Last updated on 2026-11-10 17:52:45 CET.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 1.3.1 | 23.42 | 129.71 | 153.13 | ERROR | |
| r-devel-linux-x86_64-debian-gcc | 1.3.1 | 16.69 | 91.76 | 108.45 | ERROR | |
| r-devel-linux-x86_64-fedora-clang | 1.3.1 | 17.00 | OK | |||
| r-devel-linux-x86_64-fedora-gcc | 1.3.1 | 17.00 | 95.59 | 112.59 | ERROR | |
| r-devel-windows-x86_64 | 1.3.1 | 26.00 | 154.00 | 180.00 | OK | |
| r-patched-linux-x86_64 | 1.3.1 | OK | ||||
| r-release-linux-x86_64 | 1.3.1 | 24.49 | 123.73 | 148.22 | OK | |
| r-release-macos-arm64 | 1.3.1 | 6.00 | 46.00 | 52.00 | OK | |
| r-release-macos-x86_64 | 1.3.1 | 19.00 | 327.00 | 346.00 | OK | |
| r-release-windows-x86_64 | 1.3.1 | 25.00 | 145.00 | 170.00 | OK | |
| r-oldrel-macos-arm64 | 1.3.1 | 6.00 | 46.00 | 52.00 | OK | |
| r-oldrel-macos-x86_64 | 1.3.1 | 18.00 | 313.00 | 331.00 | OK | |
| r-oldrel-windows-x86_64 | 1.3.1 | 34.00 | 194.00 | 228.00 | OK |
Version: 1.3.1
Check: examples
Result: ERROR
Running examples in ‘mi-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: 02missing_data.frame
> ### Title: Class "missing_data.frame"
> ### Aliases: 02missing_data.frame missing_data.frame-class
> ### missing_data.frame
> ### Keywords: classes manip AimedAtUseRs
>
> ### ** Examples
>
> # STEP 0: Get data
> data(CHAIN, package = "mi")
>
> # STEP 1: Convert to a missing_data.frame
> mdf <- missing_data.frame(CHAIN) # warnings about missingness patterns
NOTE: The following pairs of variables appear to have the same missingness pattern.
Please verify whether they are in fact logically distinct variables.
[,1] [,2]
[1,] "age" "healthy"
[2,] "age" "mental"
[3,] "age" "treatment"
[4,] "healthy" "mental"
[5,] "healthy" "treatment"
[6,] "mental" "treatment"
Warning in .local(.Object, ...) :
Some observations are missing on all included variables.
Often, this indicates a more complicated model is needed for this missingness mechanism
> show(mdf)
Object of class missing_data.frame with 532 observations on 7 variables
There are 9 missing data patterns
Append '@patterns' to this missing_data.frame to access the corresponding pattern for every observation or perhaps use table()
type missing method model
log_virus continuous 179 ppd linear
age continuous 24 ppd linear
income continuous 38 ppd linear
healthy continuous 24 ppd linear
mental binary 24 ppd logit
damage ordered-categorical 63 ppd ologit
treatment ordered-categorical 24 ppd ologit
family link transformation
log_virus gaussian identity standardize
age gaussian identity standardize
income gaussian identity standardize
healthy gaussian identity standardize
mental binomial logit <NA>
damage multinomial logit <NA>
treatment multinomial logit <NA>
>
> # STEP 2: change things
> mdf <- change(mdf, y = "log_virus", what = "transformation", to = "identity")
>
> # STEP 3: look deeper
> summary(mdf)
log_virus age income healthy
Min. : 0.000 Min. :21.00 Min. : 1.000 Min. :16.67
1st Qu.: 0.000 1st Qu.:37.00 1st Qu.: 2.000 1st Qu.:35.00
Median : 0.000 Median :43.00 Median : 3.000 Median :45.37
Mean : 4.324 Mean :42.56 Mean : 3.377 Mean :44.40
3rd Qu.: 9.105 3rd Qu.:48.00 3rd Qu.: 5.000 3rd Qu.:54.89
Max. :13.442 Max. :70.00 Max. :10.000 Max. :70.11
NAs :179 NAs :24 NAs :38 NAs :24
mental damage treatment
Min. :0.0000 Min. :1.000 Min. :0.0000
1st Qu.:0.0000 1st Qu.:3.000 1st Qu.:0.0000
Median :0.0000 Median :4.000 Median :1.0000
Mean :0.2717 Mean :3.578 Mean :0.8602
3rd Qu.:1.0000 3rd Qu.:5.000 3rd Qu.:2.0000
Max. :1.0000 Max. :5.000 Max. :2.0000
NAs :24 NAs :63 NAs :24
> hist(mdf)
> image(mdf)
>
> # STEP 4: impute
> ## Not run:
> ##D imputations <- mi(mdf)
> ## End(Not run)
>
> ## An example with subsetting on a fully observed variable
> data(nlsyV, package = "mi")
> mdfs <- missing_data.frame(nlsyV, favor_positive = TRUE, favor_ordered = FALSE, by = "first")
Error in if ((l <- length(slot(object, i))) > 1) { :
argument is of length zero
Calls: missing_data.frame ... validObject -> anyStrings -> isTRUE -> validityMethod
Execution halted
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc
Version: 1.3.1
Check: tests
Result: ERROR
Running ‘missing_data.frame.R’ [5s/7s]
Running ‘missing_variable.R’ [3s/4s]
Running the tests in ‘tests/missing_variable.R’ failed.
Complete output:
> stopifnot(require(mi))
Loading required package: mi
Loading required package: Matrix
Loading required package: stats4
mi (Version 1.3.1, packaged: 2026-07-28 02:55:47 UTC; bgoodri)
mi Copyright (C) 2008, 2009, 2010, 2011, 2012, 2013, 2014, 2015 Trustees of Columbia University
This program comes with ABSOLUTELY NO WARRANTY.
This is free software, and you are welcome to redistribute it
under the General Public License version 2 or later.
Execute RShowDoc('COPYING') for details.
> set.seed(1)
> x <- rnorm(10)
> x[1] <- NA
> y <- missing_variable(x, type = "continuous")
>
> y <- missing_variable(x, type = "irrelevant")
> x <- rep(1, 10)
> y <- missing_variable(x, type = "fixed")
> x <- rep(1:5, each = 2)
> y <- missing_variable(x, type = "group")
>
> x[1] <- NA
> y <- missing_variable(x, type = "unordered-categorical")
> y <- missing_variable(x, type = "ordered-categorical")
> y <- missing_variable(x, type = "interval")
>
> x <- rbinom(10, size = 1, prob = 0.5)
> x[1] <- NA
> if (all(x == 1, na.rm = TRUE) || all(x == 0, na.rm = TRUE)) x[10] <- 1 - x[10]
> y <- missing_variable(x, type = "binary")
> y <- missing_variable(x, type = "grouped-binary", strata = rep(c("A", "B"), each = 5))
Error in validObject(.Object) :
invalid class "grouped-binary" object: y : length of strata must be 0 or 1 but is 10
Calls: missing_variable ... .local -> callNextMethod -> .nextMethod -> validObject
Execution halted
Flavor: r-devel-linux-x86_64-debian-clang
Version: 1.3.1
Check: tests
Result: ERROR
Running ‘missing_data.frame.R’ [3s/5s]
Running ‘missing_variable.R’ [2s/3s]
Running the tests in ‘tests/missing_variable.R’ failed.
Complete output:
> stopifnot(require(mi))
Loading required package: mi
Loading required package: Matrix
Loading required package: stats4
mi (Version 1.3.1, packaged: 2026-07-28 02:55:47 UTC; bgoodri)
mi Copyright (C) 2008, 2009, 2010, 2011, 2012, 2013, 2014, 2015 Trustees of Columbia University
This program comes with ABSOLUTELY NO WARRANTY.
This is free software, and you are welcome to redistribute it
under the General Public License version 2 or later.
Execute RShowDoc('COPYING') for details.
> set.seed(1)
> x <- rnorm(10)
> x[1] <- NA
> y <- missing_variable(x, type = "continuous")
>
> y <- missing_variable(x, type = "irrelevant")
> x <- rep(1, 10)
> y <- missing_variable(x, type = "fixed")
> x <- rep(1:5, each = 2)
> y <- missing_variable(x, type = "group")
>
> x[1] <- NA
> y <- missing_variable(x, type = "unordered-categorical")
> y <- missing_variable(x, type = "ordered-categorical")
> y <- missing_variable(x, type = "interval")
>
> x <- rbinom(10, size = 1, prob = 0.5)
> x[1] <- NA
> if (all(x == 1, na.rm = TRUE) || all(x == 0, na.rm = TRUE)) x[10] <- 1 - x[10]
> y <- missing_variable(x, type = "binary")
> y <- missing_variable(x, type = "grouped-binary", strata = rep(c("A", "B"), each = 5))
Error in validObject(.Object) :
invalid class "grouped-binary" object: y : length of strata must be 0 or 1 but is 10
Calls: missing_variable ... .local -> callNextMethod -> .nextMethod -> validObject
Execution halted
Flavor: r-devel-linux-x86_64-debian-gcc
Version: 1.3.1
Check: examples
Result: ERROR
Running examples in ‘mi-Ex.R’ failed
The error most likely occurred in:
> ### Name: 02missing_data.frame
> ### Title: Class "missing_data.frame"
> ### Aliases: 02missing_data.frame missing_data.frame-class
> ### missing_data.frame
> ### Keywords: classes manip AimedAtUseRs
>
> ### ** Examples
>
> # STEP 0: Get data
> data(CHAIN, package = "mi")
>
> # STEP 1: Convert to a missing_data.frame
> mdf <- missing_data.frame(CHAIN) # warnings about missingness patterns
NOTE: The following pairs of variables appear to have the same missingness pattern.
Please verify whether they are in fact logically distinct variables.
[,1] [,2]
[1,] "age" "healthy"
[2,] "age" "mental"
[3,] "age" "treatment"
[4,] "healthy" "mental"
[5,] "healthy" "treatment"
[6,] "mental" "treatment"
Warning in .local(.Object, ...) :
Some observations are missing on all included variables.
Often, this indicates a more complicated model is needed for this missingness mechanism
> show(mdf)
Object of class missing_data.frame with 532 observations on 7 variables
There are 9 missing data patterns
Append '@patterns' to this missing_data.frame to access the corresponding pattern for every observation or perhaps use table()
type missing method model
log_virus continuous 179 ppd linear
age continuous 24 ppd linear
income continuous 38 ppd linear
healthy continuous 24 ppd linear
mental binary 24 ppd logit
damage ordered-categorical 63 ppd ologit
treatment ordered-categorical 24 ppd ologit
family link transformation
log_virus gaussian identity standardize
age gaussian identity standardize
income gaussian identity standardize
healthy gaussian identity standardize
mental binomial logit <NA>
damage multinomial logit <NA>
treatment multinomial logit <NA>
>
> # STEP 2: change things
> mdf <- change(mdf, y = "log_virus", what = "transformation", to = "identity")
>
> # STEP 3: look deeper
> summary(mdf)
log_virus age income healthy
Min. : 0.000 Min. :21.00 Min. : 1.000 Min. :16.67
1st Qu.: 0.000 1st Qu.:37.00 1st Qu.: 2.000 1st Qu.:35.00
Median : 0.000 Median :43.00 Median : 3.000 Median :45.37
Mean : 4.324 Mean :42.56 Mean : 3.377 Mean :44.40
3rd Qu.: 9.105 3rd Qu.:48.00 3rd Qu.: 5.000 3rd Qu.:54.89
Max. :13.442 Max. :70.00 Max. :10.000 Max. :70.11
NAs :179 NAs :24 NAs :38 NAs :24
mental damage treatment
Min. :0.0000 Min. :1.000 Min. :0.0000
1st Qu.:0.0000 1st Qu.:3.000 1st Qu.:0.0000
Median :0.0000 Median :4.000 Median :1.0000
Mean :0.2717 Mean :3.578 Mean :0.8602
3rd Qu.:1.0000 3rd Qu.:5.000 3rd Qu.:2.0000
Max. :1.0000 Max. :5.000 Max. :2.0000
NAs :24 NAs :63 NAs :24
> hist(mdf)
> image(mdf)
>
> # STEP 4: impute
> ## Not run:
> ##D imputations <- mi(mdf)
> ## End(Not run)
>
> ## An example with subsetting on a fully observed variable
> data(nlsyV, package = "mi")
> mdfs <- missing_data.frame(nlsyV, favor_positive = TRUE, favor_ordered = FALSE, by = "first")
Error in if ((l <- length(slot(object, i))) > 1) { :
argument is of length zero
Calls: missing_data.frame ... validObject -> anyStrings -> isTRUE -> validityMethod
Execution halted
Flavor: r-devel-linux-x86_64-fedora-gcc
Version: 1.3.1
Check: tests
Result: ERROR
Running ‘missing_data.frame.R’
Running ‘missing_variable.R’
Running the tests in ‘tests/missing_variable.R’ failed.
Complete output:
> stopifnot(require(mi))
Loading required package: mi
Loading required package: Matrix
Loading required package: stats4
mi (Version 1.3.1, packaged: 2026-07-28 02:55:47 UTC; bgoodri)
mi Copyright (C) 2008, 2009, 2010, 2011, 2012, 2013, 2014, 2015 Trustees of Columbia University
This program comes with ABSOLUTELY NO WARRANTY.
This is free software, and you are welcome to redistribute it
under the General Public License version 2 or later.
Execute RShowDoc('COPYING') for details.
> set.seed(1)
> x <- rnorm(10)
> x[1] <- NA
> y <- missing_variable(x, type = "continuous")
>
> y <- missing_variable(x, type = "irrelevant")
> x <- rep(1, 10)
> y <- missing_variable(x, type = "fixed")
> x <- rep(1:5, each = 2)
> y <- missing_variable(x, type = "group")
>
> x[1] <- NA
> y <- missing_variable(x, type = "unordered-categorical")
> y <- missing_variable(x, type = "ordered-categorical")
> y <- missing_variable(x, type = "interval")
>
> x <- rbinom(10, size = 1, prob = 0.5)
> x[1] <- NA
> if (all(x == 1, na.rm = TRUE) || all(x == 0, na.rm = TRUE)) x[10] <- 1 - x[10]
> y <- missing_variable(x, type = "binary")
> y <- missing_variable(x, type = "grouped-binary", strata = rep(c("A", "B"), each = 5))
Error in validObject(.Object) :
invalid class "grouped-binary" object: y : length of strata must be 0 or 1 but is 10
Calls: missing_variable ... .local -> callNextMethod -> .nextMethod -> validObject
Execution halted
Flavor: r-devel-linux-x86_64-fedora-gcc
Version: 1.3.1
Check: re-building of vignette outputs
Result: ERROR
Error(s) in re-building vignettes:
--- re-building ‘mi_vignette.Rmd’ using rmarkdown
Quitting from mi_vignette.Rmd:52-56 [step2]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `if ((l <- length(slot(object, i))) > 1) ...`:
! argument is of length zero
---
Backtrace:
x
1. +-mi::change(...)
2. \-mi::change(...)
3. +-mi::change_type(data = data, y = y, to = to, ...)
4. \-mi::change_type(data = data, y = y, to = to, ...)
5. +-mi::change_type(y = data@variables[[y[i]]], to = to[i], ...)
6. \-mi::change_type(y = data@variables[[y[i]]], to = to[i], ...)
7. \-methods::new(...)
8. +-methods::initialize(value, ...)
9. \-mi (local) initialize(value, ...)
10. +-methods::callNextMethod()
11. \-mi (local) .nextMethod(.Object = .Object, ... = ...)
12. +-methods::callNextMethod()
13. \-mi (local) .nextMethod(.Object = .Object, ... = ...)
14. \-mi (local) .local(.Object, ...)
15. +-methods::callNextMethod()
16. \-methods (local) .nextMethod(.Object = .Object, ... = ...)
17. \-methods::validObject(.Object)
18. +-methods (local) anyStrings(...)
19. | \-base::isTRUE(x)
20. \-mi (local) validityMethod(if (exti@simple) object else as(object, superClass))
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'mi_vignette.Rmd' failed with diagnostics:
argument is of length zero
--- failed re-building ‘mi_vignette.Rmd’
SUMMARY: processing the following file failed:
‘mi_vignette.Rmd’
Error: Vignette re-building failed.
Execution halted
Flavor: r-devel-linux-x86_64-fedora-gcc