Last updated on 2020-08-07 01:50:22 CEST.
| Package | ERROR | OK |
|---|---|---|
| bootImpute | 1 | 11 |
| InformativeCensoring | 2 | 10 |
| mlmi | 12 | |
| smcfcs | 12 |
Current CRAN status: ERROR: 1, OK: 11
Version: 1.1.0
Check: examples
Result: ERROR
Running examples in 'bootImpute-Ex.R' failed
The error most likely occurred in:
> ### Name: bootImpute
> ### Title: Bootstrap then impute an incomplete dataset
> ### Aliases: bootImpute
>
> ### ** Examples
>
> #this example shows how you can use bootImpute to impute using the mice
> #package. If you do want to impute using MICE you can instead use the
> #bootMice function, which essentially contains the code below
> library(mice)
Attaching package: 'mice'
The following objects are masked from 'package:base':
cbind, rbind
>
> #write a wrapper function to call mice with one imputation and return
> #the imputed dataset
> impOnce <- function(inputData) {
+ oneImp <- mice::mice(inputData, m=1)
+ mice::complete(oneImp)
+ }
>
> #bootstrap twice and impute each twice
> #in practice you should bootstrap many more times, e.g. at least 200
> imps <- bootImpute(ex_linquad, impOnce, nBoot=2, nImp=2, seed=564764)
Warning in bootImpute(ex_linquad, impOnce, nBoot = 2, nImp = 2, seed = 564764) :
It is recommended to use at least 200 bootstraps.
iter imp variable
1 1 xError in matcher(yhatobs, yhatmis, k = donors) :
function 'enterRNGScope' not provided by package 'Rcpp'
Calls: bootImpute ... sampler.univ -> do.call -> mice.impute.pmm -> matcher
Execution halted
Flavor: r-release-windows-ix86+x86_64
Version: 1.1.0
Check: tests
Result: ERROR
Running 'testthat.R' [18s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
> library(testthat)
> library(bootImpute)
>
> test_check("bootImpute")
Estimate Std. error 95% CI lower 95% CI upper p
(Intercept) 0.07915058 0.19747184 -0.3108593 0.4691604 6.890917e-01
x 0.87482487 0.16079989 0.5572895 1.1923603 1.931226e-07
x2 -0.01858405 0.06370239 -0.1451103 0.1079422 7.711511e-01
Estimate Std. error 95% CI lower 95% CI upper p
[1,] 1 0 NaN NaN NaN
iter imp variable
1 1 x-- 1. Failure: Testing bootMice works (@test_bootImpute.r#75) -----------------
`{ ... }` threw an error.
Message: function 'enterRNGScope' not provided by package 'Rcpp'
Class: simpleError/error/condition
Backtrace:
1. testthat::expect_error(...)
6. bootImpute::bootMice(ex_linquad, nBoot = 10, nImp = 2)
7. bootImpute::bootImpute(...)
8. bootImpute:::impfun(obsdata[bsIndices, ], ...)
9. mice::mice(inputData, m = 1, ...)
10. mice:::sampler(...)
11. mice:::sampler.univ(...)
13. mice::mice.impute.pmm(...)
14. mice:::matcher(yhatobs, yhatmis, k = donors)
[1] "Outcome variable(s): y"
[1] "Passive variables: xsq"
[1] "Partially obs. variables: x"
[1] "Fully obs. substantive model variables: z"
[1] "Imputation 1"
[1] "Imputing: x using z plus outcome"
[1] "Outcome variable(s): y"
[1] "Passive variables: xsq"
[1] "Partially obs. variables: x"
[1] "Fully obs. substantive model variables: z"
[1] "Imputation 1"
[1] "Imputing: x using z plus outcome"
[1] "Outcome variable(s): y"
[1] "Passive variables: xsq"
[1] "Partially obs. variables: x"
[1] "Fully obs. substantive model variables: z"
[1] "Imputation 1"
[1] "Imputing: x using z plus outcome"
[1] "Outcome variable(s): y"
[1] "Passive variables: xsq"
[1] "Partially obs. variables: x"
[1] "Fully obs. substantive model variables: z"
[1] "Imputation 1"
[1] "Imputing: x using z plus outcome"
Estimate Std. error 95% CI lower 95% CI upper p
(Intercept) 0.07324015 0.17813009 -0.2786614 0.4251417 6.815276e-01
x 0.87813736 0.15575323 0.5706295 1.1856452 7.227343e-08
x2 -0.01727423 0.06691675 -0.1501987 0.1156503 7.968788e-01
Estimate Std. error 95% CI lower 95% CI upper p
(Intercept) 0.07324015 0.17813009 -0.2786614 0.4251417 6.815276e-01
x 0.87813736 0.15575323 0.5706295 1.1856452 7.227343e-08
x2 -0.01727423 0.06691675 -0.1501987 0.1156503 7.968788e-01
-- 2. Failure: Test bootImpute runs using multiple cores with mice (@test_parall
`{ ... }` threw an error.
Message: 2 nodes produced errors; first error: function 'enterRNGScope' not provided by package 'Rcpp'
Class: simpleError/error/condition
Backtrace:
1. testthat::expect_error(...)
6. bootImpute::bootMice(...)
7. bootImpute::bootImpute(...)
8. parallel::parLapply(...)
10. parallel::clusterApply(...)
11. parallel:::staticClusterApply(cl, fun, length(x), argfun)
12. parallel:::checkForRemoteErrors(val)
-- 3. Failure: Test bootImpute runs using multiple cores with mice with extra ar
`{ ... }` threw an error.
Message: 2 nodes produced errors; first error: function 'enterRNGScope' not provided by package 'Rcpp'
Class: simpleError/error/condition
Backtrace:
1. testthat::expect_error(...)
6. bootImpute::bootMice(...)
7. bootImpute::bootImpute(...)
8. parallel::parLapply(...)
10. parallel::clusterApply(...)
11. parallel:::staticClusterApply(cl, fun, length(x), argfun)
12. parallel:::checkForRemoteErrors(val)
Estimate Std. error 95% CI lower 95% CI upper p
(Intercept) -0.01028169 0.2680221 -0.6223072 0.6017438 0.9702874228
x 0.96952393 0.1163650 0.6835377 1.2555102 0.0001782262
Estimate Std. error 95% CI lower 95% CI upper p
(Intercept) -0.01028169 0.2680221 -0.6223072 0.6017438 0.9702874228
x 0.96952393 0.1163650 0.6835377 1.2555102 0.0001782262
== testthat results ===========================================================
[ OK: 7 | SKIPPED: 0 | WARNINGS: 3 | FAILED: 3 ]
1. Failure: Testing bootMice works (@test_bootImpute.r#75)
2. Failure: Test bootImpute runs using multiple cores with mice (@test_parallel.R#35)
3. Failure: Test bootImpute runs using multiple cores with mice with extra arguments (@test_parallel.R#49)
Error: testthat unit tests failed
In addition: Warning messages:
1: In for (i in seq_len(n)) { :
closing unused connection 7 (<-CRANwin.fb05.statistik.uni-dortmund.de:11071)
2: In for (i in seq_len(n)) { :
closing unused connection 6 (<-CRANwin.fb05.statistik.uni-dortmund.de:11071)
3: In for (i in seq_len(n)) { :
closing unused connection 5 (<-CRANwin.fb05.statistik.uni-dortmund.de:11071)
4: In for (i in seq_len(n)) { :
closing unused connection 4 (<-CRANwin.fb05.statistik.uni-dortmund.de:11071)
Execution halted
Flavor: r-release-windows-ix86+x86_64
Current CRAN status: ERROR: 2, OK: 10
Version: 0.3.5
Check: tests
Result: ERROR
Running ‘testthat.R’ [151s/151s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
══ testthat results ═══════════════════════════════════════════════════════════
[ OK: 491 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 10 ]
1. Failure: GammaImputeSet_object (@test-gammaImputedata.R#25)
2. Failure: GammaImputeSet_object (@test-gammaImputedata.R#26)
3. Failure: GammaStatSet (@test-gammaStat.R#115)
4. Failure: GammaStatSet (@test-gammaStat.R#116)
5. Failure: GammaStatSet_multiplecovar (@test-gammaStat.R#140)
6. Failure: GammaStatSet_multiplecovar (@test-gammaStat.R#141)
7. Failure: summary_1_covar (@test-gammaStat.R#171)
8. Failure: ScoreImputeSet_extract (@test-scoreExtract.R#32)
9. Failure: ScoreImputeSet_extract (@test-scoreExtract.R#33)
10. Failure: Logrank_Wilcoxon_usersupplied_formula (@test-scoreStat.R#168)
Error: testthat unit tests failed
Execution halted
Flavor: r-oldrel-macos-x86_64
Version: 0.3.5
Flags: --no-vignettes
Check: tests
Result: ERROR
Running 'testthat.R' [251s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
> library(testthat)
> library("InformativeCensoring")
Loading required package: survival
Attaching package: 'InformativeCensoring'
The following object is masked from 'package:survival':
cox.zph
>
> test_check("InformativeCensoring")
-- 1. Failure: GammaImputeSet_object (@test-gammaImputedata.R#25) -------------
c("matrix", "array") not equal to class(imputed.data.sets$impute.time).
Lengths differ: 2 is not 1
-- 2. Failure: GammaImputeSet_object (@test-gammaImputedata.R#26) -------------
c("matrix", "array") not equal to class(imputed.data.sets$impute.event).
Lengths differ: 2 is not 1
-- 3. Failure: GammaStatSet (@test-gammaStat.R#115) ---------------------------
c("matrix", "array") not equal to class(ans$statistics$estimates).
Lengths differ: 2 is not 1
-- 4. Failure: GammaStatSet (@test-gammaStat.R#116) ---------------------------
c("matrix", "array") not equal to class(ans$statistics$vars).
Lengths differ: 2 is not 1
-- 5. Failure: GammaStatSet_multiplecovar (@test-gammaStat.R#140) -------------
c("matrix", "array") not equal to class(ans$statistics$estimates).
Lengths differ: 2 is not 1
-- 6. Failure: GammaStatSet_multiplecovar (@test-gammaStat.R#141) -------------
c("matrix", "array") not equal to class(ans$statistics$vars).
Lengths differ: 2 is not 1
-- 7. Failure: summary_1_covar (@test-gammaStat.R#171) ------------------------
c("matrix", "array") not equal to class(ans).
Lengths differ: 2 is not 1
-- 8. Failure: ScoreImputeSet_extract (@test-scoreExtract.R#32) ---------------
c("matrix", "array") not equal to class(ans$impute.time).
Lengths differ: 2 is not 1
-- 9. Failure: ScoreImputeSet_extract (@test-scoreExtract.R#33) ---------------
c("matrix", "array") not equal to class(ans$impute.event).
Lengths differ: 2 is not 1
-- 10. Failure: Logrank_Wilcoxon_usersupplied_formula (@test-scoreStat.R#168) -
a$statistic not equal to `/`(...).
1/1 mismatches
[1] -0.0292 - -1.53 == 1.5
== testthat results ===========================================================
[ OK: 491 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 10 ]
1. Failure: GammaImputeSet_object (@test-gammaImputedata.R#25)
2. Failure: GammaImputeSet_object (@test-gammaImputedata.R#26)
3. Failure: GammaStatSet (@test-gammaStat.R#115)
4. Failure: GammaStatSet (@test-gammaStat.R#116)
5. Failure: GammaStatSet_multiplecovar (@test-gammaStat.R#140)
6. Failure: GammaStatSet_multiplecovar (@test-gammaStat.R#141)
7. Failure: summary_1_covar (@test-gammaStat.R#171)
8. Failure: ScoreImputeSet_extract (@test-scoreExtract.R#32)
9. Failure: ScoreImputeSet_extract (@test-scoreExtract.R#33)
10. Failure: Logrank_Wilcoxon_usersupplied_formula (@test-scoreStat.R#168)
Error: testthat unit tests failed
Execution halted
Flavor: r-oldrel-windows-ix86+x86_64
Current CRAN status: OK: 12
Current CRAN status: OK: 12