CRAN submission RC 0.13.1

[strengejacke]

I'm running devtools::check_win*() now, @DominiqueMakowski you'll get notified. Once revdep-checks successfully passed, we can submit, I'd say.

[codecov-commenter]

Codecov Report

Merging #593 (562fc50) into main (a00f5a0) will decrease coverage by 1.92%. The diff coverage is 0.00%.

:exclamation: Current head 562fc50 differs from pull request most recent head 391f628. Consider uploading reports for the commit 391f628 to get more accurate results

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@@            Coverage Diff             @@
##             main     #593      +/-   ##
==========================================
- Coverage   50.94%   49.03%   -1.92%     
==========================================
  Files          65       65              
  Lines        5115     5115              
==========================================
- Hits         2606     2508      -98     
- Misses       2509     2607      +98     

Impacted Files	Coverage Δ
R/bayesfactor_restricted.R	66.66% <ø> (ø)
R/mediation.R	0.00% <0.00%> (ø)
R/p_to_bf.R	75.67% <0.00%> (ø)

... and 15 files with indirect coverage changes

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[strengejacke]

revdep checks were ok!

[IndrajeetPatil]

I have fixed the revdepcheck workflow. It stalled because of the new glmmTMB CRAN release.

[strengejacke]

I'm afraid @DominiqueMakowski lost his GitHub account in Singapore, so not sure this will ever be submitted... 🤣

[DominiqueMakowski]

https://win-builder.r-project.org/5mL8PdSFJJBi

https://win-builder.r-project.org/fTl4Y2bIj0go

https://win-builder.r-project.org/g095P2q940X5

I'm here 🙈 so sorry I missed that

[DominiqueMakowski]

checks error because of insight

[strengejacke]

Ok, looks good. Do you want to submit?

[DominiqueMakowski]

submitted

[DominiqueMakowski]

package bayestestR_0.13.1.tar.gz does not pass the incoming checks automatically, please see the following pre-tests: Windows: https://win-builder.r-project.org/incoming_pretest/bayestestR_0.13.1_20230323_131038/Windows/00check.log Status: 2 NOTEs Debian: https://win-builder.r-project.org/incoming_pretest/bayestestR_0.13.1_20230323_131038/Debian/00check.log Status: 1 ERROR, 1 NOTE

[DominiqueMakowski]

🥲

  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure ('test-emmGrid.R:205:5'): emmGrid bayesfactor_parameters ────────────
  xsdbf1$log_BF (`actual`) not equal to xsdbf2$log_BF (`expected`).

    `actual`: 5.71 4.91 2.91

[strengejacke]

Increase tolerance, or skip on Linux?

[strengejacke]

maybe both 😆

[IndrajeetPatil]

Was it resubmitted?

[strengejacke]

bump

[DominiqueMakowski]

resubmitted

[DominiqueMakowski]

https://win-builder.r-project.org/incoming_pretest/bayestestR_0.13.1_20230327_193101/Debian/00check.log fails on Debian because of tolerance

[strengejacke]

[strengejacke]

bump

[DominiqueMakowski]

submitted

[strengejacke]

were win-builder checks ok?

[DominiqueMakowski]

just NOTEs with mispelled "et" "al" & co

[DominiqueMakowski]

it passed the winbuilder checks earlier but it failed upon submission, should we increase the tol again?

https://win-builder.r-project.org/incoming_pretest/bayestestR_0.13.1_20230405_095418/Debian/00check.log

  ══ Skipped tests ═══════════════════════════════════════════════════════════════
  • On CRAN (72)
  • TODO: check hard-coded values (1)
  • Test creates error, must check why... (1)

  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure ('test-emmGrid.R:204:3'): emmGrid bayesfactor_parameters ────────────
  xsdbf1$log_BF (`actual`) not equal to xsdbf2$log_BF (`expected`).

    `actual`: 5.71 4.91 2.91
  `expected`: 5.76 4.92 2.99

[strengejacke]

Would be nice if the complete file was tested, so we don't need to fix test failures step by step with each resubmit ^^ Should be fixed now.

[IndrajeetPatil]

On mac-M1, I still see one test failing:

Failure (test-check_prior.R:120:3): check_prior - brms (not linux or windows)
check_prior(model2)$Prior_Quality (`actual`) not equal to c(...) (`expected`).

    actual          | expected           
[1] "uninformative" | "uninformative" [1]
[2] "informative"   - "uninformative" [2]
[3] "informative"   | "informative"   [3]
[4] "uninformative" | "uninformative" [4]
[5] "uninformative" | "uninformative" [5]

[strengejacke]

Only local? If it works on GH CI, then it's ok. We skip it on CRAN, anyway.

[IndrajeetPatil]

Only local? If it works on GH CI, then it's ok. We skip it on CRAN, anyway.

Ah, okay. If we skip it on CRAN, then it shouldn't be an issue. CRAN also runs an additional check on M1mac, and so wanted to point out this failure.

[DominiqueMakowski]

How come it also keeps flagging misspelling when it is in the wordlist??

Possibly misspelled words in DESCRIPTION:
  Makowski (66:37)
  al (66:49)
  et (66:46)

[strengejacke]

I think CRAN doesn't use the spellcheck package and hence not the wordlist - but I'm not sure.

[IndrajeetPatil]

CRAN machines actually know nothing about inst/WORDLIST. It’s an idiom we use to avoid spelling mistakes.

I had complained to Uwe about these false positives and he had told me that CRAN maintainers typically ignore NOTEs related to spelling mistakes in DESCRIPTION.

I had also asked him to suggest a way to avoid the issue altogether. I never got a reply to that question. There is nothing about this in “Writing R Extensions” either.

On Thu 6. Apr 2023 at 15:01, Daniel @.***> wrote:

I think CRAN doesn't use the spellcheck package and hence not the wordlist

• but I'm not sure.

— Reply to this email directly, view it on GitHub https://github.com/easystats/bayestestR/pull/593#issuecomment-1499029651, or unsubscribe https://github.com/notifications/unsubscribe-auth/ACWOHFJLDQHBGQG6II4NMEDW725BDANCNFSM6AAAAAAWCBBMDA . You are receiving this because you commented.Message ID: @.***>

[DominiqueMakowski]

You should join CRAN and improve their workflow

(I'm resubmitting now)

[DominiqueMakowski]

Good enough for now, hence:
Thanks, reverse dependency checks have been triggered.

[strengejacke]

CRAN team when seeing bayestestR submission: