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ARROW-17252: [R] Intermittent valgrind failure #13773

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Merged
nealrichardson merged 8 commits into from
Aug 9, 2022
Merged

ARROW-17252: [R] Intermittent valgrind failure #13773

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73e68de
don't collect with an event loop unless requested
paleolimbot Aug 2, 2022
3647aa3
modify example that needs special handling, skip a test on linux devel
paleolimbot Aug 2, 2022
46d7ef3
auto opt-in to user-defined function-friendly collect
paleolimbot Aug 2, 2022
f9f9e85
better documentation of test skipping
paleolimbot Aug 2, 2022
10a9815
Update r/R/compute.R
paleolimbot Aug 2, 2022
3b71868
document
paleolimbot Aug 2, 2022
2efade7
more explicit and more correct cleaning up of env var
paleolimbot Aug 7, 2022
37e6e2e
more reliable unsetting of environment variable, remove references to…
paleolimbot Aug 7, 2022
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9 changes: 8 additions & 1 deletion r/R/compute.R
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Original file line number Diff line number Diff line change
Expand Up @@ -344,7 +344,7 @@ cast_options <- function(safe = TRUE, ...) {
#' @return `NULL`, invisibly
#' @export
#'
#' @examplesIf arrow_with_dataset()
#' @examplesIf arrow_with_dataset() && identical(Sys.getenv("NOT_CRAN"), "true")
#' library(dplyr, warn.conflicts = FALSE)
#'
#' some_model <- lm(mpg ~ disp + cyl, data = mtcars)
Expand Down Expand Up @@ -385,6 +385,13 @@ register_scalar_function <- function(name, fun, in_type, out_type,
update_cache = TRUE
)

# User-defined functions require some special handling
# in the query engine which currently require an opt-in using
# the R_ARROW_COLLECT_WITH_UDF environment variable while this
# behaviour is stabilized.
# TODO(ARROW-17178) remove the need for this!
Sys.setenv(R_ARROW_COLLECT_WITH_UDF = "true")

invisible(NULL)
}

Expand Down
9 changes: 8 additions & 1 deletion r/R/table.R
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Expand Up @@ -331,5 +331,12 @@ as_arrow_table.arrow_dplyr_query <- function(x, ...) {
# See query-engine.R for ExecPlan/Nodes
plan <- ExecPlan$create()
final_node <- plan$Build(x)
plan$Run(final_node, as_table = TRUE)

run_with_event_loop <- identical(
Sys.getenv("R_ARROW_COLLECT_WITH_UDF", ""),
"true"
)

result <- plan$Run(final_node, as_table = run_with_event_loop)
as_arrow_table(result)
}
2 changes: 1 addition & 1 deletion r/man/register_scalar_function.Rd
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51 changes: 40 additions & 11 deletions r/tests/testthat/test-compute.R
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Expand Up @@ -81,14 +81,21 @@ test_that("arrow_scalar_function() works with auto_convert = TRUE", {

test_that("register_scalar_function() adds a compute function to the registry", {
skip_if_not(CanRunWithCapturedR())
# TODO(ARROW-17178): User-defined function-friendly ExecPlan execution has
# occasional valgrind errors
skip_on_linux_devel()

register_scalar_function(
"times_32",
function(context, x) x * 32.0,
int32(), float64(),
auto_convert = TRUE
)
on.exit(unregister_binding("times_32", update_cache = TRUE))
on.exit({
unregister_binding("times_32", update_cache = TRUE)
# TODO(ARROW-17178) remove the need for this!
Sys.unsetenv("R_ARROW_COLLECT_WITH_UDF")
})

expect_true("times_32" %in% names(asNamespace("arrow")$.cache$functions))
expect_true("times_32" %in% list_compute_functions())
Expand Down Expand Up @@ -120,9 +127,11 @@ test_that("arrow_scalar_function() with bad return type errors", {
int32(),
float64()
)
on.exit(
on.exit({
unregister_binding("times_32_bad_return_type_array", update_cache = TRUE)
)
# TODO(ARROW-17178) remove the need for this!
Sys.unsetenv("R_ARROW_COLLECT_WITH_UDF")
})

expect_error(
call_function("times_32_bad_return_type_array", Array$create(1L)),
Expand All @@ -135,17 +144,19 @@ test_that("arrow_scalar_function() with bad return type errors", {
int32(),
float64()
)
on.exit(
on.exit({
unregister_binding("times_32_bad_return_type_scalar", update_cache = TRUE)
)
# TODO(ARROW-17178) remove the need for this!
Sys.unsetenv("R_ARROW_COLLECT_WITH_UDF")
})

expect_error(
call_function("times_32_bad_return_type_scalar", Array$create(1L)),
"Expected return Array or Scalar with type 'double'"
)
})

test_that("register_user_defined_function() can register multiple kernels", {
test_that("register_scalar_function() can register multiple kernels", {
skip_if_not(CanRunWithCapturedR())

register_scalar_function(
Expand All @@ -155,7 +166,11 @@ test_that("register_user_defined_function() can register multiple kernels", {
out_type = function(in_types) in_types[[1]],
auto_convert = TRUE
)
on.exit(unregister_binding("times_32", update_cache = TRUE))
on.exit({
unregister_binding("times_32", update_cache = TRUE)
# TODO(ARROW-17178) remove the need for this!
Sys.unsetenv("R_ARROW_COLLECT_WITH_UDF")
})

expect_equal(
call_function("times_32", Scalar$create(1L, int32())),
Expand All @@ -173,7 +188,10 @@ test_that("register_user_defined_function() can register multiple kernels", {
)
})

test_that("register_user_defined_function() errors for unsupported specifications", {
test_that("register_scalar_function() errors for unsupported specifications", {
# TODO(ARROW-17178) remove the need for this!
on.exit(Sys.unsetenv("R_ARROW_COLLECT_WITH_UDF"))

expect_error(
register_scalar_function(
"no_kernels",
Expand Down Expand Up @@ -208,7 +226,10 @@ test_that("register_user_defined_function() errors for unsupported specification
test_that("user-defined functions work during multi-threaded execution", {
skip_if_not(CanRunWithCapturedR())
skip_if_not_available("dataset")
# Snappy has a UBSan issue: https://github.com/google/snappy/pull/148
# Skip on linux devel because:
# TODO(ARROW-17283): Snappy has a UBSan issue that is fixed in the dev version
# TODO(ARROW-17178): User-defined function-friendly ExecPlan execution has
# occasional valgrind errors
skip_on_linux_devel()

n_rows <- 10000
Expand All @@ -235,7 +256,11 @@ test_that("user-defined functions work during multi-threaded execution", {
float64(),
auto_convert = TRUE
)
on.exit(unregister_binding("times_32", update_cache = TRUE))
on.exit({
unregister_binding("times_32", update_cache = TRUE)
# TODO(ARROW-17178) remove the need for this!
Sys.unsetenv("R_ARROW_COLLECT_WITH_UDF")
})

# check a regular collect()
result <- open_dataset(tf_dataset) %>%
Expand Down Expand Up @@ -268,7 +293,11 @@ test_that("user-defined error when called from an unsupported context", {
float64(),
auto_convert = TRUE
)
on.exit(unregister_binding("times_32", update_cache = TRUE))
on.exit({
unregister_binding("times_32", update_cache = TRUE)
# TODO(ARROW-17178) remove the need for this!
Sys.unsetenv("R_ARROW_COLLECT_WITH_UDF")
})

stream_plan_with_udf <- function() {
record_batch(a = 1:1000) %>%
Expand Down