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Posted to issues@spark.apache.org by "Hyukjin Kwon (Jira)" <ji...@apache.org> on 2020/02/05 04:30:00 UTC
[jira] [Updated] (SPARK-30733) Fix SparkR tests per testthat and R
version upgrade
[ https://issues.apache.org/jira/browse/SPARK-30733?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ]
Hyukjin Kwon updated SPARK-30733:
---------------------------------
Description:
5 SparkR tests seem being failed after upgrading testthat 2.0.0 and R 3.5.x
{code}
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
{code}
{code}
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.
{code}
{code}
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
test_sparkSQL.R:504: warning: SPARK-17811: can create DataFrame containing NA as date and time
Your system is mis-configured: ���/etc/localtime��� is not a symlink
{code}
{code}
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)
test_sparkSQL.R:504: 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
{code}
{code}
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/SparkPullRequestBuilder@2/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(fdef@generic), 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(fdef@generic), sQuote(cnames)), domain = NA)
{code}
was:
5 SparkR tests seem being failed after upgrading testthat 2.0.0 and R 3.5.x
{code}
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.
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
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)
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/SparkPullRequestBuilder@2/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(fdef@generic), 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(fdef@generic), sQuote(cnames)), domain = NA)
{code}
> Fix SparkR tests per testthat and R version upgrade
> ---------------------------------------------------
>
> Key: SPARK-30733
> URL: https://issues.apache.org/jira/browse/SPARK-30733
> Project: Spark
> Issue Type: Test
> Components: SparkR, SQL
> Affects Versions: 2.4.5, 3.0.0, 3.1.0
> Reporter: Hyukjin Kwon
> Priority: Critical
>
> 5 SparkR tests seem being failed after upgrading testthat 2.0.0 and R 3.5.x
> {code}
> 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
> {code}
> {code}
> 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.
> {code}
> {code}
> 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
> test_sparkSQL.R:504: warning: SPARK-17811: can create DataFrame containing NA as date and time
> Your system is mis-configured: ���/etc/localtime��� is not a symlink
> {code}
> {code}
> 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)
> test_sparkSQL.R:504: 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
> {code}
> {code}
> 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/SparkPullRequestBuilder@2/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(fdef@generic), 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(fdef@generic), sQuote(cnames)), domain = NA)
> {code}
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