e2d984aa1c
### 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 <gurwls223@apache.org>
Signed-off-by: HyukjinKwon <gurwls223@apache.org>
66 lines
2.8 KiB
Bash
Executable file
66 lines
2.8 KiB
Bash
Executable file
#!/bin/bash
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#
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# Licensed to the Apache Software Foundation (ASF) under one or more
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# contributor license agreements. See the NOTICE file distributed with
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# this work for additional information regarding copyright ownership.
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# The ASF licenses this file to You under the Apache License, Version 2.0
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# (the "License"); you may not use this file except in compliance with
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# the License. You may obtain a copy of the License at
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#
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# http://www.apache.org/licenses/LICENSE-2.0
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#
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# Unless required by applicable law or agreed to in writing, software
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# distributed under the License is distributed on an "AS IS" BASIS,
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# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
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# See the License for the specific language governing permissions and
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# limitations under the License.
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#
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FWDIR="$(cd `dirname $0`; pwd)"
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FAILED=0
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LOGFILE=$FWDIR/unit-tests.out
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rm -f $LOGFILE
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SPARK_TESTING=1 NOT_CRAN=true $FWDIR/../bin/spark-submit --driver-java-options "-Dlog4j.configuration=file:$FWDIR/log4j.properties" --conf spark.hadoop.fs.defaultFS="file:///" --conf spark.driver.extraJavaOptions="-Dio.netty.tryReflectionSetAccessible=true" --conf spark.executor.extraJavaOptions="-Dio.netty.tryReflectionSetAccessible=true" $FWDIR/pkg/tests/run-all.R 2>&1 | tee -a $LOGFILE
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FAILED=$((PIPESTATUS[0]||$FAILED))
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NUM_TEST_WARNING="$(grep -c -e 'Warnings ----------------' $LOGFILE)"
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# Also run the documentation tests for CRAN
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CRAN_CHECK_LOG_FILE=$FWDIR/cran-check.out
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rm -f $CRAN_CHECK_LOG_FILE
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# TODO(SPARK-30737) reenable this once packages are correctly installed in Jenkins
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# NO_TESTS=1 NO_MANUAL=1 $FWDIR/check-cran.sh 2>&1 | tee -a $CRAN_CHECK_LOG_FILE
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# FAILED=$((PIPESTATUS[0]||$FAILED))
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touch $CRAN_CHECK_LOG_FILE
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NUM_CRAN_WARNING="$(grep -c WARNING$ $CRAN_CHECK_LOG_FILE)"
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NUM_CRAN_ERROR="$(grep -c ERROR$ $CRAN_CHECK_LOG_FILE)"
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NUM_CRAN_NOTES="$(grep -c NOTE$ $CRAN_CHECK_LOG_FILE)"
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HAS_PACKAGE_VERSION_WARN="$(grep -c "Insufficient package version" $CRAN_CHECK_LOG_FILE)"
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if [[ $FAILED != 0 || $NUM_TEST_WARNING != 0 ]]; then
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cat $LOGFILE
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echo -en "\033[31m" # Red
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echo "Had test warnings or failures; see logs."
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echo -en "\033[0m" # No color
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exit -1
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else
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# We have 2 NOTEs: for RoxygenNote and one in Jenkins only "No repository set"
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# For non-latest version branches, one WARNING for package version
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if [[ ($NUM_CRAN_WARNING != 0 || $NUM_CRAN_ERROR != 0 || $NUM_CRAN_NOTES -gt 2) &&
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($HAS_PACKAGE_VERSION_WARN != 1 || $NUM_CRAN_WARNING != 1 || $NUM_CRAN_ERROR != 0 || $NUM_CRAN_NOTES -gt 1) ]]; then
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cat $CRAN_CHECK_LOG_FILE
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echo -en "\033[31m" # Red
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echo "Had CRAN check errors; see logs."
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echo -en "\033[0m" # No color
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exit -1
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else
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echo -en "\033[32m" # Green
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echo "Tests passed."
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echo -en "\033[0m" # No color
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fi
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fi
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