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Posted to commits@mxnet.apache.org by GitBox <gi...@apache.org> on 2020/03/27 02:54:57 UTC
[GitHub] [incubator-mxnet] aaronmarkham opened a new issue #17920: R docs
generation error
aaronmarkham opened a new issue #17920: R docs generation error
URL: https://github.com/apache/incubator-mxnet/issues/17920
## Description
When CI tries to create the R docs, it fails, blocking website creation and CI's website test.
This particular error happens with v1.6.x.
### Error Message
```
[2020-03-27T01:45:31.428Z] Error in setRefClass("mx.metric.logger", fields = list(train = "numeric", (from callback.R#19) :
[2020-03-27T01:45:31.428Z] could not find function "setRefClass"
```
## To Reproduce
(If you developed your own code, please provide a short script that reproduces the error. For existing examples, please provide link.)
### Steps to reproduce
http://jenkins.mxnet-ci.amazon-ml.com/blue/organizations/jenkins/mxnet-validation%2Fwebsite/detail/PR-17919/2/pipeline
1. `ci/build.py --docker-registry mxnetci --platform ubuntu_cpu_lite /work/runtime_functions.sh build_ubuntu_cpu_docs`
2. `ci/build.py --docker-registry mxnetci --platform ubuntu_cpu_r /work/runtime_functions.sh build_r_docs`
## What have you tried to solve it?
1. Google error... not much luck there so far.
2. ?
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[GitHub] [incubator-mxnet] ChaiBapchya commented on issue #17920: R docs
generation error
Posted by GitBox <gi...@apache.org>.
ChaiBapchya commented on issue #17920: R docs generation error
URL: https://github.com/apache/incubator-mxnet/issues/17920#issuecomment-611120781
Alright, thanks for pointing it out. Testing locally if moving all CI from py2 to py3 fixes doc issue.
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[GitHub] [incubator-mxnet] leezu commented on issue #17920: R docs
generation error
Posted by GitBox <gi...@apache.org>.
leezu commented on issue #17920: R docs generation error
URL: https://github.com/apache/incubator-mxnet/issues/17920#issuecomment-606154016
The patch changes the build system for R, so it's not good to backport to 1.6.x. But you can try backporting the single line mentioned above, adding `library(methods)` to the `callback.R` file.
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[GitHub] [incubator-mxnet] ChaiBapchya commented on issue #17920: R docs
generation error
Posted by GitBox <gi...@apache.org>.
ChaiBapchya commented on issue #17920: R docs generation error
URL: https://github.com/apache/incubator-mxnet/issues/17920#issuecomment-611100432
> Maybe the backports broke it? https://github.com/apache/incubator-mxnet/blob/v1.6.x/python/mxnet/metric.py
@aaronmarkham testing if back ports broke it, by reverting it on branch 1.6 and testing locally.
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[GitHub] [incubator-mxnet] leezu commented on issue #17920: R docs
generation error
Posted by GitBox <gi...@apache.org>.
leezu commented on issue #17920: R docs generation error
URL: https://github.com/apache/incubator-mxnet/issues/17920#issuecomment-605204908
I think I experienced this error locally before. I fixed it by importing the function first, using `library(methods)`. https://github.com/apache/incubator-mxnet/commit/9f2e73f39b405ec24cab254076f964452382c224#diff-a926015f30adb97767a7e80d67fbacbd
Not sure why this error appears and persists on 1.6 branch. Did you confirm it doesn't happen master?
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[GitHub] [incubator-mxnet] aaronmarkham commented on issue #17920: R docs
generation error
Posted by GitBox <gi...@apache.org>.
aaronmarkham commented on issue #17920: R docs generation error
URL: https://github.com/apache/incubator-mxnet/issues/17920#issuecomment-605117306
Maybe the backports broke it? https://github.com/apache/incubator-mxnet/blob/v1.6.x/python/mxnet/metric.py
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[GitHub] [incubator-mxnet] ChaiBapchya commented on issue #17920: R docs
generation error
Posted by GitBox <gi...@apache.org>.
ChaiBapchya commented on issue #17920: R docs generation error
URL: https://github.com/apache/incubator-mxnet/issues/17920#issuecomment-611036754
> Maybe the backports broke it? https://github.com/apache/incubator-mxnet/blob/v1.6.x/python/mxnet/metric.py
@aaronmarkham This backport : https://github.com/apache/incubator-mxnet/pull/17029/files in metric.py changed parts within Pearson Correlation. Not sure why that would break the file.
> But you can try backporting the single line mentioned above, adding library(methods) to the callback.R file.
@leezu Tried backporting `library(methods)` in #17993 but now it gives error for finding the library
```
Loading mxnet
[1] "Loading local: inst/libs/libmxnet.so"
<simpleError in find.package(package, lib.loc, verbose = verbose): there is no package called 'mxnet'
>
[1] "Loading local: src/mxnet.so"
<simpleError in find.package(package, lib.loc, verbose = verbose): there is no package called 'mxnet'
>
Error in loadModule("mxnet", TRUE) : could not find function "loadModule"
```
@aaronmarkham @leezu any suggestions for this?
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[GitHub] [incubator-mxnet] ChaiBapchya edited a comment on issue #17920: R
docs generation error
Posted by GitBox <gi...@apache.org>.
ChaiBapchya edited a comment on issue #17920: R docs generation error
URL: https://github.com/apache/incubator-mxnet/issues/17920#issuecomment-610501295
Added that patch on v1.6.x
Testing it locally first. If it passes, will create a PR to fix the issue.
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[GitHub] [incubator-mxnet] leezu commented on issue #17920: R docs
generation error
Posted by GitBox <gi...@apache.org>.
leezu commented on issue #17920: R docs generation error
URL: https://github.com/apache/incubator-mxnet/issues/17920#issuecomment-611112275
I don't think there is any single / separate PR to change different parts of the CI to Python 3. Instead of backporting, it may be simplest to create a new PR
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[GitHub] [incubator-mxnet] leezu commented on issue #17920: R docs
generation error
Posted by GitBox <gi...@apache.org>.
leezu commented on issue #17920: R docs generation error
URL: https://github.com/apache/incubator-mxnet/issues/17920#issuecomment-605205420
Regarding the backports you linked: Why would changes to the python code affect the R package?
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[GitHub] [incubator-mxnet] aaronmarkham commented on issue #17920: R docs
generation error
Posted by GitBox <gi...@apache.org>.
aaronmarkham commented on issue #17920: R docs generation error
URL: https://github.com/apache/incubator-mxnet/issues/17920#issuecomment-606145810
> I think I experienced this error locally before. I fixed it by importing the function first, using `library(methods)`. [9f2e73f#diff-a926015f30adb97767a7e80d67fbacbd](https://github.com/apache/incubator-mxnet/commit/9f2e73f39b405ec24cab254076f964452382c224#diff-a926015f30adb97767a7e80d67fbacbd)
>
> Not sure why this error appears and persists on 1.6 branch. Did you confirm it doesn't happen master?
> Regarding the backports you linked: Why would changes to the python code affect the R package?
Doesn't happen on master, and it didn't happen before when we were operating on that codebase, so I can assume it is introduced with the back-porting.
As far as Python impacting R... we have some bootstrapping going on... Scala does it... and I think R does too... so it'll use Python to generate some of its functions. You can notice this when you look at the docstrings and see how Python examples are in the docs for Scala or R.
Can your R patch be back-ported to v1.6.x?
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[GitHub] [incubator-mxnet] ChaiBapchya commented on issue #17920: R docs
generation error
Posted by GitBox <gi...@apache.org>.
ChaiBapchya commented on issue #17920: R docs generation error
URL: https://github.com/apache/incubator-mxnet/issues/17920#issuecomment-610501295
Add that patch on v1.6.x
Testing it locally first. If it passes, will create a PR to fix the issue.
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[GitHub] [incubator-mxnet] ChaiBapchya edited a comment on issue #17920: R
docs generation error
Posted by GitBox <gi...@apache.org>.
ChaiBapchya edited a comment on issue #17920: R docs generation error
URL: https://github.com/apache/incubator-mxnet/issues/17920#issuecomment-611036754
> Maybe the backports broke it? https://github.com/apache/incubator-mxnet/blob/v1.6.x/python/mxnet/metric.py
@aaronmarkham This backport : https://github.com/apache/incubator-mxnet/pull/17029/files in metric.py changed parts within Pearson Correlation. Not sure why that would break the file.
> But you can try backporting the single line mentioned above, adding library(methods) to the callback.R file.
@leezu Tried backporting `library(methods)` in #17993 but now it gives error for finding the library
```
Loading mxnet
[1] "Loading local: inst/libs/libmxnet.so"
<simpleError in find.package(package, lib.loc, verbose = verbose): there is no package called 'mxnet'
>
[1] "Loading local: src/mxnet.so"
<simpleError in find.package(package, lib.loc, verbose = verbose): there is no package called 'mxnet'
>
Error in loadModule("mxnet", TRUE) : could not find function "loadModule"
```
@aaronmarkham @leezu any suggestions for this?
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[GitHub] [incubator-mxnet] ChaiBapchya edited a comment on issue #17920: R
docs generation error
Posted by GitBox <gi...@apache.org>.
ChaiBapchya edited a comment on issue #17920: R docs generation error
URL: https://github.com/apache/incubator-mxnet/issues/17920#issuecomment-611036754
> Maybe the backports broke it? https://github.com/apache/incubator-mxnet/blob/v1.6.x/python/mxnet/metric.py
@aaronmarkham This backport : https://github.com/apache/incubator-mxnet/pull/17029/files in metric.py changed parts within Pearson Correlation. Not sure why that would break the file.
> But you can try backporting the single line mentioned above, adding library(methods) to the callback.R file.
@leezu Tried backporting `library(methods)` in #17993 but now it gives error for finding the library
```
Loading mxnet
[1] "Loading local: inst/libs/libmxnet.so"
<simpleError in find.package(package, lib.loc, verbose = verbose): there is no package called 'mxnet'
>
[1] "Loading local: src/mxnet.so"
<simpleError in find.package(package, lib.loc, verbose = verbose): there is no package called 'mxnet'
>
Error in loadModule("mxnet", TRUE) : could not find function "loadModule"
```
Since aaron's investigation revealed, backporting py2->py3 for CI would probably be helpful. I'm trying to backport 2 PRs #17853 #17593 [only 2 I could find relevant to py2->py3 update for CI] [though I'm skeptical if it will resolve package not found issue in R Docs]
@aaronmarkham @leezu any suggestions for this?
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