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Posted to issues@spark.apache.org by "Hyukjin Kwon (Jira)" <ji...@apache.org> on 2020/06/22 14:11:00 UTC
[jira] [Comment Edited] (SPARK-31918) SparkR CRAN check gives a
warning with R 4.0.0 on OSX
[ https://issues.apache.org/jira/browse/SPARK-31918?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel&focusedCommentId=17142073#comment-17142073 ]
Hyukjin Kwon edited comment on SPARK-31918 at 6/22/20, 2:10 PM:
----------------------------------------------------------------
It affects Spark 3.0 too, and seems failing with a different message in my local:
{code}
* creating vignettes ... ERROR
--- re-building ‘sparkr-vignettes.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Attaching package: 'SparkR'
The following objects are masked from 'package:stats':
cov, filter, lag, na.omit, predict, sd, var, window
The following objects are masked from 'package:base':
as.data.frame, colnames, colnames<-, drop, endsWith, intersect,
rank, rbind, sample, startsWith, subset, summary, transform, union
Picked up _JAVA_OPTIONS: -XX:-UsePerfData
Picked up _JAVA_OPTIONS: -XX:-UsePerfData
20/06/22 15:07:34 WARN NativeCodeLoader: Unable to load native-hadoop library for your platform... using builtin-java classes where applicable
Using Spark's default log4j profile: org/apache/spark/log4j-defaults.properties
Setting default log level to "WARN".
To adjust logging level use sc.setLogLevel(newLevel). For SparkR, use setLogLevel(newLevel).
[Stage 0:> (0 + 1) / 1]
20/06/22 15:07:43 ERROR Executor: Exception in task 0.0 in stage 0.0 (TID 0)
org.apache.spark.SparkException: R unexpectedly exited.
R worker produced errors: Error in lapply(part, FUN) : attempt to bind a variable to R_UnboundValue
{code}
Assuming the errors from R execution itself, the root cause might be same.
was (Author: hyukjin.kwon):
It affects Spark 3.0 too, and seems failing with a different message in my local:
{code}
* creating vignettes ... ERROR
--- re-building ‘sparkr-vignettes.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Attaching package: 'SparkR'
The following objects are masked from 'package:stats':
cov, filter, lag, na.omit, predict, sd, var, window
The following objects are masked from 'package:base':
as.data.frame, colnames, colnames<-, drop, endsWith, intersect,
rank, rbind, sample, startsWith, subset, summary, transform, union
Picked up _JAVA_OPTIONS: -XX:-UsePerfData
Picked up _JAVA_OPTIONS: -XX:-UsePerfData
20/06/22 15:07:34 WARN NativeCodeLoader: Unable to load native-hadoop library for your platform... using builtin-java classes where applicable
Using Spark's default log4j profile: org/apache/spark/log4j-defaults.properties
Setting default log level to "WARN".
To adjust logging level use sc.setLogLevel(newLevel). For SparkR, use setLogLevel(newLevel).
[Stage 0:> (0 + 1) / 1]
20/06/22 15:07:43 ERROR Executor: Exception in task 0.0 in stage 0.0 (TID 0)
org.apache.spark.SparkException: R unexpectedly exited.
{code}
Assuming the errors from R execution itself, the root cause might be same.
> SparkR CRAN check gives a warning with R 4.0.0 on OSX
> -----------------------------------------------------
>
> Key: SPARK-31918
> URL: https://issues.apache.org/jira/browse/SPARK-31918
> Project: Spark
> Issue Type: Bug
> Components: SparkR
> Affects Versions: 2.4.6, 3.0.0
> Reporter: Shivaram Venkataraman
> Priority: Major
>
> When the SparkR package is run through a CRAN check (i.e. with something like R CMD check --as-cran ~/Downloads/SparkR_2.4.6.tar.gz), we rebuild the SparkR vignette as a part of the checks.
> However this seems to be failing with R 4.0.0 on OSX -- both on my local machine and on CRAN https://cran.r-project.org/web/checks/check_results_SparkR.html
> cc [~felixcheung]
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