[jira] [Commented] (SPARK-38174) SparkR documentation build fails in CI
[
https://issues.apache.org/jira/browse/SPARK-38174?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel&focusedCommentId=17490878#comment-17490878
]
Hyukjin Kwon commented on SPARK-38174:
--
Awesome!!!
> SparkR documentation build fails in CI
> --
>
> Key: SPARK-38174
> URL: https://issues.apache.org/jira/browse/SPARK-38174
> Project: Spark
> Issue Type: Test
> Components: Build, SparkR
>Affects Versions: 3.3.0
>Reporter: Hyukjin Kwon
>Priority: Major
>
> SparkR documentation job in GitHub Actions seems to be broken now as below
> (https://github.com/apache/spark/runs/5138914521?check_suite_focus=true):
> {code}
> Writing 'reference/head.html'
> Reading 'man/hint.Rd'
> Writing 'reference/hint.html'
> Reading 'man/histogram.Rd'
> Error in .f(.x[[i]], ...) : Failed to parse Rd in histogram.Rd
> ℹ ReadItem: unknown type 73, perhaps written by later version of R
> Caused by error in `readRDS()`:
> ! ReadItem: unknown type 73, perhaps written by later version of R
> Error: histogram.Rd
> ℹ ReadItem: unknown type 73, perhaps written by later version of R
> Caused by error in `readRDS()`:
> ! ReadItem: unknown type 73, perhaps written by later version of R>
> -->
> Failed to parse Rd in histogram.Rd
> ℹ ReadItem: unknown type 73, perhaps written by later version of R
> Caused by error in `readRDS()`:
> ! ReadItem: unknown type 73, perhaps written by later version of R>
> in process 13417
> Stack trace:
> Process 13346:
> 1. pkgdown::build_site("..")
> 2. pkgdown:::build_site_external(pkg = pkg, examples = examples, ...
> 3. callr::r(function(..., crayon_enabled, crayon_colors, pkgdown_internet) {
> ...
> 4. callr:::get_result(output = out, options)
> 5. throw(newerr, parent = remerr[[2]])
> x callr subprocess failed: Failed to parse Rd in histogram.Rd
> ℹ ReadItem: unknown type 73, perhaps written by later version of R
> Caused by error in `readRDS()`:
> ! ReadItem: unknown type 73, perhaps written by later version of R
> Process 13417:
> 17. (function (..., crayon_enabled, crayon_colors, pkgdown_internet) ...
> 18. pkgdown::build_site(...)
> 19. pkgdown:::build_site_local(pkg = pkg, examples = examples, run_do ...
> 20. pkgdown:::build_reference(pkg, lazy = lazy, examples = examples, ...
> 21. purrr::map(topics, build_reference_topic, pkg = pkg, lazy = lazy, ...
> {code}
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[jira] [Commented] (SPARK-38174) SparkR documentation build fails in CI
[
https://issues.apache.org/jira/browse/SPARK-38174?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel&focusedCommentId=17490877#comment-17490877
]
Maciej Szymkiewicz commented on SPARK-38174:
Done some more digging, and I believe it has been caused by malformed response
from [https://cran.rstudio.com/web/packages/packages.rds.]
{{histogram}} example loads {{ggplot2}}
https://github.com/apache/spark/blob/d4a2e5c55d127218f6ae42925443f7d0588d5875/R/pkg/R/DataFrame.R#L3645
which caused attempt to fetch data from CRAN:
https://github.com/r-lib/downlit/blob/d5622d665ebe4d3529b297aa926fe3c0132c8b81/R/metadata.R#L132-L137
and {{CRAN_package_db}} loads RDS object
{code:r}
> tools::CRAN_package_db
function ()
as.data.frame(read_CRAN_object(CRAN_baseurl_for_web_area(),
"web/packages/packages.rds"),
stringsAsFactors = FALSE)
{code}
If the problem repeats we might try to see if setting
{{deploy.install_metadata: true}} in pkgdown and installing {{ggplot2}} (and
other incidental doc build dependencies), resolves the issue.
> SparkR documentation build fails in CI
> --
>
> Key: SPARK-38174
> URL: https://issues.apache.org/jira/browse/SPARK-38174
> Project: Spark
> Issue Type: Test
> Components: Build, SparkR
>Affects Versions: 3.3.0
>Reporter: Hyukjin Kwon
>Priority: Major
>
> SparkR documentation job in GitHub Actions seems to be broken now as below
> (https://github.com/apache/spark/runs/5138914521?check_suite_focus=true):
> {code}
> Writing 'reference/head.html'
> Reading 'man/hint.Rd'
> Writing 'reference/hint.html'
> Reading 'man/histogram.Rd'
> Error in .f(.x[[i]], ...) : Failed to parse Rd in histogram.Rd
> ℹ ReadItem: unknown type 73, perhaps written by later version of R
> Caused by error in `readRDS()`:
> ! ReadItem: unknown type 73, perhaps written by later version of R
> Error: histogram.Rd
> ℹ ReadItem: unknown type 73, perhaps written by later version of R
> Caused by error in `readRDS()`:
> ! ReadItem: unknown type 73, perhaps written by later version of R>
> -->
> Failed to parse Rd in histogram.Rd
> ℹ ReadItem: unknown type 73, perhaps written by later version of R
> Caused by error in `readRDS()`:
> ! ReadItem: unknown type 73, perhaps written by later version of R>
> in process 13417
> Stack trace:
> Process 13346:
> 1. pkgdown::build_site("..")
> 2. pkgdown:::build_site_external(pkg = pkg, examples = examples, ...
> 3. callr::r(function(..., crayon_enabled, crayon_colors, pkgdown_internet) {
> ...
> 4. callr:::get_result(output = out, options)
> 5. throw(newerr, parent = remerr[[2]])
> x callr subprocess failed: Failed to parse Rd in histogram.Rd
> ℹ ReadItem: unknown type 73, perhaps written by later version of R
> Caused by error in `readRDS()`:
> ! ReadItem: unknown type 73, perhaps written by later version of R
> Process 13417:
> 17. (function (..., crayon_enabled, crayon_colors, pkgdown_internet) ...
> 18. pkgdown::build_site(...)
> 19. pkgdown:::build_site_local(pkg = pkg, examples = examples, run_do ...
> 20. pkgdown:::build_reference(pkg, lazy = lazy, examples = examples, ...
> 21. purrr::map(topics, build_reference_topic, pkg = pkg, lazy = lazy, ...
> {code}
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[jira] [Commented] (SPARK-38174) SparkR documentation build fails in CI
[
https://issues.apache.org/jira/browse/SPARK-38174?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel&focusedCommentId=17490590#comment-17490590
]
Hyukjin Kwon commented on SPARK-38174:
--
Thanks for investigation and monitoring [~zero323] and [~dongjoon]. Seems it
got fixed so let me resolve this for now.
> SparkR documentation build fails in CI
> --
>
> Key: SPARK-38174
> URL: https://issues.apache.org/jira/browse/SPARK-38174
> Project: Spark
> Issue Type: Test
> Components: Build, SparkR
>Affects Versions: 3.3.0
>Reporter: Hyukjin Kwon
>Priority: Major
>
> SparkR documentation job in GitHub Actions seems to be broken now as below
> (https://github.com/apache/spark/runs/5138914521?check_suite_focus=true):
> {code}
> Writing 'reference/head.html'
> Reading 'man/hint.Rd'
> Writing 'reference/hint.html'
> Reading 'man/histogram.Rd'
> Error in .f(.x[[i]], ...) : Failed to parse Rd in histogram.Rd
> ℹ ReadItem: unknown type 73, perhaps written by later version of R
> Caused by error in `readRDS()`:
> ! ReadItem: unknown type 73, perhaps written by later version of R
> Error: histogram.Rd
> ℹ ReadItem: unknown type 73, perhaps written by later version of R
> Caused by error in `readRDS()`:
> ! ReadItem: unknown type 73, perhaps written by later version of R>
> -->
> Failed to parse Rd in histogram.Rd
> ℹ ReadItem: unknown type 73, perhaps written by later version of R
> Caused by error in `readRDS()`:
> ! ReadItem: unknown type 73, perhaps written by later version of R>
> in process 13417
> Stack trace:
> Process 13346:
> 1. pkgdown::build_site("..")
> 2. pkgdown:::build_site_external(pkg = pkg, examples = examples, ...
> 3. callr::r(function(..., crayon_enabled, crayon_colors, pkgdown_internet) {
> ...
> 4. callr:::get_result(output = out, options)
> 5. throw(newerr, parent = remerr[[2]])
> x callr subprocess failed: Failed to parse Rd in histogram.Rd
> ℹ ReadItem: unknown type 73, perhaps written by later version of R
> Caused by error in `readRDS()`:
> ! ReadItem: unknown type 73, perhaps written by later version of R
> Process 13417:
> 17. (function (..., crayon_enabled, crayon_colors, pkgdown_internet) ...
> 18. pkgdown::build_site(...)
> 19. pkgdown:::build_site_local(pkg = pkg, examples = examples, run_do ...
> 20. pkgdown:::build_reference(pkg, lazy = lazy, examples = examples, ...
> 21. purrr::map(topics, build_reference_topic, pkg = pkg, lazy = lazy, ...
> {code}
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[jira] [Commented] (SPARK-38174) SparkR documentation build fails in CI
[
https://issues.apache.org/jira/browse/SPARK-38174?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel&focusedCommentId=17490574#comment-17490574
]
Maciej Szymkiewicz commented on SPARK-38174:
I also compared the last failing log and the next that passed
(https://github.com/apache/spark/runs/5144322617?check_suite_focus=true), but
nothing really stands out, and virtual image version is still 20220207.1.
Histogram looks unremarkable and, since files are written for each build, we
can reject "later version" as a plausible explanation.
It seems like the issue can arise if files were somehow corrupt, but I cannot
see why on this particular one.
It seems like it failed pretty deep into core R utilities
{code}
45. base:::as.data.frame(read_CRAN_object(CRAN_baseurl_for_web_area() ...
46. tools:::read_CRAN_object(CRAN_baseurl_for_web_area(), "web/packag ...
47. base:::readRDS(con)
48. base:::.handleSimpleError(function (err) ...
49. pkgdown:::h(simpleError(msg, call))
50. rlang:::abort(msg, parent = err)
51. rlang:::signal_abort(cnd, .file)
52. base:::signalCondition(cnd)
53. (function (e) ...
{code}
and I none of the packages that we install specifically for docs R builds are
likely to the culprit ‒ these are mostly font utils.
Doesn't seem like CRAN deb repos provide changelogs, so I am not sure if
something changed there.
I guess it is something to monitor, unless anyone has any other ideas where to
look for the source of the problem.
> SparkR documentation build fails in CI
> --
>
> Key: SPARK-38174
> URL: https://issues.apache.org/jira/browse/SPARK-38174
> Project: Spark
> Issue Type: Test
> Components: Build, SparkR
>Affects Versions: 3.3.0
>Reporter: Hyukjin Kwon
>Priority: Major
>
> SparkR documentation job in GitHub Actions seems to be broken now as below
> (https://github.com/apache/spark/runs/5138914521?check_suite_focus=true):
> {code}
> Writing 'reference/head.html'
> Reading 'man/hint.Rd'
> Writing 'reference/hint.html'
> Reading 'man/histogram.Rd'
> Error in .f(.x[[i]], ...) : Failed to parse Rd in histogram.Rd
> ℹ ReadItem: unknown type 73, perhaps written by later version of R
> Caused by error in `readRDS()`:
> ! ReadItem: unknown type 73, perhaps written by later version of R
> Error: histogram.Rd
> ℹ ReadItem: unknown type 73, perhaps written by later version of R
> Caused by error in `readRDS()`:
> ! ReadItem: unknown type 73, perhaps written by later version of R>
> -->
> Failed to parse Rd in histogram.Rd
> ℹ ReadItem: unknown type 73, perhaps written by later version of R
> Caused by error in `readRDS()`:
> ! ReadItem: unknown type 73, perhaps written by later version of R>
> in process 13417
> Stack trace:
> Process 13346:
> 1. pkgdown::build_site("..")
> 2. pkgdown:::build_site_external(pkg = pkg, examples = examples, ...
> 3. callr::r(function(..., crayon_enabled, crayon_colors, pkgdown_internet) {
> ...
> 4. callr:::get_result(output = out, options)
> 5. throw(newerr, parent = remerr[[2]])
> x callr subprocess failed: Failed to parse Rd in histogram.Rd
> ℹ ReadItem: unknown type 73, perhaps written by later version of R
> Caused by error in `readRDS()`:
> ! ReadItem: unknown type 73, perhaps written by later version of R
> Process 13417:
> 17. (function (..., crayon_enabled, crayon_colors, pkgdown_internet) ...
> 18. pkgdown::build_site(...)
> 19. pkgdown:::build_site_local(pkg = pkg, examples = examples, run_do ...
> 20. pkgdown:::build_reference(pkg, lazy = lazy, examples = examples, ...
> 21. purrr::map(topics, build_reference_topic, pkg = pkg, lazy = lazy, ...
> {code}
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[jira] [Commented] (SPARK-38174) SparkR documentation build fails in CI
[
https://issues.apache.org/jira/browse/SPARK-38174?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel&focusedCommentId=17490457#comment-17490457
]
Dongjoon Hyun commented on SPARK-38174:
---
Yes, it's green now. It must be some transient issue.
- https://github.com/apache/spark/commits/master
> SparkR documentation build fails in CI
> --
>
> Key: SPARK-38174
> URL: https://issues.apache.org/jira/browse/SPARK-38174
> Project: Spark
> Issue Type: Test
> Components: Build, SparkR
>Affects Versions: 3.3.0
>Reporter: Hyukjin Kwon
>Priority: Major
>
> SparkR documentation job in GitHub Actions seems to be broken now as below
> (https://github.com/apache/spark/runs/5138914521?check_suite_focus=true):
> {code}
> Writing 'reference/head.html'
> Reading 'man/hint.Rd'
> Writing 'reference/hint.html'
> Reading 'man/histogram.Rd'
> Error in .f(.x[[i]], ...) : Failed to parse Rd in histogram.Rd
> ℹ ReadItem: unknown type 73, perhaps written by later version of R
> Caused by error in `readRDS()`:
> ! ReadItem: unknown type 73, perhaps written by later version of R
> Error: histogram.Rd
> ℹ ReadItem: unknown type 73, perhaps written by later version of R
> Caused by error in `readRDS()`:
> ! ReadItem: unknown type 73, perhaps written by later version of R>
> -->
> Failed to parse Rd in histogram.Rd
> ℹ ReadItem: unknown type 73, perhaps written by later version of R
> Caused by error in `readRDS()`:
> ! ReadItem: unknown type 73, perhaps written by later version of R>
> in process 13417
> Stack trace:
> Process 13346:
> 1. pkgdown::build_site("..")
> 2. pkgdown:::build_site_external(pkg = pkg, examples = examples, ...
> 3. callr::r(function(..., crayon_enabled, crayon_colors, pkgdown_internet) {
> ...
> 4. callr:::get_result(output = out, options)
> 5. throw(newerr, parent = remerr[[2]])
> x callr subprocess failed: Failed to parse Rd in histogram.Rd
> ℹ ReadItem: unknown type 73, perhaps written by later version of R
> Caused by error in `readRDS()`:
> ! ReadItem: unknown type 73, perhaps written by later version of R
> Process 13417:
> 17. (function (..., crayon_enabled, crayon_colors, pkgdown_internet) ...
> 18. pkgdown::build_site(...)
> 19. pkgdown:::build_site_local(pkg = pkg, examples = examples, run_do ...
> 20. pkgdown:::build_reference(pkg, lazy = lazy, examples = examples, ...
> 21. purrr::map(topics, build_reference_topic, pkg = pkg, lazy = lazy, ...
> {code}
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[jira] [Commented] (SPARK-38174) SparkR documentation build fails in CI
[
https://issues.apache.org/jira/browse/SPARK-38174?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel&focusedCommentId=17490344#comment-17490344
]
Maciej Szymkiewicz commented on SPARK-38174:
And now, it is green again :/
> SparkR documentation build fails in CI
> --
>
> Key: SPARK-38174
> URL: https://issues.apache.org/jira/browse/SPARK-38174
> Project: Spark
> Issue Type: Test
> Components: Build, SparkR
>Affects Versions: 3.3.0
>Reporter: Hyukjin Kwon
>Priority: Major
>
> SparkR documentation job in GitHub Actions seems to be broken now as below
> (https://github.com/apache/spark/runs/5138914521?check_suite_focus=true):
> {code}
> Writing 'reference/head.html'
> Reading 'man/hint.Rd'
> Writing 'reference/hint.html'
> Reading 'man/histogram.Rd'
> Error in .f(.x[[i]], ...) : Failed to parse Rd in histogram.Rd
> ℹ ReadItem: unknown type 73, perhaps written by later version of R
> Caused by error in `readRDS()`:
> ! ReadItem: unknown type 73, perhaps written by later version of R
> Error: histogram.Rd
> ℹ ReadItem: unknown type 73, perhaps written by later version of R
> Caused by error in `readRDS()`:
> ! ReadItem: unknown type 73, perhaps written by later version of R>
> -->
> Failed to parse Rd in histogram.Rd
> ℹ ReadItem: unknown type 73, perhaps written by later version of R
> Caused by error in `readRDS()`:
> ! ReadItem: unknown type 73, perhaps written by later version of R>
> in process 13417
> Stack trace:
> Process 13346:
> 1. pkgdown::build_site("..")
> 2. pkgdown:::build_site_external(pkg = pkg, examples = examples, ...
> 3. callr::r(function(..., crayon_enabled, crayon_colors, pkgdown_internet) {
> ...
> 4. callr:::get_result(output = out, options)
> 5. throw(newerr, parent = remerr[[2]])
> x callr subprocess failed: Failed to parse Rd in histogram.Rd
> ℹ ReadItem: unknown type 73, perhaps written by later version of R
> Caused by error in `readRDS()`:
> ! ReadItem: unknown type 73, perhaps written by later version of R
> Process 13417:
> 17. (function (..., crayon_enabled, crayon_colors, pkgdown_internet) ...
> 18. pkgdown::build_site(...)
> 19. pkgdown:::build_site_local(pkg = pkg, examples = examples, run_do ...
> 20. pkgdown:::build_reference(pkg, lazy = lazy, examples = examples, ...
> 21. purrr::map(topics, build_reference_topic, pkg = pkg, lazy = lazy, ...
> {code}
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[jira] [Commented] (SPARK-38174) SparkR documentation build fails in CI
[
https://issues.apache.org/jira/browse/SPARK-38174?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel&focusedCommentId=17490227#comment-17490227
]
Maciej Szymkiewicz commented on SPARK-38174:
I run R doc builds against 3d285c11b611e63d6ebb0b209f52d6ec7a61debe using R
4.0.3, 4.1.1 and 4.1.2 conda envs, but so far couldn't reproduce the error.
> SparkR documentation build fails in CI
> --
>
> Key: SPARK-38174
> URL: https://issues.apache.org/jira/browse/SPARK-38174
> Project: Spark
> Issue Type: Test
> Components: Build, SparkR
>Affects Versions: 3.3.0
>Reporter: Hyukjin Kwon
>Priority: Major
>
> SparkR documentation job in GitHub Actions seems to be broken now as below
> (https://github.com/apache/spark/runs/5138914521?check_suite_focus=true):
> {code}
> Writing 'reference/head.html'
> Reading 'man/hint.Rd'
> Writing 'reference/hint.html'
> Reading 'man/histogram.Rd'
> Error in .f(.x[[i]], ...) : Failed to parse Rd in histogram.Rd
> ℹ ReadItem: unknown type 73, perhaps written by later version of R
> Caused by error in `readRDS()`:
> ! ReadItem: unknown type 73, perhaps written by later version of R
> Error: histogram.Rd
> ℹ ReadItem: unknown type 73, perhaps written by later version of R
> Caused by error in `readRDS()`:
> ! ReadItem: unknown type 73, perhaps written by later version of R>
> -->
> Failed to parse Rd in histogram.Rd
> ℹ ReadItem: unknown type 73, perhaps written by later version of R
> Caused by error in `readRDS()`:
> ! ReadItem: unknown type 73, perhaps written by later version of R>
> in process 13417
> Stack trace:
> Process 13346:
> 1. pkgdown::build_site("..")
> 2. pkgdown:::build_site_external(pkg = pkg, examples = examples, ...
> 3. callr::r(function(..., crayon_enabled, crayon_colors, pkgdown_internet) {
> ...
> 4. callr:::get_result(output = out, options)
> 5. throw(newerr, parent = remerr[[2]])
> x callr subprocess failed: Failed to parse Rd in histogram.Rd
> ℹ ReadItem: unknown type 73, perhaps written by later version of R
> Caused by error in `readRDS()`:
> ! ReadItem: unknown type 73, perhaps written by later version of R
> Process 13417:
> 17. (function (..., crayon_enabled, crayon_colors, pkgdown_internet) ...
> 18. pkgdown::build_site(...)
> 19. pkgdown:::build_site_local(pkg = pkg, examples = examples, run_do ...
> 20. pkgdown:::build_reference(pkg, lazy = lazy, examples = examples, ...
> 21. purrr::map(topics, build_reference_topic, pkg = pkg, lazy = lazy, ...
> {code}
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[jira] [Commented] (SPARK-38174) SparkR documentation build fails in CI
[
https://issues.apache.org/jira/browse/SPARK-38174?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel&focusedCommentId=17490180#comment-17490180
]
Maciej Szymkiewicz commented on SPARK-38174:
The most obvious change, but maybe unrelated is switch from
{code}
Environment: ubuntu-20.04
Version: 20220131.1
{code}
to
{code}
Environment: ubuntu-20.04
Version: 20220207.1
{code}
> SparkR documentation build fails in CI
> --
>
> Key: SPARK-38174
> URL: https://issues.apache.org/jira/browse/SPARK-38174
> Project: Spark
> Issue Type: Test
> Components: Build, SparkR
>Affects Versions: 3.3.0
>Reporter: Hyukjin Kwon
>Priority: Major
>
> SparkR documentation job in GitHub Actions seems to be broken now as below
> (https://github.com/apache/spark/runs/5138914521?check_suite_focus=true):
> {code}
> Writing 'reference/head.html'
> Reading 'man/hint.Rd'
> Writing 'reference/hint.html'
> Reading 'man/histogram.Rd'
> Error in .f(.x[[i]], ...) : Failed to parse Rd in histogram.Rd
> ℹ ReadItem: unknown type 73, perhaps written by later version of R
> Caused by error in `readRDS()`:
> ! ReadItem: unknown type 73, perhaps written by later version of R
> Error: histogram.Rd
> ℹ ReadItem: unknown type 73, perhaps written by later version of R
> Caused by error in `readRDS()`:
> ! ReadItem: unknown type 73, perhaps written by later version of R>
> -->
> Failed to parse Rd in histogram.Rd
> ℹ ReadItem: unknown type 73, perhaps written by later version of R
> Caused by error in `readRDS()`:
> ! ReadItem: unknown type 73, perhaps written by later version of R>
> in process 13417
> Stack trace:
> Process 13346:
> 1. pkgdown::build_site("..")
> 2. pkgdown:::build_site_external(pkg = pkg, examples = examples, ...
> 3. callr::r(function(..., crayon_enabled, crayon_colors, pkgdown_internet) {
> ...
> 4. callr:::get_result(output = out, options)
> 5. throw(newerr, parent = remerr[[2]])
> x callr subprocess failed: Failed to parse Rd in histogram.Rd
> ℹ ReadItem: unknown type 73, perhaps written by later version of R
> Caused by error in `readRDS()`:
> ! ReadItem: unknown type 73, perhaps written by later version of R
> Process 13417:
> 17. (function (..., crayon_enabled, crayon_colors, pkgdown_internet) ...
> 18. pkgdown::build_site(...)
> 19. pkgdown:::build_site_local(pkg = pkg, examples = examples, run_do ...
> 20. pkgdown:::build_reference(pkg, lazy = lazy, examples = examples, ...
> 21. purrr::map(topics, build_reference_topic, pkg = pkg, lazy = lazy, ...
> {code}
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[jira] [Commented] (SPARK-38174) SparkR documentation build fails in CI
[
https://issues.apache.org/jira/browse/SPARK-38174?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel&focusedCommentId=17490173#comment-17490173
]
Maciej Szymkiewicz commented on SPARK-38174:
Also, all R dependencies for documentation build seem to be unchanged between
https://github.com/apache/spark/runs/5136885171?check_suite_focus=true and
https://github.com/apache/spark/runs/5138402728?check_suite_focus=true
> SparkR documentation build fails in CI
> --
>
> Key: SPARK-38174
> URL: https://issues.apache.org/jira/browse/SPARK-38174
> Project: Spark
> Issue Type: Test
> Components: Build, SparkR
>Affects Versions: 3.3.0
>Reporter: Hyukjin Kwon
>Priority: Major
>
> SparkR documentation job in GitHub Actions seems to be broken now as below
> (https://github.com/apache/spark/runs/5138914521?check_suite_focus=true):
> {code}
> Writing 'reference/head.html'
> Reading 'man/hint.Rd'
> Writing 'reference/hint.html'
> Reading 'man/histogram.Rd'
> Error in .f(.x[[i]], ...) : Failed to parse Rd in histogram.Rd
> ℹ ReadItem: unknown type 73, perhaps written by later version of R
> Caused by error in `readRDS()`:
> ! ReadItem: unknown type 73, perhaps written by later version of R
> Error: histogram.Rd
> ℹ ReadItem: unknown type 73, perhaps written by later version of R
> Caused by error in `readRDS()`:
> ! ReadItem: unknown type 73, perhaps written by later version of R>
> -->
> Failed to parse Rd in histogram.Rd
> ℹ ReadItem: unknown type 73, perhaps written by later version of R
> Caused by error in `readRDS()`:
> ! ReadItem: unknown type 73, perhaps written by later version of R>
> in process 13417
> Stack trace:
> Process 13346:
> 1. pkgdown::build_site("..")
> 2. pkgdown:::build_site_external(pkg = pkg, examples = examples, ...
> 3. callr::r(function(..., crayon_enabled, crayon_colors, pkgdown_internet) {
> ...
> 4. callr:::get_result(output = out, options)
> 5. throw(newerr, parent = remerr[[2]])
> x callr subprocess failed: Failed to parse Rd in histogram.Rd
> ℹ ReadItem: unknown type 73, perhaps written by later version of R
> Caused by error in `readRDS()`:
> ! ReadItem: unknown type 73, perhaps written by later version of R
> Process 13417:
> 17. (function (..., crayon_enabled, crayon_colors, pkgdown_internet) ...
> 18. pkgdown::build_site(...)
> 19. pkgdown:::build_site_local(pkg = pkg, examples = examples, run_do ...
> 20. pkgdown:::build_reference(pkg, lazy = lazy, examples = examples, ...
> 21. purrr::map(topics, build_reference_topic, pkg = pkg, lazy = lazy, ...
> {code}
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[jira] [Commented] (SPARK-38174) SparkR documentation build fails in CI
[
https://issues.apache.org/jira/browse/SPARK-38174?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel&focusedCommentId=17490163#comment-17490163
]
Maciej Szymkiewicz commented on SPARK-38174:
Not a clue, but I am trying to reproduce this.
Stating the obvious ‒ no changes where made to the R tree lately and pkgdown
has pinned version, so either another package or some system dependency.
> SparkR documentation build fails in CI
> --
>
> Key: SPARK-38174
> URL: https://issues.apache.org/jira/browse/SPARK-38174
> Project: Spark
> Issue Type: Test
> Components: Build, SparkR
>Affects Versions: 3.3.0
>Reporter: Hyukjin Kwon
>Priority: Major
>
> SparkR documentation job in GitHub Actions seems to be broken now as below
> (https://github.com/apache/spark/runs/5138914521?check_suite_focus=true):
> {code}
> Writing 'reference/head.html'
> Reading 'man/hint.Rd'
> Writing 'reference/hint.html'
> Reading 'man/histogram.Rd'
> Error in .f(.x[[i]], ...) : Failed to parse Rd in histogram.Rd
> ℹ ReadItem: unknown type 73, perhaps written by later version of R
> Caused by error in `readRDS()`:
> ! ReadItem: unknown type 73, perhaps written by later version of R
> Error: histogram.Rd
> ℹ ReadItem: unknown type 73, perhaps written by later version of R
> Caused by error in `readRDS()`:
> ! ReadItem: unknown type 73, perhaps written by later version of R>
> -->
> Failed to parse Rd in histogram.Rd
> ℹ ReadItem: unknown type 73, perhaps written by later version of R
> Caused by error in `readRDS()`:
> ! ReadItem: unknown type 73, perhaps written by later version of R>
> in process 13417
> Stack trace:
> Process 13346:
> 1. pkgdown::build_site("..")
> 2. pkgdown:::build_site_external(pkg = pkg, examples = examples, ...
> 3. callr::r(function(..., crayon_enabled, crayon_colors, pkgdown_internet) {
> ...
> 4. callr:::get_result(output = out, options)
> 5. throw(newerr, parent = remerr[[2]])
> x callr subprocess failed: Failed to parse Rd in histogram.Rd
> ℹ ReadItem: unknown type 73, perhaps written by later version of R
> Caused by error in `readRDS()`:
> ! ReadItem: unknown type 73, perhaps written by later version of R
> Process 13417:
> 17. (function (..., crayon_enabled, crayon_colors, pkgdown_internet) ...
> 18. pkgdown::build_site(...)
> 19. pkgdown:::build_site_local(pkg = pkg, examples = examples, run_do ...
> 20. pkgdown:::build_reference(pkg, lazy = lazy, examples = examples, ...
> 21. purrr::map(topics, build_reference_topic, pkg = pkg, lazy = lazy, ...
> {code}
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[jira] [Commented] (SPARK-38174) SparkR documentation build fails in CI
[
https://issues.apache.org/jira/browse/SPARK-38174?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel&focusedCommentId=17490151#comment-17490151
]
Hyukjin Kwon commented on SPARK-38174:
--
Possibly related to SPARK-37474. [~zero323], do you have any clue on this? cc
[~dongjoon] FYI
> SparkR documentation build fails in CI
> --
>
> Key: SPARK-38174
> URL: https://issues.apache.org/jira/browse/SPARK-38174
> Project: Spark
> Issue Type: Test
> Components: Build, SparkR
>Affects Versions: 3.3.0
>Reporter: Hyukjin Kwon
>Priority: Major
>
> SparkR documentation job in GitHub Actions seems to be broken now as below
> (https://github.com/apache/spark/runs/5138914521?check_suite_focus=true):
> {code}
> Writing 'reference/head.html'
> Reading 'man/hint.Rd'
> Writing 'reference/hint.html'
> Reading 'man/histogram.Rd'
> Error in .f(.x[[i]], ...) : Failed to parse Rd in histogram.Rd
> ℹ ReadItem: unknown type 73, perhaps written by later version of R
> Caused by error in `readRDS()`:
> ! ReadItem: unknown type 73, perhaps written by later version of R
> Error: histogram.Rd
> ℹ ReadItem: unknown type 73, perhaps written by later version of R
> Caused by error in `readRDS()`:
> ! ReadItem: unknown type 73, perhaps written by later version of R>
> -->
> Failed to parse Rd in histogram.Rd
> ℹ ReadItem: unknown type 73, perhaps written by later version of R
> Caused by error in `readRDS()`:
> ! ReadItem: unknown type 73, perhaps written by later version of R>
> in process 13417
> Stack trace:
> Process 13346:
> 1. pkgdown::build_site("..")
> 2. pkgdown:::build_site_external(pkg = pkg, examples = examples, ...
> 3. callr::r(function(..., crayon_enabled, crayon_colors, pkgdown_internet) {
> ...
> 4. callr:::get_result(output = out, options)
> 5. throw(newerr, parent = remerr[[2]])
> x callr subprocess failed: Failed to parse Rd in histogram.Rd
> ℹ ReadItem: unknown type 73, perhaps written by later version of R
> Caused by error in `readRDS()`:
> ! ReadItem: unknown type 73, perhaps written by later version of R
> Process 13417:
> 17. (function (..., crayon_enabled, crayon_colors, pkgdown_internet) ...
> 18. pkgdown::build_site(...)
> 19. pkgdown:::build_site_local(pkg = pkg, examples = examples, run_do ...
> 20. pkgdown:::build_reference(pkg, lazy = lazy, examples = examples, ...
> 21. purrr::map(topics, build_reference_topic, pkg = pkg, lazy = lazy, ...
> {code}
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