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Posted to reviews@spark.apache.org by felixcheung <gi...@git.apache.org> on 2017/08/22 06:44:17 UTC
[GitHub] spark pull request #19016: [SPARK-21805] Disable R vignettes code on Windows
GitHub user felixcheung opened a pull request:
https://github.com/apache/spark/pull/19016
[SPARK-21805] Disable R vignettes code on Windows
## What changes were proposed in this pull request?
Code in vignettes requires winutils on windows to run, when publishing to CRAN or building from source, winutils might not be available, so it's better to disable code run (so resulting vigenttes will not have output from code, but text is still there and code is still there)
fix * checking re-building of vignette outputs ... WARNING
and
> %LOCALAPPDATA% not found. Please define the environment variable or restart and enter an installation path in localDir.
## How was this patch tested?
jenkins, appveyor, r-hub
before: https://artifacts.r-hub.io/SparkR_2.2.0.tar.gz-49cecef3bb09db1db130db31604e0293/SparkR.Rcheck/00check.log
after: https://artifacts.r-hub.io/SparkR_2.2.0.tar.gz-86a066c7576f46794930ad114e5cff7c/SparkR.Rcheck/00check.log
You can merge this pull request into a Git repository by running:
$ git pull https://github.com/felixcheung/spark rvigwind
Alternatively you can review and apply these changes as the patch at:
https://github.com/apache/spark/pull/19016.patch
To close this pull request, make a commit to your master/trunk branch
with (at least) the following in the commit message:
This closes #19016
----
commit ba65d6e7d5f503c1d5da4cc17586aed67e7955c3
Author: Felix Cheung <fe...@hotmail.com>
Date: 2017-08-06T22:52:59Z
disable eval on windows
commit 7c75073a0bbf9ef489244d58b678a8b2dda3c287
Author: Felix Cheung <fe...@hotmail.com>
Date: 2017-08-21T02:09:34Z
add support for no localappdata
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[GitHub] spark issue #19016: [SPARK-21805] Disable R vignettes code on Windows
Posted by SparkQA <gi...@git.apache.org>.
Github user SparkQA commented on the issue:
https://github.com/apache/spark/pull/19016
**[Test build #80965 has started](https://amplab.cs.berkeley.edu/jenkins/job/SparkPullRequestBuilder/80965/testReport)** for PR 19016 at commit [`7c75073`](https://github.com/apache/spark/commit/7c75073a0bbf9ef489244d58b678a8b2dda3c287).
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[GitHub] spark issue #19016: [SPARK-21805][SPARKR] Disable R vignettes code on Window...
Posted by AmplabJenkins <gi...@git.apache.org>.
Github user AmplabJenkins commented on the issue:
https://github.com/apache/spark/pull/19016
Merged build finished. Test FAILed.
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[GitHub] spark issue #19016: [SPARK-21805][SPARKR] Disable R vignettes code on Window...
Posted by shivaram <gi...@git.apache.org>.
Github user shivaram commented on the issue:
https://github.com/apache/spark/pull/19016
Sure - change LGTM. Lets see if @HyukjinKwon has any more comments ? If not we can merge to master, branch-2.2 and then do some more tests.
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[GitHub] spark issue #19016: [SPARK-21805][SPARKR] Disable R vignettes code on Window...
Posted by SparkQA <gi...@git.apache.org>.
Github user SparkQA commented on the issue:
https://github.com/apache/spark/pull/19016
**[Test build #80972 has finished](https://amplab.cs.berkeley.edu/jenkins/job/SparkPullRequestBuilder/80972/testReport)** for PR 19016 at commit [`7c75073`](https://github.com/apache/spark/commit/7c75073a0bbf9ef489244d58b678a8b2dda3c287).
* This patch passes all tests.
* This patch merges cleanly.
* This patch adds no public classes.
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[GitHub] spark issue #19016: [SPARK-21805][SPARKR] Disable R vignettes code on Window...
Posted by AmplabJenkins <gi...@git.apache.org>.
Github user AmplabJenkins commented on the issue:
https://github.com/apache/spark/pull/19016
Test FAILed.
Refer to this link for build results (access rights to CI server needed):
https://amplab.cs.berkeley.edu/jenkins//job/SparkPullRequestBuilder/80965/
Test FAILed.
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[GitHub] spark issue #19016: [SPARK-21805][SPARKR] Disable R vignettes code on Window...
Posted by felixcheung <gi...@git.apache.org>.
Github user felixcheung commented on the issue:
https://github.com/apache/spark/pull/19016
I think that is caused by the way I build the source package - I use the option --no-build-vignettes so the source package I test with doesn't have the PDF in it
Similarly for the failed test - I change the version to 2.2.0 to get it to run without setting the download URL and there is a change on the wrapper class parameter list.
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[GitHub] spark issue #19016: [SPARK-21805][SPARKR] Disable R vignettes code on Window...
Posted by felixcheung <gi...@git.apache.org>.
Github user felixcheung commented on the issue:
https://github.com/apache/spark/pull/19016
thanks, merged to master/2.2.
will check for nightly build from tonight.
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[GitHub] spark pull request #19016: [SPARK-21805][SPARKR] Disable R vignettes code on...
Posted by felixcheung <gi...@git.apache.org>.
Github user felixcheung closed the pull request at:
https://github.com/apache/spark/pull/19016
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[GitHub] spark issue #19016: [SPARK-21805][SPARKR] Disable R vignettes code on Window...
Posted by SparkQA <gi...@git.apache.org>.
Github user SparkQA commented on the issue:
https://github.com/apache/spark/pull/19016
**[Test build #80972 has started](https://amplab.cs.berkeley.edu/jenkins/job/SparkPullRequestBuilder/80972/testReport)** for PR 19016 at commit [`7c75073`](https://github.com/apache/spark/commit/7c75073a0bbf9ef489244d58b678a8b2dda3c287).
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[GitHub] spark issue #19016: [SPARK-21805][SPARKR] Disable R vignettes code on Window...
Posted by HyukjinKwon <gi...@git.apache.org>.
Github user HyukjinKwon commented on the issue:
https://github.com/apache/spark/pull/19016
Sure, I have no more comments and it looks good to me too.
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[GitHub] spark issue #19016: [SPARK-21805][SPARKR] Disable R vignettes code on Window...
Posted by SparkQA <gi...@git.apache.org>.
Github user SparkQA commented on the issue:
https://github.com/apache/spark/pull/19016
**[Test build #80965 has finished](https://amplab.cs.berkeley.edu/jenkins/job/SparkPullRequestBuilder/80965/testReport)** for PR 19016 at commit [`7c75073`](https://github.com/apache/spark/commit/7c75073a0bbf9ef489244d58b678a8b2dda3c287).
* This patch **fails due to an unknown error code, -9**.
* This patch merges cleanly.
* This patch adds no public classes.
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[GitHub] spark issue #19016: [SPARK-21805][SPARKR] Disable R vignettes code on Window...
Posted by shivaram <gi...@git.apache.org>.
Github user shivaram commented on the issue:
https://github.com/apache/spark/pull/19016
Ah I see. Yeah the failed tests makes sense. We can also try to submit a custom tar.gz to r-hub to test it with the PDF and a different version number ?
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[GitHub] spark issue #19016: [SPARK-21805][SPARKR] Disable R vignettes code on Window...
Posted by shivaram <gi...@git.apache.org>.
Github user shivaram commented on the issue:
https://github.com/apache/spark/pull/19016
Thats great ! I will also run this by winbuilder later today.
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[GitHub] spark issue #19016: [SPARK-21805][SPARKR] Disable R vignettes code on Window...
Posted by AmplabJenkins <gi...@git.apache.org>.
Github user AmplabJenkins commented on the issue:
https://github.com/apache/spark/pull/19016
Merged build finished. Test PASSed.
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[GitHub] spark issue #19016: [SPARK-21805][SPARKR] Disable R vignettes code on Window...
Posted by felixcheung <gi...@git.apache.org>.
Github user felixcheung commented on the issue:
https://github.com/apache/spark/pull/19016
what's with jenkins? looks like JIRA is not updated either...
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[GitHub] spark pull request #19016: [SPARK-21805][SPARKR] Disable R vignettes code on...
Posted by asfgit <gi...@git.apache.org>.
Github user asfgit closed the pull request at:
https://github.com/apache/spark/pull/19016
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[GitHub] spark issue #19016: [SPARK-21805][SPARKR] Disable R vignettes code on Window...
Posted by HyukjinKwon <gi...@git.apache.org>.
Github user HyukjinKwon commented on the issue:
https://github.com/apache/spark/pull/19016
retest this please
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[GitHub] spark issue #19016: [SPARK-21805][SPARKR] Disable R vignettes code on Window...
Posted by felixcheung <gi...@git.apache.org>.
Github user felixcheung commented on the issue:
https://github.com/apache/spark/pull/19016
It likely best to back port this to branch-2.2 so the test can pass with matching API in a released jar.
Then we can see everything passing (except having to hand edit the version number)
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[GitHub] spark pull request #19016: [SPARK-21805][SPARKR] Disable R vignettes code on...
Posted by felixcheung <gi...@git.apache.org>.
GitHub user felixcheung reopened a pull request:
https://github.com/apache/spark/pull/19016
[SPARK-21805][SPARKR] Disable R vignettes code on Windows
## What changes were proposed in this pull request?
Code in vignettes requires winutils on windows to run, when publishing to CRAN or building from source, winutils might not be available, so it's better to disable code run (so resulting vigenttes will not have output from code, but text is still there and code is still there)
fix * checking re-building of vignette outputs ... WARNING
and
> %LOCALAPPDATA% not found. Please define the environment variable or restart and enter an installation path in localDir.
## How was this patch tested?
jenkins, appveyor, r-hub
before: https://artifacts.r-hub.io/SparkR_2.2.0.tar.gz-49cecef3bb09db1db130db31604e0293/SparkR.Rcheck/00check.log
after: https://artifacts.r-hub.io/SparkR_2.2.0.tar.gz-86a066c7576f46794930ad114e5cff7c/SparkR.Rcheck/00check.log
You can merge this pull request into a Git repository by running:
$ git pull https://github.com/felixcheung/spark rvigwind
Alternatively you can review and apply these changes as the patch at:
https://github.com/apache/spark/pull/19016.patch
To close this pull request, make a commit to your master/trunk branch
with (at least) the following in the commit message:
This closes #19016
----
commit ba65d6e7d5f503c1d5da4cc17586aed67e7955c3
Author: Felix Cheung <fe...@hotmail.com>
Date: 2017-08-06T22:52:59Z
disable eval on windows
commit 7c75073a0bbf9ef489244d58b678a8b2dda3c287
Author: Felix Cheung <fe...@hotmail.com>
Date: 2017-08-21T02:09:34Z
add support for no localappdata
----
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[GitHub] spark issue #19016: [SPARK-21805][SPARKR] Disable R vignettes code on Window...
Posted by shivaram <gi...@git.apache.org>.
Github user shivaram commented on the issue:
https://github.com/apache/spark/pull/19016
Thanks @felixcheung ! Are the warnings about the missing PDF unavoidable ? I see something like
```
checking package vignettes in 'inst/doc' ... WARNING
Package vignette without corresponding PDF/HTML:
'sparkr-vignettes.Rmd'
```
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[GitHub] spark issue #19016: [SPARK-21805][SPARKR] Disable R vignettes code on Window...
Posted by SparkQA <gi...@git.apache.org>.
Github user SparkQA commented on the issue:
https://github.com/apache/spark/pull/19016
**[Test build #81040 has finished](https://amplab.cs.berkeley.edu/jenkins/job/SparkPullRequestBuilder/81040/testReport)** for PR 19016 at commit [`23f9d5e`](https://github.com/apache/spark/commit/23f9d5ec42b57d296d67353019b6fa5ea28a6ba6).
* This patch passes all tests.
* This patch merges cleanly.
* This patch adds no public classes.
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[GitHub] spark issue #19016: [SPARK-21805][SPARKR] Disable R vignettes code on Window...
Posted by AmplabJenkins <gi...@git.apache.org>.
Github user AmplabJenkins commented on the issue:
https://github.com/apache/spark/pull/19016
Test PASSed.
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[GitHub] spark issue #19016: [SPARK-21805][SPARKR] Disable R vignettes code on Window...
Posted by HyukjinKwon <gi...@git.apache.org>.
Github user HyukjinKwon commented on the issue:
https://github.com/apache/spark/pull/19016
Yes ... for JIRA linking problem, there are some information here - http://apache-spark-developers-list.1001551.n3.nabble.com/Some-PRs-not-automatically-linked-to-JIRAs-td22067.html just FYI. I think -9 has increased recently..
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[GitHub] spark pull request #19016: [SPARK-21805][SPARKR] Disable R vignettes code on...
Posted by shivaram <gi...@git.apache.org>.
Github user shivaram commented on a diff in the pull request:
https://github.com/apache/spark/pull/19016#discussion_r134815709
--- Diff: R/pkg/vignettes/sparkr-vignettes.Rmd ---
@@ -27,6 +27,17 @@ vignette: >
limitations under the License.
-->
+```{r setup, include=FALSE}
+library(knitr)
--- End diff --
Just to clarify, the opt_hooks is provided by knitr ?
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[GitHub] spark issue #19016: [SPARK-21805][SPARKR] Disable R vignettes code on Window...
Posted by AmplabJenkins <gi...@git.apache.org>.
Github user AmplabJenkins commented on the issue:
https://github.com/apache/spark/pull/19016
Test PASSed.
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[GitHub] spark issue #19016: [SPARK-21805][SPARKR] Disable R vignettes code on Window...
Posted by felixcheung <gi...@git.apache.org>.
Github user felixcheung commented on the issue:
https://github.com/apache/spark/pull/19016
I tested with the nightly, it passed
https://builder.r-hub.io/status/SparkR_2.2.0.tar.gz-fba296d2142edeb8bcdb082e311d8462
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[GitHub] spark issue #19016: [SPARK-21805][SPARKR] Disable R vignettes code on Window...
Posted by AmplabJenkins <gi...@git.apache.org>.
Github user AmplabJenkins commented on the issue:
https://github.com/apache/spark/pull/19016
Merged build finished. Test PASSed.
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[GitHub] spark issue #19016: [SPARK-21805][SPARKR] Disable R vignettes code on Window...
Posted by SparkQA <gi...@git.apache.org>.
Github user SparkQA commented on the issue:
https://github.com/apache/spark/pull/19016
**[Test build #81040 has started](https://amplab.cs.berkeley.edu/jenkins/job/SparkPullRequestBuilder/81040/testReport)** for PR 19016 at commit [`23f9d5e`](https://github.com/apache/spark/commit/23f9d5ec42b57d296d67353019b6fa5ea28a6ba6).
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[GitHub] spark pull request #19016: [SPARK-21805][SPARKR] Disable R vignettes code on...
Posted by felixcheung <gi...@git.apache.org>.
Github user felixcheung commented on a diff in the pull request:
https://github.com/apache/spark/pull/19016#discussion_r134816715
--- Diff: R/pkg/vignettes/sparkr-vignettes.Rmd ---
@@ -27,6 +27,17 @@ vignette: >
limitations under the License.
-->
+```{r setup, include=FALSE}
+library(knitr)
--- End diff --
yes!
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