[jira] [Commented] (SPARK-21367) R older version of Roxygen2 on Jenkins
[ https://issues.apache.org/jira/browse/SPARK-21367?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel=16838771#comment-16838771 ] Dongjoon Hyun commented on SPARK-21367: --- Thank you, [~shaneknapp]! > R older version of Roxygen2 on Jenkins > -- > > Key: SPARK-21367 > URL: https://issues.apache.org/jira/browse/SPARK-21367 > Project: Spark > Issue Type: Bug > Components: SparkR >Affects Versions: 2.3.0 >Reporter: Felix Cheung >Assignee: shane knapp >Priority: Major > Attachments: R.paks > > > Getting this message from a recent build. > https://amplab.cs.berkeley.edu/jenkins/job/SparkPullRequestBuilder/79461/console > Warning messages: > 1: In check_dep_version(pkg, version, compare) : > Need roxygen2 >= 5.0.0 but loaded version is 4.1.1 > 2: In check_dep_version(pkg, version, compare) : > Need roxygen2 >= 5.0.0 but loaded version is 4.1.1 > * installing *source* package 'SparkR' ... > ** R > We have been running with 5.0.1 and haven't changed for a year. > NOTE: Roxygen 6.x has some big changes and IMO we should not move to that yet. -- This message was sent by Atlassian JIRA (v7.6.3#76005) - To unsubscribe, e-mail: issues-unsubscr...@spark.apache.org For additional commands, e-mail: issues-h...@spark.apache.org
[jira] [Commented] (SPARK-21367) R older version of Roxygen2 on Jenkins
[ https://issues.apache.org/jira/browse/SPARK-21367?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel=16838188#comment-16838188 ] Felix Cheung commented on SPARK-21367: -- great thx! > R older version of Roxygen2 on Jenkins > -- > > Key: SPARK-21367 > URL: https://issues.apache.org/jira/browse/SPARK-21367 > Project: Spark > Issue Type: Bug > Components: SparkR >Affects Versions: 2.3.0 >Reporter: Felix Cheung >Assignee: shane knapp >Priority: Major > Attachments: R.paks > > > Getting this message from a recent build. > https://amplab.cs.berkeley.edu/jenkins/job/SparkPullRequestBuilder/79461/console > Warning messages: > 1: In check_dep_version(pkg, version, compare) : > Need roxygen2 >= 5.0.0 but loaded version is 4.1.1 > 2: In check_dep_version(pkg, version, compare) : > Need roxygen2 >= 5.0.0 but loaded version is 4.1.1 > * installing *source* package 'SparkR' ... > ** R > We have been running with 5.0.1 and haven't changed for a year. > NOTE: Roxygen 6.x has some big changes and IMO we should not move to that yet. -- This message was sent by Atlassian JIRA (v7.6.3#76005) - To unsubscribe, e-mail: issues-unsubscr...@spark.apache.org For additional commands, e-mail: issues-h...@spark.apache.org
[jira] [Commented] (SPARK-21367) R older version of Roxygen2 on Jenkins
[
https://issues.apache.org/jira/browse/SPARK-21367?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel=16837440#comment-16837440
]
shane knapp commented on SPARK-21367:
-
after deciding to clear out my JIRA queue this morning, i found this unresolved
ticket and just installed roxygen2 from source on all of the jenkins workers:
{noformat}
$ pssh -h jenkins_workers.txt -i "/home/eecs/sknapp/r-wtf.sh"
[1] 09:54:30 [SUCCESS] amp-jenkins-worker-02
[1] ‘5.0.1’
[2] 09:54:30 [SUCCESS] amp-jenkins-worker-05
[1] ‘5.0.1’
[3] 09:54:30 [SUCCESS] amp-jenkins-worker-06
[1] ‘5.0.1’
[4] 09:54:30 [SUCCESS] amp-jenkins-worker-04
[1] ‘5.0.1’
[5] 09:54:31 [SUCCESS] amp-jenkins-worker-03
[1] ‘5.0.1’
[6] 09:54:31 [SUCCESS] amp-jenkins-worker-01
[1] ‘5.0.1’
{noformat}
> R older version of Roxygen2 on Jenkins
> --
>
> Key: SPARK-21367
> URL: https://issues.apache.org/jira/browse/SPARK-21367
> Project: Spark
> Issue Type: Bug
> Components: SparkR
>Affects Versions: 2.3.0
>Reporter: Felix Cheung
>Assignee: shane knapp
>Priority: Major
> Attachments: R.paks
>
>
> Getting this message from a recent build.
> https://amplab.cs.berkeley.edu/jenkins/job/SparkPullRequestBuilder/79461/console
> Warning messages:
> 1: In check_dep_version(pkg, version, compare) :
> Need roxygen2 >= 5.0.0 but loaded version is 4.1.1
> 2: In check_dep_version(pkg, version, compare) :
> Need roxygen2 >= 5.0.0 but loaded version is 4.1.1
> * installing *source* package 'SparkR' ...
> ** R
> We have been running with 5.0.1 and haven't changed for a year.
> NOTE: Roxygen 6.x has some big changes and IMO we should not move to that yet.
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[jira] [Commented] (SPARK-21367) R older version of Roxygen2 on Jenkins
[ https://issues.apache.org/jira/browse/SPARK-21367?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel=16113145#comment-16113145 ] Felix Cheung commented on SPARK-21367: -- still seeing it Warning messages: 1: In check_dep_version(pkg, version, compare) : Need roxygen2 >= 5.0.0 but loaded version is 4.1.1 2: In check_dep_version(pkg, version, compare) : Need roxygen2 >= 5.0.0 but loaded version is 4.1.1 * installing *source* package 'SparkR' ... https://amplab.cs.berkeley.edu/jenkins/job/SparkPullRequestBuilder/80213/console > R older version of Roxygen2 on Jenkins > -- > > Key: SPARK-21367 > URL: https://issues.apache.org/jira/browse/SPARK-21367 > Project: Spark > Issue Type: Bug > Components: SparkR >Affects Versions: 2.3.0 >Reporter: Felix Cheung >Assignee: shane knapp > Attachments: R.paks > > > Getting this message from a recent build. > https://amplab.cs.berkeley.edu/jenkins/job/SparkPullRequestBuilder/79461/console > Warning messages: > 1: In check_dep_version(pkg, version, compare) : > Need roxygen2 >= 5.0.0 but loaded version is 4.1.1 > 2: In check_dep_version(pkg, version, compare) : > Need roxygen2 >= 5.0.0 but loaded version is 4.1.1 > * installing *source* package 'SparkR' ... > ** R > We have been running with 5.0.1 and haven't changed for a year. > NOTE: Roxygen 6.x has some big changes and IMO we should not move to that yet. -- This message was sent by Atlassian JIRA (v6.4.14#64029) - To unsubscribe, e-mail: issues-unsubscr...@spark.apache.org For additional commands, e-mail: issues-h...@spark.apache.org
[jira] [Commented] (SPARK-21367) R older version of Roxygen2 on Jenkins
[
https://issues.apache.org/jira/browse/SPARK-21367?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel=16082757#comment-16082757
]
shane knapp commented on SPARK-21367:
-
here's what version of knitr is installed:
{noformat}
knitr"knitr""/usr/lib64/R/library" "1.16" NA
knitr"R (>= 3.1.0)"
knitr"evaluate (>= 0.10), digest, highr, markdown, stringr (>=
0.6),\nyaml, methods, tools"
{noformat}
> R older version of Roxygen2 on Jenkins
> --
>
> Key: SPARK-21367
> URL: https://issues.apache.org/jira/browse/SPARK-21367
> Project: Spark
> Issue Type: Bug
> Components: SparkR
>Affects Versions: 2.3.0
>Reporter: Felix Cheung
>Assignee: shane knapp
> Attachments: R.paks
>
>
> Getting this message from a recent build.
> https://amplab.cs.berkeley.edu/jenkins/job/SparkPullRequestBuilder/79461/console
> Warning messages:
> 1: In check_dep_version(pkg, version, compare) :
> Need roxygen2 >= 5.0.0 but loaded version is 4.1.1
> 2: In check_dep_version(pkg, version, compare) :
> Need roxygen2 >= 5.0.0 but loaded version is 4.1.1
> * installing *source* package 'SparkR' ...
> ** R
> We have been running with 5.0.1 and haven't changed for a year.
> NOTE: Roxygen 6.x has some big changes and IMO we should not move to that yet.
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[jira] [Commented] (SPARK-21367) R older version of Roxygen2 on Jenkins
[
https://issues.apache.org/jira/browse/SPARK-21367?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel=16082780#comment-16082780
]
shane knapp commented on SPARK-21367:
-
[~shivaram] that error code 1 is grep failing to find anything matching pandoc
in /var/log/yum.log (meaning pandoc and pandoc-citeproc weren't updating when i
did the system update).
here are the versions we have installed:
{noformat}
[root@amp-jenkins-worker-05 R]# rpm -qa | grep pandoc
pandoc-citeproc-0.9.1.1-1.el6.x86_64
pandoc-1.17.0.3-1.el6.x86_64
{noformat}
> R older version of Roxygen2 on Jenkins
> --
>
> Key: SPARK-21367
> URL: https://issues.apache.org/jira/browse/SPARK-21367
> Project: Spark
> Issue Type: Bug
> Components: SparkR
>Affects Versions: 2.3.0
>Reporter: Felix Cheung
>Assignee: shane knapp
> Attachments: R.paks
>
>
> Getting this message from a recent build.
> https://amplab.cs.berkeley.edu/jenkins/job/SparkPullRequestBuilder/79461/console
> Warning messages:
> 1: In check_dep_version(pkg, version, compare) :
> Need roxygen2 >= 5.0.0 but loaded version is 4.1.1
> 2: In check_dep_version(pkg, version, compare) :
> Need roxygen2 >= 5.0.0 but loaded version is 4.1.1
> * installing *source* package 'SparkR' ...
> ** R
> We have been running with 5.0.1 and haven't changed for a year.
> NOTE: Roxygen 6.x has some big changes and IMO we should not move to that yet.
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[jira] [Commented] (SPARK-21367) R older version of Roxygen2 on Jenkins
[ https://issues.apache.org/jira/browse/SPARK-21367?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel=16082775#comment-16082775 ] Shivaram Venkataraman commented on SPARK-21367: --- Is there anyway to get more info on the pandoc error ? I think that is the root cause of the problem - Error code 1 does not seem to show up anything useful in searches > R older version of Roxygen2 on Jenkins > -- > > Key: SPARK-21367 > URL: https://issues.apache.org/jira/browse/SPARK-21367 > Project: Spark > Issue Type: Bug > Components: SparkR >Affects Versions: 2.3.0 >Reporter: Felix Cheung >Assignee: shane knapp > Attachments: R.paks > > > Getting this message from a recent build. > https://amplab.cs.berkeley.edu/jenkins/job/SparkPullRequestBuilder/79461/console > Warning messages: > 1: In check_dep_version(pkg, version, compare) : > Need roxygen2 >= 5.0.0 but loaded version is 4.1.1 > 2: In check_dep_version(pkg, version, compare) : > Need roxygen2 >= 5.0.0 but loaded version is 4.1.1 > * installing *source* package 'SparkR' ... > ** R > We have been running with 5.0.1 and haven't changed for a year. > NOTE: Roxygen 6.x has some big changes and IMO we should not move to that yet. -- This message was sent by Atlassian JIRA (v6.4.14#64029) - To unsubscribe, e-mail: issues-unsubscr...@spark.apache.org For additional commands, e-mail: issues-h...@spark.apache.org
[jira] [Commented] (SPARK-21367) R older version of Roxygen2 on Jenkins
[
https://issues.apache.org/jira/browse/SPARK-21367?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel=16082741#comment-16082741
]
shane knapp commented on SPARK-21367:
-
here's what we install during server setup:
{noformat}
Rscript -e 'install.packages("digest", repos="http://cran.stat.ucla.edu/;)'
Rscript -e 'install.packages("testthat", repos="http://cran.stat.ucla.edu/;)'
Rscript -e 'install.packages("knitr", repos="http://cran.stat.ucla.edu/;)'
Rscript -e 'install.packages("devtools", repos="http://cran.stat.ucla.edu/;)'
Rscript -e 'devtools::install_github("jimhester/lintr")'
Rscript -e 'install.packages("e1071", repos="http://cran.stat.ucla.edu/;)'
Rscript -e 'install.packages("rmarkdown", repos="http://cran.stat.ucla.edu/;)'
$YUM pandoc
$YUM pandoc-citeproc
{noformat}
note: pandoc and pandoc-citeproc were installed via yum, but did not get
updated on june 20th.
{noformat}
$ pssh -h jenkins_workers.txt -i -t 0 "grep pandoc /var/log/yum.log"
[1] 11:43:49 [FAILURE] amp-jenkins-worker-04 Exited with error code 1
[2] 11:43:49 [FAILURE] amp-jenkins-worker-05 Exited with error code 1
[3] 11:43:49 [FAILURE] amp-jenkins-worker-07 Exited with error code 1
[4] 11:43:49 [FAILURE] amp-jenkins-worker-03 Exited with error code 1
[5] 11:43:49 [FAILURE] amp-jenkins-worker-06 Exited with error code 1
[6] 11:43:49 [FAILURE] amp-jenkins-worker-02 Exited with error code 1
[7] 11:43:49 [FAILURE] amp-jenkins-worker-08 Exited with error code 1
[8] 11:43:50 [FAILURE] amp-jenkins-worker-01 Exited with error code 1
{noformat}
> R older version of Roxygen2 on Jenkins
> --
>
> Key: SPARK-21367
> URL: https://issues.apache.org/jira/browse/SPARK-21367
> Project: Spark
> Issue Type: Bug
> Components: SparkR
>Affects Versions: 2.3.0
>Reporter: Felix Cheung
>Assignee: shane knapp
> Attachments: R.paks
>
>
> Getting this message from a recent build.
> https://amplab.cs.berkeley.edu/jenkins/job/SparkPullRequestBuilder/79461/console
> Warning messages:
> 1: In check_dep_version(pkg, version, compare) :
> Need roxygen2 >= 5.0.0 but loaded version is 4.1.1
> 2: In check_dep_version(pkg, version, compare) :
> Need roxygen2 >= 5.0.0 but loaded version is 4.1.1
> * installing *source* package 'SparkR' ...
> ** R
> We have been running with 5.0.1 and haven't changed for a year.
> NOTE: Roxygen 6.x has some big changes and IMO we should not move to that yet.
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[jira] [Commented] (SPARK-21367) R older version of Roxygen2 on Jenkins
[ https://issues.apache.org/jira/browse/SPARK-21367?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel=16082708#comment-16082708 ] Shivaram Venkataraman commented on SPARK-21367: --- >From [~felixcheung]'s earlier parsing of the error messages, my guess is that >the knitr package probably has some issues working with roxygen2 5.0.0 ? In >other words I wonder if the problem is caused due to incompatible versions >across packages. [~shaneknapp] Could you list down all the versions of packages installed right now on Jenkins ? We can then try to use that and see if we can piece together why this problem comes up > R older version of Roxygen2 on Jenkins > -- > > Key: SPARK-21367 > URL: https://issues.apache.org/jira/browse/SPARK-21367 > Project: Spark > Issue Type: Bug > Components: SparkR >Affects Versions: 2.3.0 >Reporter: Felix Cheung >Assignee: shane knapp > > Getting this message from a recent build. > https://amplab.cs.berkeley.edu/jenkins/job/SparkPullRequestBuilder/79461/console > Warning messages: > 1: In check_dep_version(pkg, version, compare) : > Need roxygen2 >= 5.0.0 but loaded version is 4.1.1 > 2: In check_dep_version(pkg, version, compare) : > Need roxygen2 >= 5.0.0 but loaded version is 4.1.1 > * installing *source* package 'SparkR' ... > ** R > We have been running with 5.0.1 and haven't changed for a year. > NOTE: Roxygen 6.x has some big changes and IMO we should not move to that yet. -- This message was sent by Atlassian JIRA (v6.4.14#64029) - To unsubscribe, e-mail: issues-unsubscr...@spark.apache.org For additional commands, e-mail: issues-h...@spark.apache.org
[jira] [Commented] (SPARK-21367) R older version of Roxygen2 on Jenkins
[ https://issues.apache.org/jira/browse/SPARK-21367?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel=16082692#comment-16082692 ] Felix Cheung commented on SPARK-21367: -- *SOMETIMES*? :) > R older version of Roxygen2 on Jenkins > -- > > Key: SPARK-21367 > URL: https://issues.apache.org/jira/browse/SPARK-21367 > Project: Spark > Issue Type: Bug > Components: SparkR >Affects Versions: 2.3.0 >Reporter: Felix Cheung >Assignee: shane knapp > > Getting this message from a recent build. > https://amplab.cs.berkeley.edu/jenkins/job/SparkPullRequestBuilder/79461/console > Warning messages: > 1: In check_dep_version(pkg, version, compare) : > Need roxygen2 >= 5.0.0 but loaded version is 4.1.1 > 2: In check_dep_version(pkg, version, compare) : > Need roxygen2 >= 5.0.0 but loaded version is 4.1.1 > * installing *source* package 'SparkR' ... > ** R > We have been running with 5.0.1 and haven't changed for a year. > NOTE: Roxygen 6.x has some big changes and IMO we should not move to that yet. -- This message was sent by Atlassian JIRA (v6.4.14#64029) - To unsubscribe, e-mail: issues-unsubscr...@spark.apache.org For additional commands, e-mail: issues-h...@spark.apache.org
[jira] [Commented] (SPARK-21367) R older version of Roxygen2 on Jenkins
[ https://issues.apache.org/jira/browse/SPARK-21367?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel=16082661#comment-16082661 ] shane knapp commented on SPARK-21367: - ok, so i dug through the old build logs and the warning started happening during the R version rollback that happened on june 20th. here's the first build that had the warning in it: https://amplab.cs.berkeley.edu/jenkins/job/SparkPullRequestBuilder/78353/ note the timing: - R accidentally upgraded @ ~7am june 20th - no warnings between ~7am and ~9pm - we started getting the Roxygen2 warnings @ ~9pm (the build linked above) - i rolled back R ~9pm (about the same time) here's what i rolled back: libRmath-devel-3.1.1-7.el6.x86_64.rpm R-core-3.1.1-7.el6.x86_64.rpm R-java-3.1.1-7.el6.x86_64.rpm R-3.1.1-7.el6.x86_64.rpm R-core-devel-3.1.1-7.el6.x86_64.rpm R-java-devel-3.1.1-7.el6.x86_64.rpm libRmath-3.1.1-7.el6.x86_64.rpm R-devel-3.1.1-7.el6.x86_64.rpm sadly, all the logs from the build failures yesterday are gone, so i'll see if i can reproduce locally on another centos box set up the same way... and since i will need to deploy this box from scratch, it'll take a couple of hours. Y R BUILDS SOMETIMES SO HARD? > R older version of Roxygen2 on Jenkins > -- > > Key: SPARK-21367 > URL: https://issues.apache.org/jira/browse/SPARK-21367 > Project: Spark > Issue Type: Bug > Components: SparkR >Affects Versions: 2.3.0 >Reporter: Felix Cheung >Assignee: shane knapp > > Getting this message from a recent build. > https://amplab.cs.berkeley.edu/jenkins/job/SparkPullRequestBuilder/79461/console > Warning messages: > 1: In check_dep_version(pkg, version, compare) : > Need roxygen2 >= 5.0.0 but loaded version is 4.1.1 > 2: In check_dep_version(pkg, version, compare) : > Need roxygen2 >= 5.0.0 but loaded version is 4.1.1 > * installing *source* package 'SparkR' ... > ** R > We have been running with 5.0.1 and haven't changed for a year. > NOTE: Roxygen 6.x has some big changes and IMO we should not move to that yet. -- This message was sent by Atlassian JIRA (v6.4.14#64029) - To unsubscribe, e-mail: issues-unsubscr...@spark.apache.org For additional commands, e-mail: issues-h...@spark.apache.org
[jira] [Commented] (SPARK-21367) R older version of Roxygen2 on Jenkins
[
https://issues.apache.org/jira/browse/SPARK-21367?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel=16081744#comment-16081744
]
Felix Cheung commented on SPARK-21367:
--
I think I found the first error, it's one build before the build failures
listed above, 79470
https://amplab.cs.berkeley.edu/jenkins/job/SparkPullRequestBuilder/79470/console
{code}
Updating roxygen version in
/home/jenkins/workspace/SparkPullRequestBuilder/R/pkg/DESCRIPTION
Deleting AFTSurvivalRegressionModel-class.Rd
Deleting ALSModel-class.Rd
...
There were 50 or more warnings (use warnings() to see the first 50)
{code}
> R older version of Roxygen2 on Jenkins
> --
>
> Key: SPARK-21367
> URL: https://issues.apache.org/jira/browse/SPARK-21367
> Project: Spark
> Issue Type: Bug
> Components: SparkR
>Affects Versions: 2.3.0
>Reporter: Felix Cheung
>Assignee: shane knapp
>
> Getting this message from a recent build.
> https://amplab.cs.berkeley.edu/jenkins/job/SparkPullRequestBuilder/79461/console
> Warning messages:
> 1: In check_dep_version(pkg, version, compare) :
> Need roxygen2 >= 5.0.0 but loaded version is 4.1.1
> 2: In check_dep_version(pkg, version, compare) :
> Need roxygen2 >= 5.0.0 but loaded version is 4.1.1
> * installing *source* package 'SparkR' ...
> ** R
> We have been running with 5.0.1 and haven't changed for a year.
> NOTE: Roxygen 6.x has some big changes and IMO we should not move to that yet.
--
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[jira] [Commented] (SPARK-21367) R older version of Roxygen2 on Jenkins
[ https://issues.apache.org/jira/browse/SPARK-21367?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel=16081723#comment-16081723 ] Felix Cheung commented on SPARK-21367: -- And I'm pretty sure we should build with Roxygen2 5.0.1 https://github.com/apache/spark/blob/master/R/pkg/DESCRIPTION#L60 RoxygenNote: 5.0.1 > R older version of Roxygen2 on Jenkins > -- > > Key: SPARK-21367 > URL: https://issues.apache.org/jira/browse/SPARK-21367 > Project: Spark > Issue Type: Bug > Components: SparkR >Affects Versions: 2.3.0 >Reporter: Felix Cheung >Assignee: shane knapp > > Getting this message from a recent build. > https://amplab.cs.berkeley.edu/jenkins/job/SparkPullRequestBuilder/79461/console > Warning messages: > 1: In check_dep_version(pkg, version, compare) : > Need roxygen2 >= 5.0.0 but loaded version is 4.1.1 > 2: In check_dep_version(pkg, version, compare) : > Need roxygen2 >= 5.0.0 but loaded version is 4.1.1 > * installing *source* package 'SparkR' ... > ** R > We have been running with 5.0.1 and haven't changed for a year. > NOTE: Roxygen 6.x has some big changes and IMO we should not move to that yet. -- This message was sent by Atlassian JIRA (v6.4.14#64029) - To unsubscribe, e-mail: issues-unsubscr...@spark.apache.org For additional commands, e-mail: issues-h...@spark.apache.org
[jira] [Commented] (SPARK-21367) R older version of Roxygen2 on Jenkins
[ https://issues.apache.org/jira/browse/SPARK-21367?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel=16081720#comment-16081720 ] Felix Cheung commented on SPARK-21367: -- I'm not sure exactly why yet, but comparing the working and non-working buid working: First time using roxygen2 4.0. Upgrading automatically... Writing SparkDataFrame.Rd Writing printSchema.Rd Writing schema.Rd Writing explain.Rd ... Warning messages: 1: In check_dep_version(pkg, version, compare) : Need roxygen2 >= 5.0.0 but loaded version is 4.1.1 2: In check_dep_version(pkg, version, compare) : Need roxygen2 >= 5.0.0 but loaded version is 4.1.1 * installing *source* package 'SparkR' ... not working: First time using roxygen2 4.0. Upgrading automatically... There were 50 or more warnings (use warnings() to see the first 50) * installing *source* package 'SparkR' ... Bascially, the .Rd files are not getting created (because of warnings that are not captured) That cause the CRAN check to fail with "checking for missing documentation entries ... WARNING Undocumented code objects: '%<=>%' 'add_months' 'agg' 'approxCountDistinc" (which would be to be expected) As explained in the description above, I"m pretty sure these are not in the build a while ago " Warning messages: 1: In check_dep_version(pkg, version, compare) : Need roxygen2 >= 5.0.0 but loaded version is 4.1.1 " > R older version of Roxygen2 on Jenkins > -- > > Key: SPARK-21367 > URL: https://issues.apache.org/jira/browse/SPARK-21367 > Project: Spark > Issue Type: Bug > Components: SparkR >Affects Versions: 2.3.0 >Reporter: Felix Cheung >Assignee: shane knapp > > Getting this message from a recent build. > https://amplab.cs.berkeley.edu/jenkins/job/SparkPullRequestBuilder/79461/console > Warning messages: > 1: In check_dep_version(pkg, version, compare) : > Need roxygen2 >= 5.0.0 but loaded version is 4.1.1 > 2: In check_dep_version(pkg, version, compare) : > Need roxygen2 >= 5.0.0 but loaded version is 4.1.1 > * installing *source* package 'SparkR' ... > ** R > We have been running with 5.0.1 and haven't changed for a year. > NOTE: Roxygen 6.x has some big changes and IMO we should not move to that yet. -- This message was sent by Atlassian JIRA (v6.4.14#64029) - To unsubscribe, e-mail: issues-unsubscr...@spark.apache.org For additional commands, e-mail: issues-h...@spark.apache.org
[jira] [Commented] (SPARK-21367) R older version of Roxygen2 on Jenkins
[ https://issues.apache.org/jira/browse/SPARK-21367?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel=16081712#comment-16081712 ] Felix Cheung commented on SPARK-21367: -- it looks like instead of 5.x, the older 4.0 is being loaded? First time using roxygen2 4.0. Upgrading automatically... > R older version of Roxygen2 on Jenkins > -- > > Key: SPARK-21367 > URL: https://issues.apache.org/jira/browse/SPARK-21367 > Project: Spark > Issue Type: Bug > Components: SparkR >Affects Versions: 2.3.0 >Reporter: Felix Cheung >Assignee: shane knapp > > Getting this message from a recent build. > https://amplab.cs.berkeley.edu/jenkins/job/SparkPullRequestBuilder/79461/console > Warning messages: > 1: In check_dep_version(pkg, version, compare) : > Need roxygen2 >= 5.0.0 but loaded version is 4.1.1 > 2: In check_dep_version(pkg, version, compare) : > Need roxygen2 >= 5.0.0 but loaded version is 4.1.1 > * installing *source* package 'SparkR' ... > ** R > We have been running with 5.0.1 and haven't changed for a year. > NOTE: Roxygen 6.x has some big changes and IMO we should not move to that yet. -- This message was sent by Atlassian JIRA (v6.4.14#64029) - To unsubscribe, e-mail: issues-unsubscr...@spark.apache.org For additional commands, e-mail: issues-h...@spark.apache.org
[jira] [Commented] (SPARK-21367) R older version of Roxygen2 on Jenkins
[ https://issues.apache.org/jira/browse/SPARK-21367?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel=16081206#comment-16081206 ] shane knapp commented on SPARK-21367: - reverting now. > R older version of Roxygen2 on Jenkins > -- > > Key: SPARK-21367 > URL: https://issues.apache.org/jira/browse/SPARK-21367 > Project: Spark > Issue Type: Bug > Components: SparkR >Affects Versions: 2.3.0 >Reporter: Felix Cheung >Assignee: shane knapp > > Getting this message from a recent build. > https://amplab.cs.berkeley.edu/jenkins/job/SparkPullRequestBuilder/79461/console > Warning messages: > 1: In check_dep_version(pkg, version, compare) : > Need roxygen2 >= 5.0.0 but loaded version is 4.1.1 > 2: In check_dep_version(pkg, version, compare) : > Need roxygen2 >= 5.0.0 but loaded version is 4.1.1 > * installing *source* package 'SparkR' ... > ** R > We have been running with 5.0.1 and haven't changed for a year. > NOTE: Roxygen 6.x has some big changes and IMO we should not move to that yet. -- This message was sent by Atlassian JIRA (v6.4.14#64029) - To unsubscribe, e-mail: issues-unsubscr...@spark.apache.org For additional commands, e-mail: issues-h...@spark.apache.org
[jira] [Commented] (SPARK-21367) R older version of Roxygen2 on Jenkins
[ https://issues.apache.org/jira/browse/SPARK-21367?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel=16081274#comment-16081274 ] Dongjoon Hyun commented on SPARK-21367: --- Thank you, [~shaneknapp]. It seems to be `Had CRAN check errors; see logs.`. - https://amplab.cs.berkeley.edu/jenkins/view/Spark%20QA%20Test%20(Dashboard)/job/SparkPullRequestBuilder/79474/console - https://amplab.cs.berkeley.edu/jenkins/view/Spark%20QA%20Test%20(Dashboard)/job/SparkPullRequestBuilder/79473/console - https://amplab.cs.berkeley.edu/jenkins/view/Spark%20QA%20Test%20(Dashboard)/job/SparkPullRequestBuilder/79472/console - https://amplab.cs.berkeley.edu/jenkins/view/Spark%20QA%20Test%20(Dashboard)/job/SparkPullRequestBuilder/79471/console > R older version of Roxygen2 on Jenkins > -- > > Key: SPARK-21367 > URL: https://issues.apache.org/jira/browse/SPARK-21367 > Project: Spark > Issue Type: Bug > Components: SparkR >Affects Versions: 2.3.0 >Reporter: Felix Cheung >Assignee: shane knapp > > Getting this message from a recent build. > https://amplab.cs.berkeley.edu/jenkins/job/SparkPullRequestBuilder/79461/console > Warning messages: > 1: In check_dep_version(pkg, version, compare) : > Need roxygen2 >= 5.0.0 but loaded version is 4.1.1 > 2: In check_dep_version(pkg, version, compare) : > Need roxygen2 >= 5.0.0 but loaded version is 4.1.1 > * installing *source* package 'SparkR' ... > ** R > We have been running with 5.0.1 and haven't changed for a year. > NOTE: Roxygen 6.x has some big changes and IMO we should not move to that yet. -- This message was sent by Atlassian JIRA (v6.4.14#64029) - To unsubscribe, e-mail: issues-unsubscr...@spark.apache.org For additional commands, e-mail: issues-h...@spark.apache.org
[jira] [Commented] (SPARK-21367) R older version of Roxygen2 on Jenkins
[ https://issues.apache.org/jira/browse/SPARK-21367?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel=16081230#comment-16081230 ] shane knapp commented on SPARK-21367: - shiv: some of the builds that launched post-upgrade were showing a v4 version of roxygen2 being imported (from https://amplab.cs.berkeley.edu/jenkins/job/SparkPullRequestBuilder/79476/console) ```First time using roxygen2 4.0. Upgrading automatically...``` this build launched after the upgrade, so i'd rather roll back and un-break things and take a closer look in a little bit (i have an appt in ~30 mins). i'll check back later this afternoon and see if anything has turned up. > R older version of Roxygen2 on Jenkins > -- > > Key: SPARK-21367 > URL: https://issues.apache.org/jira/browse/SPARK-21367 > Project: Spark > Issue Type: Bug > Components: SparkR >Affects Versions: 2.3.0 >Reporter: Felix Cheung >Assignee: shane knapp > > Getting this message from a recent build. > https://amplab.cs.berkeley.edu/jenkins/job/SparkPullRequestBuilder/79461/console > Warning messages: > 1: In check_dep_version(pkg, version, compare) : > Need roxygen2 >= 5.0.0 but loaded version is 4.1.1 > 2: In check_dep_version(pkg, version, compare) : > Need roxygen2 >= 5.0.0 but loaded version is 4.1.1 > * installing *source* package 'SparkR' ... > ** R > We have been running with 5.0.1 and haven't changed for a year. > NOTE: Roxygen 6.x has some big changes and IMO we should not move to that yet. -- This message was sent by Atlassian JIRA (v6.4.14#64029) - To unsubscribe, e-mail: issues-unsubscr...@spark.apache.org For additional commands, e-mail: issues-h...@spark.apache.org
[jira] [Commented] (SPARK-21367) R older version of Roxygen2 on Jenkins
[ https://issues.apache.org/jira/browse/SPARK-21367?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel=16081226#comment-16081226 ] shane knapp commented on SPARK-21367: - ill take a closer look at this tomorrow. > R older version of Roxygen2 on Jenkins > -- > > Key: SPARK-21367 > URL: https://issues.apache.org/jira/browse/SPARK-21367 > Project: Spark > Issue Type: Bug > Components: SparkR >Affects Versions: 2.3.0 >Reporter: Felix Cheung >Assignee: shane knapp > > Getting this message from a recent build. > https://amplab.cs.berkeley.edu/jenkins/job/SparkPullRequestBuilder/79461/console > Warning messages: > 1: In check_dep_version(pkg, version, compare) : > Need roxygen2 >= 5.0.0 but loaded version is 4.1.1 > 2: In check_dep_version(pkg, version, compare) : > Need roxygen2 >= 5.0.0 but loaded version is 4.1.1 > * installing *source* package 'SparkR' ... > ** R > We have been running with 5.0.1 and haven't changed for a year. > NOTE: Roxygen 6.x has some big changes and IMO we should not move to that yet. -- This message was sent by Atlassian JIRA (v6.4.14#64029) - To unsubscribe, e-mail: issues-unsubscr...@spark.apache.org For additional commands, e-mail: issues-h...@spark.apache.org
[jira] [Commented] (SPARK-21367) R older version of Roxygen2 on Jenkins
[ https://issues.apache.org/jira/browse/SPARK-21367?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel=16081223#comment-16081223 ] Shivaram Venkataraman commented on SPARK-21367: --- [~dongjoon] Do you have a particular output file that we can use to debug ? > R older version of Roxygen2 on Jenkins > -- > > Key: SPARK-21367 > URL: https://issues.apache.org/jira/browse/SPARK-21367 > Project: Spark > Issue Type: Bug > Components: SparkR >Affects Versions: 2.3.0 >Reporter: Felix Cheung >Assignee: shane knapp > > Getting this message from a recent build. > https://amplab.cs.berkeley.edu/jenkins/job/SparkPullRequestBuilder/79461/console > Warning messages: > 1: In check_dep_version(pkg, version, compare) : > Need roxygen2 >= 5.0.0 but loaded version is 4.1.1 > 2: In check_dep_version(pkg, version, compare) : > Need roxygen2 >= 5.0.0 but loaded version is 4.1.1 > * installing *source* package 'SparkR' ... > ** R > We have been running with 5.0.1 and haven't changed for a year. > NOTE: Roxygen 6.x has some big changes and IMO we should not move to that yet. -- This message was sent by Atlassian JIRA (v6.4.14#64029) - To unsubscribe, e-mail: issues-unsubscr...@spark.apache.org For additional commands, e-mail: issues-h...@spark.apache.org
[jira] [Commented] (SPARK-21367) R older version of Roxygen2 on Jenkins
[ https://issues.apache.org/jira/browse/SPARK-21367?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel=16081220#comment-16081220 ] shane knapp commented on SPARK-21367: - reverted > R older version of Roxygen2 on Jenkins > -- > > Key: SPARK-21367 > URL: https://issues.apache.org/jira/browse/SPARK-21367 > Project: Spark > Issue Type: Bug > Components: SparkR >Affects Versions: 2.3.0 >Reporter: Felix Cheung >Assignee: shane knapp > > Getting this message from a recent build. > https://amplab.cs.berkeley.edu/jenkins/job/SparkPullRequestBuilder/79461/console > Warning messages: > 1: In check_dep_version(pkg, version, compare) : > Need roxygen2 >= 5.0.0 but loaded version is 4.1.1 > 2: In check_dep_version(pkg, version, compare) : > Need roxygen2 >= 5.0.0 but loaded version is 4.1.1 > * installing *source* package 'SparkR' ... > ** R > We have been running with 5.0.1 and haven't changed for a year. > NOTE: Roxygen 6.x has some big changes and IMO we should not move to that yet. -- This message was sent by Atlassian JIRA (v6.4.14#64029) - To unsubscribe, e-mail: issues-unsubscr...@spark.apache.org For additional commands, e-mail: issues-h...@spark.apache.org
[jira] [Commented] (SPARK-21367) R older version of Roxygen2 on Jenkins
[
https://issues.apache.org/jira/browse/SPARK-21367?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel=16081173#comment-16081173
]
Dongjoon Hyun commented on SPARK-21367:
---
Hi, All.
After this, many builds seems to fail consecutively.
{code}
This patch fails SparkR unit tests.
{code}
> R older version of Roxygen2 on Jenkins
> --
>
> Key: SPARK-21367
> URL: https://issues.apache.org/jira/browse/SPARK-21367
> Project: Spark
> Issue Type: Bug
> Components: SparkR
>Affects Versions: 2.3.0
>Reporter: Felix Cheung
>Assignee: shane knapp
>
> Getting this message from a recent build.
> https://amplab.cs.berkeley.edu/jenkins/job/SparkPullRequestBuilder/79461/console
> Warning messages:
> 1: In check_dep_version(pkg, version, compare) :
> Need roxygen2 >= 5.0.0 but loaded version is 4.1.1
> 2: In check_dep_version(pkg, version, compare) :
> Need roxygen2 >= 5.0.0 but loaded version is 4.1.1
> * installing *source* package 'SparkR' ...
> ** R
> We have been running with 5.0.1 and haven't changed for a year.
> NOTE: Roxygen 6.x has some big changes and IMO we should not move to that yet.
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[jira] [Commented] (SPARK-21367) R older version of Roxygen2 on Jenkins
[ https://issues.apache.org/jira/browse/SPARK-21367?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel=16080827#comment-16080827 ] shane knapp commented on SPARK-21367: - copy that. installing this version now... > R older version of Roxygen2 on Jenkins > -- > > Key: SPARK-21367 > URL: https://issues.apache.org/jira/browse/SPARK-21367 > Project: Spark > Issue Type: Bug > Components: SparkR >Affects Versions: 2.3.0 >Reporter: Felix Cheung > > Getting this message from a recent build. > https://amplab.cs.berkeley.edu/jenkins/job/SparkPullRequestBuilder/79461/console > Warning messages: > 1: In check_dep_version(pkg, version, compare) : > Need roxygen2 >= 5.0.0 but loaded version is 4.1.1 > 2: In check_dep_version(pkg, version, compare) : > Need roxygen2 >= 5.0.0 but loaded version is 4.1.1 > * installing *source* package 'SparkR' ... > ** R > We have been running with 5.0.1 and haven't changed for a year. > NOTE: Roxygen 6.x has some big changes and IMO we should not move to that yet. -- This message was sent by Atlassian JIRA (v6.4.14#64029) - To unsubscribe, e-mail: issues-unsubscr...@spark.apache.org For additional commands, e-mail: issues-h...@spark.apache.org
[jira] [Commented] (SPARK-21367) R older version of Roxygen2 on Jenkins
[ https://issues.apache.org/jira/browse/SPARK-21367?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel=16080830#comment-16080830 ] shane knapp commented on SPARK-21367: - ...and this is done. > R older version of Roxygen2 on Jenkins > -- > > Key: SPARK-21367 > URL: https://issues.apache.org/jira/browse/SPARK-21367 > Project: Spark > Issue Type: Bug > Components: SparkR >Affects Versions: 2.3.0 >Reporter: Felix Cheung > > Getting this message from a recent build. > https://amplab.cs.berkeley.edu/jenkins/job/SparkPullRequestBuilder/79461/console > Warning messages: > 1: In check_dep_version(pkg, version, compare) : > Need roxygen2 >= 5.0.0 but loaded version is 4.1.1 > 2: In check_dep_version(pkg, version, compare) : > Need roxygen2 >= 5.0.0 but loaded version is 4.1.1 > * installing *source* package 'SparkR' ... > ** R > We have been running with 5.0.1 and haven't changed for a year. > NOTE: Roxygen 6.x has some big changes and IMO we should not move to that yet. -- This message was sent by Atlassian JIRA (v6.4.14#64029) - To unsubscribe, e-mail: issues-unsubscr...@spark.apache.org For additional commands, e-mail: issues-h...@spark.apache.org
[jira] [Commented] (SPARK-21367) R older version of Roxygen2 on Jenkins
[ https://issues.apache.org/jira/browse/SPARK-21367?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel=16080826#comment-16080826 ] Shivaram Venkataraman commented on SPARK-21367: --- I just checked the transitive dependencies and I think it should be fine to manually install roxygen 5.0.0 > R older version of Roxygen2 on Jenkins > -- > > Key: SPARK-21367 > URL: https://issues.apache.org/jira/browse/SPARK-21367 > Project: Spark > Issue Type: Bug > Components: SparkR >Affects Versions: 2.3.0 >Reporter: Felix Cheung > > Getting this message from a recent build. > https://amplab.cs.berkeley.edu/jenkins/job/SparkPullRequestBuilder/79461/console > Warning messages: > 1: In check_dep_version(pkg, version, compare) : > Need roxygen2 >= 5.0.0 but loaded version is 4.1.1 > 2: In check_dep_version(pkg, version, compare) : > Need roxygen2 >= 5.0.0 but loaded version is 4.1.1 > * installing *source* package 'SparkR' ... > ** R > We have been running with 5.0.1 and haven't changed for a year. > NOTE: Roxygen 6.x has some big changes and IMO we should not move to that yet. -- This message was sent by Atlassian JIRA (v6.4.14#64029) - To unsubscribe, e-mail: issues-unsubscr...@spark.apache.org For additional commands, e-mail: issues-h...@spark.apache.org
[jira] [Commented] (SPARK-21367) R older version of Roxygen2 on Jenkins
[ https://issues.apache.org/jira/browse/SPARK-21367?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel=16080801#comment-16080801 ] shane knapp commented on SPARK-21367: - we haven't ever explicitly installed any version of Roxygen2, so whatever is there was installed via deps on other packages. that being said, i should be able to upgrade this to 5.0.0 pretty easily. let me check w/[~shivaram] before proceeding, however. > R older version of Roxygen2 on Jenkins > -- > > Key: SPARK-21367 > URL: https://issues.apache.org/jira/browse/SPARK-21367 > Project: Spark > Issue Type: Bug > Components: SparkR >Affects Versions: 2.3.0 >Reporter: Felix Cheung > > Getting this message from a recent build. > https://amplab.cs.berkeley.edu/jenkins/job/SparkPullRequestBuilder/79461/console > Warning messages: > 1: In check_dep_version(pkg, version, compare) : > Need roxygen2 >= 5.0.0 but loaded version is 4.1.1 > 2: In check_dep_version(pkg, version, compare) : > Need roxygen2 >= 5.0.0 but loaded version is 4.1.1 > * installing *source* package 'SparkR' ... > ** R > We have been running with 5.0.1 and haven't changed for a year. > NOTE: Roxygen 6.x has some big changes and IMO we should not move to that yet. -- This message was sent by Atlassian JIRA (v6.4.14#64029) - To unsubscribe, e-mail: issues-unsubscr...@spark.apache.org For additional commands, e-mail: issues-h...@spark.apache.org
[jira] [Commented] (SPARK-21367) R older version of Roxygen2 on Jenkins
[ https://issues.apache.org/jira/browse/SPARK-21367?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel=16080728#comment-16080728 ] Felix Cheung commented on SPARK-21367: -- @shane knapp could you check? thanks! > R older version of Roxygen2 on Jenkins > -- > > Key: SPARK-21367 > URL: https://issues.apache.org/jira/browse/SPARK-21367 > Project: Spark > Issue Type: Bug > Components: SparkR >Affects Versions: 2.3.0 >Reporter: Felix Cheung > > Getting this message from a recent build. > https://amplab.cs.berkeley.edu/jenkins/job/SparkPullRequestBuilder/79461/console > Warning messages: > 1: In check_dep_version(pkg, version, compare) : > Need roxygen2 >= 5.0.0 but loaded version is 4.1.1 > 2: In check_dep_version(pkg, version, compare) : > Need roxygen2 >= 5.0.0 but loaded version is 4.1.1 > * installing *source* package 'SparkR' ... > ** R > We have been running with 5.0.1 and haven't changed for a year. > NOTE: Roxygen 6.x has some big changes and IMO we should not move to that yet. -- This message was sent by Atlassian JIRA (v6.4.14#64029) - To unsubscribe, e-mail: issues-unsubscr...@spark.apache.org For additional commands, e-mail: issues-h...@spark.apache.org
