[GitHub] [arrow] pitrou commented on a change in pull request #10237: ARROW-12571: [R][CI] Run nightly R with valgrind

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pitrou commented on a change in pull request #10237:
URL: https://github.com/apache/arrow/pull/10237#discussion_r625619463



##########
File path: ci/scripts/r_valgrind.sh
##########
@@ -0,0 +1,81 @@
+#!/usr/bin/env bash
+# Licensed to the Apache Software Foundation (ASF) under one
+# or more contributor license agreements.  See the NOTICE file
+# distributed with this work for additional information
+# regarding copyright ownership.  The ASF licenses this file
+# to you under the Apache License, Version 2.0 (the
+# "License"); you may not use this file except in compliance
+# with the License.  You may obtain a copy of the License at
+#
+#   http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing,
+# software distributed under the License is distributed on an
+# "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
+# KIND, either express or implied.  See the License for the
+# specific language governing permissions and limitations
+# under the License.
+
+set -ex
+
+: ${R_BIN:=RDvalgrind}
+
+printenv
+
+source_dir=${1}/r
+
+${R_BIN} CMD INSTALL ${source_dir}
+pushd ${source_dir}/tests
+
+export TEST_R_WITH_ARROW=TRUE
+${R_BIN} --vanilla -d "valgrind --tool=memcheck --leak-check=full --track-origins=yes" -f testthat.R > testthat.out 2>&1 || true
+
+# TODO: examples? vignettes? R CMD check with valgrind on?
+
+cat testthat.out
+
+# Check the valgrind output
+# We might also considering using the greps that LibthGBM uses:
+# https://github.com/microsoft/LightGBM/blob/fa6d356555f9ef888acf5f5e259dca958ca24f6d/.ci/test_r_package_valgrind.sh#L20-L85
+
+# No errors at all

Review comment:
       You should use `valgrind --error-exitcode=1` instead of grepping.

##########
File path: ci/scripts/r_valgrind.sh
##########
@@ -0,0 +1,81 @@
+#!/usr/bin/env bash
+# Licensed to the Apache Software Foundation (ASF) under one
+# or more contributor license agreements.  See the NOTICE file
+# distributed with this work for additional information
+# regarding copyright ownership.  The ASF licenses this file
+# to you under the Apache License, Version 2.0 (the
+# "License"); you may not use this file except in compliance
+# with the License.  You may obtain a copy of the License at
+#
+#   http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing,
+# software distributed under the License is distributed on an
+# "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
+# KIND, either express or implied.  See the License for the
+# specific language governing permissions and limitations
+# under the License.
+
+set -ex
+
+: ${R_BIN:=RDvalgrind}
+
+printenv
+
+source_dir=${1}/r
+
+${R_BIN} CMD INSTALL ${source_dir}
+pushd ${source_dir}/tests
+
+export TEST_R_WITH_ARROW=TRUE
+${R_BIN} --vanilla -d "valgrind --tool=memcheck --leak-check=full --track-origins=yes" -f testthat.R > testthat.out 2>&1 || true
+
+# TODO: examples? vignettes? R CMD check with valgrind on?
+
+cat testthat.out
+
+# Check the valgrind output
+# We might also considering using the greps that LibthGBM uses:
+# https://github.com/microsoft/LightGBM/blob/fa6d356555f9ef888acf5f5e259dca958ca24f6d/.ci/test_r_package_valgrind.sh#L20-L85
+
+# No errors at all
+if [[ "$(grep -c 'ERROR SUMMARY: 0 errors' testthat.out)" == 1 ]]; then
+  no_errors=true
+else
+  no_errors=false
+fi
+
+# This error happens in our CI when there is a `skip()` of any sort. It does not show up on the cran 
+# logs so we should be able to ignore it.
+# ==273== Conditional jump or move depends on uninitialised value(s)
+# ==273==    at 0x49CFFB6: gregexpr_Regexc (grep.c:2413)
+# ==273==    by 0x49D2CB2: do_regexpr (grep.c:3050)
+# ==273==    by 0x49A08C8: bcEval (eval.c:7115)
+# ==273==    by 0x498BF52: Rf_eval (eval.c:727)
+# ==273==    by 0x498ECC1: R_execClosure (eval.c:1897)
+# ==273==    by 0x498E974: Rf_applyClosure (eval.c:1823)
+# ==273==    by 0x49A04FC: bcEval (eval.c:7083)
+# ==273==    by 0x498BF52: Rf_eval (eval.c:727)
+# ==273==    by 0x498BA9E: forcePromise (eval.c:555)
+# ==273==    by 0x4996C1B: FORCE_PROMISE (eval.c:5136)
+# ==273==    by 0x4996DD6: getvar (eval.c:5177)
+# ==273==    by 0x499DA15: bcEval (eval.c:6867)
+# ==273==  Uninitialised value was created by a stack allocation
+# ==273==    at 0x49CFAB5: gregexpr_Regexc (grep.c:2343)
+# ==273==
+if [[   "$(grep -c 'ERROR SUMMARY: 2 errors' testthat.out)" = 1 &&
+  "$(grep -c 'Conditional jump or move depends on uninitialised value' testthat.out)" = 1 &&
+  "$(grep -c 'Uninitialised value was created by a stack allocation' testthat.out)" = 1 ]]; then

Review comment:
       We should use a Valgrind suppressions file instead of grepping:
   https://stackoverflow.com/questions/17159578/generating-suppressions-for-memory-leaks
   

##########
File path: r/tests/testthat/test-compute-aggregate.R
##########
@@ -37,7 +37,8 @@ test_that("sum.Array", {
 
   floats <- c(floats, NA)
   na <- Array$create(floats)
-  expect_identical(as.numeric(sum(na)), sum(floats))
+  # expect_identical(as.numeric(sum(na)), sum(floats))
+  expect_identical(as.numeric(sum(na)), NA_real_)

Review comment:
       Why these changes? If they have a specific purpose, there should be a comment explaining them.




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