[R] [CI] Test reorganization triggering valgrind errors

[asfimport]

It looks like the test reorganization that was part of ARROW-15010 means that some of the tests that were being skipped because re2 is known to (purposefully) not pass valgrind.

For example, the format_ISO8601 tests that are now in test-dplyr-funcs-datetime.R

used to be in test-dplyr-funcs-string.R below a skip_if_not_available("re2")

arrow/r/tests/testthat/test-dplyr-funcs-string.R

Lines 861 to 919 in 0ead7c9

	test_that("format_ISO8601", {
	skip_on_os("windows") # https://issues.apache.org/jira/browse/ARROW-13168
	times <- tibble(x = c(lubridate::ymd_hms("2018-10-07 19:04:05", tz = "Etc/GMT+6"), NA))
	compare_dplyr_binding(
	.input %>%
	mutate(x = format_ISO8601(x, precision = "ymd", usetz = FALSE)) %>%
	collect(),
	times
	)
	if (getRversion() < "3.5") {
	# before 3.5, times$x will have no timezone attribute, so Arrow faithfully
	# errors that there is no timezone to format:
	expect_error(
	times %>%
	Table$create() %>%
	mutate(x = format_ISO8601(x, precision = "ymd", usetz = TRUE)) %>%
	collect(),
	"Timezone not present, cannot convert to string with timezone: %Y-%m-%d%z"
	)
	# See comment regarding %S flag in strftime tests
	expect_error(
	times %>%
	Table$create() %>%
	mutate(x = format_ISO8601(x, precision = "ymdhms", usetz = TRUE)) %>%
	mutate(x = gsub("\\.0*", "", x)) %>%
	collect(),
	"Timezone not present, cannot convert to string with timezone: %Y-%m-%dT%H:%M:%S%z"
	)
	} else {
	compare_dplyr_binding(
	.input %>%
	mutate(x = format_ISO8601(x, precision = "ymd", usetz = TRUE)) %>%
	collect(),
	times
	)
	# See comment regarding %S flag in strftime tests
	compare_dplyr_binding(
	.input %>%
	mutate(x = format_ISO8601(x, precision = "ymdhms", usetz = TRUE)) %>%
	mutate(x = gsub("\\.0*", "", x)) %>%
	collect(),
	times
	)
	}
	# See comment regarding %S flag in strftime tests
	compare_dplyr_binding(
	.input %>%
	mutate(x = format_ISO8601(x, precision = "ymdhms", usetz = FALSE)) %>%
	mutate(x = gsub("\\.0*", "", x)) %>%
	collect(),
	times
	)
	})

A bit counter-intuitively "not available" for re2 includes being run on the systems that run valgrind: https://github.com/apache/arrow/blob/master/r/tests/testthat/helper-skip.R#L25-L27

We can add in that re2 skip gatting those tests (though, there might be more that need that gating too!)

https://dev.azure.com/ursacomputing/crossbow/_build/results?buildId=18175&view=logs&j=0da5d1d9-276d-5173-c4c4-9d4d4ed14fdb&t=d9b15392-e4ce-5e4c-0c8c-b69645229181&l=8758

==10242==    by 0xE266301: __invoke_impl<arrow::Result<arrow::compute::ExecBatch>, arrow::compute::(anonymous namespace)::ProjectNode::InputReceived(arrow::compute::ExecNode*, arrow::compute::ExecBatch)::<lambda(arrow::compute::ExecBatch)>&, arrow::compute::ExecBatch> (invoke.h:60)
==10242==    by 0xE266301: __invoke_r<arrow::Result<arrow::compute::ExecBatch>, arrow::compute::(anonymous namespace)::ProjectNode::InputReceived(arrow::compute::ExecNode*, arrow::compute::ExecBatch)::<lambda(arrow::compute::ExecBatch)>&, arrow::compute::ExecBatch> (invoke.h:142)
==10242==    by 0xE266301: std::_Function_handler<arrow::Result<arrow::compute::ExecBatch> (arrow::compute::ExecBatch), arrow::compute::(anonymous namespace)::ProjectNode::InputReceived(arrow::compute::ExecNode*, arrow::compute::ExecBatch)::{lambda(arrow::compute::ExecBatch)#1}>::_M_invoke(std::_Any_data const&, arrow::compute::ExecBatch&&) (std_function.h:292)
==10242==  Uninitialised value was created by a heap allocation
==10242==    at 0x483BE63: operator new(unsigned long) (in /usr/lib/x86_64-linux-gnu/valgrind/vgpreload_memcheck-amd64-linux.so)
==10242==    by 0xEC22BD5: allocate (new_allocator.h:115)
==10242==    by 0xEC22BD5: PODArray (pod_array.h:22)
==10242==    by 0xEC22BD5: re2::SparseSetT<void>::SparseSetT(int) (sparse_set.h:241)
==10242==    by 0xEC208E9: re2::Prog::Optimize() (prog.cc:225)
==10242==    by 0xEC393BB: re2::Compiler::Finish(re2::Regexp*) (compile.cc:1172)
==10242==    by 0xEC3B48E: re2::Compiler::Compile(re2::Regexp*, bool, long) (compile.cc:1156)
==10242==    by 0xEC1B8AE: re2::RE2::Init(re2::StringPiece const&, re2::RE2::Options const&) (re2.cc:223)
==10242==    by 0xEC1C480: re2::RE2::RE2(re2::StringPiece const&, re2::RE2::Options const&) (re2.cc:126)
==10242==    by 0xE7032B7: RegexSubstringReplacer (scalar_string.cc:3178)
==10242==    by 0xE7032B7: make_unique<arrow::compute::internal::(anonymous namespace)::RegexSubstringReplacer<arrow::StringType>, const arrow::compute::ReplaceSubstringOptions&> (make_unique.h:30)
==10242==    by 0xE7032B7: arrow::compute::internal::(anonymous namespace)::RegexSubstringReplacer<arrow::StringType>::Make(arrow::compute::ReplaceSubstringOptions const&) (scalar_string.cc:3158)
==10242==    by 0xE7063C0: arrow::compute::internal::(anonymous namespace)::ReplaceSubstring<arrow::StringType, arrow::compute::internal::(anonymous namespace)::RegexSubstringReplacer<arrow::StringType> >::Exec(arrow::compute::KernelContext*, arrow::compute::ExecBatch const&, arrow::Datum*) (scalar_string.cc:3060)
==10242==    by 0xE2FF61E: __invoke_impl<arrow::Status, arrow::Status (*&)(arrow::compute::KernelContext*, const arrow::compute::ExecBatch&, arrow::Datum*), arrow::compute::KernelContext*, const arrow::compute::ExecBatch&, arrow::Datum*> (invoke.h:60)
==10242==    by 0xE2FF61E: __invoke_r<arrow::Status, arrow::Status (*&)(arrow::compute::KernelContext*, const arrow::compute::ExecBatch&, arrow::Datum*), arrow::compute::KernelContext*, const arrow::compute::ExecBatch&, arrow::Datum*> (invoke.h:142)
==10242==    by 0xE2FF61E: std::_Function_handler<arrow::Status (arrow::compute::KernelContext*, arrow::compute::ExecBatch const&, arrow::Datum*), arrow::Status (*)(arrow::compute::KernelContext*, arrow::compute::ExecBatch const&, arrow::Datum*)>::_M_invoke(std::_Any_data const&, arrow::compute::KernelContext*&&, arrow::compute::ExecBatch const&, arrow::Datum*&&) (std_function.h:292)
==10242==    by 0xE2290E4: operator() (std_function.h:622)
==10242==    by 0xE2290E4: ExecuteBatch (exec.cc:700)
==10242==    by 0xE2290E4: arrow::compute::detail::(anonymous namespace)::ScalarExecutor::Execute(std::vector<arrow::Datum, std::allocator<arrow::Datum> > const&, arrow::compute::detail::ExecListener*) (exec.cc:641)
==10242==    by 0xE243D54: arrow::compute::ExecuteScalarExpression(arrow::compute::Expression const&, arrow::compute::ExecBatch const&, arrow::compute::ExecContext*) (expression.cc:547)
==10242== 

Reporter: Jonathan Keane / @jonkeane
Assignee: Dewey Dunnington / @paleolimbot

PRs and other links:

• GitHub Pull Request #12090

_{Note: This issue was originally created as ARROW-15266. Please see the migration documentation for further details.}

[asfimport]

Jonathan Keane / @jonkeane:
Issue resolved by pull request 12090
#12090