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Posted to reviews@spark.apache.org by zero323 <gi...@git.apache.org> on 2017/05/21 18:32:23 UTC
[GitHub] spark pull request #18051: [SPARK-18825][SPARKR][DOCS][WIP] Eliminate duplic...
GitHub user zero323 opened a pull request:
https://github.com/apache/spark/pull/18051
[SPARK-18825][SPARKR][DOCS][WIP] Eliminate duplicate links in SparkR API doc index
## What changes were proposed in this pull request?
Duplicate links come from the `00Index.html` created during package installation. The file has a regular structure, where each link is a table row, slitted into two lines:
```r
<tr><td style="width: 25%;"><a href="atan.html">atan-method</a></td>
<td>atan</td></tr>
```
This PR adds an additional steps to the `R/create-docs.sh`:
- Copy `00Index.html` to the current working directory;
index_path = file.path(libDir, "SparkR", "html", "00Index.html");
invisible(file.copy(index_path, "00Index.html.bck"));writeLines(txt, index_path);
- Reads file and removes problematic lines
txt = readLines(index_path); method_lines = grep("-method</a>", txt, fixed = TRUE);
txt = txt[-c(method_lines, method_lines + 1)];
- Writes file back:
writeLines(txt, index_path)
- Executes current pipeline.
- Restores original content:
invisible(file.rename("00Index.html.bck", index_path))
Arguably this is not the most reliable approach, but doesn't require any parser, and can be embedded in the current `create-docs.sh`
## How was this patch tested?
Manual inspection of the docs.
You can merge this pull request into a Git repository by running:
$ git pull https://github.com/zero323/spark SPARK-18825
Alternatively you can review and apply these changes as the patch at:
https://github.com/apache/spark/pull/18051.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 #18051
----
commit b28ec94b0c0589736b4e3377d160642b0b6181a6
Author: zero323 <ze...@users.noreply.github.com>
Date: 2017-05-21T18:19:22Z
Initial implementation
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[GitHub] spark issue #18051: [SPARK-18825][SPARKR][DOCS][WIP] Eliminate duplicate lin...
Posted by SparkQA <gi...@git.apache.org>.
Github user SparkQA commented on the issue:
https://github.com/apache/spark/pull/18051
**[Test build #77206 has finished](https://amplab.cs.berkeley.edu/jenkins/job/SparkPullRequestBuilder/77206/testReport)** for PR 18051 at commit [`8392ba5`](https://github.com/apache/spark/commit/8392ba51f4e0b096e9731b0f63f38942555e6f46).
* This patch **fails SparkR unit tests**.
* This patch merges cleanly.
* This patch adds no public classes.
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[GitHub] spark issue #18051: [SPARK-18825][SPARKR][DOCS][WIP] Eliminate duplicate lin...
Posted by zero323 <gi...@git.apache.org>.
Github user zero323 commented on the issue:
https://github.com/apache/spark/pull/18051
It doesn't, but `R CMD build pkg` doesn't generate html index. This happens somewhere in the `R CMD INSTALL` so even if we create custom build script (with `devtools`), it won't helps us here.
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[GitHub] spark issue #18051: [SPARK-18825][SPARKR][DOCS][WIP] Eliminate duplicate lin...
Posted by felixcheung <gi...@git.apache.org>.
Github user felixcheung commented on the issue:
https://github.com/apache/spark/pull/18051
Improvements to R API doc online can be useful.
But I think that is somewhat independent of this change/PR. Let's focus on your points on `Cleaning duplicate links` and `Trying to clean see also` - what do you think what @actuaryzhang is asking?
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[GitHub] spark issue #18051: [SPARK-18825][SPARKR][DOCS][WIP] Eliminate duplicate lin...
Posted by SparkQA <gi...@git.apache.org>.
Github user SparkQA commented on the issue:
https://github.com/apache/spark/pull/18051
**[Test build #77152 has finished](https://amplab.cs.berkeley.edu/jenkins/job/SparkPullRequestBuilder/77152/testReport)** for PR 18051 at commit [`b28ec94`](https://github.com/apache/spark/commit/b28ec94b0c0589736b4e3377d160642b0b6181a6).
* This patch passes all tests.
* This patch merges cleanly.
* This patch adds no public classes.
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[GitHub] spark issue #18051: [SPARK-18825][SPARKR][DOCS][WIP] Eliminate duplicate lin...
Posted by actuaryzhang <gi...@git.apache.org>.
Github user actuaryzhang commented on the issue:
https://github.com/apache/spark/pull/18051
Maybe I'm missing something completely, but I still don't get the point why we are removing the `xx-method` link since we are defining methods as S4 using `setMethod`. Lots of packages have these entries in the index. Below is a snapshot from the `sp` package. You can find a lot more there.
Even for S3 methods, they tend to repeat as well. Below is a snapshot of the `gamm4` package.
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[GitHub] spark issue #18051: [SPARK-18825][SPARKR][DOCS][WIP] Eliminate duplicate lin...
Posted by zero323 <gi...@git.apache.org>.
Github user zero323 commented on the issue:
https://github.com/apache/spark/pull/18051
If we consider improvement of the online documentation to be a separate problem, then I fully agree with @actuaryzhang.
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[GitHub] spark issue #18051: [SPARK-18825][SPARKR][DOCS][WIP] Eliminate duplicate lin...
Posted by AmplabJenkins <gi...@git.apache.org>.
Github user AmplabJenkins commented on the issue:
https://github.com/apache/spark/pull/18051
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[GitHub] spark issue #18051: [SPARK-18825][SPARKR][DOCS][WIP] Eliminate duplicate lin...
Posted by zero323 <gi...@git.apache.org>.
Github user zero323 commented on the issue:
https://github.com/apache/spark/pull/18051
I think there are two different problems here:
- Quality of the internal R documentation. I think that fixing this is non-goal. It is not only a normal state of R packages, but also impossible to fix without hacks or serious trade-offs.
- Quality of the online documentation. This is subjective but I think there is a lot to do there including, but not limited to:
- Removing this IFrame nonsense. It doesn't serve any real purpose and is completely useless.
- Cleaning duplicate links. Since almost everything here is S4 we duplicate the size of the index with each addition make it only harder to use. It also affects _ee also_ sections.
- Trying to clean _see also_. Something like this (example SQL function):
is just useless.
- Adding some kind of search functionality.
- Running all examples as a part of the internal docs build process. Having readable, highlighted examples, with actual output, would be awesome.
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[GitHub] spark issue #18051: [SPARK-18825][SPARKR][DOCS][WIP] Eliminate duplicate lin...
Posted by felixcheung <gi...@git.apache.org>.
Github user felixcheung commented on the issue:
https://github.com/apache/spark/pull/18051
@actuaryzhang - we were just talking this in the other PR. what do you think?
@zero323 - right, I do agree `?abs-method` is kind of a big problem...
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[GitHub] spark issue #18051: [SPARK-18825][SPARKR][DOCS][WIP] Eliminate duplicate lin...
Posted by actuaryzhang <gi...@git.apache.org>.
Github user actuaryzhang commented on the issue:
https://github.com/apache/spark/pull/18051
That makes sense!
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[GitHub] spark issue #18051: [SPARK-18825][SPARKR][DOCS][WIP] Eliminate duplicate lin...
Posted by SparkQA <gi...@git.apache.org>.
Github user SparkQA commented on the issue:
https://github.com/apache/spark/pull/18051
**[Test build #77207 has finished](https://amplab.cs.berkeley.edu/jenkins/job/SparkPullRequestBuilder/77207/testReport)** for PR 18051 at commit [`4843950`](https://github.com/apache/spark/commit/4843950694ca3d2dbd607ee889306fcbd8d83fac).
* This patch passes all tests.
* This patch merges cleanly.
* This patch adds no public classes.
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[GitHub] spark issue #18051: [SPARK-18825][SPARKR][DOCS][WIP] Eliminate duplicate lin...
Posted by zero323 <gi...@git.apache.org>.
Github user zero323 commented on the issue:
https://github.com/apache/spark/pull/18051
To be honest I thought mostly about online docs here. Duplicate links in the bundled documentation never bothered me before (in SparkR, or any other package for that matter) and don't I think these have to be fixed. Maybe just close this PR, mark upstream ticket as won't fix, and focus on bigger issues? Just saying...
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[GitHub] spark issue #18051: [SPARK-18825][SPARKR][DOCS][WIP] Eliminate duplicate lin...
Posted by zero323 <gi...@git.apache.org>.
Github user zero323 commented on the issue:
https://github.com/apache/spark/pull/18051
OK, take two. Instead of modifying `00index.html`let's process `Rd` files. This will remove `-method` aliases before html version is created.
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[GitHub] spark issue #18051: [SPARK-18825][SPARKR][DOCS][WIP] Eliminate duplicate lin...
Posted by AmplabJenkins <gi...@git.apache.org>.
Github user AmplabJenkins commented on the issue:
https://github.com/apache/spark/pull/18051
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[GitHub] spark issue #18051: [SPARK-18825][SPARKR][DOCS][WIP] Eliminate duplicate lin...
Posted by felixcheung <gi...@git.apache.org>.
Github user felixcheung commented on the issue:
https://github.com/apache/spark/pull/18051
given the work we are doing in #18025 to reorganize a lot of the pages, this might become a very minor issue when the dust settles. So I'm good also just to track this (wouldn't resolve the JIRA just yet) and revisit later.
also looking forward to your proposal on getting online help doc better, @zero323 !
could you put your comment above into a JIRA please?
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[GitHub] spark issue #18051: [SPARK-18825][SPARKR][DOCS][WIP] Eliminate duplicate lin...
Posted by AmplabJenkins <gi...@git.apache.org>.
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https://github.com/apache/spark/pull/18051
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[GitHub] spark issue #18051: [SPARK-18825][SPARKR][DOCS][WIP] Eliminate duplicate lin...
Posted by felixcheung <gi...@git.apache.org>.
Github user felixcheung commented on the issue:
https://github.com/apache/spark/pull/18051
hmm,.. we do want people to be able to install it as a package...
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[GitHub] spark issue #18051: [SPARK-18825][SPARKR][DOCS][WIP] Eliminate duplicate lin...
Posted by felixcheung <gi...@git.apache.org>.
Github user felixcheung commented on the issue:
https://github.com/apache/spark/pull/18051
I see - I think this doesn't address doc build via `R CMD build pkg`?
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Github user AmplabJenkins commented on the issue:
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[GitHub] spark issue #18051: [SPARK-18825][SPARKR][DOCS][WIP] Eliminate duplicate lin...
Posted by SparkQA <gi...@git.apache.org>.
Github user SparkQA commented on the issue:
https://github.com/apache/spark/pull/18051
**[Test build #77207 has started](https://amplab.cs.berkeley.edu/jenkins/job/SparkPullRequestBuilder/77207/testReport)** for PR 18051 at commit [`4843950`](https://github.com/apache/spark/commit/4843950694ca3d2dbd607ee889306fcbd8d83fac).
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[GitHub] spark issue #18051: [SPARK-18825][SPARKR][DOCS][WIP] Eliminate duplicate lin...
Posted by felixcheung <gi...@git.apache.org>.
Github user felixcheung commented on the issue:
https://github.com/apache/spark/pull/18051
hmm, so what would be the approach to fix the dup links then, change every `@rdname` to `-method`?
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[GitHub] spark issue #18051: [SPARK-18825][SPARKR][DOCS][WIP] Eliminate duplicate lin...
Posted by actuaryzhang <gi...@git.apache.org>.
Github user actuaryzhang commented on the issue:
https://github.com/apache/spark/pull/18051
@zero323 I really like your thoughts on the docs. As @felixcheung mentioned above, we are doing some cleaning in #18025, which will improve readability and fix the SeeAlso issue.
Regarding making the examples runnable, I would really like to do that. This is not an issue for Jenkins since the examples are tiny. However, that will increase the cran check time significantly and I'm not sure CRAN will allow that.
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[GitHub] spark issue #18051: [SPARK-18825][SPARKR][DOCS][WIP] Eliminate duplicate lin...
Posted by SparkQA <gi...@git.apache.org>.
Github user SparkQA commented on the issue:
https://github.com/apache/spark/pull/18051
**[Test build #77152 has started](https://amplab.cs.berkeley.edu/jenkins/job/SparkPullRequestBuilder/77152/testReport)** for PR 18051 at commit [`b28ec94`](https://github.com/apache/spark/commit/b28ec94b0c0589736b4e3377d160642b0b6181a6).
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[GitHub] spark issue #18051: [SPARK-18825][SPARKR][DOCS][WIP] Eliminate duplicate lin...
Posted by zero323 <gi...@git.apache.org>.
Github user zero323 commented on the issue:
https://github.com/apache/spark/pull/18051
For a moment I thought I found another solution but I was wrong.
I don't think there is a conflict between this and installable package. It won't help with the packaged version (but other packages depending on S4 suffer from the same issue), but we can have an improved online version.
There is one possible alternative - converting all `names` to long version:
```r
#' abs
#'
#' Computes the absolute value.
#'
#' @param x Column to compute on.
#'
#' @rdname abs
#' @name abs-method
#' @family non-aggregate functions
#' @export
#' @examples \dontrun{abs(df$c)}
#' @aliases abs,Column-method
```
This would keep CRAN checks happy and removed duplicates but at the cost of having docs like this:
and making help unusable from R session, requiring:
?SparkR::`abs-method`
instead
?SparkR::abs
I am not sure if you agree, but IMHO this just makes things worse.
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[GitHub] spark pull request #18051: [SPARK-18825][SPARKR][DOCS][WIP] Eliminate duplic...
Posted by zero323 <gi...@git.apache.org>.
Github user zero323 closed the pull request at:
https://github.com/apache/spark/pull/18051
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[GitHub] spark issue #18051: [SPARK-18825][SPARKR][DOCS][WIP] Eliminate duplicate lin...
Posted by SparkQA <gi...@git.apache.org>.
Github user SparkQA commented on the issue:
https://github.com/apache/spark/pull/18051
**[Test build #77206 has started](https://amplab.cs.berkeley.edu/jenkins/job/SparkPullRequestBuilder/77206/testReport)** for PR 18051 at commit [`8392ba5`](https://github.com/apache/spark/commit/8392ba51f4e0b096e9731b0f63f38942555e6f46).
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[GitHub] spark issue #18051: [SPARK-18825][SPARKR][DOCS][WIP] Eliminate duplicate lin...
Posted by felixcheung <gi...@git.apache.org>.
Github user felixcheung commented on the issue:
https://github.com/apache/spark/pull/18051
re: example - agreed, I think @zero323 is proposing that we only run the example when creating the online doc, but not as CRAN (so we keep the dontrun)
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[GitHub] spark issue #18051: [SPARK-18825][SPARKR][DOCS][WIP] Eliminate duplicate lin...
Posted by SparkQA <gi...@git.apache.org>.
Github user SparkQA commented on the issue:
https://github.com/apache/spark/pull/18051
**[Test build #77156 has started](https://amplab.cs.berkeley.edu/jenkins/job/SparkPullRequestBuilder/77156/testReport)** for PR 18051 at commit [`4843950`](https://github.com/apache/spark/commit/4843950694ca3d2dbd607ee889306fcbd8d83fac).
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[GitHub] spark issue #18051: [SPARK-18825][SPARKR][DOCS][WIP] Eliminate duplicate lin...
Posted by AmplabJenkins <gi...@git.apache.org>.
Github user AmplabJenkins commented on the issue:
https://github.com/apache/spark/pull/18051
Test PASSed.
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Test PASSed.
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[GitHub] spark issue #18051: [SPARK-18825][SPARKR][DOCS][WIP] Eliminate duplicate lin...
Posted by zero323 <gi...@git.apache.org>.
Github user zero323 commented on the issue:
https://github.com/apache/spark/pull/18051
Exactly my point. Run examples internally ([it is not hard to patch knitr](https://github.com/zero323/knitr/commit/7a0d8f9ddb9d77a9c235f25aca26131e83c1f6cc) or even `tools::Rd2ex`) to validate examples and improve online docs. #18025 looks great - I'll try to review it when I have a spare moment.
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[GitHub] spark issue #18051: [SPARK-18825][SPARKR][DOCS][WIP] Eliminate duplicate lin...
Posted by SparkQA <gi...@git.apache.org>.
Github user SparkQA commented on the issue:
https://github.com/apache/spark/pull/18051
**[Test build #77156 has finished](https://amplab.cs.berkeley.edu/jenkins/job/SparkPullRequestBuilder/77156/testReport)** for PR 18051 at commit [`4843950`](https://github.com/apache/spark/commit/4843950694ca3d2dbd607ee889306fcbd8d83fac).
* This patch passes all tests.
* This patch merges cleanly.
* This patch adds no public classes.
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[GitHub] spark issue #18051: [SPARK-18825][SPARKR][DOCS][WIP] Eliminate duplicate lin...
Posted by AmplabJenkins <gi...@git.apache.org>.
Github user AmplabJenkins commented on the issue:
https://github.com/apache/spark/pull/18051
Merged build finished. Test PASSed.
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