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Update reverse dependencies check
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@stefvanbuuren
stefvanbuuren committed Nov 27, 2024
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37 changes: 19 additions & 18 deletions revdep/README.md
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# Platform

|field |value |
|:--------|:------------------------------------------|
|version |R version 4.4.2 (2024-10-31) |
|os |macOS Sequoia 15.1.1 |
|system |aarch64, darwin20 |
|ui |RStudio |
|language |(EN) |
|collate |en_US.UTF-8 |
|ctype |en_US.UTF-8 |
|tz |Europe/Amsterdam |
|date |2024-11-22 |
|rstudio |2024.09.1+394 Cranberry Hibiscus (desktop) |
|pandoc |1.17.1 @ /usr/local/bin/pandoc |
|field |value |
|:--------|:------------------------------------------------------------------------------------------------|
|version |R version 4.4.2 (2024-10-31) |
|os |macOS Sequoia 15.1.1 |
|system |aarch64, darwin20 |
|ui |RStudio |
|language |(EN) |
|collate |en_US.UTF-8 |
|ctype |en_US.UTF-8 |
|tz |Europe/Amsterdam |
|date |2024-11-27 |
|rstudio |2024.09.1+394 Cranberry Hibiscus (desktop) |
|pandoc |3.2 @ /Applications/RStudio.app/Contents/Resources/app/quarto/bin/tools/aarch64/ (via rmarkdown) |

# Dependencies

|package |old |new |Δ |
|:-----------|:-----------|:-----------|:--|
|mice |3.16.0 |3.16.17 |* |
|mice |3.16.0 |3.17.0 |* |
|backports |1.5.0 |1.5.0 | |
|bit |4.5.0 |4.5.0 | |
|bit64 |4.5.2 |4.5.2 | |
Expand Down Expand Up @@ -82,12 +82,13 @@
|Replication |0.1.2 |1 | | |
|rmsb |1.1-1 |1 | |1 |

## New problems (4)
## New problems (5)

|package |version |error |warning |note |
|:--------|:-------|:------|:-------|:---------|
|package |version |error |warning |note |
|:----------|:-------|:------|:-------|:---------|
|[autoReg](problems.md#autoreg)|0.3.3 |__+2__ | | |
|[bipd](problems.md#bipd)|0.3 |1 | |-1 __+1__ |
|[finalfit](problems.md#finalfit)|1.0.8 |__+2__ | |1 |
|[pre](problems.md#pre)|1.0.7 |__+1__ | | |
|[gFormulaMI](problems.md#gformulami)|1.0.0 |__+3__ | | |
|[micd](problems.md#micd)|1.1.1 | |__+1__ | |

11 changes: 8 additions & 3 deletions revdep/cran.md
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We checked 132 reverse dependencies (127 from CRAN + 5 from Bioconductor), comparing R CMD check results across CRAN and dev versions of this package.

* We saw 4 new problems
* We saw 5 new problems
* We failed to check 5 packages

Issues with CRAN packages are summarised below.
Expand All @@ -15,14 +15,19 @@ Issues with CRAN packages are summarised below.
checking running R code from vignettes ...

* bipd
checking dependencies in R code ...sh: line 1: 28198 Segmentation fault: 11 R_DEFAULT_PACKAGES=NULL '/Library/Frameworks/R.framework/Resources/bin/R' --vanilla --no-echo 2>&1 < '/var/folders/5_/g85d42yj50b6lrjq4rzjzg8w0000gn/T//Rtmp8uxG38/file6ad8527d0366'
checking dependencies in R code ...sh: line 1: 6660 Segmentation fault: 11 R_DEFAULT_PACKAGES=NULL '/Library/Frameworks/R.framework/Resources/bin/R' --vanilla --no-echo 2>&1 < '/var/folders/5_/g85d42yj50b6lrjq4rzjzg8w0000gn/T//RtmpY4Kslj/file17bf4758620f'

* finalfit
checking examples ... ERROR
checking running R code from vignettes ...

* pre
* gFormulaMI
checking examples ... ERROR
checking tests ...
checking running R code from vignettes ...

* micd
checking Rd cross-references ... WARNING

### Failed to check

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108 changes: 88 additions & 20 deletions revdep/problems.md
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Expand Up @@ -50,7 +50,7 @@ Run `revdepcheck::revdep_details(, "autoReg")` for more info
Errors in running code in vignettes:
when running code in ‘Automatic_Regression_Modeling.Rmd’
...
virginica (N=50) Mean ± SD 6.6 ± 0.6 1.95 (1.75 to 2.14, p<.001) 1.91 (1.68 to 2.14, p<.001)
virginica (N=50) Mean ± SD 6.6 ± 0.6 1.95 (1.75 to 2.14, p<.001) 1.85 (1.62 to 2.07, p<.001)
...
Male 489 (52.9%) 463 (51.6%) 0.95 (0.79-1.14, p=.594) 0.95 (0.78-1.15, p=.589)
——————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————
Expand Down Expand Up @@ -80,7 +80,7 @@ Run `revdepcheck::revdep_details(, "bipd")` for more info

## Newly broken

* checking dependencies in R code ...sh: line 1: 28198 Segmentation fault: 11 R_DEFAULT_PACKAGES=NULL '/Library/Frameworks/R.framework/Resources/bin/R' --vanilla --no-echo 2>&1 < '/var/folders/5_/g85d42yj50b6lrjq4rzjzg8w0000gn/T//Rtmp8uxG38/file6ad8527d0366'
* checking dependencies in R code ...sh: line 1: 6660 Segmentation fault: 11 R_DEFAULT_PACKAGES=NULL '/Library/Frameworks/R.framework/Resources/bin/R' --vanilla --no-echo 2>&1 < '/var/folders/5_/g85d42yj50b6lrjq4rzjzg8w0000gn/T//RtmpY4Kslj/file17bf4758620f'
```
NOTE
Expand All @@ -107,7 +107,7 @@ Run `revdepcheck::revdep_details(, "bipd")` for more info

## Newly fixed

* checking dependencies in R code ...sh: line 1: 28180 Segmentation fault: 11 R_DEFAULT_PACKAGES=NULL '/Library/Frameworks/R.framework/Resources/bin/R' --vanilla --no-echo 2>&1 < '/var/folders/5_/g85d42yj50b6lrjq4rzjzg8w0000gn/T//Rtmpw6OWhC/file6a76216c4045'
* checking dependencies in R code ...sh: line 1: 6641 Segmentation fault: 11 R_DEFAULT_PACKAGES=NULL '/Library/Frameworks/R.framework/Resources/bin/R' --vanilla --no-echo 2>&1 < '/var/folders/5_/g85d42yj50b6lrjq4rzjzg8w0000gn/T//Rtmpt5u94R/file17892b19b039'
```
NOTE
Expand Down Expand Up @@ -234,42 +234,110 @@ Run `revdepcheck::revdep_details(, "finalfit")` for more info
doc 4.9Mb
```

# pre
# gFormulaMI

<details>

* Version: 1.0.7
* GitHub: https://github.com/marjoleinF/pre
* Source code: https://github.com/cran/pre
* Date/Publication: 2024-01-12 19:30:02 UTC
* Number of recursive dependencies: 150
* Version: 1.0.0
* GitHub: NA
* Source code: https://github.com/cran/gFormulaMI
* Date/Publication: 2023-05-25 20:00:08 UTC
* Number of recursive dependencies: 93

Run `revdepcheck::revdep_details(, "pre")` for more info
Run `revdepcheck::revdep_details(, "gFormulaMI")` for more info

</details>

## Newly broken

* checking examples ... ERROR
```
Running examples in ‘gFormulaMI-Ex.R’ failed
The error most likely occurred in:
> ### Name: gFormulaImpute
> ### Title: G-formula multiple imputation
> ### Aliases: gFormulaImpute
>
> ### ** Examples
>
> set.seed(7626)
...
l2 1 1 1 1 0 0 0 0
a2 1 1 1 1 1 0 0 0
y 1 1 1 1 1 1 0 0
regime 1 1 1 1 1 1 1 0
> #fit linear model to final outcome with regime as covariate
> fits <- with(imps, lm(y~factor(regime)))
Error in mira(call = call, call1 = data$call, nmis = data$nmis, analyses = analyses) :
Argument 'nmis' must be an integer vector.
Calls: with -> with.mids -> mira
Execution halted
```

* checking tests ...
```
Running ‘testthat.R’
ERROR
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
> test_check("pre")
[ FAIL 1 | WARN 0 | SKIP 0 | PASS 127 ]
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test_pre_misc.R:94:3'): cvpre gives previous results with airquality data ──
Error in `serverSocket(port = port)`: creation of server socket failed: port 11508 cannot be opened
9. └─mice::mira(...)
── Error ('test-gFormulaMI.R:49:5'): Check 95% confidence interval includes true value, two regimes ──
Error in `mira(call = call, call1 = data$call, nmis = data$nmis, analyses = analyses)`: Argument 'nmis' must be an integer vector.
Backtrace:
▆
1. └─parallel::makeCluster(2L) at test_pre_misc.R:94:3
2. └─parallel::makePSOCKcluster(names = spec, ...)
3. └─base::serverSocket(port = port)
1. ├─testthat::expect_equal(...) at test-gFormulaMI.R:45:3
2. │ └─testthat::quasi_label(enquo(object), label, arg = "object")
3. │ └─rlang::eval_bare(expr, quo_get_env(quo))
4. ├─base::with(impRes, lm(y ~ factor(regime))) at test-gFormulaMI.R:49:5
5. └─mice:::with.mids(impRes, lm(y ~ factor(regime)))
6. └─mice::mira(...)
[ FAIL 1 | WARN 0 | SKIP 0 | PASS 127 ]
[ FAIL 5 | WARN 0 | SKIP 2 | PASS 11 ]
Error: Test failures
Execution halted
```

* checking running R code from vignettes ...
```
‘gFormulaMI.Rmd’ using ‘UTF-8’... failed
ERROR
Errors in running code in vignettes:
when running code in ‘gFormulaMI.Rmd’
...
3 0.4327859 0 -0.3925652 0 -0.7555212806 0 -1.5840459 1
4 0.6059553 0 2.4764117 0 0.7312018102 0 0.6342567 1
5 0.2985589 0 0.9223022 0 0.0734605439 0 -1.1511625 1
6 -0.1763264 0 0.6122369 0 0.8838681514 0 2.0858243 1
> fits <- with(imps, lm(y ~ factor(regime)))
When sourcing ‘gFormulaMI.R’:
Error: Argument 'nmis' must be an integer vector.
Execution halted
```

# micd

<details>

* Version: 1.1.1
* GitHub: https://github.com/bips-hb/micd
* Source code: https://github.com/cran/micd
* Date/Publication: 2023-02-17 17:40:02 UTC
* Number of recursive dependencies: 104

Run `revdepcheck::revdep_details(, "micd")` for more info

</details>

## Newly broken

* checking Rd cross-references ... WARNING
```
Missing link or links in Rd file 'with_graph.Rd':
‘[mice]{mira-class}’
See section 'Cross-references' in the 'Writing R Extensions' manual.
```

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