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[SPARK-30733][R][HOTFIX] Fix SparkR tests per testthat and R version upgrade, and disable CRAN #27460

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[SPARK-30733][R][HOTFIX] Fix SparkR tests per testthat and R version upgrade, and disable CRAN #27460

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3113c53
Fix SparkR tests per testthat and R version upgrade
HyukjinKwon Feb 5, 2020
9aa87c3
Skip with id'ed todo
HyukjinKwon Feb 5, 2020
d0f8e72
Revert "Skip with id'ed todo"
HyukjinKwon Feb 5, 2020
d97794d
Skip CRAN
HyukjinKwon Feb 5, 2020
2acfab5
touch log file
HyukjinKwon Feb 5, 2020
b5c0e08
Match with previous disable fix
HyukjinKwon Feb 5, 2020
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3 changes: 2 additions & 1 deletion R/pkg/tests/fulltests/test_context.R
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Expand Up @@ -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`
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8 changes: 4 additions & 4 deletions R/pkg/tests/fulltests/test_includePackage.R
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Expand Up @@ -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)
Expand All @@ -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))
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10 changes: 8 additions & 2 deletions R/pkg/tests/fulltests/test_sparkSQL.R
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Expand Up @@ -496,7 +496,12 @@ 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", {
Expand Down Expand Up @@ -1810,7 +1815,8 @@ 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$minor) >= 3) {
expect_true(startsWith("Hello World", "Hello"))
expect_false(endsWith("Hello World", "a"))
}
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7 changes: 4 additions & 3 deletions R/run-tests.sh
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Expand Up @@ -31,9 +31,10 @@ NUM_TEST_WARNING="$(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)"
Expand Down