Tests and vignettes failures

maelle commented 2 years ago

:wave: @jdeck88!

I was looking at this repo because of the docs building failure https://github.com/r-universe/ropensci/runs/4512022947?check_suite_focus=true

The vignette fails with the error in the log above.
Some tests also fail.

I see this repo used to be tested on Travis CI which we no longer recommend https://ropensci.org/blog/2020/11/19/moving-away-travis/ You can explore GitHub Actions, cf usethis support https://usethis.r-lib.org/reference/github_actions.html and r-lib examples https://github.com/r-lib/actions#readme

As your package wraps a web API I can also suggest skimming through https://books.ropensci.org/http-testing/

Happy to help if needed!

jdeck88 commented 2 years ago

Thanks, i made some updates to the code... this should solve the vignette issue...

John

On Tue, Dec 14, 2021 at 4:27 AM Maëlle Salmon @.***> wrote:

👋 @jdeck88 https://github.com/jdeck88!

I was looking at this repo because of the docs building failure https://github.com/r-universe/ropensci/runs/4512022947?check_suite_focus=true

The vignette fails with the error in the log above.

Some tests also fail.

I see this repo used to be tested on Travis CI which we no longer recommend https://ropensci.org/blog/2020/11/19/moving-away-travis/ You can explore GitHub Actions, cf usethis support https://usethis.r-lib.org/reference/github_actions.html and r-lib examples https://github.com/r-lib/actions#readme

As your package wraps a web API I can also suggest skimming through https://books.ropensci.org/http-testing/

Happy to help if needed!

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/ropensci/rppo/issues/8, or unsubscribe https://github.com/notifications/unsubscribe-auth/AAIZ3RNN7GA745AATFUVUM3UQ4Z3RANCNFSM5KAYFGNQ . Triage notifications on the go with GitHub Mobile for iOS https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675 or Android https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub.

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maelle commented 2 years ago

Cool! However there is still an error on https://github.com/r-universe/ropensci/runs/4730373763?check_suite_focus=true

Writing 'articles/index.html'
Reading 'vignettes/rppo-vignette.Rmd'
-- RMarkdown error -------------------------------------------------------------
sending request for terms ...
No encoding supplied: defaulting to UTF-8.
sending request for data ...
plantphenology.org/api/v3/download/_search?q=%2Bgenus:Quercus+AND+%2BtermID:"obo:PPO_0002313"+AND+%2Byear:>=2013+AND+%2Byear:<=2013+AND+%2BdayOfYear:>=100+AND+%2BdayOfYear:<=110+AND+source:USA-NPN&source=latitude,longitude,year,dayOfYear,termID&limit=10
/bin/tar: This does not look like a tar archive
/bin/tar: Skipping to next header
/bin/tar: Exiting with failure status due to previous errors
Quitting from lines 40-43 (rppo-vignette.Rmd) 
Error in file(file, "rt") : cannot open the connection
In addition: Warning messages:
1: In untar(tf, exdir = "./ppo_download") :
  '/bin/tar -xf '/tmp/RtmpwSEKHa/file2af16a73aba' -C './ppo_download'' returned error code 2
2: In file(file, "rt") :
  cannot open file 'ppo_download/data.csv': No such file or directory
--------------------------------------------------------------------------------
Error : Failed to render RMarkdown

If you can't reproduce this locally I can have a closer look this week or next.

jdeck88 commented 2 years ago

what command do you run for this test? i just ran check() and it was fine for me. john

On Thu, Jan 6, 2022 at 10:51 AM Maëlle Salmon @.***> wrote:

Cool! However there is still an error on https://github.com/r-universe/ropensci/runs/4730373763?check_suite_focus=true

Writing 'articles/index.html' Reading 'vignettes/rppo-vignette.Rmd' -- RMarkdown error ------------------------------------------------------------- sending request for terms ... No encoding supplied: defaulting to UTF-8. sending request for data ...plantphenology.org/api/v3/download/_search?q=%2Bgenus:Quercus+AND+%2BtermID:"obo:PPO_0002313"+AND+%2Byear:>=2013+AND+%2Byear:<=2013+AND+%2BdayOfYear:>=100+AND+%2BdayOfYear:<=110+AND+source:USA-NPN&source=latitude,longitude,year,dayOfYear,termID&limit=10 /bin/tar: This does not look like a tar archive /bin/tar: Skipping to next header /bin/tar: Exiting with failure status due to previous errors Quitting from lines 40-43 (rppo-vignette.Rmd) Error in file(file, "rt") : cannot open the connection In addition: Warning messages: 1: In untar(tf, exdir = "./ppo_download") : '/bin/tar -xf '/tmp/RtmpwSEKHa/file2af16a73aba' -C './ppo_download'' returned error code 2 2: In file(file, "rt") : cannot open file 'ppo_download/data.csv': No such file or directory

Error : Failed to render RMarkdown

If you can't reproduce this locally I can have a closer look this week or next.

— Reply to this email directly, view it on GitHub https://github.com/ropensci/rppo/issues/8#issuecomment-1006833310, or unsubscribe https://github.com/notifications/unsubscribe-auth/AAIZ3RIX7PFHMWLPQZINDMTUUXQDFANCNFSM5KAYFGNQ . Triage notifications on the go with GitHub Mobile for iOS https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675 or Android https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub.

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maelle commented 2 years ago

:wave: @jdeck88!

You have a folder called ppo_download/ in .gitignore. If it needs to remain so (as opposed to "just" being in .Rbuildignore) then you should

skip the tests that use it, based on an environment variable for instance, so that you'd still run them locally.
speaking of tests you might be interested in https://books.ropensci.org/http-testing/
pre-build the vignettes as rOpenSci docs building does not have access to that folder. See https://ropensci.org/blog/2019/12/08/precompute-vignettes/
unrelated to build servers on the cloud but potentially relevant, regarding caching data locally (so that each rppo user might be able to download it only once per computer for a given period of time) see https://blog.r-hub.io/2020/03/12/user-preferences/

maelle commented 2 years ago

:wave: @jdeck88 Friendly reminder :smile_cat:

jdeck88 commented 2 years ago

i came up with a solution regarding that directory which i think will help pass your tests... i could not replicate the results you received on your end so i'm keeping my fingers crossed that this solution works!

John

On Tue, Jan 25, 2022 at 7:23 AM Maëlle Salmon @.***> wrote:

👋 @jdeck88 https://github.com/jdeck88 Friendly reminder 😸

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maelle commented 2 years ago

See https://github.com/r-universe/ropensci/runs/4982345166?check_suite_focus=true, as ppo_downloads is listed in .gitignore that folder is present on your machine but not in the GitHub repo which creates the failure

 Quitting from lines 40-43 (rppo-vignette.Rmd) 
Error in file(file, "rt") : cannot open the connection
In addition: Warning messages:
1: In untar(tf, exdir = "./ppo_download") :
  '/bin/tar -xf '/tmp/RtmpuUCQlp/file2da7ca3f1ad' -C './ppo_download'' returned error code 2
2: In file(file, "rt") :
  cannot open file 'ppo_download/data.csv': No such file or directory

jdeck88 commented 2 years ago

I added a README.md to that directory so the script would not remove the directory. John

On Mon, Jan 31, 2022 at 6:37 AM Maëlle Salmon @.***> wrote:

See https://github.com/r-universe/ropensci/runs/4982345166?check_suite_focus=true, as ppo_downloads is listed in .gitignore that folder is present on your machine but not in the GitHub repo which creates the failure

Quitting from lines 40-43 (rppo-vignette.Rmd) Error in file(file, "rt") : cannot open the connection In addition: Warning messages: 1: In untar(tf, exdir = "./ppo_download") : '/bin/tar -xf '/tmp/RtmpuUCQlp/file2da7ca3f1ad' -C './ppo_download'' returned error code 2 2: In file(file, "rt") : cannot open file 'ppo_download/data.csv': No such file or directory

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maelle commented 2 years ago

Right but the folder does not have the csv that the vignette needs?

Maybe the vignette should be pre-computed? https://ropensci.org/blog/2019/12/08/precompute-vignettes/

Sorry if I'm missing something.

jdeck88 commented 2 years ago

the data.csv is downloaded dynamically. it is a small lift for the server to return this so i don't think i need to pre-download this file. Did you try to run with the new commit?

On Mon, Jan 31, 2022 at 7:46 AM Maëlle Salmon @.***> wrote:

Right but the folder does not have the csv that the vignette needs?

Maybe the vignette should be pre-computed? https://ropensci.org/blog/2019/12/08/precompute-vignettes/

Sorry if I'm missing something.

— Reply to this email directly, view it on GitHub https://github.com/ropensci/rppo/issues/8#issuecomment-1025755220, or unsubscribe https://github.com/notifications/unsubscribe-auth/AAIZ3RO5VAUE7FUKJEIO5RLUY2HC5ANCNFSM5KAYFGNQ . Triage notifications on the go with GitHub Mobile for iOS https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675 or Android https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub.

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maelle commented 2 years ago

I haven't tried anything again locally, I've just noticed the failure on the dashboard, the log can be found at https://github.com/r-universe/ropensci/runs/4982345166?check_suite_focus=true

Is https://github.com/r-universe/ropensci/commit/0fbb8e7badc56cb64dab73b7da0c9d55f33e3c75 the latest commit? I think so?

maelle commented 2 years ago

the error is

 plantphenology.org/api/v3/download/_search?q=%2Bgenus:Quercus+AND+%2BtermID:"obo:PPO_0002313"+AND+%2Byear:>=2013+AND+%2Byear:<=2013+AND+%2BdayOfYear:>=100+AND+%2BdayOfYear:<=110+AND+source:USA-NPN&source=latitude,longitude,year,dayOfYear,termID&limit=10
/bin/tar: This does not look like a tar archive
/bin/tar: Skipping to next header
/bin/tar: Exiting with failure status due to previous errors

jdeck88 commented 2 years ago

See latest commit: e03c427 https://github.com/ropensci/rppo/commit/e03c427ca50b6b6213a50a32744673785924b167

I added the github CI with associated badge on the git homepage: https://github.com/ropensci/rppo

should be passing now John

On Mon, Jan 31, 2022 at 8:02 AM Maëlle Salmon @.***> wrote:

FWIW I get a 504 for https://biscicol.org/api/v3/download/_search?q=%2Bgenus:Quercus+AND+%2BtermID :

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maelle commented 2 years ago

Thanks!

For reference the dashboard is at https://ropensci.r-universe.dev/ui#builds

It will have an updated build within one hour or so. I'll look at it again tomorrow but you can look earlier if you want.

We're making good progress, thanks for your work on this, looking forward to seeing green icons :grin:

maelle commented 2 years ago

All green! :tada: :clap:

ropensci / rppo

Tests and vignettes failures #8