[jira] [Commented] (SPARK-22344) Prevent R CMD check from using /tmp
[
https://issues.apache.org/jira/browse/SPARK-22344?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel=16238843#comment-16238843
]
Apache Spark commented on SPARK-22344:
--
User 'felixcheung' has created a pull request for this issue:
https://github.com/apache/spark/pull/19657
> Prevent R CMD check from using /tmp
> ---
>
> Key: SPARK-22344
> URL: https://issues.apache.org/jira/browse/SPARK-22344
> Project: Spark
> Issue Type: Bug
> Components: SparkR
>Affects Versions: 1.6.3, 2.1.2, 2.2.0, 2.3.0
>Reporter: Shivaram Venkataraman
>Priority: Major
>
> When R CMD check is run on the SparkR package it leaves behind files in /tmp
> which is a violation of CRAN policy. We should instead write to Rtmpdir.
> Notes from CRAN are below
> {code}
> Checking this leaves behind dirs
>hive/$USER
>$USER
> and files named like
>b4f6459b-0624-4100-8358-7aa7afbda757_resources
> in /tmp, in violation of the CRAN Policy.
> {code}
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[jira] [Commented] (SPARK-22344) Prevent R CMD check from using /tmp
[
https://issues.apache.org/jira/browse/SPARK-22344?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel=16236103#comment-16236103
]
Felix Cheung commented on SPARK-22344:
--
Yes to both. If SPARK_HOME is set before calling install.spark then we are not
installing it.
Boy it's getting complicated.
> Prevent R CMD check from using /tmp
> ---
>
> Key: SPARK-22344
> URL: https://issues.apache.org/jira/browse/SPARK-22344
> Project: Spark
> Issue Type: Bug
> Components: SparkR
>Affects Versions: 1.6.3, 2.1.2, 2.2.0, 2.3.0
>Reporter: Shivaram Venkataraman
>Priority: Major
>
> When R CMD check is run on the SparkR package it leaves behind files in /tmp
> which is a violation of CRAN policy. We should instead write to Rtmpdir.
> Notes from CRAN are below
> {code}
> Checking this leaves behind dirs
>hive/$USER
>$USER
> and files named like
>b4f6459b-0624-4100-8358-7aa7afbda757_resources
> in /tmp, in violation of the CRAN Policy.
> {code}
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[jira] [Commented] (SPARK-22344) Prevent R CMD check from using /tmp
[
https://issues.apache.org/jira/browse/SPARK-22344?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel=16234372#comment-16234372
]
Shivaram Venkataraman commented on SPARK-22344:
---
Right I was considering that - but everytime we run `check-cran.sh` in Jenkins
or locally we are running with `NOT_CRAN` false and `SPARK_HOME` set ?
> Prevent R CMD check from using /tmp
> ---
>
> Key: SPARK-22344
> URL: https://issues.apache.org/jira/browse/SPARK-22344
> Project: Spark
> Issue Type: Bug
> Components: SparkR
>Affects Versions: 1.6.3, 2.1.2, 2.2.0, 2.3.0
>Reporter: Shivaram Venkataraman
>Priority: Major
>
> When R CMD check is run on the SparkR package it leaves behind files in /tmp
> which is a violation of CRAN policy. We should instead write to Rtmpdir.
> Notes from CRAN are below
> {code}
> Checking this leaves behind dirs
>hive/$USER
>$USER
> and files named like
>b4f6459b-0624-4100-8358-7aa7afbda757_resources
> in /tmp, in violation of the CRAN Policy.
> {code}
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[jira] [Commented] (SPARK-22344) Prevent R CMD check from using /tmp
[
https://issues.apache.org/jira/browse/SPARK-22344?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel=16233762#comment-16233762
]
Felix Cheung commented on SPARK-22344:
--
Maybe just delete the directory returned from sparkCachePath() if NOT CRAN
false?
> Prevent R CMD check from using /tmp
> ---
>
> Key: SPARK-22344
> URL: https://issues.apache.org/jira/browse/SPARK-22344
> Project: Spark
> Issue Type: Bug
> Components: SparkR
>Affects Versions: 1.6.3, 2.1.2, 2.2.0, 2.3.0
>Reporter: Shivaram Venkataraman
>Priority: Major
>
> When R CMD check is run on the SparkR package it leaves behind files in /tmp
> which is a violation of CRAN policy. We should instead write to Rtmpdir.
> Notes from CRAN are below
> {code}
> Checking this leaves behind dirs
>hive/$USER
>$USER
> and files named like
>b4f6459b-0624-4100-8358-7aa7afbda757_resources
> in /tmp, in violation of the CRAN Policy.
> {code}
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[jira] [Commented] (SPARK-22344) Prevent R CMD check from using /tmp
[
https://issues.apache.org/jira/browse/SPARK-22344?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel=16233751#comment-16233751
]
Felix Cheung commented on SPARK-22344:
--
Hmm yes we do have to know if it has just found it, or downloaded it.
I guess the logic is fairly deep inside several call frames?
> Prevent R CMD check from using /tmp
> ---
>
> Key: SPARK-22344
> URL: https://issues.apache.org/jira/browse/SPARK-22344
> Project: Spark
> Issue Type: Bug
> Components: SparkR
>Affects Versions: 1.6.3, 2.1.2, 2.2.0, 2.3.0
>Reporter: Shivaram Venkataraman
>Priority: Major
>
> When R CMD check is run on the SparkR package it leaves behind files in /tmp
> which is a violation of CRAN policy. We should instead write to Rtmpdir.
> Notes from CRAN are below
> {code}
> Checking this leaves behind dirs
>hive/$USER
>$USER
> and files named like
>b4f6459b-0624-4100-8358-7aa7afbda757_resources
> in /tmp, in violation of the CRAN Policy.
> {code}
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[jira] [Commented] (SPARK-22344) Prevent R CMD check from using /tmp
[
https://issues.apache.org/jira/browse/SPARK-22344?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel=16233683#comment-16233683
]
Shivaram Venkataraman commented on SPARK-22344:
---
So I started working on this but this is a little non-trivial because if the
user had supplied a `SPARK_HOME` then we would end up deleting JARs from that
directory ?
> Prevent R CMD check from using /tmp
> ---
>
> Key: SPARK-22344
> URL: https://issues.apache.org/jira/browse/SPARK-22344
> Project: Spark
> Issue Type: Bug
> Components: SparkR
>Affects Versions: 1.6.3, 2.1.2, 2.2.0, 2.3.0
>Reporter: Shivaram Venkataraman
>Priority: Major
>
> When R CMD check is run on the SparkR package it leaves behind files in /tmp
> which is a violation of CRAN policy. We should instead write to Rtmpdir.
> Notes from CRAN are below
> {code}
> Checking this leaves behind dirs
>hive/$USER
>$USER
> and files named like
>b4f6459b-0624-4100-8358-7aa7afbda757_resources
> in /tmp, in violation of the CRAN Policy.
> {code}
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[jira] [Commented] (SPARK-22344) Prevent R CMD check from using /tmp
[
https://issues.apache.org/jira/browse/SPARK-22344?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel=16226197#comment-16226197
]
Felix Cheung commented on SPARK-22344:
--
Yes I think we should do just that. Might need to delete the parent .cache
directory also though.
> Prevent R CMD check from using /tmp
> ---
>
> Key: SPARK-22344
> URL: https://issues.apache.org/jira/browse/SPARK-22344
> Project: Spark
> Issue Type: Bug
> Components: SparkR
>Affects Versions: 1.6.3, 2.1.2, 2.2.0, 2.3.0
>Reporter: Shivaram Venkataraman
>
> When R CMD check is run on the SparkR package it leaves behind files in /tmp
> which is a violation of CRAN policy. We should instead write to Rtmpdir.
> Notes from CRAN are below
> {code}
> Checking this leaves behind dirs
>hive/$USER
>$USER
> and files named like
>b4f6459b-0624-4100-8358-7aa7afbda757_resources
> in /tmp, in violation of the CRAN Policy.
> {code}
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[jira] [Commented] (SPARK-22344) Prevent R CMD check from using /tmp
[
https://issues.apache.org/jira/browse/SPARK-22344?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel=16225924#comment-16225924
]
Shivaram Venkataraman commented on SPARK-22344:
---
To consider this narrow case of CRAN checks -- we explicitly call install.spark
from run-all.R and that returns the directory where it put Spark. So we could
just delete that returned value when we exit ?
> Prevent R CMD check from using /tmp
> ---
>
> Key: SPARK-22344
> URL: https://issues.apache.org/jira/browse/SPARK-22344
> Project: Spark
> Issue Type: Bug
> Components: SparkR
>Affects Versions: 1.6.3, 2.1.2, 2.2.0, 2.3.0
>Reporter: Shivaram Venkataraman
>
> When R CMD check is run on the SparkR package it leaves behind files in /tmp
> which is a violation of CRAN policy. We should instead write to Rtmpdir.
> Notes from CRAN are below
> {code}
> Checking this leaves behind dirs
>hive/$USER
>$USER
> and files named like
>b4f6459b-0624-4100-8358-7aa7afbda757_resources
> in /tmp, in violation of the CRAN Policy.
> {code}
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[jira] [Commented] (SPARK-22344) Prevent R CMD check from using /tmp
[
https://issues.apache.org/jira/browse/SPARK-22344?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel=16225770#comment-16225770
]
Felix Cheung commented on SPARK-22344:
--
Kinda. We have some alternate code paths and the packageName might not be the
package version (e.g. When we have the URL override)
> Prevent R CMD check from using /tmp
> ---
>
> Key: SPARK-22344
> URL: https://issues.apache.org/jira/browse/SPARK-22344
> Project: Spark
> Issue Type: Bug
> Components: SparkR
>Affects Versions: 1.6.3, 2.1.2, 2.2.0, 2.3.0
>Reporter: Shivaram Venkataraman
>
> When R CMD check is run on the SparkR package it leaves behind files in /tmp
> which is a violation of CRAN policy. We should instead write to Rtmpdir.
> Notes from CRAN are below
> {code}
> Checking this leaves behind dirs
>hive/$USER
>$USER
> and files named like
>b4f6459b-0624-4100-8358-7aa7afbda757_resources
> in /tmp, in violation of the CRAN Policy.
> {code}
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[jira] [Commented] (SPARK-22344) Prevent R CMD check from using /tmp
[
https://issues.apache.org/jira/browse/SPARK-22344?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel=16224301#comment-16224301
]
Shivaram Venkataraman commented on SPARK-22344:
---
well uninstall is just removing `sparkCachePath()/` -- Should be
relatively easy to put together ?
> Prevent R CMD check from using /tmp
> ---
>
> Key: SPARK-22344
> URL: https://issues.apache.org/jira/browse/SPARK-22344
> Project: Spark
> Issue Type: Bug
> Components: SparkR
>Affects Versions: 1.6.3, 2.1.2, 2.2.0, 2.3.0
>Reporter: Shivaram Venkataraman
>
> When R CMD check is run on the SparkR package it leaves behind files in /tmp
> which is a violation of CRAN policy. We should instead write to Rtmpdir.
> Notes from CRAN are below
> {code}
> Checking this leaves behind dirs
>hive/$USER
>$USER
> and files named like
>b4f6459b-0624-4100-8358-7aa7afbda757_resources
> in /tmp, in violation of the CRAN Policy.
> {code}
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[jira] [Commented] (SPARK-22344) Prevent R CMD check from using /tmp
[
https://issues.apache.org/jira/browse/SPARK-22344?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel=16224139#comment-16224139
]
Felix Cheung commented on SPARK-22344:
--
Kinda we don't have any uninstall feature though
> Prevent R CMD check from using /tmp
> ---
>
> Key: SPARK-22344
> URL: https://issues.apache.org/jira/browse/SPARK-22344
> Project: Spark
> Issue Type: Bug
> Components: SparkR
>Affects Versions: 1.6.3, 2.1.2, 2.2.0, 2.3.0
>Reporter: Shivaram Venkataraman
>
> When R CMD check is run on the SparkR package it leaves behind files in /tmp
> which is a violation of CRAN policy. We should instead write to Rtmpdir.
> Notes from CRAN are below
> {code}
> Checking this leaves behind dirs
>hive/$USER
>$USER
> and files named like
>b4f6459b-0624-4100-8358-7aa7afbda757_resources
> in /tmp, in violation of the CRAN Policy.
> {code}
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[jira] [Commented] (SPARK-22344) Prevent R CMD check from using /tmp
[
https://issues.apache.org/jira/browse/SPARK-22344?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel=16223844#comment-16223844
]
Shivaram Venkataraman commented on SPARK-22344:
---
The ~/.cache is created by `install.spark` -- so its in our control whether we
want to "uninstall" spark at the end of the tests ?
> Prevent R CMD check from using /tmp
> ---
>
> Key: SPARK-22344
> URL: https://issues.apache.org/jira/browse/SPARK-22344
> Project: Spark
> Issue Type: Bug
> Components: SparkR
>Affects Versions: 1.6.3, 2.1.2, 2.2.0, 2.3.0
>Reporter: Shivaram Venkataraman
>
> When R CMD check is run on the SparkR package it leaves behind files in /tmp
> which is a violation of CRAN policy. We should instead write to Rtmpdir.
> Notes from CRAN are below
> {code}
> Checking this leaves behind dirs
>hive/$USER
>$USER
> and files named like
>b4f6459b-0624-4100-8358-7aa7afbda757_resources
> in /tmp, in violation of the CRAN Policy.
> {code}
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[jira] [Commented] (SPARK-22344) Prevent R CMD check from using /tmp
[
https://issues.apache.org/jira/browse/SPARK-22344?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel=16223228#comment-16223228
]
Felix Cheung commented on SPARK-22344:
--
I think the PR addresses other cases, but what do we want to do with:
~/.cache
/tmp/hsperfdata_ubuntu/
> Prevent R CMD check from using /tmp
> ---
>
> Key: SPARK-22344
> URL: https://issues.apache.org/jira/browse/SPARK-22344
> Project: Spark
> Issue Type: Bug
> Components: SparkR
>Affects Versions: 1.6.3, 2.1.2, 2.2.0, 2.3.0
>Reporter: Shivaram Venkataraman
>
> When R CMD check is run on the SparkR package it leaves behind files in /tmp
> which is a violation of CRAN policy. We should instead write to Rtmpdir.
> Notes from CRAN are below
> {code}
> Checking this leaves behind dirs
>hive/$USER
>$USER
> and files named like
>b4f6459b-0624-4100-8358-7aa7afbda757_resources
> in /tmp, in violation of the CRAN Policy.
> {code}
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[jira] [Commented] (SPARK-22344) Prevent R CMD check from using /tmp
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]
Apache Spark commented on SPARK-22344:
--
User 'shivaram' has created a pull request for this issue:
https://github.com/apache/spark/pull/19589
> Prevent R CMD check from using /tmp
> ---
>
> Key: SPARK-22344
> URL: https://issues.apache.org/jira/browse/SPARK-22344
> Project: Spark
> Issue Type: Bug
> Components: SparkR
>Affects Versions: 1.6.3, 2.1.2, 2.2.0, 2.3.0
>Reporter: Shivaram Venkataraman
>
> When R CMD check is run on the SparkR package it leaves behind files in /tmp
> which is a violation of CRAN policy. We should instead write to Rtmpdir.
> Notes from CRAN are below
> {code}
> Checking this leaves behind dirs
>hive/$USER
>$USER
> and files named like
>b4f6459b-0624-4100-8358-7aa7afbda757_resources
> in /tmp, in violation of the CRAN Policy.
> {code}
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[jira] [Commented] (SPARK-22344) Prevent R CMD check from using /tmp
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]
Hossein Falaki commented on SPARK-22344:
I don't have solid pointer as to why we are creating these temp directories for
hive. I think it would be nicer to fix them in Spark. It is a good practice not
to leave files on /tmp.
> Prevent R CMD check from using /tmp
> ---
>
> Key: SPARK-22344
> URL: https://issues.apache.org/jira/browse/SPARK-22344
> Project: Spark
> Issue Type: Bug
> Components: SparkR
>Affects Versions: 1.6.3, 2.1.2, 2.2.0, 2.3.0
>Reporter: Shivaram Venkataraman
>
> When R CMD check is run on the SparkR package it leaves behind files in /tmp
> which is a violation of CRAN policy. We should instead write to Rtmpdir.
> Notes from CRAN are below
> {code}
> Checking this leaves behind dirs
>hive/$USER
>$USER
> and files named like
>b4f6459b-0624-4100-8358-7aa7afbda757_resources
> in /tmp, in violation of the CRAN Policy.
> {code}
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[jira] [Commented] (SPARK-22344) Prevent R CMD check from using /tmp
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Shivaram Venkataraman commented on SPARK-22344:
---
Thanks for investigating. Is
`/tmp/ubuntu/8201eb2c-8065-458c-b564-1e61b3dc5b7d/` a symlink to
`/tmp/hive/ubuntu/8201eb2c-8065-458c-b564-1e61b3dc5b7d/` or are they just
different directories ?
We can disable the hsperfdata with the suggested flag and also change the
java.io.tmpdir which should at least fix the blockmanager I think. I will open
a PR for this.
Regarding Hive directories created even though its off, I have no idea why that
is happening. [~falaki] [~hyukjin.kwon] do you have any idea on why this
happens ?
> Prevent R CMD check from using /tmp
> ---
>
> Key: SPARK-22344
> URL: https://issues.apache.org/jira/browse/SPARK-22344
> Project: Spark
> Issue Type: Bug
> Components: SparkR
>Affects Versions: 1.6.3, 2.1.2, 2.2.0, 2.3.0
>Reporter: Shivaram Venkataraman
>
> When R CMD check is run on the SparkR package it leaves behind files in /tmp
> which is a violation of CRAN policy. We should instead write to Rtmpdir.
> Notes from CRAN are below
> {code}
> Checking this leaves behind dirs
>hive/$USER
>$USER
> and files named like
>b4f6459b-0624-4100-8358-7aa7afbda757_resources
> in /tmp, in violation of the CRAN Policy.
> {code}
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[jira] [Commented] (SPARK-22344) Prevent R CMD check from using /tmp
[
https://issues.apache.org/jira/browse/SPARK-22344?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel=16220083#comment-16220083
]
Felix Cheung commented on SPARK-22344:
--
why is hive there when enableHiveSupport should be off?
what do we do with .cache/?
https://stackoverflow.com/questions/76327/how-can-i-prevent-java-from-creating-hsperfdata-files
> Prevent R CMD check from using /tmp
> ---
>
> Key: SPARK-22344
> URL: https://issues.apache.org/jira/browse/SPARK-22344
> Project: Spark
> Issue Type: Bug
> Components: SparkR
>Affects Versions: 1.6.3, 2.1.2, 2.2.0, 2.3.0
>Reporter: Shivaram Venkataraman
>
> When R CMD check is run on the SparkR package it leaves behind files in /tmp
> which is a violation of CRAN policy. We should instead write to Rtmpdir.
> Notes from CRAN are below
> {code}
> Checking this leaves behind dirs
>hive/$USER
>$USER
> and files named like
>b4f6459b-0624-4100-8358-7aa7afbda757_resources
> in /tmp, in violation of the CRAN Policy.
> {code}
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[jira] [Commented] (SPARK-22344) Prevent R CMD check from using /tmp
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https://issues.apache.org/jira/browse/SPARK-22344?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel=16220080#comment-16220080
]
Felix Cheung commented on SPARK-22344:
--
this is what I see on a clean machine tracking access/create/modify to file
system.
I run this command:
R CMD check --as-cran SparkR_2.1.2.tar.gz
And matching the report these are accessed:
/tmp/hive/
/tmp/hive/ubuntu/8201eb2c-8065-458c-b564-1e61b3dc5b7d/_tmp_space.db/
/tmp/ubuntu/8201eb2c-8065-458c-b564-1e61b3dc5b7d/
But these are also there:
~/.cache
/tmp/blockmgr-b27976f3-b66a-44e1-94c2-7360525af321/
/tmp/hsperfdata_ubuntu/
/tmp/1993ae7a-f553-4de5-9f74-6c8393e3cd5a_resources/
/tmp/8201eb2c-8065-458c-b564-1e61b3dc5b7d_resources/
> Prevent R CMD check from using /tmp
> ---
>
> Key: SPARK-22344
> URL: https://issues.apache.org/jira/browse/SPARK-22344
> Project: Spark
> Issue Type: Bug
> Components: SparkR
>Affects Versions: 1.6.3, 2.1.2, 2.2.0, 2.3.0
>Reporter: Shivaram Venkataraman
>
> When R CMD check is run on the SparkR package it leaves behind files in /tmp
> which is a violation of CRAN policy. We should instead write to Rtmpdir.
> Notes from CRAN are below
> {code}
> Checking this leaves behind dirs
>hive/$USER
>$USER
> and files named like
>b4f6459b-0624-4100-8358-7aa7afbda757_resources
> in /tmp, in violation of the CRAN Policy.
> {code}
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