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Posted to commits@spark.apache.org by gu...@apache.org on 2020/02/05 07:49:14 UTC
[spark] branch branch-2.4 updated: [SPARK-30733][R][HOTFIX] Fix
SparkR tests per testthat and R version upgrade, and disable CRAN
This is an automated email from the ASF dual-hosted git repository.
gurwls223 pushed a commit to branch branch-2.4
in repository https://gitbox.apache.org/repos/asf/spark.git
The following commit(s) were added to refs/heads/branch-2.4 by this push:
new f674d88 [SPARK-30733][R][HOTFIX] Fix SparkR tests per testthat and R version upgrade, and disable CRAN
f674d88 is described below
commit f674d883723cfa53d19e4988975b4fefd2e7b021
Author: HyukjinKwon <gu...@apache.org>
AuthorDate: Wed Feb 5 16:45:54 2020 +0900
[SPARK-30733][R][HOTFIX] Fix SparkR tests per testthat and R version upgrade, and disable CRAN
### What changes were proposed in this pull request?
There are currently the R test failures after upgrading `testthat` to 2.0.0, and R version 3.5.2 as of SPARK-23435. This PR targets to fix the tests and make the tests pass. See the explanations and causes below:
```
test_context.R:49: failure: Check masked functions
length(maskedCompletely) not equal to length(namesOfMaskedCompletely).
1/1 mismatches
[1] 6 - 4 == 2
test_context.R:53: failure: Check masked functions
sort(maskedCompletely, na.last = TRUE) not equal to sort(namesOfMaskedCompletely, na.last = TRUE).
5/6 mismatches
x[2]: "endsWith"
y[2]: "filter"
x[3]: "filter"
y[3]: "not"
x[4]: "not"
y[4]: "sample"
x[5]: "sample"
y[5]: NA
x[6]: "startsWith"
y[6]: NA
```
From my cursory look, R base and R's version are mismatched. I fixed accordingly and Jenkins will test it out.
```
test_includePackage.R:31: error: include inside function
package or namespace load failed for ���plyr���:
package ���plyr��� was installed by an R version with different internals; it needs to be reinstalled for use with this R version
Seems it's a package installation issue. Looks like plyr has to be re-installed.
```
From my cursory look, previously installed `plyr` remains and it's not compatible with the new R version. I fixed accordingly and Jenkins will test it out.
```
test_sparkSQL.R:499: warning: SPARK-17811: can create DataFrame containing NA as date and time
Your system is mis-configured: ���/etc/localtime��� is not a symlink
```
Seems a env problem. I suppressed the warnings for now.
```
test_sparkSQL.R:499: warning: SPARK-17811: can create DataFrame containing NA as date and time
It is strongly recommended to set envionment variable TZ to ���America/Los_Angeles��� (or equivalent)
```
Seems a env problem. I suppressed the warnings for now.
```
test_sparkSQL.R:1814: error: string operators
unable to find an inherited method for function ���startsWith��� for signature ���"character"���
1: expect_true(startsWith("Hello World", "Hello")) at /home/jenkins/workspace/SparkPullRequestBuilder2/R/pkg/tests/fulltests/test_sparkSQL.R:1814
2: quasi_label(enquo(object), label)
3: eval_bare(get_expr(quo), get_env(quo))
4: startsWith("Hello World", "Hello")
5: (function (classes, fdef, mtable)
{
methods <- .findInheritedMethods(classes, fdef, mtable)
if (length(methods) == 1L)
return(methods[[1L]])
else if (length(methods) == 0L) {
cnames <- paste0("\"", vapply(classes, as.character, ""), "\"", collapse = ", ")
stop(gettextf("unable to find an inherited method for function %s for signature %s",
sQuote(fdefgeneric), sQuote(cnames)), domain = NA)
}
else stop("Internal error in finding inherited methods; didn't return a unique method",
domain = NA)
})(list("character"), new("nonstandardGenericFunction", .Data = function (x, prefix)
{
standardGeneric("startsWith")
}, generic = structure("startsWith", package = "SparkR"), package = "SparkR", group = list(),
valueClass = character(0), signature = c("x", "prefix"), default = NULL, skeleton = (function (x,
prefix)
stop("invalid call in method dispatch to 'startsWith' (no default method)", domain = NA))(x,
prefix)), <environment>)
6: stop(gettextf("unable to find an inherited method for function %s for signature %s",
sQuote(fdefgeneric), sQuote(cnames)), domain = NA)
```
From my cursory look, R base and R's version are mismatched. I fixed accordingly and Jenkins will test it out.
Also, this PR causes a CRAN check failure as below:
```
* creating vignettes ... ERROR
Error: processing vignette 'sparkr-vignettes.Rmd' failed with diagnostics:
package ���htmltools��� was installed by an R version with different internals; it needs to be reinstalled for use with this R version
```
This PR disables it for now.
### Why are the changes needed?
To unblock other PRs.
### Does this PR introduce any user-facing change?
No. Test only and dev only.
### How was this patch tested?
No. I am going to use Jenkins to test.
Closes #27460 from HyukjinKwon/r-test-failure.
Authored-by: HyukjinKwon <gu...@apache.org>
Signed-off-by: HyukjinKwon <gu...@apache.org>
(cherry picked from commit e2d984aa1c79eb389cc8d333f656196b17af1c32)
Signed-off-by: HyukjinKwon <gu...@apache.org>
---
R/pkg/tests/fulltests/test_context.R | 3 ++-
R/pkg/tests/fulltests/test_includePackage.R | 8 ++++----
R/pkg/tests/fulltests/test_sparkSQL.R | 10 ++++++++--
R/run-tests.sh | 7 ++++---
4 files changed, 18 insertions(+), 10 deletions(-)
diff --git a/R/pkg/tests/fulltests/test_context.R b/R/pkg/tests/fulltests/test_context.R
index 0e5af3c..776efdc 100644
--- a/R/pkg/tests/fulltests/test_context.R
+++ b/R/pkg/tests/fulltests/test_context.R
@@ -25,7 +25,8 @@ test_that("Check masked functions", {
namesOfMasked <- c("describe", "cov", "filter", "lag", "na.omit", "predict", "sd", "var",
"colnames", "colnames<-", "intersect", "rank", "rbind", "sample", "subset",
"summary", "transform", "drop", "window", "as.data.frame", "union", "not")
- if (as.numeric(R.version$major) >= 3 && as.numeric(R.version$minor) >= 3) {
+ version <- packageVersion("base")
+ if (as.numeric(version$major) >= 3 && as.numeric(version$minor) >= 3) {
namesOfMasked <- c("endsWith", "startsWith", namesOfMasked)
}
masked <- conflicts(detail = TRUE)$`package:SparkR`
diff --git a/R/pkg/tests/fulltests/test_includePackage.R b/R/pkg/tests/fulltests/test_includePackage.R
index 916361f..1d16b26 100644
--- a/R/pkg/tests/fulltests/test_includePackage.R
+++ b/R/pkg/tests/fulltests/test_includePackage.R
@@ -27,8 +27,8 @@ rdd <- parallelize(sc, nums, 2L)
test_that("include inside function", {
# Only run the test if plyr is installed.
- if ("plyr" %in% rownames(installed.packages())) {
- suppressPackageStartupMessages(library(plyr))
+ if ("plyr" %in% rownames(installed.packages()) &&
+ suppressPackageStartupMessages(suppressWarnings(library(plyr, logical.return = TRUE)))) {
generateData <- function(x) {
suppressPackageStartupMessages(library(plyr))
attach(airquality)
@@ -44,8 +44,8 @@ test_that("include inside function", {
test_that("use include package", {
# Only run the test if plyr is installed.
- if ("plyr" %in% rownames(installed.packages())) {
- suppressPackageStartupMessages(library(plyr))
+ if ("plyr" %in% rownames(installed.packages()) &&
+ suppressPackageStartupMessages(suppressWarnings(library(plyr, logical.return = TRUE)))) {
generateData <- function(x) {
attach(airquality)
result <- transform(Ozone, logOzone = log(Ozone))
diff --git a/R/pkg/tests/fulltests/test_sparkSQL.R b/R/pkg/tests/fulltests/test_sparkSQL.R
index 38fb258..542a2bb 100644
--- a/R/pkg/tests/fulltests/test_sparkSQL.R
+++ b/R/pkg/tests/fulltests/test_sparkSQL.R
@@ -505,7 +505,12 @@ test_that("SPARK-17811: can create DataFrame containing NA as date and time", {
expect_true(is.na(DF$date[2]))
expect_equal(DF$date[1], as.Date("2016-10-01"))
expect_true(is.na(DF$time[2]))
- expect_equal(DF$time[1], as.POSIXlt("2016-01-10"))
+ # Warnings were suppressed due to Jenkins environment issues.
+ # It shows both warnings as below in Jenkins:
+ # - Your system is mis-configured: /etc/localtime is not a symlink
+ # - It is strongly recommended to set environment variable TZ to
+ # America/Los_Angeles (or equivalent)
+ suppressWarnings(expect_equal(DF$time[1], as.POSIXlt("2016-01-10")))
})
test_that("create DataFrame with complex types", {
@@ -1772,7 +1777,8 @@ test_that("string operators", {
expect_true(first(select(df, endsWith(df$name, "el")))[[1]])
expect_equal(first(select(df, substr(df$name, 1, 2)))[[1]], "Mi")
expect_equal(first(select(df, substr(df$name, 4, 6)))[[1]], "hae")
- if (as.numeric(R.version$major) >= 3 && as.numeric(R.version$minor) >= 3) {
+ version <- packageVersion("base")
+ if (as.numeric(version$major) >= 3 && as.numeric(version$minor) >= 3) {
expect_true(startsWith("Hello World", "Hello"))
expect_false(endsWith("Hello World", "a"))
}
diff --git a/R/run-tests.sh b/R/run-tests.sh
index 86bd8aa..557f121 100755
--- a/R/run-tests.sh
+++ b/R/run-tests.sh
@@ -31,9 +31,10 @@ NUM_TEST_WARNING="$(grep -c -e 'Warnings ----------------' $LOGFILE)"
# Also run the documentation tests for CRAN
CRAN_CHECK_LOG_FILE=$FWDIR/cran-check.out
rm -f $CRAN_CHECK_LOG_FILE
-
-NO_TESTS=1 NO_MANUAL=1 $FWDIR/check-cran.sh 2>&1 | tee -a $CRAN_CHECK_LOG_FILE
-FAILED=$((PIPESTATUS[0]||$FAILED))
+# TODO(SPARK-30737) reenable this once packages are correctly installed in Jenkins
+# NO_TESTS=1 NO_MANUAL=1 $FWDIR/check-cran.sh 2>&1 | tee -a $CRAN_CHECK_LOG_FILE
+# FAILED=$((PIPESTATUS[0]||$FAILED))
+touch $CRAN_CHECK_LOG_FILE
NUM_CRAN_WARNING="$(grep -c WARNING$ $CRAN_CHECK_LOG_FILE)"
NUM_CRAN_ERROR="$(grep -c ERROR$ $CRAN_CHECK_LOG_FILE)"
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