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neurogenomics / rworkflows

Continuous integration for R packages. 🔀 Automates testing ✅, documentation website building 📦, & containerised deployment 🐳.
https://neurogenomics.github.io/rworkflows/
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Windows GHA: `Error: Error: node stack overflow` #56

Closed bschilder closed 1 year ago

bschilder commented 1 year ago

1. Bug description

Error: Error: node stack overflow error on Windows GHA.

Console output

One of the tests fails, but can't seem to find which one or why.

[ FAIL 1 | WARN 0 | SKIP 1 | PASS 84 ]

══ Skipped tests ═══════════════════════════════════════════════════════════════
• empty test (1)

══ Failed tests ════════════════════════════════════════════════════════════════
Error: Error: node stack overflow
Execution halted

Expected behaviour

Runs all the way through on all OS

2. Reproducible example

https://github.com/neurogenomics/rworkflows/actions/runs/4863237498/jobs/8670667942

bschilder commented 1 year ago

Here's the full output. Seems to be related to the usage of "...". Perhaps me using "..." in the Roxygen notes of get_description causes this (only on windows)?

2023-06-17T12:02:28.0513055Z ── Test failures ───────────────────────────────────────────────── testthat ────
2023-06-17T12:02:28.0513361Z 
2023-06-17T12:02:28.0513832Z > # This file is part of the standard setup for testthat.
2023-06-17T12:02:28.0514347Z > # It is recommended that you do not modify it.
2023-06-17T12:02:28.0514714Z > #
2023-06-17T12:02:28.0515156Z > # Where should you do additional test configuration?
2023-06-17T12:02:28.0515640Z > # Learn more about the roles of various files in:
2023-06-17T12:02:28.0516154Z > # * https://r-pkgs.org/tests.html
2023-06-17T12:02:28.0516807Z > # * https://testthat.r-lib.org/reference/test_package.html#special-files
2023-06-17T12:02:28.0517172Z > 
2023-06-17T12:02:28.0517474Z > library(testthat)
2023-06-17T12:02:28.0517817Z > library(rworkflows)
2023-06-17T12:02:28.0518107Z > 
2023-06-17T12:02:28.0518430Z > test_check("rworkflows")
2023-06-17T12:02:28.0518877Z Constructing DESCRIPTION files for 1 R packages.
2023-06-17T12:02:28.0519342Z Constructing DESCRIPTION for: GenomicRanges
2023-06-17T12:02:28.0519985Z trying URL 'https://github.com/neurogenomics/templateR/raw/master/DESCRIPTION'
2023-06-17T12:02:28.0520621Z Content type 'text/plain; charset=utf-8' length 707 bytes
2023-06-17T12:02:28.0521067Z ==================================================
2023-06-17T12:02:28.0521418Z downloaded 707 bytes
2023-06-17T12:02:28.0521645Z 
2023-06-17T12:02:28.0521959Z Updating: Package --> MyPackageName
2023-06-17T12:02:28.0522497Z Updating: Title --> This Package Does Awesome Stuff
2023-06-17T12:02:28.0523312Z Updating: Description --> MyPackageName does several awesome things. Describe thing1. Describe thing2. Describe thing3.
2023-06-17T12:02:28.0524129Z Updating: Authors --> yourGivenName yourFamilyName <yourEmail@email.com> [cre] (yourOrcidId)
2023-06-17T12:02:28.0524677Z Updating: Depends --> R (>= 4.3)
2023-06-17T12:02:28.0525028Z Deleting field: Suggests
2023-06-17T12:02:28.0525533Z Updating: biocViews --> Genetics, SystemsBiology
2023-06-17T12:02:28.0526132Z Updating: URL --> https://github.com/OwnerName/MyPackageName
2023-06-17T12:02:28.0526820Z Updating: BugReports --> https://github.com/OwnerName/MyPackageName/issues
2023-06-17T12:02:28.0527587Z Saving updated file: C:\Users\RUNNER~1\AppData\Local\Temp\RtmpElszvU/working_dir\Rtmp4KHWyF\DESCRIPTIONbd4403e41d7
2023-06-17T12:02:28.0528440Z Cannot find DESCRIPTION for: typoooo
2023-06-17T12:02:28.0528884Z Cannot find DESCRIPTION file for: typoooo
2023-06-17T12:02:28.0529515Z Searching for DESCRIPTION file(s) in R repositories: BioCsoft, BioCann, BioCexp, BioCworkflows, CRAN
2023-06-17T12:02:28.0530005Z Importing database: BioCsoft
2023-06-17T12:02:28.0530361Z Importing database: BioCann
2023-06-17T12:02:28.0557403Z Importing database: BioCexp
2023-06-17T12:02:28.0557785Z Importing database: BioCworkflows
2023-06-17T12:02:28.0558103Z Importing database: CRAN
2023-06-17T12:02:28.0558497Z 0 DESCRIPTION files found in CRAN/Bioc. Returning NULL.
2023-06-17T12:02:28.0558874Z Cannot import DESCRIPTION file: typo
2023-06-17T12:02:28.0559230Z Cannot import DESCRIPTION file: DESCRIPTION
2023-06-17T12:02:28.0559969Z trying URL 'https://github.com/neurogenomics/MAGMA_Celltyping/raw/master/DESCRIPTION'
2023-06-17T12:02:28.0560561Z Content type 'text/plain; charset=utf-8' length 2110 bytes
2023-06-17T12:02:28.0561192Z ==================================================
2023-06-17T12:02:28.0561478Z downloaded 2110 bytes
2023-06-17T12:02:28.0561631Z 
2023-06-17T12:02:28.0561845Z Cannot find DESCRIPTION for: MAGMA_Celltyping
2023-06-17T12:02:28.0562203Z Cannot find DESCRIPTION for: ggtree
2023-06-17T12:02:28.0562716Z Requested package ("ggtree") != retrieved package ("rworkflows") in DESCRIPTION. Returning NULL.
2023-06-17T12:02:28.0563362Z Searching for DESCRIPTION file(s) in R repositories: BioCsoft, BioCann, BioCexp, BioCworkflows, CRAN
2023-06-17T12:02:28.0563788Z Importing database: BioCsoft
2023-06-17T12:02:28.0564093Z Importing database: BioCann
2023-06-17T12:02:28.0564391Z Importing database: BioCexp
2023-06-17T12:02:28.0564691Z Importing database: BioCworkflows
2023-06-17T12:02:28.0564995Z Importing database: CRAN
2023-06-17T12:02:28.0565366Z Constructing DESCRIPTION files for 1 R packages.
2023-06-17T12:02:28.0565737Z Constructing DESCRIPTION for: ggtree
2023-06-17T12:02:28.0566174Z Currently running on GITHUB_ACTION: __neurogenomics_rworkflows
2023-06-17T12:02:28.0566569Z Finding hex sticker(s) for 1 package(s).
2023-06-17T12:02:28.0566900Z Finding hex sticker(s) for 1 package(s).
2023-06-17T12:02:28.0567324Z Currently running on GITHUB_ACTION: __neurogenomics_rworkflows
2023-06-17T12:02:28.0567636Z Hello world
2023-06-17T12:02:28.0567834Z [1] 0
2023-06-17T12:02:28.0568125Z Finding hex sticker(s) for 1 package(s).
2023-06-17T12:02:28.0568420Z Adding CRAN release version.
2023-06-17T12:02:28.0568694Z Adding CRAN checks.
2023-06-17T12:02:28.0569069Z Adding CRAN downloads: last-month
2023-06-17T12:02:28.0569457Z Adding CRAN downloads: grand-total
2023-06-17T12:02:28.0569730Z Adding license.
2023-06-17T12:02:28.0569961Z Adding DOI.
2023-06-17T12:02:28.0570186Z Adding lifecycle.
2023-06-17T12:02:28.0570432Z Adding version.
2023-06-17T12:02:28.0570674Z Adding code size
2023-06-17T12:02:28.0570912Z Adding commit.
2023-06-17T12:02:28.0571155Z Adding actions.
2023-06-17T12:02:28.0571376Z Adding codecov.
2023-06-17T12:02:28.0571611Z Adding authors.
2023-06-17T12:02:28.0572221Z <img src="https://github.com/neurogenomics/rworkflows/raw/master/inst/hex/hex.png" title="Hex sticker for rworkflows" height="300"><br>
2023-06-17T12:02:28.0573078Z [![](https://www.r-pkg.org/badges/version/rworkflows?color=black)](https://cran.r-project.org/package=rworkflows)
2023-06-17T12:02:28.0574239Z [![CRAN checks](https://badges.cranchecks.info/summary/rworkflows.svg)](https://cran.r-project.org/web/checks/check_results_rworkflows.html)
2023-06-17T12:02:28.0575174Z [![](http://cranlogs.r-pkg.org/badges/last-month/rworkflows?color=black)](https://cran.r-project.org/package=rworkflows)
2023-06-17T12:02:28.0576060Z [![](http://cranlogs.r-pkg.org/badges/grand-total/rworkflows?color=black)](https://cran.r-project.org/package=rworkflows)
2023-06-17T12:02:28.0576948Z [![License: GPL-3](https://img.shields.io/badge/license-GPL--3-blue.svg)](https://cran.r-project.org/web/licenses/GPL-3)
2023-06-17T12:02:28.0577899Z [![](https://img.shields.io/badge/doi-doi:000000-blue.svg)](https://doi.org/doi:000000)
2023-06-17T12:02:28.0579013Z ##[error]Error: R CMD check found ERRORs
2023-06-17T12:02:28.0580268Z [![](https://img.shields.io/badge/lifecycle-experimental-orange.svg)](https://lifecycle.r-lib.org/articles/stages.html#experimental)
2023-06-17T12:02:28.0581009Z <br>
2023-06-17T12:02:28.0581871Z [![](https://img.shields.io/badge/devel%20version-0.99.10-black.svg)](https://github.com/neurogenomics/rworkflows)
2023-06-17T12:02:28.0582918Z [![](https://img.shields.io/github/languages/code-size/neurogenomics/rworkflows.svg)](https://github.com/neurogenomics/rworkflows)
2023-06-17T12:02:28.0583982Z [![](https://img.shields.io/github/last-commit/neurogenomics/rworkflows.svg)](https://github.com/neurogenomics/rworkflows/commits/master)
2023-06-17T12:02:28.0584503Z <br>
2023-06-17T12:02:28.0585247Z [![R build status](https://github.com/neurogenomics/rworkflows/workflows/rworkflow/badge.svg)](https://github.com/neurogenomics/rworkflows/actions)
2023-06-17T12:02:28.0586354Z [![](https://codecov.io/gh/neurogenomics/rworkflows/branch/master/graph/badge.svg)](https://codecov.io/gh/neurogenomics/rworkflows)
2023-06-17T12:02:28.0586861Z <br>
2023-06-17T12:02:28.0588144Z <a href="https://app.codecov.io/gh/neurogenomics/rworkflows/tree/master" target='_blank'><img src="https://codecov.io/gh/neurogenomics/rworkflows/branch/master/graphs/sunburst.svg" title="Codecov sunburst graph" width="200" height="50" style="vertical-align: top;"></a>
2023-06-17T12:02:28.0589781Z <a href="https://app.codecov.io/gh/neurogenomics/rworkflows/tree/master" target='_blank'><img src="https://codecov.io/gh/neurogenomics/rworkflows/branch/master/graphs/tree.svg" title="Codecov tree graph" width="200" height="50" style="vertical-align: top;"></a>
2023-06-17T12:02:28.0591384Z <a href="https://app.codecov.io/gh/neurogenomics/rworkflows/tree/master" target='_blank'><img src="https://codecov.io/gh/neurogenomics/rworkflows/branch/master/graphs/icicle.svg" title="Codecov icicle graph" width="200" height="50" style="vertical-align: top;"></a>
2023-06-17T12:02:28.0592344Z <h4>Authors: <i>Brian Schilder, Alan Murphy, Nathan Skene</i></h4>Adding Bioconductor release version.
2023-06-17T12:02:28.0592963Z package is up-to-date release version
2023-06-17T12:02:28.0593459Z Adding Bioc downloads: by month
2023-06-17T12:02:28.0593873Z Adding Bioc downloads: by total
2023-06-17T12:02:28.0594254Z Adding license.
2023-06-17T12:02:28.0594615Z Adding code size
2023-06-17T12:02:28.0594992Z Adding commit.
2023-06-17T12:02:28.0595340Z Adding actions.
2023-06-17T12:02:28.0595689Z Adding codecov.
2023-06-17T12:02:28.0596329Z Creating new Docker file ==> C:\Users\RUNNER~1\AppData\Local\Temp\RtmpElszvU/working_dir\Rtmp4KHWyF/Dockerfile
2023-06-17T12:02:28.0597127Z Using existing Docker file: C:\Users\RUNNER~1\AppData\Local\Temp\RtmpElszvU/working_dir\Rtmp4KHWyF/Dockerfile
2023-06-17T12:02:28.0597648Z Docker file preview:
2023-06-17T12:02:28.0598340Z Creating new Issue Template ==> C:\Users\RUNNER~1\AppData\Local\Temp\RtmpElszvU/working_dir\Rtmp4KHWyF/bug_report.md
2023-06-17T12:02:28.0599185Z Creating new Issue Template ==> C:\Users\RUNNER~1\AppData\Local\Temp\RtmpElszvU/working_dir\Rtmp4KHWyF/feature_request.md
2023-06-17T12:02:28.0600021Z Using existing Issue Template: C:\Users\RUNNER~1\AppData\Local\Temp\RtmpElszvU/working_dir\Rtmp4KHWyF/bug_report.md
2023-06-17T12:02:28.0600561Z Issue Template preview:
2023-06-17T12:02:28.0601264Z Using existing Issue Template: C:\Users\RUNNER~1\AppData\Local\Temp\RtmpElszvU/working_dir\Rtmp4KHWyF/feature_request.md
2023-06-17T12:02:28.0601815Z Issue Template preview:
2023-06-17T12:02:28.0602476Z Creating new README file ==> C:\Users\RUNNER~1\AppData\Local\Temp\RtmpElszvU/working_dir\Rtmp4KHWyF/README.Rmd
2023-06-17T12:02:28.0603255Z Using existing README file: C:\Users\RUNNER~1\AppData\Local\Temp\RtmpElszvU/working_dir\Rtmp4KHWyF/README.Rmd
2023-06-17T12:02:28.0603796Z README file preview:
2023-06-17T12:02:28.0604653Z Creating new vignette file ==> C:\Users\RUNNER~1\AppData\Local\Temp\RtmpElszvU/working_dir\Rtmp4KHWyF/vignettes/docker.Rmd
2023-06-17T12:02:28.0605513Z Using existing vignette file: C:\Users\RUNNER~1\AppData\Local\Temp\RtmpElszvU/working_dir\Rtmp4KHWyF/vignettes/docker.Rmd
2023-06-17T12:02:28.0606051Z Vignette file preview:
2023-06-17T12:02:28.0606761Z Creating new vignette file ==> C:\Users\RUNNER~1\AppData\Local\Temp\RtmpElszvU/working_dir\Rtmp4KHWyF/vignettes/mypackage.Rmd
2023-06-17T12:02:28.0607627Z Saving workflow ==> C:\Users\RUNNER~1\AppData\Local\Temp\RtmpElszvU/working_dir\Rtmp4KHWyF/.github/workflows/rworkflows.yml
2023-06-17T12:02:28.0608428Z Saving workflow ==> C:\Users\RUNNER~1\AppData\Local\Temp\RtmpElszvU/working_dir\Rtmp4KHWyF/rworkflows.yml
2023-06-17T12:02:28.0609236Z Using existing workflow file: C:\Users\RUNNER~1\AppData\Local\Temp\RtmpElszvU/working_dir\Rtmp4KHWyF/rworkflows.yml
2023-06-17T12:02:28.0609803Z [ FAIL 2 | WARN 0 | SKIP 1 | PASS 93 ]
2023-06-17T12:02:28.0610191Z 
2023-06-17T12:02:28.0610795Z ══ Skipped tests (1) ═══════════════════════════════════════════════════════════
2023-06-17T12:02:28.0611398Z • empty test (1): 'test-infer_biocviews.R:1:1'
2023-06-17T12:02:28.0611686Z 
2023-06-17T12:02:28.0612522Z ══ Failed tests ════════════════════════════════════════════════════════════════
2023-06-17T12:02:28.0613322Z ##[error]Error in check_dots_empty0(...) : node stack overflow
2023-06-17T12:02:28.0614353Z Calls: test_check ... .rlang_purrr_map_mold -> as_function -> check_dots_empty0
2023-06-17T12:02:28.0614784Z Execution halted
2023-06-17T12:02:28.0615033Z 
2023-06-17T12:02:28.0615477Z 1 error ✖ | 0 warnings ✔ | 1 note ✖
2023-06-17T12:02:28.0672064Z Execution halted
2023-06-17T12:02:28.1041836Z ##[error]Process completed with exit code 1.
bschilder commented 1 year ago

Removing the vignette function tests didn't seem to do anything, so seems it's unrelated to that.

e.g. test-use_vignette_docker / 

if(.Platform$OS.type!="windows"){
...
}
bschilder commented 1 year ago

This seems to have resolved itself (GHA VMs updated perhaps?)