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License: Creative Commons Zero v1.0 Universal
GitHub Actions for the R community
License: Creative Commons Zero v1.0 Universal
Hi,
I have been having issues with setting up tinytex
for windows-latest
. My workflow is here and the failed action and log can be found here. As you can see, the windows installation just hangs and times out, while the Linux and OSX installations happen quick and proceed forward without issue.
It looks like the Windows install is expecting user input, which is what causes it to hang:
Press any key to continue . . .
##[error]The operation was canceled.
Am I missing something in my YAML doc? Thanks for your help.
I think a /reprex
trigger would be useful, similar to /document
and /style
in pr-commands.yaml
.
In the pkgdown repo, we are asking for a reprex more often to debug obscure issues, and it would be nice to provide some consistency to these messages.
A /reprex
trigger would:
The section about getting help in the README is great!
I was wondering whether it'd make sense to add an item about using a search engine and when doing so paying attention to the dates i.e. something like "Look for your error/idea in a search engine. Note that questions and answers prior to <date>
refer to the now defunct beta version of GH Actions"?
First of all, thank you so much for these awesome actions. They've helped immensely transition over to GH actions from Travis.
I've noticed a bit of instability with what TeX packages end up being installed when using the setup-tinyetex
action. After reading the source, I found that by default TinyTeX is installing the list of packages at https://raw.githubusercontent.com/yihui/tinytex/master/tools/pkgs-custom.txt and it looks like the oberdiek package has been changed and no longer includes kvoptions
and pdftexcmds
(among others) https://ctan.org/ctan-ann/id/[email protected]
I've also submitted an issue to TinyTeX to resolve this up stream, but in the interim, I forked this repo and added an explicit check/install of all of the packages I've found necessary in the manual creation process. I'm happy to submit a PR for this, though if it's resolved in TinyTeX it's not strictly necessary any more.
I've made an incredibly minimal (and useless!) package to show the issue at https://github.com/jonkeane/simple-package see the error in the action around https://github.com/jonkeane/simple-package/runs/329317228#step:7:71 The setup-tinytex stage completes fine, but when R CMD check is run, the manual isn't able to be built because it can't find pdftexcmds.sty
_R_CHECK_LENGTH_1_LOGIC2_=true
I can no longer set up R on Ubuntu through the setup-r action. This happened spontaneously about 3 hours ago. The setup-r step "succeeds" with the below error, but subsequent steps fail because Rscript
cannot be found.
Run r-lib/actions/setup-r@master
Added matchers: 'rcmdcheck'. Problem matchers scan action output for known warning or error strings and report these inline.
Added matchers: 'testthat'. Problem matchers scan action output for known warning or error strings and report these inline.
Added matchers: 'r'. Problem matchers scan action output for known warning or error strings and report these inline.
sudo DEBIAN_FRONTEND=noninteractive apt-get update -qq
W: Conflicting distribution: https://packages.microsoft.com/repos/microsoft-ubuntu-bionic-prod bionic InRelease (expected bionic but got stable)
E: Repository 'https://packages.microsoft.com/repos/microsoft-ubuntu-bionic-prod bionic InRelease' changed its 'Origin' value from 'microsoft-ubuntu-bionic-prod bionic' to 'vscode stable'
E: Repository 'https://packages.microsoft.com/repos/microsoft-ubuntu-bionic-prod bionic InRelease' changed its 'Label' value from 'microsoft-ubuntu-bionic-prod bionic' to 'vscode stable'
E: Repository 'https://packages.microsoft.com/repos/microsoft-ubuntu-bionic-prod bionic InRelease' changed its 'Suite' value from 'bionic' to 'stable'
E: Repository 'https://packages.microsoft.com/repos/microsoft-ubuntu-bionic-prod bionic InRelease' changed its 'Codename' value from 'bionic' to 'stable'
W: Conflicting distribution: https://packages.microsoft.com/ubuntu/16.04/prod xenial InRelease (expected xenial but got stable)
E: Repository 'https://packages.microsoft.com/ubuntu/16.04/prod xenial InRelease' changed its 'Origin' value from 'microsoft-ubuntu-xenial-prod xenial' to 'vscode stable'
E: Repository 'https://packages.microsoft.com/ubuntu/16.04/prod xenial InRelease' changed its 'Label' value from 'microsoft-ubuntu-xenial-prod xenial' to 'vscode stable'
E: Repository 'https://packages.microsoft.com/ubuntu/16.04/prod xenial InRelease' changed its 'Suite' value from 'xenial' to 'stable'
E: Repository 'https://packages.microsoft.com/ubuntu/16.04/prod xenial InRelease' changed its 'Codename' value from 'xenial' to 'stable'
(node:4886) UnhandledPromiseRejectionWarning: Failed to install R: Error: The process 'sudo' failed with exit code 100
(node:4886) UnhandledPromiseRejectionWarning: Unhandled promise rejection. This error originated either by throwing inside of an async function without a catch block, or by rejecting a promise which was not handled with .catch(). (rejection id: 1)
(node:4886) [DEP0018] DeprecationWarning: Unhandled promise rejections are deprecated. In the future, promise rejections that are not handled will terminate the Node.js process with a non-zero exit code.
I've set up an empty R package with a basic workflow to reproduce the error. I've used the yaml file as generated by usethis::use_github_actions()
, but I've changed the runner to ubuntu-latest
. You can find the failed workflow here.
R-CMD-check.yaml contents:
on: [push, pull_request]
name: R-CMD-check
jobs:
R-CMD-check:
runs-on: ubuntu-latest
steps:
- uses: actions/checkout@v1
- uses: r-lib/actions/setup-r@master
- name: Install dependencies
run: Rscript -e "install.packages(c('remotes', 'rcmdcheck'))" -e "remotes::install_deps(dependencies = TRUE)"
- name: Check
run: Rscript -e "rcmdcheck::rcmdcheck(args = '--no-manual', error_on = 'error')"
Bug
On the Windows build [only], it's not finding the knitr
package:
Run Rscript -e "rcmdcheck::rcmdcheck(args = '--no-manual', error_on = 'error', check_dir = 'check')"
Rscript -e "rcmdcheck::rcmdcheck(args = '--no-manual', error_on = 'error', check_dir = 'check')"
shell: C:\Program Files\PowerShell\6\pwsh.EXE -command ". '{0}'"
env:
R_REMOTES_NO_ERRORS_FROM_WARNINGS: true
CRAN:
BOTOMETER_KEY: ***
TWITTER_ACCESS_TOKEN: ***
TWITTER_ACCESS_SECRET: ***
R_LIBS_USER: d:\a\_temp\Library
CI: true
TZ: UTC
NOT_CRAN: true
-- R CMD build -----------------------------------------------------------------
* checking for file 'D:\a\tweetbotornot2\tweetbotornot2/DESCRIPTION' ... OK
* preparing 'tweetbotornot2':
* checking DESCRIPTION meta-information ... OK
Error in loadVignetteBuilder(pkgdir, TRUE) :
vignette builder 'knitr' not found
Execution halted
##[error]Error in proc$get_built_file() : Build process failed
Logs
Link to the full logs of the failed build: https://github.com/mkearney/tweetbotornot2
Expected behavior
The build works on Ubuntu and MacOS
Additional context
It seems knitr
failed to install because it couldn't find stringi
(see relevant portion of log below). So I don't know if this is a problem with knitr
or just a momentary Windows bug (b/c it's being built from source). It seems like something I can fix (so I'm not worried about my build), but I figured you might want to know about it because maybe there is some underlying cause that is useful to know about?
2020-02-09T16:31:26.2020937Z * installing *source* package 'knitr' ...
2020-02-09T16:31:26.2374920Z ** package 'knitr' successfully unpacked and MD5 sums checked
2020-02-09T16:31:26.2376823Z ** using staged installation
2020-02-09T16:31:26.5377949Z ** R
2020-02-09T16:31:26.6165482Z ** demo
2020-02-09T16:31:26.6210157Z ** inst
2020-02-09T16:31:26.9458491Z ** byte-compile and prepare package for lazy loading
2020-02-09T16:31:27.5003007Z Error in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]) :
2020-02-09T16:31:27.5003428Z ERROR: lazy loading failed for package 'knitr'
2020-02-09T16:31:27.5003641Z there is no package called 'stringi'
2020-02-09T16:31:27.5005186Z ##[error]Error: unable to load R code in package 'knitr'
2020-02-09T16:31:27.5008648Z * removing 'd:/a/_temp/Library/knitr'
2020-02-09T16:31:27.5009041Z Execution halted
2020-02-09T16:31:31.9463648Z * installing *source* package 'stringi' ...
Thanks for this repo, and sorry if issues aren't welcome at the moment (I imagine this repo isn't very mature yet). I noticed that the render README example will push to master no matter what the current branch is.
The build process of R takes a much longer time due to package installations. This happens every time the action is triggered.
I think we can reduce time using https://github.com/actions/cache.
But, I'm not sure how to implement.
Dear developer,
I found the action workflow does not work for me in Windows. The installing dependency step did not finish successfully but got passed.
config yml: https://github.com/ropensci/UCSCXenaTools/blob/master/.github/workflows/main.yml
action log: https://github.com/ropensci/UCSCXenaTools/runs/318933389
Best,
Shixiang
Something like this
on: [push]
jobs:
job1:
runs-on: ubuntu-latest
container: rocker/verse
steps:
- uses: actions/checkout@v1
- run: Rscript fit_model.R
- run: Rscript build_reports.R
- name: Upload results
uses: actions/upload-artifact@master
with:
name: results
path: /path/to/artifacts/
The current config in travis is (assumes that the R tensorflow
package is installed):
env:
global:
- KERAS_BACKEND="tensorflow"
before_script:
- python -m pip install --upgrade --ignore-installed --user travis pip setuptools wheel virtualenv
- python -m pip install --upgrade --ignore-installed --user travis keras h5py pyyaml requests Pillow scipy theano
- R -e 'tensorflow::install_tensorflow()'
before_install:
- sudo apt-get update
- sudo apt-get -y install python3
Hi!
Wouldn't it be better if the name
in
actions/examples/check-release.yaml
Line 3 in ef3ed83
name: R CMD check
). Then the status badge would also show up nicely with spaces.
Thanks,
Bela
Hi,
Not sure if this is the best place to ask this but I've been testing usethis::use_github_actions_check_release
for my package.
It generally has been working however occasionally it fails due to a timeout error during the rebuilding of vignettes. It seems that the timeout is set to 10000ms (i.e. 10s).
The checks all pass fine locally, on travis-CI and seem to sometimes pass on github actions. You can see an example PR that passes on travis-CI but fails on github actions due to timeout here
Example error below (from here)
Quitting from lines 36-42 (elo-ratings-example.Rmd)
##[error]Error: processing vignette 'elo-ratings-example.Rmd' failed with diagnostics:
Timeout was reached: [afltables.com] Operation timed out after 10091 milliseconds with 0 out of 0 bytes received
--- failed re-building ‘elo-ratings-example.Rmd’
Is there a way to increase this timeout at all in the YML for the R-CMD-CHECK
action?
Sorry a silly one really but just to note that the first 3 action links in the README.md all point to the setup-r
action rather than setup-pandoc
and setup-tinytex
respectively.
Will leave just as a note if it's too trivial to PR and happy for you to just absorb and close if you aren't accepting contributions!
Unrelated: I stumbled across this (thank you!) when I was writing up an Actions workflow for publishing using bookdown/gh-pages; happy to put together a PR with this too if you think it's worthwhile in addition to pkgdown.
Based on discussion in maxheld83/ghpages#1, maxheld83/ghpages#18, and reading GitHub's Authenticating with the GITHUB_TOKEN
help doc, I think the Pkgdown
github action example needs to be switched from:
Lines 21 to 23 in 0636e8a
To:
run: |
pkgdown:::deploy_local(new_process = FALSE, remote_url = 'https://x-access-token:${{secrets.DEPLOY_PAT}}@github.com/${{github.repository}}.git')
shell: Rscript {0}
Emphasize that DEPLOY_PAT
needs to be generated once and manually set for each repo under Secrets.
I think there is an issue with the logic of the steps in the check full workflow which prevents the caching feature from being used.
The depends.Rds
gets created before the caching step. That means that even during a run where a cache gets restored, the depends.Rds
gets created against an empty library.
Here is a sample output I see on the depends.Rds
in a run where there is a cache available
Needs update -----------------------------
package installed available is_cran remote
clisymbols NA 1.2.0 TRUE CRAN
crayon NA 1.3.4 TRUE CRAN
digest NA 0.6.23 TRUE CRAN
dplyr NA 0.8.4 TRUE CRAN
glue NA 1.3.1 TRUE CRAN
httr NA 1.4.1 TRUE CRAN
jsonlite NA 1.6.1 TRUE CRAN
knitr NA 1.28 TRUE CRAN
kableExtra NA 1.1.0 TRUE CRAN
purrr NA 0.3.3 TRUE CRAN
readr NA 1.3.1 TRUE CRAN
Notice the NA
in the installed
column.
Because this depends.Rds
gets used in the 'install dependencies' step, all the packages get installed regardless of whether or not they have been restored in the library from the cache.
A possible solution would be to replace in
actions/examples/check-full.yaml
Line 66 in e85841c
depends.Rds
with another call to remotes::dev_package_deps(dependencies = TRUE)
The checkout action now sets up GitHub Authentication for you, e.g. https://github.com/r-lib/rlang/runs/441234372?check_suite_focus=true#step:2:20.
We might be able to use this to deploy to GitHub pages without needing to setup any secrets.
The docker containers, e.g. rocker/tidyverse
, use latest
to refer to the latest release of R. I think it's a good idea to also support latest
in the setup-r actions to make the flow more consistent.
On Windows, it would be useful to cache the R installation. I've been informed that the r-lib/actions/setup-r
action doesn't just install R (and Rtools); it also sets up environment variables and PATH.
I used the "Tidyverse CI workflow" example, but I had to add install.packages('covr')
obtaining
- name: Test coverage
if: matrix.config.os == 'macOS-latest' && matrix.config.r == '3.6'
run: |
install.packages('covr')
covr::codecov(token = "${{secrets.CODECOV_TOKEN}}")
shell: Rscript {0}
before it worked.
Not sure if that is indeed needed or not, but for me it didn't work unless I installed covr
first.
Is the path to the renv package cache correct here? It seems to be trying to append it as a relative path to the current directory.
actions/examples/bookdown.yaml
Line 25 in 155c137
For me, I see:
https://github.com/DavisVaughan/r-extensions/runs/579215093?check_suite_focus=true
Post job cleanup.
/usr/bin/tar -cz -f /Users/runner/runners/2.168.0/work/_temp/194d01a0-7d29-4e36-ae3f-8dab3742b905/cache.tgz -C /Users/runner/runners/2.168.0/work/r-extensions/r-extensions/$HOME/.local/share/renv .
tar: could not chdir to '/Users/runner/runners/2.168.0/work/r-extensions/r-extensions/$HOME/.local/share/renv'
[warning]Tar failed with error: The process '/usr/bin/tar' failed with exit code 1
And then on subsequent runs I get stuck in a loop where the pre-cache step says that there is no cache found:
Run actions/cache@v1
Cache not found for input keys: r-453a2d65c821c2b42619477860dc167ca1a5033ddd8e234267b681f9b7b9894f, r-.
But the cache step says there is already a cache:
Post job cleanup.
[warning]Cache already exists. Scope: refs/heads/master, Key: r-453a2d65c821c2b42619477860dc167ca1a5033ddd8e234267b681f9b7b9894f, Version: (null)
https://github.com/DavisVaughan/r-extensions/runs/579268046?check_suite_focus=true
The only way to break out of that loop seems to be to set a new cache key, as described here, but that still doesn't fix the path issue
Since 2 days all our macOS devel runners fail setting up R during CRON builds. Everything works for normal push events.
Here is an example: https://github.com/mlr-org/mlr3proba/runs/499591060?check_suite_focus=true
AFAICS, R is not getting installed after gfortran
was installed and all other steps are skipped therefore.
Don't really want to go this route, but here is some code for it https://github.com/1138-4EB/vunit/blob/migrate-to-gha/.github/workflows/push.yml#L63-L74
Two days ago Simon announced that R4.0 will use gfortran 8.2 and Apples native compiler along with the SDK 10.13.
There is a new alpha R4.0 branch that contains the latest R-devel changes: https://mac.r-project.org/.
There is a need to switch to the new gfortran version and change the URL for getting the R-devel tarball.
The R-devel el-capitan build is stuck at March-25 and might no longer be updated (not 100% sure about this though).
FYI: There are known issues with the 10.15 SDK (Rcpp issues you are most likely aware of, igraph issues). Therefore I am using a custom install of the 10.13 SDK. Maybe you also want to use that as the default SDK on Actions to mimic CRAN behavior?
wget https://github.com/phracker/MacOSX-SDKs/releases/download/10.15/MacOSX10.13.sdk.tar.xz
tar fxz MacOSX10.13.sdk.tar.xz
sudo mv MacOSX10.13.sdk /Library/Developer/CommandLineTools/SDKs/
rm -rf MacOSX10.13*
.R/Makevars
CFLAGS=-isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX10.13.sdk
CCFLAGS=-isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX10.13.sdk
CXXFLAGS=-isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX10.13.sdk
CPPFLAGS=-isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX10.13.sdk
Hi Jim,
thanks a lot for the effort in getting GH actions to work easily for R packages. Just browsed your rstudio::conf slides.
We are in the process to support GH actions also in {tic}, building on your "actions".
I see that your are putting in a lot of effort to move towards using R package binaries, even on Linux.
While this comes with a nice speed up for dependency installation, it comes with the issues of R packages which need to link against a system library.
Let's use {rJava} as the best example here ;)
I am wondering if using binaries might introduce more problems in CI than it helps - and if using source installs only (even on Windows) combined with caching the R user library might be the more robust way for most users.
However, installing certain system libs on Windows is of course a medium pain and that's also one reason why binaries exist.
If one wants to test on R-devel, source is the only option anyways.
Also I also like the idea of having the same "build process" for the dep installs across all platforms and pulling away the pain of thinking about binary/source differences at all.
Curious about your view on this.
All my CI GitHub actions selectively fail for macOS-devel version because some packages are not available:
https://github.com/IndrajeetPatil/broomExtra/runs/299273606
But I checked that these packages are indeed available for R-devel here:
https://cloud.r-project.org/bin/windows/contrib/4.0/PACKAGES
So not sure why the builds fail for this system.
Open an issue here only if you have a bug in one of the
custom R specific actions themselves. -> Please tell me if it's not the right place, i thought for this kind of bug installing a R package this might be the right place, but i might be wrong.
Describe the bug
The fs
package does not install on the mac-os devel plateform.
To Reproduce
See the github action repport of my package there : https://github.com/lrnv/cort/runs/522178146#step:15:2856 , lines 2856 -> 2923
Expected behavior
The package should install properly. fs
is a dependency of pkgdown
, and i dont get why it does not work as other builds for other packages do install pkgdown without encountering this issue.
Additional context
I used tic::use_tic() so setup the whole thing.
I have written a docker based action for running rchk: https://github.com/randy3k/github-action-rchk
I could prepare a PR if there are any interests.
My builds are selectively failing for Mac OS 3.6
config-
with the following error:
##[warning]LaTeX errors when creating PDF version.
This typically indicates Rd problems.
LaTeX errors found:
!pdfTeX error: pdflatex (file tcrm1000): Font tcrm1000 at 600 not found
==> Fatal error occurred, no output PDF file produced!
* checking PDF version of manual without hyperrefs or index ... ERROR
##[error]* DONE
Status: 1 ERROR, 1 WARNING
See
‘/Users/runner/runners/2.163.1/work/broomExtra/broomExtra/check/broomExtra.Rcheck/00check.log’
for details.
Detailed log: https://github.com/IndrajeetPatil/broomExtra/runs/372837238
Workflows: https://github.com/IndrajeetPatil/broomExtra/tree/master/.github/workflows
How can I change the workflow to avoid this?
I'm surprised this example does not have a step where it installs the package:
https://github.com/r-lib/actions/tree/master/examples#render-readme
Expected behaviour:
After installing R, expect to see the following environment variables sets: R_LIBS_USER
, CI
, TZ
and NOT_CRAN
per what is specified in the setREnvironmentVariables()
function.
Actual behaviour:
The first two envvars are set correctly. However:
NOT_CRAN
does not appear to set on any platform andTZ
appears to be set in a malformed way on Windows only (?) and needs to be overridden by specifying this in the env
step in the workflow.You can see the TZ behaviour by comparing two builds: before setting TZ in the workflow and after setting TZ in the workflow
There was a failure for the CI build of embed
but only for ubuntu-16.04 (3.5)
:
Run Rscript -e "remotes::install_github('r-hub/sysreqs')"
Rscript -e "remotes::install_github('r-hub/sysreqs')"
sysreqs=$(Rscript -e "cat(sysreqs::sysreq_commands('DESCRIPTION'))")
sudo -s eval "$sysreqs"
shell: /bin/bash -e {0}
env:
R_REMOTES_NO_ERRORS_FROM_WARNINGS: true
PIP_NO_WARN_SCRIPT_LOCATION: false
RSPM: https://demo.rstudiopm.com/all/__linux__/xenial/latest
R_LIBS_USER: /home/runner/work/_temp/Library
CI: true
TZ: UTC
NOT_CRAN: true
RHUB_PLATFORM: linux-x86_64-ubuntu-gcc
Error in rbind(info, getNamespaceInfo(env, "S3methods")) :
number of columns of matrices must match (see arg 2)
Calls: :: ... tryCatch -> tryCatchList -> tryCatchOne -> <Anonymous>
Execution halted
##[error]Process completed with exit code 1.
Perhaps this is a bad R version for a dependency (it is the only 3.5 build that I did) but it was previously working yesterday.
Is your feature request related to a problem? Please describe.
I am trying to cache Ubuntu apt but it is failing with permission errors: https://github.com/evandroforks/anki/runs/527868018?check_suite_focus=true#step:32:3
- name: Cache /var/lib/apt
uses: actions/cache@v1
with:
path: /var/lib/apt
key: ${{ runner.os }}-/var/lib/apt-${{ hashFiles('**/linux_checks.yml') }}
- name: Cache /var/cache/apt
uses: actions/cache@v1
with:
path: /var/cache/apt
key: ${{ runner.os }}-/var/cache/apt-${{ hashFiles('**/linux_checks.yml') }}
- name: Set up ripgrep, pyaudio, gettext, rename
run: |
sudo apt update
sudo apt install portaudio19-dev gettext rename
sudo snap install ripgrep --classic
Describe the solution you'd like
Run /bin/tar
with sudo
, so I can cache anything I would like.
On Windows, this is are already working because there is no sudo restrictions. There, I am caching the Git
directory because I am installing the Unix Package manager (pacman) on it: https://github.com/evandroforks/anki/runs/527868075?check_suite_focus=true#step:6:16
Describe alternatives you've considered
I tried to run:
- name: Fix ~/.cache permissions
run: |
sudo chown -R $(whoami):$(id -ng) /var/lib/apt/
sudo chown -R $(whoami):$(id -ng) /var/cache/apt/
But I still got permissions issues.
I made a small reproducible example on SO: https://stackoverflow.com/q/59197177/6103040.
Basically, I get this issue only on GH actions for Windows using a similar template as you provide here (https://github.com/privefl/minipkg/blob/master/.github/workflows/main.yml).
I don't get this issue locally on Windows, nor on AppVeyor (nor on Mac or Linux builds).
I'm very confused on what is the problem.
Have you any idea where it can come from?
Describe the bug
I have a build that is passing on all systems except macOS. The error occurs when trying to install the package gdtools (https://github.com/davidgohel/gdtools). The main page for the package lists additional software that needs to be available for this package, X11. The software requirement is additionally documented here: https://cran.r-project.org/bin/macosx/
To Reproduce
Here is a link to the most recent failed build log: https://github.com/ddsjoberg/gtsummary/pull/437/checks?check_run_id=574965508
Expected behavior
As this is only occurring on macOS with the package that needs X11, I assume this is the reason for the error.
Additional context
Apologies if this is not the correct space for reporting! Thank you!
I'm looking to use r-lib/actions/setup-pandoc
for manubot/manubot#197. Our install command is:
- name: Install Pandoc
uses: r-lib/actions/setup-pandoc@v1
with:
pandoc-version: 2.9.1
We're getting failure on windows:
pandoc : The term 'pandoc' is not recognized as the name of a cmdlet, function, script file, or operable program.
Check the spelling of the name, or if a path was included, verify that the path is correct and try again.
At D:\a\_temp\13e5f803-7724-40c7-9f0c-bf38ac617eb9.ps1:2 char:17
+ echo "# Test" | pandoc -t html
+ ~~~~~~
+ CategoryInfo : ObjectNotFound: (pandoc:String) [], ParentContainsErrorRecordException
+ FullyQualifiedErrorId : CommandNotFoundException
It seems that mac and linux installation succeeded. CC @jimhester
During ropensci/ozunconf19#7, a group investigated the new GitHub actions and provided a set of R-specific extended documentation within their unconf repository. One workflow that might be useful to add as an example is the bookdown
one generated to host the notes. Details at:
Describe the bug
The check-full.yaml
workflow has YAML fold block notation on some run
statements, which don't seem to be parsed correctly. With the folds:
run: >
Rscript
-e "install.packages('remotes')"
-e "saveRDS(remotes::dev_package_deps(dependencies = TRUE), 'depends.Rds', version = 2)"
Rscript does not receive the -e
arguments and thus expects a file, which is does not receive.
To Reproduce
Create a new repository with the most recent check-full.yaml
workflow and let the workflow run. The workflow should fail at the "Query dependencies" stage (example run logs). Output should be the Rscript usage statements and an error:
Usage: /path/to/Rscript [--options] [-e expr [-e expr2 ...] | file] [args]
--options accepted are
--help Print usage and exit
--version Print version and exit
--verbose Print information on progress
--default-packages=list
Where 'list' is a comma-separated set
of package names, or 'NULL'
or options to R, in addition to --slave --no-restore, such as
--save Do save workspace at the end of the session
--no-environ Don't read the site and user environment files
--no-site-file Don't read the site-wide Rprofile
--no-init-file Don't read the user R profile
--restore Do restore previously saved objects at startup
--vanilla Combine --no-save, --no-restore, --no-site-file
--no-init-file and --no-environ
'file' may contain spaces but not shell metacharacters
Expressions (one or more '-e <expr>') may be used *instead* of 'file'
See also ?Rscript from within R
##[error]Process completed with exit code 1.
Expected behavior
The workflow should run as if the run commands were written in a single line (example workflow success with single line revisions)
Additional context
I decided to open an issue because usethis
pulls from these example scripts, which would be causing downstream workflow failures.
The post cache R package clean up seems to fail in different ways on different platforms:
On macOS:
Post job cleanup.
Cache hit occurred on the primary key macOS-r-3.6-9d6d6298c76f4d3f6969ba02e70924fc899df6ede745c821d69e7bc6c7583a2c, not saving cache.
On Windows:
Post job cleanup.
C:\Rtools\bin\tar.exe -cz --force-local -f d:/a/_temp/b77bb8ee-0267-4c3e-a392-f0271711ce95/cache.tgz -C d:/a/_temp/Library .
tar (child): gzip: Cannot exec: No such file or directory
tar (child): Error is not recoverable: exiting now
/Rtools/bin/tar: d\:/a/_temp/b77bb8ee-0267-4c3e-a392-f0271711ce95/cache.tgz: Cannot write: Broken pipe
/Rtools/bin/tar: Child returned status 2
/Rtools/bin/tar: Error is not recoverable: exiting now
##[warning]The process 'C:\Rtools\bin\tar.exe' failed with exit code 2
On Ubuntu:
Post job cleanup.
Cache hit occurred on the primary key Linux-r-3.6-9d6d6298c76f4d3f6969ba02e70924fc899df6ede745c821d69e7bc6c7583a2c, not saving cache
Describe the bug
When jobs are re-run, a race condition (? or similar) in checkout@v1
causes jobs to error with the message fatal: reference is not a tree
. 🚫 🌳
The Actions team has fixed this problem in actions/checkout@v2
(discussion in actions/checkout#23) so it would be great to move up the checkout version in check-full.yaml and similar.
To Reproduce
Here is a PR that is experiencing this behavior. Every time I click "Re-run jobs", it fails at actions/checkout@v1
.
Expected behavior
When jobs are re-run, the checkout succeeds.
I'm seeing a failure thrown in this build as I install package dependencies. I can't see why a failure is being thrown by this. There are some Rd compilation warnings, but it doesn't look like the matcher regex's you've set up should catch those.
Currently selecting - { os: ubuntu-18.04, r: "release" }
fails with
Run r-lib/actions/setup-r@master
##[error]Node run failed with exit code 1
We currently are developing several teaching related actions (https://github.com/rundel/ghclass-actions) and it would be nice to follow the lead of the tooling being built here and in usethis. Most of our yaml files require some form of templating to customize for each class or assignment and some unified approach for this would be helpful.
The goal of this issue is to start a discussion of possible approaches and tooling either in this package or usethis.
E: Failed to fetch https://packages.microsoft.com/ubuntu/16.04/prod/dists/xenial/main/binary-amd64/Packages.bz2 Hash Sum mismatch
E: Some index files failed to download. They have been ignored, or old ones used instead.
To Reproduce
Expected behavior
successfully pass the stage
- uses: r-lib/actions/setup-r@master
with:
r-version: ${{ matrix.config.r }}
It would be nice to have a good solution for lintr. A simple workflow is something like this
jobs:
lintr:
runs-on: macOS-latest
steps:
- uses: actions/checkout@master
- uses: r-lib/actions/setup-r@master
- name: Install dependencies
run: |
install.packages(c("remotes", "lintr"))
remotes::install_deps(dependencies = TRUE)
shell: Rscript {0}
- name: Install package
run: R CMD INSTALL .
- name: Lint package
run: lintr::lint_package()
shell: Rscript {0}
However it would also be nice
Perhaps this is a repeat of #6
But, is there a way to avoid specifying version numbers for oldrel
? Similar to:
https://docs.travis-ci.com/user/languages/r/#r-versions
The current example shows only fixed version numbers and a tag for devel
.
actions/examples/check-full.yaml
Lines 21 to 28 in 0636e8a
Problem
The command \style
takes long because styler is generally slow (I am allowed to say it because I wrote most of it -.- haha).
Solution: use the cache
As of styler v1.3.0
, repeated styling is almost instantaneous because of caching (of whole files but also of top-level expressions). If the cache is activated. And I think it's fair to say that in a PR, only a minority of top-level expressions is changed. {styler}
uses the {R.cache}
backend for caching, and the location of the cache can be specified with R.cache::setCacheRootPath("/path/to/cache")
, best in the same R session we call styler::style_pkg()
. Then, we'd have to cache that directory to benefit from speed gains.
I think it's a small thing to implement this, but I have no clue about GitHub Actions, so I hope someone else shows interest in making a code contribution.
I wonder if it is possible to e.g. use a keyword (e.g. -notest
) in the commit message, and look for this in the build to skip it.
For example, if I'm only correcting a typo, it feels like wasting resources to run the tests again.
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