Last updated on 2022-11-06 08:57:26 CET.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 1.0.0 | 33.69 | 491.29 | 524.98 | ERROR | |
| r-devel-linux-x86_64-debian-gcc | 1.0.0 | 24.50 | 359.66 | 384.16 | ERROR | |
| r-devel-linux-x86_64-fedora-clang | 1.0.0 | 639.35 | ERROR | |||
| r-devel-linux-x86_64-fedora-gcc | 1.0.0 | 612.30 | ERROR | |||
| r-devel-windows-x86_64 | 1.0.0 | 65.00 | 537.00 | 602.00 | ERROR | |
| r-patched-linux-x86_64 | 1.0.0 | 30.11 | 459.17 | 489.28 | ERROR | |
| r-release-linux-x86_64 | 1.0.0 | 29.26 | 449.63 | 478.89 | ERROR | |
| r-release-macos-arm64 | 1.0.0 | 224.00 | NOTE | |||
| r-release-macos-x86_64 | 1.0.0 | 379.00 | NOTE | |||
| r-release-windows-x86_64 | 1.0.0 | 72.00 | 539.00 | 611.00 | ERROR | |
| r-oldrel-macos-arm64 | 1.0.0 | 261.00 | NOTE | |||
| r-oldrel-macos-x86_64 | 1.0.0 | 320.00 | NOTE | |||
| r-oldrel-windows-ix86+x86_64 | 1.0.0 | 62.00 | 611.00 | 673.00 | ERROR |
Version: 1.0.0
Check: examples
Result: ERROR
Running examples in 'psfmi-Ex.R' failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: psfmi_validate
> ### Title: Internal validation and performance of logistic prediction
> ### models across Multiply Imputed datasets
> ### Aliases: psfmi_validate
>
> ### ** Examples
>
> pool_lr <- psfmi_lr(data=lbpmilr, formula = Chronic ~ Pain + JobDemands + rcs(Tampascale, 3) +
+ factor(Satisfaction) + Smoking, p.crit = 1, direction="FW",
+ nimp=5, impvar="Impnr", method="D1")
>
> pool_lr$RR_model
$`Step 1 - no variables removed -`
term estimate std.error statistic df
1 (Intercept) -18.194984918 7.46386123 -2.4377443 66.86346
2 Pain 0.787297519 0.28791031 2.7345236 23.89602
3 JobDemands -0.009136444 0.05316641 -0.1718462 50.22157
4 Smoking 0.078959504 0.47947339 0.1646796 72.71887
5 factor(Satisfaction)2 -0.439137053 0.58056883 -0.7563910 132.98121
6 factor(Satisfaction)3 -2.255502423 0.71238726 -3.1661184 113.70396
7 rcs(Tampascale, 3)Tampascale 0.404284518 0.19688244 2.0534311 96.31169
8 rcs(Tampascale, 3)Tampascale' -0.335633226 0.24663776 -1.3608347 28.85941
p.value OR lower.EXP upper.EXP
1 0.017444622 1.253194e-08 4.243137e-15 0.03701262
2 0.011578833 2.197450e+00 1.212814e+00 3.98147379
3 0.864249071 9.909052e-01 8.905530e-01 1.10256554
4 0.869653055 1.082160e+00 4.161574e-01 2.81401089
5 0.450752704 6.445924e-01 2.044399e-01 2.03237915
6 0.001983287 1.048209e-01 2.555875e-02 0.42988853
7 0.042741589 1.498230e+00 1.013584e+00 2.21461135
8 0.184099209 7.148853e-01 4.316368e-01 1.18400693
>
> res_perf <- psfmi_validate(pool_lr, val_method = "cv_MI", data_orig = lbp_orig, folds=3,
+ nimp_cv = 2, p.crit=0.05, BW=TRUE, miceImp = miceImp, printFlag = FALSE)
Imp run 1
Error in `strata_check()`:
! `strata` should be a single name or character value.
Backtrace:
x
1. \-psfmi::psfmi_validate(...)
2. \-psfmi::cv_MI(...)
3. +-purrr::map(...)
4. \-rsample::vfold_cv(data_orig, v = folds, strata = unlist(data_orig[pobj$Outcome]))
5. \-rsample:::strata_check(strata, data)
6. \-rlang::abort("`strata` should be a single name or character value.")
Execution halted
Flavor: r-devel-linux-x86_64-debian-clang
Version: 1.0.0
Check: re-building of vignette outputs
Result: ERROR
Error(s) in re-building vignettes:
...
--- re-building 'MI_boot.Rmd' using rmarkdown
--- finished re-building 'MI_boot.Rmd'
--- re-building 'MI_cv_naive.Rmd' using rmarkdown
--- finished re-building 'MI_cv_naive.Rmd'
--- re-building 'Pool_Model_Performance.Rmd' using rmarkdown
--- finished re-building 'Pool_Model_Performance.Rmd'
--- re-building 'Pooling_AUC_values.Rmd' using rmarkdown
--- finished re-building 'Pooling_AUC_values.Rmd'
--- re-building 'boot_MI.Rmd' using rmarkdown
--- finished re-building 'boot_MI.Rmd'
--- re-building 'cv_MI.Rmd' using rmarkdown
Quitting from lines 51-64 (cv_MI.Rmd)
Error: processing vignette 'cv_MI.Rmd' failed with diagnostics:
`strata` should be a single name or character value.
--- failed re-building 'cv_MI.Rmd'
--- re-building 'cv_MI_RR.Rmd' using rmarkdown
Quitting from lines 48-61 (cv_MI_RR.Rmd)
Error: processing vignette 'cv_MI_RR.Rmd' failed with diagnostics:
`strata` should be a single name or character value.
--- failed re-building 'cv_MI_RR.Rmd'
--- re-building 'development_workflow.Rmd' using rmarkdown
Attaching package: 'mice'
The following object is masked from 'package:stats':
filter
The following objects are masked from 'package:base':
cbind, rbind
Quitting from lines 136-148 (development_workflow.Rmd)
Error: processing vignette 'development_workflow.Rmd' failed with diagnostics:
`strata` should be a single name or character value.
--- failed re-building 'development_workflow.Rmd'
--- re-building 'psfmi_CoxModels.Rmd' using rmarkdown
--- finished re-building 'psfmi_CoxModels.Rmd'
--- re-building 'psfmi_LinearModels.Rmd' using rmarkdown
--- finished re-building 'psfmi_LinearModels.Rmd'
--- re-building 'psfmi_LogisticModels.Rmd' using rmarkdown
--- finished re-building 'psfmi_LogisticModels.Rmd'
--- re-building 'psfmi_StabilityAnalysis.Rmd' using rmarkdown
--- finished re-building 'psfmi_StabilityAnalysis.Rmd'
--- re-building 'psfmi_mice.Rmd' using rmarkdown
--- finished re-building 'psfmi_mice.Rmd'
SUMMARY: processing the following files failed:
'cv_MI.Rmd' 'cv_MI_RR.Rmd' 'development_workflow.Rmd'
Error: Vignette re-building failed.
Execution halted
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-patched-linux-x86_64, r-release-linux-x86_64
Version: 1.0.0
Check: examples
Result: ERROR
Running examples in ‘psfmi-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: psfmi_validate
> ### Title: Internal validation and performance of logistic prediction
> ### models across Multiply Imputed datasets
> ### Aliases: psfmi_validate
>
> ### ** Examples
>
> pool_lr <- psfmi_lr(data=lbpmilr, formula = Chronic ~ Pain + JobDemands + rcs(Tampascale, 3) +
+ factor(Satisfaction) + Smoking, p.crit = 1, direction="FW",
+ nimp=5, impvar="Impnr", method="D1")
>
> pool_lr$RR_model
$`Step 1 - no variables removed -`
term estimate std.error statistic df
1 (Intercept) -18.194984918 7.46386123 -2.4377443 66.86346
2 Pain 0.787297519 0.28791031 2.7345236 23.89602
3 JobDemands -0.009136444 0.05316641 -0.1718462 50.22157
4 Smoking 0.078959504 0.47947339 0.1646796 72.71887
5 factor(Satisfaction)2 -0.439137053 0.58056883 -0.7563910 132.98121
6 factor(Satisfaction)3 -2.255502423 0.71238726 -3.1661184 113.70396
7 rcs(Tampascale, 3)Tampascale 0.404284518 0.19688244 2.0534311 96.31169
8 rcs(Tampascale, 3)Tampascale' -0.335633226 0.24663776 -1.3608347 28.85941
p.value OR lower.EXP upper.EXP
1 0.017444622 1.253194e-08 4.243137e-15 0.03701262
2 0.011578833 2.197450e+00 1.212814e+00 3.98147379
3 0.864249071 9.909052e-01 8.905530e-01 1.10256554
4 0.869653055 1.082160e+00 4.161574e-01 2.81401089
5 0.450752704 6.445924e-01 2.044399e-01 2.03237915
6 0.001983287 1.048209e-01 2.555875e-02 0.42988853
7 0.042741589 1.498230e+00 1.013584e+00 2.21461135
8 0.184099209 7.148853e-01 4.316368e-01 1.18400693
>
> res_perf <- psfmi_validate(pool_lr, val_method = "cv_MI", data_orig = lbp_orig, folds=3,
+ nimp_cv = 2, p.crit=0.05, BW=TRUE, miceImp = miceImp, printFlag = FALSE)
Imp run 1
Error in `strata_check()`:
! `strata` should be a single name or character value.
Backtrace:
▆
1. └─psfmi::psfmi_validate(...)
2. └─psfmi::cv_MI(...)
3. ├─purrr::map(...)
4. └─rsample::vfold_cv(data_orig, v = folds, strata = unlist(data_orig[pobj$Outcome]))
5. └─rsample:::strata_check(strata, data)
6. └─rlang::abort("`strata` should be a single name or character value.")
Execution halted
Flavors: r-devel-linux-x86_64-debian-gcc, r-patched-linux-x86_64, r-release-linux-x86_64
Version: 1.0.0
Check: dependencies in R code
Result: NOTE
Namespace in Imports field not imported from: ‘miceadds’
All declared Imports should be used.
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-release-macos-arm64, r-release-macos-x86_64, r-oldrel-macos-arm64, r-oldrel-macos-x86_64
Version: 1.0.0
Check: examples
Result: ERROR
Running examples in ‘psfmi-Ex.R’ failed
The error most likely occurred in:
> ### Name: psfmi_validate
> ### Title: Internal validation and performance of logistic prediction
> ### models across Multiply Imputed datasets
> ### Aliases: psfmi_validate
>
> ### ** Examples
>
> pool_lr <- psfmi_lr(data=lbpmilr, formula = Chronic ~ Pain + JobDemands + rcs(Tampascale, 3) +
+ factor(Satisfaction) + Smoking, p.crit = 1, direction="FW",
+ nimp=5, impvar="Impnr", method="D1")
>
> pool_lr$RR_model
$`Step 1 - no variables removed -`
term estimate std.error statistic df
1 (Intercept) -18.194984918 7.46386123 -2.4377443 66.86346
2 Pain 0.787297519 0.28791031 2.7345236 23.89602
3 JobDemands -0.009136444 0.05316641 -0.1718462 50.22157
4 Smoking 0.078959504 0.47947339 0.1646796 72.71887
5 factor(Satisfaction)2 -0.439137053 0.58056883 -0.7563910 132.98121
6 factor(Satisfaction)3 -2.255502423 0.71238726 -3.1661184 113.70396
7 rcs(Tampascale, 3)Tampascale 0.404284518 0.19688244 2.0534311 96.31169
8 rcs(Tampascale, 3)Tampascale' -0.335633226 0.24663776 -1.3608347 28.85941
p.value OR lower.EXP upper.EXP
1 0.017444622 1.253194e-08 4.243137e-15 0.03701262
2 0.011578833 2.197450e+00 1.212814e+00 3.98147379
3 0.864249071 9.909052e-01 8.905530e-01 1.10256554
4 0.869653055 1.082160e+00 4.161574e-01 2.81401089
5 0.450752704 6.445924e-01 2.044399e-01 2.03237915
6 0.001983287 1.048209e-01 2.555875e-02 0.42988853
7 0.042741589 1.498230e+00 1.013584e+00 2.21461135
8 0.184099209 7.148853e-01 4.316368e-01 1.18400693
>
> res_perf <- psfmi_validate(pool_lr, val_method = "cv_MI", data_orig = lbp_orig, folds=3,
+ nimp_cv = 2, p.crit=0.05, BW=TRUE, miceImp = miceImp, printFlag = FALSE)
Imp run 1
Error in `strata_check()`:
! `strata` should be a single name or character value.
Backtrace:
▆
1. └─psfmi::psfmi_validate(...)
2. └─psfmi::cv_MI(...)
3. ├─purrr::map(...)
4. └─rsample::vfold_cv(data_orig, v = folds, strata = unlist(data_orig[pobj$Outcome]))
5. └─rsample:::strata_check(strata, data)
6. └─rlang::abort("`strata` should be a single name or character value.")
Execution halted
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-devel-windows-x86_64, r-release-windows-x86_64
Version: 1.0.0
Check: re-building of vignette outputs
Result: ERROR
Error(s) in re-building vignettes:
--- re-building ‘MI_boot.Rmd’ using rmarkdown
--- finished re-building ‘MI_boot.Rmd’
--- re-building ‘MI_cv_naive.Rmd’ using rmarkdown
--- finished re-building ‘MI_cv_naive.Rmd’
--- re-building ‘Pool_Model_Performance.Rmd’ using rmarkdown
--- finished re-building ‘Pool_Model_Performance.Rmd’
--- re-building ‘Pooling_AUC_values.Rmd’ using rmarkdown
--- finished re-building ‘Pooling_AUC_values.Rmd’
--- re-building ‘boot_MI.Rmd’ using rmarkdown
--- finished re-building ‘boot_MI.Rmd’
--- re-building ‘cv_MI.Rmd’ using rmarkdown
Quitting from lines 51-64 (cv_MI.Rmd)
Error: processing vignette 'cv_MI.Rmd' failed with diagnostics:
`strata` should be a single name or character value.
--- failed re-building ‘cv_MI.Rmd’
--- re-building ‘cv_MI_RR.Rmd’ using rmarkdown
Quitting from lines 48-61 (cv_MI_RR.Rmd)
Error: processing vignette 'cv_MI_RR.Rmd' failed with diagnostics:
`strata` should be a single name or character value.
--- failed re-building ‘cv_MI_RR.Rmd’
--- re-building ‘development_workflow.Rmd’ using rmarkdown
Attaching package: 'mice'
The following object is masked from 'package:stats':
filter
The following objects are masked from 'package:base':
cbind, rbind
Quitting from lines 136-148 (development_workflow.Rmd)
Error: processing vignette 'development_workflow.Rmd' failed with diagnostics:
`strata` should be a single name or character value.
--- failed re-building ‘development_workflow.Rmd’
--- re-building ‘psfmi_CoxModels.Rmd’ using rmarkdown
--- finished re-building ‘psfmi_CoxModels.Rmd’
--- re-building ‘psfmi_LinearModels.Rmd’ using rmarkdown
--- finished re-building ‘psfmi_LinearModels.Rmd’
--- re-building ‘psfmi_LogisticModels.Rmd’ using rmarkdown
--- finished re-building ‘psfmi_LogisticModels.Rmd’
--- re-building ‘psfmi_StabilityAnalysis.Rmd’ using rmarkdown
--- finished re-building ‘psfmi_StabilityAnalysis.Rmd’
--- re-building ‘psfmi_mice.Rmd’ using rmarkdown
--- finished re-building ‘psfmi_mice.Rmd’
SUMMARY: processing the following files failed:
‘cv_MI.Rmd’ ‘cv_MI_RR.Rmd’ ‘development_workflow.Rmd’
Error: Vignette re-building failed.
Execution halted
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-devel-windows-x86_64, r-release-windows-x86_64
Version: 1.0.0
Check: examples
Result: ERROR
Running examples in 'psfmi-Ex.R' failed
The error most likely occurred in:
> ### Name: psfmi_validate
> ### Title: Internal validation and performance of logistic prediction
> ### models across Multiply Imputed datasets
> ### Aliases: psfmi_validate
>
> ### ** Examples
>
> pool_lr <- psfmi_lr(data=lbpmilr, formula = Chronic ~ Pain + JobDemands + rcs(Tampascale, 3) +
+ factor(Satisfaction) + Smoking, p.crit = 1, direction="FW",
+ nimp=5, impvar="Impnr", method="D1")
>
> pool_lr$RR_model
$`Step 1 - no variables removed -`
term estimate std.error statistic df
1 (Intercept) -18.194984918 7.46386123 -2.4377443 66.86346
2 Pain 0.787297519 0.28791031 2.7345236 23.89602
3 JobDemands -0.009136444 0.05316641 -0.1718462 50.22157
4 Smoking 0.078959504 0.47947339 0.1646796 72.71887
5 factor(Satisfaction)2 -0.439137053 0.58056883 -0.7563910 132.98121
6 factor(Satisfaction)3 -2.255502423 0.71238726 -3.1661184 113.70396
7 rcs(Tampascale, 3)Tampascale 0.404284518 0.19688244 2.0534311 96.31169
8 rcs(Tampascale, 3)Tampascale' -0.335633226 0.24663776 -1.3608347 28.85941
p.value OR lower.EXP upper.EXP
1 0.017444622 1.253194e-08 4.243137e-15 0.03701262
2 0.011578833 2.197450e+00 1.212814e+00 3.98147379
3 0.864249071 9.909052e-01 8.905530e-01 1.10256554
4 0.869653055 1.082160e+00 4.161574e-01 2.81401089
5 0.450752704 6.445924e-01 2.044399e-01 2.03237915
6 0.001983287 1.048209e-01 2.555875e-02 0.42988853
7 0.042741589 1.498230e+00 1.013584e+00 2.21461135
8 0.184099209 7.148853e-01 4.316368e-01 1.18400693
>
> res_perf <- psfmi_validate(pool_lr, val_method = "cv_MI", data_orig = lbp_orig, folds=3,
+ nimp_cv = 2, p.crit=0.05, BW=TRUE, miceImp = miceImp, printFlag = FALSE)
Imp run 1
Error in `strata_check()`:
! `strata` should be a single name or character value.
Backtrace:
x
1. \-psfmi::psfmi_validate(...)
2. \-psfmi::cv_MI(...)
3. +-purrr::map(...)
4. \-rsample::vfold_cv(data_orig, v = folds, strata = unlist(data_orig[pobj$Outcome]))
5. \-rsample:::strata_check(strata, data)
6. \-rlang::abort("`strata` should be a single name or character value.")
Execution halted
Flavor: r-oldrel-windows-ix86+x86_64
Version: 1.0.0
Check: re-building of vignette outputs
Result: WARN
Error(s) in re-building vignettes:
--- re-building 'MI_boot.Rmd' using rmarkdown
--- finished re-building 'MI_boot.Rmd'
--- re-building 'MI_cv_naive.Rmd' using rmarkdown
--- finished re-building 'MI_cv_naive.Rmd'
--- re-building 'Pool_Model_Performance.Rmd' using rmarkdown
--- finished re-building 'Pool_Model_Performance.Rmd'
--- re-building 'Pooling_AUC_values.Rmd' using rmarkdown
--- finished re-building 'Pooling_AUC_values.Rmd'
--- re-building 'boot_MI.Rmd' using rmarkdown
--- finished re-building 'boot_MI.Rmd'
--- re-building 'cv_MI.Rmd' using rmarkdown
Quitting from lines 51-64 (cv_MI.Rmd)
Error: processing vignette 'cv_MI.Rmd' failed with diagnostics:
`strata` should be a single name or character value.
--- failed re-building 'cv_MI.Rmd'
--- re-building 'cv_MI_RR.Rmd' using rmarkdown
Quitting from lines 48-61 (cv_MI_RR.Rmd)
Error: processing vignette 'cv_MI_RR.Rmd' failed with diagnostics:
`strata` should be a single name or character value.
--- failed re-building 'cv_MI_RR.Rmd'
--- re-building 'development_workflow.Rmd' using rmarkdown
Attaching package: 'mice'
The following object is masked from 'package:stats':
filter
The following objects are masked from 'package:base':
cbind, rbind
Quitting from lines 136-148 (development_workflow.Rmd)
Error: processing vignette 'development_workflow.Rmd' failed with diagnostics:
`strata` should be a single name or character value.
--- failed re-building 'development_workflow.Rmd'
--- re-building 'psfmi_CoxModels.Rmd' using rmarkdown
--- finished re-building 'psfmi_CoxModels.Rmd'
--- re-building 'psfmi_LinearModels.Rmd' using rmarkdown
--- finished re-building 'psfmi_LinearModels.Rmd'
--- re-building 'psfmi_LogisticModels.Rmd' using rmarkdown
--- finished re-building 'psfmi_LogisticModels.Rmd'
--- re-building 'psfmi_StabilityAnalysis.Rmd' using rmarkdown
--- finished re-building 'psfmi_StabilityAnalysis.Rmd'
--- re-building 'psfmi_mice.Rmd' using rmarkdown
--- finished re-building 'psfmi_mice.Rmd'
SUMMARY: processing the following files failed:
'cv_MI.Rmd' 'cv_MI_RR.Rmd' 'development_workflow.Rmd'
Error: Vignette re-building failed.
Execution halted
Flavor: r-oldrel-windows-ix86+x86_64