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Posted to github@arrow.apache.org by GitBox <gi...@apache.org> on 2021/12/06 21:05:39 UTC

[GitHub] [arrow] jonkeane opened a new pull request #11875: ARROW-14839: [R] test-fedora-r-clang-sanitizer job failing due to snappy causing a sanitizer error

jonkeane opened a new pull request #11875:
URL: https://github.com/apache/arrow/pull/11875


   This would replace (temporarily) #11796 in a way that might be ship-able as is until Snappy accepts google/snappy#148 and is released.


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[GitHub] [arrow] jonkeane commented on pull request #11875: ARROW-14839: [R] test-fedora-r-clang-sanitizer job failing due to snappy causing a sanitizer error

Posted by GitBox <gi...@apache.org>.
jonkeane commented on pull request #11875:
URL: https://github.com/apache/arrow/pull/11875#issuecomment-987977431


   @github-actions crossbow submit test-fedora-r-clang-sanitizer


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[GitHub] [arrow] github-actions[bot] commented on pull request #11875: ARROW-14839: [R] test-fedora-r-clang-sanitizer job failing due to snappy causing a sanitizer error

Posted by GitBox <gi...@apache.org>.
github-actions[bot] commented on pull request #11875:
URL: https://github.com/apache/arrow/pull/11875#issuecomment-988855668


   Revision: a9e77fde90c7094478760a3446d51636a84f2f52
   
   Submitted crossbow builds: [ursacomputing/crossbow @ actions-1269](https://github.com/ursacomputing/crossbow/branches/all?query=actions-1269)
   
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[GitHub] [arrow] github-actions[bot] commented on pull request #11875: ARROW-14839: [R] test-fedora-r-clang-sanitizer job failing due to snappy causing a sanitizer error

Posted by GitBox <gi...@apache.org>.
github-actions[bot] commented on pull request #11875:
URL: https://github.com/apache/arrow/pull/11875#issuecomment-988215297


   Revision: a9e77fde90c7094478760a3446d51636a84f2f52
   
   Submitted crossbow builds: [ursacomputing/crossbow @ actions-1266](https://github.com/ursacomputing/crossbow/branches/all?query=actions-1266)
   
   |Task|Status|
   |----|------|
   |test-fedora-r-clang-sanitizer|[![Azure](https://dev.azure.com/ursacomputing/crossbow/_apis/build/status/ursacomputing.crossbow?branchName=actions-1266-azure-test-fedora-r-clang-sanitizer)](https://dev.azure.com/ursacomputing/crossbow/_build/latest?definitionId=1&branchName=actions-1266-azure-test-fedora-r-clang-sanitizer)|


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[GitHub] [arrow] jonkeane commented on pull request #11875: ARROW-14839: [R] test-fedora-r-clang-sanitizer job failing due to snappy causing a sanitizer error

Posted by GitBox <gi...@apache.org>.
jonkeane commented on pull request #11875:
URL: https://github.com/apache/arrow/pull/11875#issuecomment-987210646


   @github-actions crossbow submit test-fedora-r-clang-sanitizer


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[GitHub] [arrow] jonkeane commented on pull request #11875: ARROW-14839: [R] test-fedora-r-clang-sanitizer job failing due to snappy causing a sanitizer error

Posted by GitBox <gi...@apache.org>.
jonkeane commented on pull request #11875:
URL: https://github.com/apache/arrow/pull/11875#issuecomment-988854735


   @github-actions crossbow submit -g r
   


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[GitHub] [arrow] jonkeane commented on a change in pull request #11875: ARROW-14839: [R] test-fedora-r-clang-sanitizer job failing due to snappy causing a sanitizer error

Posted by GitBox <gi...@apache.org>.
jonkeane commented on a change in pull request #11875:
URL: https://github.com/apache/arrow/pull/11875#discussion_r764373740



##########
File path: cpp/thirdparty/versions.txt
##########
@@ -81,6 +81,7 @@ ARROW_RAPIDJSON_BUILD_VERSION=1a803826f1197b5e30703afe4b9c0e7dd48074f5
 ARROW_RAPIDJSON_BUILD_SHA256_CHECKSUM=0b6b780b6c534bfb0b23d29910bfe361e486bcfeaf106db8bc8995792072905a
 ARROW_RE2_BUILD_VERSION=2021-02-02
 ARROW_RE2_BUILD_SHA256_CHECKSUM=1396ab50c06c1a8885fb68bf49a5ecfd989163015fd96699a180d6414937f33f
+# 1.1.9 is patched to implement https://github.com/google/snappy/pull/148 if this is bumped, remove the patch

Review comment:
       I've tried to flag this, and if we pursue this path, I'll make a Jira that points to each of these lines that need to be deleted when > 1.1.9 is released




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[GitHub] [arrow] jonkeane commented on pull request #11875: ARROW-14839: [R] test-fedora-r-clang-sanitizer job failing due to snappy causing a sanitizer error

Posted by GitBox <gi...@apache.org>.
jonkeane commented on pull request #11875:
URL: https://github.com/apache/arrow/pull/11875#issuecomment-988127441


   @github-actions autotune


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[GitHub] [arrow] ursabot edited a comment on pull request #11875: ARROW-14839: [R] test-fedora-r-clang-sanitizer job failing due to snappy causing a sanitizer error

Posted by GitBox <gi...@apache.org>.
ursabot edited a comment on pull request #11875:
URL: https://github.com/apache/arrow/pull/11875#issuecomment-989117713


   Benchmark runs are scheduled for baseline = cba23c4633f63fbbb7bde9345fa18330953c9f27 and contender = c2a89e688cf7a501ec1295a0dca5adefc4d2ce46. c2a89e688cf7a501ec1295a0dca5adefc4d2ce46 is a master commit associated with this PR. Results will be available as each benchmark for each run completes.
   Conbench compare runs links:
   [Finished :arrow_down:0.0% :arrow_up:0.0%] [ec2-t3-xlarge-us-east-2](https://conbench.ursa.dev/compare/runs/48d5fa9f859e4a23849a6a23e32b492a...813e041e913c400e8715726edc8240f5/)
   [Failed :arrow_down:0.0% :arrow_up:0.0%] [ursa-i9-9960x](https://conbench.ursa.dev/compare/runs/04560d40922e4429bf5f95e82c4a6ccf...e3e821c7123f404490b7a0c3fa31dc4a/)
   [Scheduled] [ursa-thinkcentre-m75q](https://conbench.ursa.dev/compare/runs/3b4c609346e546c3a5e1ca074832917f...f62d8521b5464cbc811b16387d2c63d0/)
   Supported benchmarks:
   ec2-t3-xlarge-us-east-2: Supported benchmark langs: Python. Runs only benchmarks with cloud = True
   ursa-i9-9960x: Supported benchmark langs: Python, R, JavaScript
   ursa-thinkcentre-m75q: Supported benchmark langs: C++, Java
   


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[GitHub] [arrow] github-actions[bot] commented on pull request #11875: ARROW-14839: [R] test-fedora-r-clang-sanitizer job failing due to snappy causing a sanitizer error

Posted by GitBox <gi...@apache.org>.
github-actions[bot] commented on pull request #11875:
URL: https://github.com/apache/arrow/pull/11875#issuecomment-987211943


   Revision: 4c426a5382b63d657c90bf968e2ba95ddf1b223b
   
   Submitted crossbow builds: [ursacomputing/crossbow @ actions-1251](https://github.com/ursacomputing/crossbow/branches/all?query=actions-1251)
   
   |Task|Status|
   |----|------|
   |test-fedora-r-clang-sanitizer|[![Azure](https://dev.azure.com/ursacomputing/crossbow/_apis/build/status/ursacomputing.crossbow?branchName=actions-1251-azure-test-fedora-r-clang-sanitizer)](https://dev.azure.com/ursacomputing/crossbow/_build/latest?definitionId=1&branchName=actions-1251-azure-test-fedora-r-clang-sanitizer)|


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[GitHub] [arrow] github-actions[bot] commented on pull request #11875: ARROW-14839: [R] test-fedora-r-clang-sanitizer job failing due to snappy causing a sanitizer error

Posted by GitBox <gi...@apache.org>.
github-actions[bot] commented on pull request #11875:
URL: https://github.com/apache/arrow/pull/11875#issuecomment-987211307






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[GitHub] [arrow] jonkeane commented on pull request #11875: ARROW-14839: [R] test-fedora-r-clang-sanitizer job failing due to snappy causing a sanitizer error

Posted by GitBox <gi...@apache.org>.
jonkeane commented on pull request #11875:
URL: https://github.com/apache/arrow/pull/11875#issuecomment-989079181


   The conda failures are known / on master. The test-r-depsource-system failure looks transient (and at the very least unrelated!) 


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[GitHub] [arrow] jonkeane closed pull request #11875: ARROW-14839: [R] test-fedora-r-clang-sanitizer job failing due to snappy causing a sanitizer error

Posted by GitBox <gi...@apache.org>.
jonkeane closed pull request #11875:
URL: https://github.com/apache/arrow/pull/11875


   


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[GitHub] [arrow] jonkeane commented on a change in pull request #11875: ARROW-14839: [R] test-fedora-r-clang-sanitizer job failing due to snappy causing a sanitizer error

Posted by GitBox <gi...@apache.org>.
jonkeane commented on a change in pull request #11875:
URL: https://github.com/apache/arrow/pull/11875#discussion_r764374055



##########
File path: r/inst/build_arrow_static.sh
##########
@@ -47,6 +47,12 @@ else
   ARROW_DEFAULT_PARAM="OFF"
 fi
 
+# Snappy 1.1.9 is patched to implement https://github.com/google/snappy/pull/148 but some platforms don't have
+# patch available, so disable snappy in those cases. If the snappy version is bumped, we should remove this.
+if [ ! $(command -v patch) ]; then
+  ARROW_WITH_SNAPPY=OFF
+fi

Review comment:
       For our CI this should not be hit, but is important incase CRAN happens to not have `patch`, it will disable snappy so we don't get a sanitizer error there.




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[GitHub] [arrow] github-actions[bot] commented on pull request #11875: ARROW-14839: [R] test-fedora-r-clang-sanitizer job failing due to snappy causing a sanitizer error

Posted by GitBox <gi...@apache.org>.
github-actions[bot] commented on pull request #11875:
URL: https://github.com/apache/arrow/pull/11875#issuecomment-987978637


   Revision: b141103f3b33fff723a50248b803b274ed9c8994
   
   Submitted crossbow builds: [ursacomputing/crossbow @ actions-1259](https://github.com/ursacomputing/crossbow/branches/all?query=actions-1259)
   
   |Task|Status|
   |----|------|
   |test-fedora-r-clang-sanitizer|[![Azure](https://dev.azure.com/ursacomputing/crossbow/_apis/build/status/ursacomputing.crossbow?branchName=actions-1259-azure-test-fedora-r-clang-sanitizer)](https://dev.azure.com/ursacomputing/crossbow/_build/latest?definitionId=1&branchName=actions-1259-azure-test-fedora-r-clang-sanitizer)|


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[GitHub] [arrow] jonkeane commented on pull request #11875: ARROW-14839: [R] test-fedora-r-clang-sanitizer job failing due to snappy causing a sanitizer error

Posted by GitBox <gi...@apache.org>.
jonkeane commented on pull request #11875:
URL: https://github.com/apache/arrow/pull/11875#issuecomment-988214659


   @github-actions crossbow submit test-fedora-r-clang-sanitizer


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[GitHub] [arrow] ursabot edited a comment on pull request #11875: ARROW-14839: [R] test-fedora-r-clang-sanitizer job failing due to snappy causing a sanitizer error

Posted by GitBox <gi...@apache.org>.
ursabot edited a comment on pull request #11875:
URL: https://github.com/apache/arrow/pull/11875#issuecomment-989117713


   Benchmark runs are scheduled for baseline = cba23c4633f63fbbb7bde9345fa18330953c9f27 and contender = c2a89e688cf7a501ec1295a0dca5adefc4d2ce46. c2a89e688cf7a501ec1295a0dca5adefc4d2ce46 is a master commit associated with this PR. Results will be available as each benchmark for each run completes.
   Conbench compare runs links:
   [Finished :arrow_down:0.0% :arrow_up:0.0%] [ec2-t3-xlarge-us-east-2](https://conbench.ursa.dev/compare/runs/48d5fa9f859e4a23849a6a23e32b492a...813e041e913c400e8715726edc8240f5/)
   [Failed :arrow_down:0.0% :arrow_up:0.0%] [ursa-i9-9960x](https://conbench.ursa.dev/compare/runs/04560d40922e4429bf5f95e82c4a6ccf...e3e821c7123f404490b7a0c3fa31dc4a/)
   [Finished :arrow_down:0.09% :arrow_up:0.09%] [ursa-thinkcentre-m75q](https://conbench.ursa.dev/compare/runs/3b4c609346e546c3a5e1ca074832917f...f62d8521b5464cbc811b16387d2c63d0/)
   Supported benchmarks:
   ec2-t3-xlarge-us-east-2: Supported benchmark langs: Python. Runs only benchmarks with cloud = True
   ursa-i9-9960x: Supported benchmark langs: Python, R, JavaScript
   ursa-thinkcentre-m75q: Supported benchmark langs: C++, Java
   


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[GitHub] [arrow] jonkeane commented on a change in pull request #11875: ARROW-14839: [R] test-fedora-r-clang-sanitizer job failing due to snappy causing a sanitizer error

Posted by GitBox <gi...@apache.org>.
jonkeane commented on a change in pull request #11875:
URL: https://github.com/apache/arrow/pull/11875#discussion_r764373314



##########
File path: cpp/cmake_modules/ThirdpartyToolchain.cmake
##########
@@ -620,6 +620,14 @@ else()
              "https://github.com/google/snappy/archive/${ARROW_SNAPPY_BUILD_VERSION}.tar.gz"
              "https://github.com/ursa-labs/thirdparty/releases/download/latest/snappy-${ARROW_SNAPPY_BUILD_VERSION}.tar.gz"
     )
+
+    # This can be removed when https://github.com/google/snappy/pull/148 is released
+    # Some platforms don't have patch, but this is probably ok to skip
+    find_program(patch "patch")
+    if(patch)
+      set(SNAPPY_PATCH_COMMAND "patch" "snappy.cc"
+                               "${CMAKE_SOURCE_DIR}/build-support/snappy-UBSAN.patch")
+    endif()

Review comment:
       Snappy works without the patch, though it has a UBSAN error, so this patches _if we can_ and moves on if not so we don't break. 




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[GitHub] [arrow] jonkeane commented on a change in pull request #11875: ARROW-14839: [R] test-fedora-r-clang-sanitizer job failing due to snappy causing a sanitizer error

Posted by GitBox <gi...@apache.org>.
jonkeane commented on a change in pull request #11875:
URL: https://github.com/apache/arrow/pull/11875#discussion_r764372413



##########
File path: ci/scripts/r_docker_configure.sh
##########
@@ -77,5 +77,19 @@ if [ "$ARROW_S3" == "ON" ] || [ "$ARROW_R_DEV" == "TRUE" ]; then
   fi
 fi
 
+# Install patch if it doesn't already exist
+if [ ! $(command -v patch) ]; then
+  if [ "`which dnf`" ]; then
+    dnf install -y patch
+  elif [ "`which yum`" ]; then
+    yum install -y patch
+  elif [ "`which zypper`" ]; then
+    zypper install -y patch
+  else
+    apt-get update
+    apt-get install -y patch
+  fi
+fi

Review comment:
       This is not strictly necessary (see below where we disable snappy if we can't find `patch`), but it makes sure that we do have `patch` available so we do exercise this code in the sanitizer in our CI




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[GitHub] [arrow] ursabot commented on pull request #11875: ARROW-14839: [R] test-fedora-r-clang-sanitizer job failing due to snappy causing a sanitizer error

Posted by GitBox <gi...@apache.org>.
ursabot commented on pull request #11875:
URL: https://github.com/apache/arrow/pull/11875#issuecomment-989117713


   Benchmark runs are scheduled for baseline = cba23c4633f63fbbb7bde9345fa18330953c9f27 and contender = c2a89e688cf7a501ec1295a0dca5adefc4d2ce46. c2a89e688cf7a501ec1295a0dca5adefc4d2ce46 is a master commit associated with this PR. Results will be available as each benchmark for each run completes.
   Conbench compare runs links:
   [Scheduled] [ec2-t3-xlarge-us-east-2](https://conbench.ursa.dev/compare/runs/48d5fa9f859e4a23849a6a23e32b492a...813e041e913c400e8715726edc8240f5/)
   [Scheduled] [ursa-i9-9960x](https://conbench.ursa.dev/compare/runs/04560d40922e4429bf5f95e82c4a6ccf...e3e821c7123f404490b7a0c3fa31dc4a/)
   [Scheduled] [ursa-thinkcentre-m75q](https://conbench.ursa.dev/compare/runs/3b4c609346e546c3a5e1ca074832917f...f62d8521b5464cbc811b16387d2c63d0/)
   Supported benchmarks:
   ec2-t3-xlarge-us-east-2: Supported benchmark langs: Python. Runs only benchmarks with cloud = True
   ursa-i9-9960x: Supported benchmark langs: Python, R, JavaScript
   ursa-thinkcentre-m75q: Supported benchmark langs: C++, Java
   


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[GitHub] [arrow] ursabot edited a comment on pull request #11875: ARROW-14839: [R] test-fedora-r-clang-sanitizer job failing due to snappy causing a sanitizer error

Posted by GitBox <gi...@apache.org>.
ursabot edited a comment on pull request #11875:
URL: https://github.com/apache/arrow/pull/11875#issuecomment-989117713


   Benchmark runs are scheduled for baseline = cba23c4633f63fbbb7bde9345fa18330953c9f27 and contender = c2a89e688cf7a501ec1295a0dca5adefc4d2ce46. c2a89e688cf7a501ec1295a0dca5adefc4d2ce46 is a master commit associated with this PR. Results will be available as each benchmark for each run completes.
   Conbench compare runs links:
   [Finished :arrow_down:0.0% :arrow_up:0.0%] [ec2-t3-xlarge-us-east-2](https://conbench.ursa.dev/compare/runs/48d5fa9f859e4a23849a6a23e32b492a...813e041e913c400e8715726edc8240f5/)
   [Scheduled] [ursa-i9-9960x](https://conbench.ursa.dev/compare/runs/04560d40922e4429bf5f95e82c4a6ccf...e3e821c7123f404490b7a0c3fa31dc4a/)
   [Scheduled] [ursa-thinkcentre-m75q](https://conbench.ursa.dev/compare/runs/3b4c609346e546c3a5e1ca074832917f...f62d8521b5464cbc811b16387d2c63d0/)
   Supported benchmarks:
   ec2-t3-xlarge-us-east-2: Supported benchmark langs: Python. Runs only benchmarks with cloud = True
   ursa-i9-9960x: Supported benchmark langs: Python, R, JavaScript
   ursa-thinkcentre-m75q: Supported benchmark langs: C++, Java
   


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[GitHub] [arrow] jonkeane commented on pull request #11875: ARROW-14839: [R] test-fedora-r-clang-sanitizer job failing due to snappy causing a sanitizer error

Posted by GitBox <gi...@apache.org>.
jonkeane commented on pull request #11875:
URL: https://github.com/apache/arrow/pull/11875#issuecomment-988127329


   @github-actions crossbow submit test-fedora-r-clang-sanitizer


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[GitHub] [arrow] github-actions[bot] commented on pull request #11875: ARROW-14839: [R] test-fedora-r-clang-sanitizer job failing due to snappy causing a sanitizer error

Posted by GitBox <gi...@apache.org>.
github-actions[bot] commented on pull request #11875:
URL: https://github.com/apache/arrow/pull/11875#issuecomment-988128164


   Revision: e1599d3d6b873abcf5eabc184cd60959438a073a
   
   Submitted crossbow builds: [ursacomputing/crossbow @ actions-1260](https://github.com/ursacomputing/crossbow/branches/all?query=actions-1260)
   
   |Task|Status|
   |----|------|
   |test-fedora-r-clang-sanitizer|[![Azure](https://dev.azure.com/ursacomputing/crossbow/_apis/build/status/ursacomputing.crossbow?branchName=actions-1260-azure-test-fedora-r-clang-sanitizer)](https://dev.azure.com/ursacomputing/crossbow/_build/latest?definitionId=1&branchName=actions-1260-azure-test-fedora-r-clang-sanitizer)|


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