/Cellar/apache-arrow/11.0.0_3/lib

Ah, #35140 uses Apache Arrow 11.0.0.
I was seeing the main branch.

Yes. The change #35147 (comment) will fix #35140. And it's already in the main branch: #34229

From the conda-side, we were able to fix it by specifying LIB_DIR=$PREFIX/lib in our build script, see conda-forge/r-arrow-feedstock#63

🤦 my mistake, sorry I missed #34229, that explains some of the confusion. I'll tidy this PR up with any remaining useful changes and get it merged.

kou · 2023-04-24T05:33:34Z

@h-vetinari Could you review conda part?

That part is fine and already working (as in: shows the build fails) in conda-forge/r-arrow-feedstock#63.

However, I don't see how the BREW-specific patch above would apply to conda-forge (we'd need $PREFIX), nor do I know what changed between 10 & 11. While taking a first look, my comment in that conda-forge PR was:

Do we need to do something like in the upstream R Makefile to discover the deps correctly?

nealrichardson · 2023-04-25T18:32:50Z

I've applied the patches and added a bunch of comments to r/configure to help with any upcoming refactoring. I want to do a bit more testing of the various branches locally before we move forward, so I've marked this as draft for now.

nealrichardson · 2023-04-28T19:00:38Z

@github-actions crossbow submit -g r

github-actions · 2023-04-28T19:05:30Z

Revision: 9dfa86d337e8428818148320c84881b3e89cb935

Submitted crossbow builds: ursacomputing/crossbow @ actions-8ccc8bc92d

Task	Status
conda-linux-aarch64-cpu-r42
conda-linux-x64-cpu-r42
conda-osx-arm64-cpu-r42
conda-osx-x64-cpu-r42
conda-win-x64-cpu-r41
homebrew-r-autobrew
homebrew-r-brew
r-binary-packages
test-fedora-r-clang-sanitizer
test-r-arrow-backwards-compatibility
test-r-depsource-bundled
test-r-depsource-system
test-r-dev-duckdb
test-r-devdocs
test-r-gcc-11
test-r-gcc-12
test-r-install-local
test-r-install-local-minsizerel
test-r-library-r-base-latest
test-r-linux-as-cran
test-r-linux-rchk
test-r-linux-valgrind
test-r-minimal-build
test-r-offline-maximal
test-r-offline-minimal
test-r-rhub-debian-gcc-devel-lto-latest
test-r-rhub-debian-gcc-release-custom-ccache
test-r-rhub-ubuntu-gcc-release-latest
test-r-rstudio-r-base-4.1-opensuse153
test-r-rstudio-r-base-4.2-centos7-devtoolset-8
test-r-rstudio-r-base-4.2-focal
test-r-ubuntu-22.04
test-r-versions
test-ubuntu-r-sanitizer

nealrichardson · 2023-04-28T20:46:18Z

I will inspect the successful builds to make sure features are enabled as they should be. Of the failures:

test-r-offline-maximal is a download timeout for orc (which we don't even use). https://github.com/ursacomputing/crossbow/actions/runs/4833915427/jobs/8614507086#step:4:50
test-r-arrow-backwards-compatibility I don't quite understand on first glance, will have to inspect, says it can't find libcurl https://github.com/ursacomputing/crossbow/actions/runs/4833911218/jobs/8614498685#step:7:27
r-binary-packages has at least one failure in parsing LIB_DIR, in which it was assumed to have only one -L in it but there were two https://github.com/ursacomputing/crossbow/actions/runs/4833911390/jobs/8614512347#step:14:25930

nealrichardson · 2023-04-29T17:02:32Z

@github-actions crossbow submit -g r

kou · 2023-05-02T13:48:29Z

I think that this problem is related to -I not -L/-l: #34523 (comment)

kou · 2023-05-02T13:52:16Z

Ah, wait. The job was passed at #35147 (comment) .
It may not be related to -I. I'll take a look at this.

nealrichardson · 2023-05-02T13:55:55Z

Ah, wait. The job was passed at #35147 (comment) . It may not be related to -I. I'll take a look at this.

It passed there because I changed it not to use the bundled build. That said, it didn't pick up the wrong absl, so maybe there's still something to learn from it.

kou · 2023-05-02T13:56:30Z

Hmm. It seems that autobrew not Homebrew was used in the passed job.

kou · 2023-05-02T13:57:22Z

Ah, OK. Thanks.

nealrichardson · 2023-05-02T13:57:41Z

In the failed build, PKG_CFLAGS=-DARROW_STATIC -DUTF8PROC_EXPORTS -I/Users/voltrondata/tmp/RtmpQAJbFi/R.INSTALLca181e5538f5/arrow/libarrow/arrow-11.0.0.100000506/include -I/opt/homebrew/include

nealrichardson · 2023-05-02T14:07:47Z

autobrew does not use pkg-config to set PKG_CFLAGS, so -I/opt/homebrew/include is not present in that build

kou · 2023-05-02T14:13:05Z

I think that this is the same problem as #34523 .
And this is a C++ part problem not an R part problem.
So I think that we can work on this as a separated pull request.

__ZN4absl12lts_2023012510FormatTimeENSt3__117basic_string_viewIcNS1_11char_traitsIcEEEENS0_4TimeENS0_8TimeZoneE is absl::lts_20230125::FormatTime(std::__1::basic_string_view<char, std::__1::char_traits<char> >, absl::lts_20230125::Time, absl::lts_20230125::TimeZone). And it's used at

arrow/cpp/src/arrow/filesystem/gcsfs_internal.cc

Line 241 in a3a0172

return absl::FormatTime(absl::RFC3339_full, absl::FromChrono(tp),

.

Abseil was mixed when we build C++'s libarrow.a not R's arrow.so.

Co-authored-by: Sutou Kouhei <kou@cozmixng.org>

nealrichardson · 2023-05-02T14:35:42Z

@github-actions crossbow submit -g r

github-actions · 2023-05-02T14:39:45Z

Revision: a769f6a

Submitted crossbow builds: ursacomputing/crossbow @ actions-674657ab73

Task	Status
conda-linux-aarch64-cpu-r42
conda-linux-x64-cpu-r42
conda-osx-arm64-cpu-r42
conda-osx-x64-cpu-r42
conda-win-x64-cpu-r41
homebrew-r-autobrew
homebrew-r-brew
r-binary-packages
test-fedora-r-clang-sanitizer
test-r-arrow-backwards-compatibility
test-r-depsource-bundled
test-r-depsource-system
test-r-dev-duckdb
test-r-devdocs
test-r-gcc-11
test-r-gcc-12
test-r-install-local
test-r-install-local-minsizerel
test-r-library-r-base-latest
test-r-linux-as-cran
test-r-linux-rchk
test-r-linux-valgrind
test-r-minimal-build
test-r-offline-maximal
test-r-offline-minimal
test-r-rhub-debian-gcc-devel-lto-latest
test-r-rhub-debian-gcc-release-custom-ccache
test-r-rhub-ubuntu-gcc-release-latest
test-r-rstudio-r-base-4.1-opensuse153
test-r-rstudio-r-base-4.2-centos7-devtoolset-8
test-r-rstudio-r-base-4.2-focal
test-r-ubuntu-22.04
test-r-versions
test-ubuntu-r-sanitizer

nealrichardson · 2023-05-02T15:48:52Z

I don't fully understand the devdocs failure, but it has to do with the fact that arrow 12.0.0 has been released (https://github.com/ursacomputing/crossbow/actions/runs/4862485406/jobs/8668915213#step:9:3878 vs. https://github.com/ursacomputing/crossbow/actions/runs/4833910722/jobs/8614497534#step:9:3880 where it passed before). The cflags/libs are identical between the two builds. Rebasing to pull in the new version number would probably solve it, though I'm not sure it's worth the electricity to confirm it (that's an expensive build for very little value, it seems).

paleolimbot · 2023-05-02T17:48:54Z

Works great on Ubuntu via Docker (arm64 and amd64)!

# docker run --rm -it ghcr.io/apache/arrow-nanoarrow:ubuntu-arm64 or amd64
git clone https://github.com/nealrichardson/arrow.git
cd arrow/r
git switch lib-dir
R CMD INSTALL .

It doesn't seem to be pulling the hosted static libraries for development, which I expected on Ubuntu/x86 (but maybe it's not supposed to?).

nealrichardson · 2023-05-02T18:05:49Z

It doesn't seem to be pulling the hosted static libraries for development, which I expected on Ubuntu/x86 (but maybe it's not supposed to?).

We don't host binaries for x.y.z.9000, the nightly versions are like x.y.z.1000123, so if you wanted it to pull a nightly for a .9000 dev build, we'd have to teach it how to find the most recent one. Something for you (or whoever) to consider on #35049 I suppose.

nealrichardson · 2023-05-02T18:13:59Z

Made #35391 for the segfault on the ubuntu force tests job, which I see on main as well.

ursabot · 2023-05-03T17:43:32Z

Benchmark runs are scheduled for baseline = f794b20 and contender = ec89360. ec89360 is a master commit associated with this PR. Results will be available as each benchmark for each run completes.
Conbench compare runs links:
[Finished ⬇️0.0% ⬆️0.0%] ec2-t3-xlarge-us-east-2
[Finished ⬇️1.22% ⬆️0.0%] test-mac-arm
[Finished ⬇️0.26% ⬆️0.0%] ursa-i9-9960x
[Finished ⬇️0.66% ⬆️0.03%] ursa-thinkcentre-m75q
Buildkite builds:
[Finished] ec893602 ec2-t3-xlarge-us-east-2
[Finished] ec893602 test-mac-arm
[Finished] ec893602 ursa-i9-9960x
[Finished] ec893602 ursa-thinkcentre-m75q
[Finished] f794b208 ec2-t3-xlarge-us-east-2
[Finished] f794b208 test-mac-arm
[Finished] f794b208 ursa-i9-9960x
[Finished] f794b208 ursa-thinkcentre-m75q
Supported benchmarks:
ec2-t3-xlarge-us-east-2: Supported benchmark langs: Python, R. Runs only benchmarks with cloud = True
test-mac-arm: Supported benchmark langs: C++, Python, R
ursa-i9-9960x: Supported benchmark langs: Python, R, JavaScript
ursa-thinkcentre-m75q: Supported benchmark langs: C++, Java

ursabot · 2023-05-03T17:45:01Z

['Python', 'R'] benchmarks have high level of regressions.
test-mac-arm

…mismatched libarrow (apache#35147) I've significantly rewritten `r/configure` to make it easier to reason about and harder for issues like apache#34229 and apache#35140 to happen. I've also added a version check to make sure that we don't obviously try to use a system C++ library that doesn't match the R package version. Making sure this was applied in all of the right places and handling what to do if the versions didn't match was the impetus for the whole refactor. `configure` has been broken up into some functions, and the flow of the script is, as is documented at the top of the file: ``` # * Find libarrow on the system. If it is present, make sure # that its version is compatible with the R package. # * If no suitable libarrow is found, download it (where allowed) # or build it from source. # * Determine what features this libarrow has and what other # flags it requires, and set them in src/Makevars for use when # compiling the bindings. # * Run a test program to confirm that arrow headers are found ``` All of the detection of CFLAGS and `-L` dirs etc. happen in one place now, and they all prefer using `pkg-config` to read from the libarrow build what libraries and flags it requires, rather than hard-coding. (autobrew is the only remaining exception, but I didn't feel like messing with that today.) This should make the builds more future proof, should make it so more build configurations work (e.g. I suspect that a static build in ARROW_HOME wouldn't have gotten picked up correctly because it didn't add `-larrow_bundled_dependencies` to the libs, but now it will), and it may eliminate the redundant `-l` and `-D` setting I've observed in some builds (not harmful but definitely sloppy). Version checking has been added in an R script for ease of testing (and for easier handling of arithmetic), and there is an accompanying `test-check-versions.R` added. These are run on all the builds that use `ci/scripts/r_test.sh`. ### Behavior changes * If libarrow is found on the system (via ARROW_HOME, pkg-config, or brew), but the version does not match, it will not be used, and we will try a bundled build. This should mean that users installing a released version will never have libarrow version problems. * If both the found C++ library and R package are on matching dev versions (i.e. not identical given the x.y.z.9000 vs x+1.y.z-SNAPSHOT difference), it will proceed with a warning that you may need to rebuild if there are issues. This means that regular developers will see an extra message in the build output. * autobrew is only used on a release version unless you set FORCE_AUTOBREW=true. This eliminates another source of version mismatches (C++ release version, R dev version). * The path where you could set `LIB_DIR` and `INCLUDE_DIR` env vars has been removed. Use `ARROW_HOME` instead. * Closes: apache#35140 * Closes: apache#31989 Lead-authored-by: Neal Richardson <neal.p.richardson@gmail.com> Co-authored-by: Sutou Kouhei <kou@cozmixng.org> Signed-off-by: Neal Richardson <neal.p.richardson@gmail.com>

nealrichardson requested a review from paleolimbot April 14, 2023 21:14

nealrichardson requested a review from assignUser as a code owner April 14, 2023 21:14

github-actions Bot added Component: R awaiting review Awaiting review labels Apr 14, 2023

nealrichardson requested review from kou and raulcd as code owners April 23, 2023 13:35

nealrichardson mentioned this pull request Apr 23, 2023

[DO NOT MERGE] test whether features are enabled in r-arrow conda packages #35294

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kou reviewed Apr 24, 2023

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github-actions Bot added awaiting changes Awaiting changes and removed awaiting review Awaiting review labels Apr 24, 2023

nealrichardson force-pushed the lib-dir branch from 1bc1a01 to 0bc8188 Compare April 25, 2023 18:28

github-actions Bot added awaiting change review Awaiting change review and removed awaiting changes Awaiting changes labels Apr 25, 2023

nealrichardson marked this pull request as draft April 25, 2023 18:29

nealrichardson mentioned this pull request Apr 26, 2023

[R] Improve configure script for contributor experience #35049

Closed

nealrichardson changed the title ~~GH-35140: [R] configure script needs LIB_DIR to find ArrowOptions.cmake~~ GH-35140: [R] Rewrite configure script and ensure we don't use mismatched libarrow Apr 28, 2023

nealrichardson marked this pull request as ready for review April 28, 2023 18:03

nealrichardson requested a review from thisisnic as a code owner April 28, 2023 18:03

nealrichardson requested a review from jonkeane April 28, 2023 18:09

nealrichardson and others added 3 commits May 2, 2023 10:19

Apply suggestions from code review

ada985b

Co-authored-by: Sutou Kouhei <kou@cozmixng.org>

Factor out find_or_build_libarrow and move up for readability

cb50393

Tweak version check messages

a769f6a

nealrichardson mentioned this pull request May 2, 2023

[R] Crash on MacOS (x86) when running tests with homebrew apache-arrow also installed #33903

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h-vetinari mentioned this pull request May 3, 2023

r-arrow v12.0.0 conda-forge/r-arrow-feedstock#64

Merged

3 tasks

Update installation vignettes to match

5942f69

nealrichardson merged commit ec89360 into apache:main May 3, 2023

nealrichardson deleted the lib-dir branch May 3, 2023 14:37

paleolimbot mentioned this pull request May 8, 2023

[R] package development builds broken for Windows and MacOS #35472

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nealrichardson mentioned this pull request Jul 3, 2023

[R] configure script for R fails to set PKG_CFLAGS #35140

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kou mentioned this pull request Jul 28, 2023

[R] Fail to install R package arrow: arrow.so: undefined symbol: _ZTIN5arrow17RecordBatchReaderE #36848

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