Closed maelle closed 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.
-- John Deck (541) 914-4739
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.
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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-- John Deck (541) 914-4739
: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
:wave: @jdeck88 Friendly reminder :smile_cat:
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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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
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
— Reply to this email directly, view it on GitHub https://github.com/ropensci/rppo/issues/8#issuecomment-1025697047, or unsubscribe https://github.com/notifications/unsubscribe-auth/AAIZ3RJ4PCNGZEOD4LL2WDLUYZ7CNANCNFSM5KAYFGNQ . 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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-- John Deck (541) 914-4739
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.
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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-- John Deck (541) 914-4739
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?
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
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 :
— Reply to this email directly, view it on GitHub https://github.com/ropensci/rppo/issues/8#issuecomment-1025768737, or unsubscribe https://github.com/notifications/unsubscribe-auth/AAIZ3RLLAYCNF5IL5HHSJ53UY2I5ZANCNFSM5KAYFGNQ . 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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-- John Deck (541) 914-4739
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:
All green! :tada: :clap:
: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
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!