[GitHub] spark issue #19290: [SPARK-22063][R] Upgrades lintr to latest commit sha1 ID

[HyukjinKwon]

Github user HyukjinKwon commented on the issue:

https://github.com/apache/spark/pull/19290
  
Ah, thank you @shaneknapp. The command below:

```
Rscript -e "devtools::install_github('jimhester/lintr@5431140')"
```

should upgrades `lintr` to the desired version here.

Actually, looks we should merge this one first before upgrading `lintr` in 
Jenkins. I realised upgrading it first could make R lintr check failures in 
other PRs up to my knowledge ..

I updated the change here back to not try to upgrade `lintr`. So, merging 
this one would not cause a problem on the build system. Let me go ahead with 
this one first and then I guess we could upgrade.

Thanks again and I am sorry for this, @shaneknapp.




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[GitHub] spark issue #19290: [SPARK-22063][R] Upgrades lintr to latest commit sha1 ID

[shaneknapp]

Github user shaneknapp commented on the issue:

https://github.com/apache/spark/pull/19290
  
hey all, i'm here.  was out sick for the past few days and trying to get
caught up.  sorry about that!

so...  what version of lintr do we need to put on the workers?

On Fri, Sep 29, 2017 at 3:32 AM, UCB AMPLab 
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[GitHub] spark issue #19290: [SPARK-22063][R] Upgrades lintr to latest commit sha1 ID

[HyukjinKwon]

Github user HyukjinKwon commented on the issue:

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retest this please


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[GitHub] spark issue #19290: [SPARK-22063][R] Upgrades lintr to latest commit sha1 ID

[HyukjinKwon]

Github user HyukjinKwon commented on the issue:

https://github.com/apache/spark/pull/19290
  
I just double checked the newer lintr, lintr@5431140, passes on the top of 
the master with the current change.


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[GitHub] spark issue #19290: [SPARK-22063][R] Upgrades lintr to latest commit sha1 ID

[HyukjinKwon]

Github user HyukjinKwon commented on the issue:

https://github.com/apache/spark/pull/19290
  
Oh! but if we upgrade it first, many builds in PRs should be broken due to 
this check failure. Probably, let me revert the script first to not upgrade it 
in order to unblock this.


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[GitHub] spark issue #19290: [SPARK-22063][R] Upgrades lintr to latest commit sha1 ID

[HyukjinKwon]

Github user HyukjinKwon commented on the issue:

https://github.com/apache/spark/pull/19290
  
Let me revert "... || packageVersion("lintr") != "1.0.1.9000" this 
condition back so that it does not try to upgrade it.


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[GitHub] spark issue #19290: [SPARK-22063][R] Upgrades lintr to latest commit sha1 ID

[felixcheung]

Github user felixcheung commented on the issue:

https://github.com/apache/spark/pull/19290
  
hmm, perhaps open a ticket to ask shane to update Jenkins to this commit 
checksum manually?


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[GitHub] spark issue #19290: [SPARK-22063][R] Upgrades lintr to latest commit sha1 ID

[HyukjinKwon]

Github user HyukjinKwon commented on the issue:

https://github.com/apache/spark/pull/19290
  
For more context, I believe `lintr` was initially installed in 
https://github.com/apache/spark/commit/004f57374b98c4df32d9f1e19221f68e92639a49.
 Upgrade to jimhester/lintr@a769c0b was proposed here in 
https://github.com/apache/spark/commit/7d1175011c976756efcd4e4e4f70a8fd6f287026 
but I believe this didn't actually upgrade the package on Jenkins as `lintr` 
was already installed  and `"lintr" %in% row.names(installed.packages())  == 
FALSE` gives `FALSE`.

So, I believe `lintr` in Jenkins is already not synced to 
jimhester/lintr@a769c0b as fixed in 
https://github.com/apache/spark/commit/7d1175011c976756efcd4e4e4f70a8fd6f287026 
unless it was manually upgraded afterwards (I can't check but this is just my 
assumption).

I believe eventually we should upgrade and match with this anyway to detect 
project's R style in each PR. I at least have been in a PR where I had to 
manually suggest to fix.





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[GitHub] spark issue #19290: [SPARK-22063][R] Upgrades lintr to latest commit sha1 ID

[HyukjinKwon]

Github user HyukjinKwon commented on the issue:

https://github.com/apache/spark/pull/19290
  
Do you maybe have some worries about this? If that worry is quite crucial, 
I think we could also consider an option, not upgrading this, leaving 
`lint-r.R` script as was, and only fixing the instances detected by the upgrade 
here.


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[GitHub] spark issue #19290: [SPARK-22063][R] Upgrades lintr to latest commit sha1 ID

[HyukjinKwon]

Github user HyukjinKwon commented on the issue:

https://github.com/apache/spark/pull/19290
  
@shaneknapp Sure, it was my bad. I will be careful next time.

It is required to fix an actual issue in order to to detect R codes that do 
not follow project's R style.


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[GitHub] spark issue #19290: [SPARK-22063][R] Upgrades lintr to latest commit sha1 ID

[shaneknapp]

Github user shaneknapp commented on the issue:

https://github.com/apache/spark/pull/19290
  
@HyukjinKwon -- you will absolutely not have builds install packages on the 
build system.  this is a really bad idea.

is this absolutely required, or just to fix a warning in the build output?


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[GitHub] spark issue #19290: [SPARK-22063][R] Upgrades lintr to latest commit sha1 ID

[HyukjinKwon]

Github user HyukjinKwon commented on the issue:

https://github.com/apache/spark/pull/19290
  
Hi @shaneknapp. I am sorry but it's me again ...

Here, this PR tries to upgrade an R package, 
[lintr](https://github.com/jimhester/lintr) for static Code analysis for R, 
which is ran via `./dev/lint-r` -> `dev/lint-r.R` as a part of Jenkins PR build.

This upgrade catches many meaningful instances that should have caught 
before in SparkR codes and if I understood correctly, we decided to upgrade 
this if it does not cause a problem.

I tried to fix the `dev/lint-r.R` script so that `lintr` can be upgraded if 
this package is not installed or not the specific version (1.0.1.9000) after 
testing this in my local, but looks failed in Jenkins due to a permission issue.

I believe the bash command below installs the package correctly:

```R
Rscript -e "devtools::install_github('jimhester/lintr@5431140')"
```

Maybe, I should have cc'ed you here first before trying this one. I 
appologise and I will cc you in such cases in the future.


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[GitHub] spark issue #19290: [SPARK-22063][R] Upgrades lintr to latest commit sha1 ID

[HyukjinKwon]

Github user HyukjinKwon commented on the issue:

https://github.com/apache/spark/pull/19290
  
Ugh.. it failed to install due to permission issue ... 

```
Downloading GitHub repo jimhester/lintr@5431140
from URL https://api.github.com/repos/jimhester/lintr/zipball/5431140
Installing lintr
Downloading GitHub repo hadley/xml2@master
from URL https://api.github.com/repos/hadley/xml2/zipball/master
Installing xml2
'/usr/lib64/R/bin/R' --no-site-file --no-environ --no-save --no-restore  \
  --quiet CMD INSTALL  \
  '/tmp/RtmprFnaBu/devtools438c516b7717/r-lib-xml2-5799cd9'  \
  --library='/usr/lib64/R/library' --install-tests 

Error: ERROR: no permission to install to directory '/usr/lib64/R/library'
Installation failed: Command failed (1)
'/usr/lib64/R/bin/R' --no-site-file --no-environ --no-save --no-restore  \
  --quiet CMD INSTALL  \
  '/tmp/RtmprFnaBu/devtools438c286c3792/jimhester-lintr-5431140'  \
  --library='/usr/lib64/R/library' --install-tests 

Error: ERROR: no permission to install to directory '/usr/lib64/R/library'
Installation failed: Command failed (1)
```


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