Last updated on 2026-06-15 01:55:54 CEST.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 1.0.3 | 25.40 | 303.90 | 329.30 | OK | |
| r-devel-linux-x86_64-debian-gcc | 1.0.3 | 17.85 | 193.74 | 211.59 | ERROR | |
| r-devel-linux-x86_64-fedora-clang | 1.0.3 | 43.00 | 437.18 | 480.18 | ERROR | |
| r-devel-linux-x86_64-fedora-gcc | 1.0.3 | 41.00 | 452.83 | 493.83 | ERROR | |
| r-devel-windows-x86_64 | 1.0.3 | 29.00 | 257.00 | 286.00 | ERROR | |
| r-patched-linux-x86_64 | 1.0.3 | 22.95 | 281.30 | 304.25 | OK | |
| r-release-linux-x86_64 | 1.0.3 | 22.71 | 242.66 | 265.37 | ERROR | |
| r-release-macos-arm64 | 1.0.3 | 6.00 | 80.00 | 86.00 | OK | |
| r-release-macos-x86_64 | 1.0.3 | 17.00 | 340.00 | 357.00 | OK | |
| r-release-windows-x86_64 | 1.0.3 | 30.00 | 307.00 | 337.00 | OK | |
| r-oldrel-macos-arm64 | 1.0.3 | OK | ||||
| r-oldrel-macos-x86_64 | 1.0.3 | 13.00 | 294.00 | 307.00 | OK | |
| r-oldrel-windows-x86_64 | 1.0.3 | 37.00 | 344.00 | 381.00 | ERROR |
Version: 1.0.3
Check: examples
Result: ERROR
Running examples in ‘missCompare-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: test_missMDA_EM
> ### Title: Testing the 'missMDA' EM missing data imputation algorithm
> ### Aliases: test_missMDA_EM
>
> ### ** Examples
>
> clindata_miss_mini <- clindata_miss[1:80,1:4]
> cleaned <- clean(clindata_miss_mini, missingness_coding = -9)
Variable(s) sex converted to numeric.
> metadata <- get_data(cleaned)
> simulated <- simulate(rownum = metadata$Rows, colnum = metadata$Columns,
+ cormat = metadata$Corr_matrix)
> miss_list <- all_patterns(simulated$Simulated_matrix,
+ MD_pattern = metadata$MD_Pattern,
+ NA_fraction = metadata$Fraction_missingness,
+ min_PDM = 2)
62.5% of observations (with at least one missing datapoint) covered by setting min_PDM to 2
62.5% of observations (with at least one missing datapoint) covered by setting min_PDM to 2
62.5% of observations (with at least one missing datapoint) covered by setting min_PDM to 2
>
> test_missMDA_EM(X_hat = simulated$Simulated_matrix, list = miss_list)
[1] "missMDA EM imputation - in progress"
Error in svd(A) : infinite or missing values in 'x'
Calls: test_missMDA_EM ... imputePCA -> impute -> <Anonymous> -> <Anonymous> -> svd
Execution halted
Flavors: r-devel-linux-x86_64-debian-gcc, r-release-linux-x86_64
Version: 1.0.3
Check: tests
Result: ERROR
Running ‘testthat.R’ [10s/23s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> library(testthat)
> library(missCompare)
Attaching package: 'missCompare'
The following object is masked from 'package:stats':
simulate
>
> test_check("missCompare")
[1] "random replacement imputation - in progress"
[1] "mice mixed imputation - in progress"
[1] "mi imputation - in progress"
starting worker pid=2711945 on localhost:11634 at 17:54:58.701
starting worker pid=2711946 on localhost:11634 at 17:54:58.806
[1] "missForest imputation - in progress"
[1] "Hmisc aregImpute imputation - in progress"
[1] "VIM kNN imputation - in progress"
[1] "random replacement imputation - in progress"
[1] "mice mixed imputation - in progress"
[1] "mi imputation - in progress"
starting worker pid=2714919 on localhost:11634 at 17:55:05.502
starting worker pid=2714920 on localhost:11634 at 17:55:05.583
[1] "missForest imputation - in progress"
[1] "Hmisc aregImpute imputation - in progress"
[1] "VIM kNN imputation - in progress"
[1] "random replacement imputation - in progress"
[1] "Median imputation - in progress"
[1] "Mean imputation - in progress"
[1] "missMDA regularized imputation - in progress"
Saving _problems/test.imp_data-34.R
[1] "random replacement imputation - in progress"
[1] "Median imputation - in progress"
[1] "Mean imputation - in progress"
[1] "missMDA regularized imputation - in progress"
Saving _problems/test.imp_data-40.R
[1] "Median imputation - in progress"
[1] "Mean imputation - in progress"
[1] "missMDA regularized imputation - in progress"
Saving _problems/test.imp_data-45.R
[1] "ITERATION 1 OF TOTAL 1 - IN PROGRESS"
[1] "random replacement imputation - in progress"
[1] "Median imputation - in progress"
[1] "Mean imputation - in progress"
[1] "missMDA regularized imputation - in progress"
Saving _problems/test.imp_simulation-23.R
[ FAIL 4 | WARN 1 | SKIP 0 | PASS 21 ]
══ Failed tests ════════════════════════════════════════════════════════════════
── Failure ('test.imp_data.R:34:3'): runs OK when all numeric and with scaling ──
`impute_data(small, n.iter = 1, scale = T, sel_method = c(1:16))` threw an error.
Message: infinite or missing values in 'x'
Class: simpleError/error/condition
Backtrace:
▆
1. ├─testthat::expect_error(...) at test.imp_data.R:34:3
2. │ └─testthat:::quasi_capture(...)
3. │ ├─testthat (local) .capture(...)
4. │ │ └─base::withCallingHandlers(...)
5. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
6. └─missCompare::impute_data(small, n.iter = 1, scale = T, sel_method = c(1:16))
7. └─missMDA::estim_ncpPCA(X, ncp.max = ncol(X) - 2)
8. └─missMDA::imputePCA(...)
9. └─missMDA (local) impute(...)
10. └─FactoMineR::svd.triplet(Xhat, row.w = row.w, ncp = ncp)
11. └─irlba::irlba(X, nu = ncp, nv = ncp)
12. └─base::svd(A)
── Failure ('test.imp_data.R:40:3'): runs OK when all numeric and without scaling ──
`suppressWarnings(impute_data(small, n.iter = 1, scale = F, sel_method = c(1:16)))` threw an error.
Message: infinite or missing values in 'x'
Class: simpleError/error/condition
Backtrace:
▆
1. ├─testthat::expect_error(...) at test.imp_data.R:40:3
2. │ └─testthat:::quasi_capture(...)
3. │ ├─testthat (local) .capture(...)
4. │ │ └─base::withCallingHandlers(...)
5. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
6. ├─base::suppressWarnings(...)
7. │ └─base::withCallingHandlers(...)
8. └─missCompare::impute_data(small, n.iter = 1, scale = F, sel_method = c(1:16))
9. └─missMDA::estim_ncpPCA(X, ncp.max = ncol(X) - 2)
10. └─missMDA::imputePCA(...)
11. └─missMDA (local) impute(...)
12. └─FactoMineR::svd.triplet(Xhat, row.w = row.w, ncp = ncp)
13. └─irlba::irlba(X, nu = ncp, nv = ncp)
14. └─base::svd(A)
── Error ('test.imp_data.R:45:1'): (code run outside of `test_that()`) ─────────
Error in `svd(A)`: infinite or missing values in 'x'
Backtrace:
▆
1. └─missCompare::impute_data(...) at test.imp_data.R:45:1
2. └─missMDA::estim_ncpPCA(X, ncp.max = ncol(X) - 2)
3. └─missMDA::imputePCA(...)
4. └─missMDA (local) impute(...)
5. └─FactoMineR::svd.triplet(Xhat, row.w = row.w, ncp = ncp)
6. └─irlba::irlba(X, nu = ncp, nv = ncp)
7. └─base::svd(A)
── Failure ('test.imp_simulation.R:17:3'): simulation runs without errors ──────
`impute_simulated(...)` threw an error.
Message: infinite or missing values in 'x'
Class: simpleError/error/condition
Backtrace:
▆
1. ├─base::suppressWarnings(...) at test.imp_simulation.R:17:3
2. │ └─base::withCallingHandlers(...)
3. ├─testthat::expect_error(...)
4. │ └─testthat:::quasi_capture(...)
5. │ ├─testthat (local) .capture(...)
6. │ │ └─base::withCallingHandlers(...)
7. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
8. └─missCompare::impute_simulated(...)
9. ├─base::as.data.frame(test_missMDA_reg(sim$Simulated_matrix, list = res))
10. └─missCompare::test_missMDA_reg(sim$Simulated_matrix, list = res)
11. ├─utils::capture.output(results <- lapply(list, missMDA_regularized_imp))
12. │ └─base::withVisible(...elt(i))
13. └─base::lapply(list, missMDA_regularized_imp)
14. └─missCompare (local) FUN(X[[i]], ...)
15. └─missMDA::estim_ncpPCA(X, ncp.max = ncol(X) - 2)
16. └─missMDA::imputePCA(...)
17. └─missMDA (local) impute(...)
18. └─FactoMineR::svd.triplet(Xhat, row.w = row.w, ncp = ncp)
19. └─irlba::irlba(X, nu = ncp, nv = ncp)
20. └─base::svd(A)
[ FAIL 4 | WARN 1 | SKIP 0 | PASS 21 ]
Error:
! Test failures.
Execution halted
Flavor: r-devel-linux-x86_64-debian-gcc
Version: 1.0.3
Check: examples
Result: ERROR
Running examples in ‘missCompare-Ex.R’ failed
The error most likely occurred in:
> ### Name: test_missMDA_EM
> ### Title: Testing the 'missMDA' EM missing data imputation algorithm
> ### Aliases: test_missMDA_EM
>
> ### ** Examples
>
> clindata_miss_mini <- clindata_miss[1:80,1:4]
> cleaned <- clean(clindata_miss_mini, missingness_coding = -9)
Variable(s) sex converted to numeric.
> metadata <- get_data(cleaned)
> simulated <- simulate(rownum = metadata$Rows, colnum = metadata$Columns,
+ cormat = metadata$Corr_matrix)
> miss_list <- all_patterns(simulated$Simulated_matrix,
+ MD_pattern = metadata$MD_Pattern,
+ NA_fraction = metadata$Fraction_missingness,
+ min_PDM = 2)
62.5% of observations (with at least one missing datapoint) covered by setting min_PDM to 2
62.5% of observations (with at least one missing datapoint) covered by setting min_PDM to 2
62.5% of observations (with at least one missing datapoint) covered by setting min_PDM to 2
>
> test_missMDA_EM(X_hat = simulated$Simulated_matrix, list = miss_list)
[1] "missMDA EM imputation - in progress"
Error in svd(A) : infinite or missing values in 'x'
Calls: test_missMDA_EM ... imputePCA -> impute -> <Anonymous> -> <Anonymous> -> svd
Execution halted
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-devel-windows-x86_64, r-oldrel-windows-x86_64
Version: 1.0.3
Check: tests
Result: ERROR
Running ‘testthat.R’ [22s/308s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> library(testthat)
> library(missCompare)
Attaching package: 'missCompare'
The following object is masked from 'package:stats':
simulate
>
> test_check("missCompare")
[1] "random replacement imputation - in progress"
[1] "mice mixed imputation - in progress"
[1] "mi imputation - in progress"
starting worker pid=345408 on localhost:11832 at 07:14:40.971
starting worker pid=345409 on localhost:11832 at 07:14:44.852
[1] "missForest imputation - in progress"
[1] "Hmisc aregImpute imputation - in progress"
[1] "VIM kNN imputation - in progress"
[1] "random replacement imputation - in progress"
[1] "mice mixed imputation - in progress"
[1] "mi imputation - in progress"
starting worker pid=350124 on localhost:11832 at 07:16:08.556
starting worker pid=350125 on localhost:11832 at 07:16:20.429
[1] "missForest imputation - in progress"
[1] "Hmisc aregImpute imputation - in progress"
[1] "VIM kNN imputation - in progress"
[1] "random replacement imputation - in progress"
[1] "Median imputation - in progress"
[1] "Mean imputation - in progress"
[1] "missMDA regularized imputation - in progress"
Saving _problems/test.imp_data-34.R
[1] "random replacement imputation - in progress"
[1] "Median imputation - in progress"
[1] "Mean imputation - in progress"
[1] "missMDA regularized imputation - in progress"
Saving _problems/test.imp_data-40.R
[1] "Median imputation - in progress"
[1] "Mean imputation - in progress"
[1] "missMDA regularized imputation - in progress"
Saving _problems/test.imp_data-45.R
[1] "ITERATION 1 OF TOTAL 1 - IN PROGRESS"
[1] "random replacement imputation - in progress"
[1] "Median imputation - in progress"
[1] "Mean imputation - in progress"
[1] "missMDA regularized imputation - in progress"
Saving _problems/test.imp_simulation-23.R
[ FAIL 4 | WARN 1 | SKIP 0 | PASS 21 ]
══ Failed tests ════════════════════════════════════════════════════════════════
── Failure ('test.imp_data.R:34:3'): runs OK when all numeric and with scaling ──
`impute_data(small, n.iter = 1, scale = T, sel_method = c(1:16))` threw an error.
Message: infinite or missing values in 'x'
Class: simpleError/error/condition
Backtrace:
▆
1. ├─testthat::expect_error(...) at test.imp_data.R:34:3
2. │ └─testthat:::quasi_capture(...)
3. │ ├─testthat (local) .capture(...)
4. │ │ └─base::withCallingHandlers(...)
5. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
6. └─missCompare::impute_data(small, n.iter = 1, scale = T, sel_method = c(1:16))
7. └─missMDA::estim_ncpPCA(X, ncp.max = ncol(X) - 2)
8. └─missMDA::imputePCA(...)
9. └─missMDA (local) impute(...)
10. └─FactoMineR::svd.triplet(Xhat, row.w = row.w, ncp = ncp)
11. └─irlba::irlba(X, nu = ncp, nv = ncp)
12. └─base::svd(A)
── Failure ('test.imp_data.R:40:3'): runs OK when all numeric and without scaling ──
`suppressWarnings(impute_data(small, n.iter = 1, scale = F, sel_method = c(1:16)))` threw an error.
Message: infinite or missing values in 'x'
Class: simpleError/error/condition
Backtrace:
▆
1. ├─testthat::expect_error(...) at test.imp_data.R:40:3
2. │ └─testthat:::quasi_capture(...)
3. │ ├─testthat (local) .capture(...)
4. │ │ └─base::withCallingHandlers(...)
5. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
6. ├─base::suppressWarnings(...)
7. │ └─base::withCallingHandlers(...)
8. └─missCompare::impute_data(small, n.iter = 1, scale = F, sel_method = c(1:16))
9. └─missMDA::estim_ncpPCA(X, ncp.max = ncol(X) - 2)
10. └─missMDA::imputePCA(...)
11. └─missMDA (local) impute(...)
12. └─FactoMineR::svd.triplet(Xhat, row.w = row.w, ncp = ncp)
13. └─irlba::irlba(X, nu = ncp, nv = ncp)
14. └─base::svd(A)
── Error ('test.imp_data.R:45:1'): (code run outside of `test_that()`) ─────────
Error in `svd(A)`: infinite or missing values in 'x'
Backtrace:
▆
1. └─missCompare::impute_data(...) at test.imp_data.R:45:1
2. └─missMDA::estim_ncpPCA(X, ncp.max = ncol(X) - 2)
3. └─missMDA::imputePCA(...)
4. └─missMDA (local) impute(...)
5. └─FactoMineR::svd.triplet(Xhat, row.w = row.w, ncp = ncp)
6. └─irlba::irlba(X, nu = ncp, nv = ncp)
7. └─base::svd(A)
── Failure ('test.imp_simulation.R:17:3'): simulation runs without errors ──────
`impute_simulated(...)` threw an error.
Message: infinite or missing values in 'x'
Class: simpleError/error/condition
Backtrace:
▆
1. ├─base::suppressWarnings(...) at test.imp_simulation.R:17:3
2. │ └─base::withCallingHandlers(...)
3. ├─testthat::expect_error(...)
4. │ └─testthat:::quasi_capture(...)
5. │ ├─testthat (local) .capture(...)
6. │ │ └─base::withCallingHandlers(...)
7. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
8. └─missCompare::impute_simulated(...)
9. ├─base::as.data.frame(test_missMDA_reg(sim$Simulated_matrix, list = res))
10. └─missCompare::test_missMDA_reg(sim$Simulated_matrix, list = res)
11. ├─utils::capture.output(results <- lapply(list, missMDA_regularized_imp))
12. │ └─base::withVisible(...elt(i))
13. └─base::lapply(list, missMDA_regularized_imp)
14. └─missCompare (local) FUN(X[[i]], ...)
15. └─missMDA::estim_ncpPCA(X, ncp.max = ncol(X) - 2)
16. └─missMDA::imputePCA(...)
17. └─missMDA (local) impute(...)
18. └─FactoMineR::svd.triplet(Xhat, row.w = row.w, ncp = ncp)
19. └─irlba::irlba(X, nu = ncp, nv = ncp)
20. └─base::svd(A)
[ FAIL 4 | WARN 1 | SKIP 0 | PASS 21 ]
Error:
! Test failures.
Execution halted
Flavor: r-devel-linux-x86_64-fedora-clang
Version: 1.0.3
Check: tests
Result: ERROR
Running ‘testthat.R’ [23s/92s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> library(testthat)
> library(missCompare)
Attaching package: 'missCompare'
The following object is masked from 'package:stats':
simulate
>
> test_check("missCompare")
[1] "random replacement imputation - in progress"
[1] "mice mixed imputation - in progress"
[1] "mi imputation - in progress"
starting worker pid=113106 on localhost:11978 at 16:25:37.520
starting worker pid=113105 on localhost:11978 at 16:25:37.632
[1] "missForest imputation - in progress"
[1] "Hmisc aregImpute imputation - in progress"
[1] "VIM kNN imputation - in progress"
[1] "random replacement imputation - in progress"
[1] "mice mixed imputation - in progress"
[1] "mi imputation - in progress"
starting worker pid=116231 on localhost:11978 at 16:26:11.708
starting worker pid=116230 on localhost:11978 at 16:26:11.773
[1] "missForest imputation - in progress"
[1] "Hmisc aregImpute imputation - in progress"
[1] "VIM kNN imputation - in progress"
[1] "random replacement imputation - in progress"
[1] "Median imputation - in progress"
[1] "Mean imputation - in progress"
[1] "missMDA regularized imputation - in progress"
Saving _problems/test.imp_data-34.R
[1] "random replacement imputation - in progress"
[1] "Median imputation - in progress"
[1] "Mean imputation - in progress"
[1] "missMDA regularized imputation - in progress"
Saving _problems/test.imp_data-40.R
[1] "Median imputation - in progress"
[1] "Mean imputation - in progress"
[1] "missMDA regularized imputation - in progress"
Saving _problems/test.imp_data-45.R
[1] "ITERATION 1 OF TOTAL 1 - IN PROGRESS"
[1] "random replacement imputation - in progress"
[1] "Median imputation - in progress"
[1] "Mean imputation - in progress"
[1] "missMDA regularized imputation - in progress"
Saving _problems/test.imp_simulation-23.R
[ FAIL 4 | WARN 1 | SKIP 0 | PASS 21 ]
══ Failed tests ════════════════════════════════════════════════════════════════
── Failure ('test.imp_data.R:34:3'): runs OK when all numeric and with scaling ──
`impute_data(small, n.iter = 1, scale = T, sel_method = c(1:16))` threw an error.
Message: infinite or missing values in 'x'
Class: simpleError/error/condition
Backtrace:
▆
1. ├─testthat::expect_error(...) at test.imp_data.R:34:3
2. │ └─testthat:::quasi_capture(...)
3. │ ├─testthat (local) .capture(...)
4. │ │ └─base::withCallingHandlers(...)
5. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
6. └─missCompare::impute_data(small, n.iter = 1, scale = T, sel_method = c(1:16))
7. └─missMDA::estim_ncpPCA(X, ncp.max = ncol(X) - 2)
8. └─missMDA::imputePCA(...)
9. └─missMDA (local) impute(...)
10. └─FactoMineR::svd.triplet(Xhat, row.w = row.w, ncp = ncp)
11. └─irlba::irlba(X, nu = ncp, nv = ncp)
12. └─base::svd(A)
── Failure ('test.imp_data.R:40:3'): runs OK when all numeric and without scaling ──
`suppressWarnings(impute_data(small, n.iter = 1, scale = F, sel_method = c(1:16)))` threw an error.
Message: infinite or missing values in 'x'
Class: simpleError/error/condition
Backtrace:
▆
1. ├─testthat::expect_error(...) at test.imp_data.R:40:3
2. │ └─testthat:::quasi_capture(...)
3. │ ├─testthat (local) .capture(...)
4. │ │ └─base::withCallingHandlers(...)
5. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
6. ├─base::suppressWarnings(...)
7. │ └─base::withCallingHandlers(...)
8. └─missCompare::impute_data(small, n.iter = 1, scale = F, sel_method = c(1:16))
9. └─missMDA::estim_ncpPCA(X, ncp.max = ncol(X) - 2)
10. └─missMDA::imputePCA(...)
11. └─missMDA (local) impute(...)
12. └─FactoMineR::svd.triplet(Xhat, row.w = row.w, ncp = ncp)
13. └─irlba::irlba(X, nu = ncp, nv = ncp)
14. └─base::svd(A)
── Error ('test.imp_data.R:45:1'): (code run outside of `test_that()`) ─────────
Error in `svd(A)`: infinite or missing values in 'x'
Backtrace:
▆
1. └─missCompare::impute_data(...) at test.imp_data.R:45:1
2. └─missMDA::estim_ncpPCA(X, ncp.max = ncol(X) - 2)
3. └─missMDA::imputePCA(...)
4. └─missMDA (local) impute(...)
5. └─FactoMineR::svd.triplet(Xhat, row.w = row.w, ncp = ncp)
6. └─irlba::irlba(X, nu = ncp, nv = ncp)
7. └─base::svd(A)
── Failure ('test.imp_simulation.R:17:3'): simulation runs without errors ──────
`impute_simulated(...)` threw an error.
Message: infinite or missing values in 'x'
Class: simpleError/error/condition
Backtrace:
▆
1. ├─base::suppressWarnings(...) at test.imp_simulation.R:17:3
2. │ └─base::withCallingHandlers(...)
3. ├─testthat::expect_error(...)
4. │ └─testthat:::quasi_capture(...)
5. │ ├─testthat (local) .capture(...)
6. │ │ └─base::withCallingHandlers(...)
7. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
8. └─missCompare::impute_simulated(...)
9. ├─base::as.data.frame(test_missMDA_reg(sim$Simulated_matrix, list = res))
10. └─missCompare::test_missMDA_reg(sim$Simulated_matrix, list = res)
11. ├─utils::capture.output(results <- lapply(list, missMDA_regularized_imp))
12. │ └─base::withVisible(...elt(i))
13. └─base::lapply(list, missMDA_regularized_imp)
14. └─missCompare (local) FUN(X[[i]], ...)
15. └─missMDA::estim_ncpPCA(X, ncp.max = ncol(X) - 2)
16. └─missMDA::imputePCA(...)
17. └─missMDA (local) impute(...)
18. └─FactoMineR::svd.triplet(Xhat, row.w = row.w, ncp = ncp)
19. └─irlba::irlba(X, nu = ncp, nv = ncp)
20. └─base::svd(A)
[ FAIL 4 | WARN 1 | SKIP 0 | PASS 21 ]
Error:
! Test failures.
Execution halted
Flavor: r-devel-linux-x86_64-fedora-gcc
Version: 1.0.3
Check: tests
Result: ERROR
Running 'testthat.R' [20s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
> library(testthat)
> library(missCompare)
Attaching package: 'missCompare'
The following object is masked from 'package:stats':
simulate
>
> test_check("missCompare")
[1] "random replacement imputation - in progress"
[1] "mice mixed imputation - in progress"
[1] "mi imputation - in progress"
starting worker pid=1545220 on localhost:11908 at 13:33:01.357
starting worker pid=2694400 on localhost:11908 at 13:33:01.363
[1] "missForest imputation - in progress"
[1] "Hmisc aregImpute imputation - in progress"
[1] "VIM kNN imputation - in progress"
[1] "random replacement imputation - in progress"
[1] "mice mixed imputation - in progress"
[1] "mi imputation - in progress"
starting worker pid=2199948 on localhost:11908 at 13:33:06.421
starting worker pid=3114776 on localhost:11908 at 13:33:06.470
[1] "missForest imputation - in progress"
[1] "Hmisc aregImpute imputation - in progress"
[1] "VIM kNN imputation - in progress"
[1] "random replacement imputation - in progress"
[1] "Median imputation - in progress"
[1] "Mean imputation - in progress"
[1] "missMDA regularized imputation - in progress"
Saving _problems/test.imp_data-34.R
[1] "random replacement imputation - in progress"
[1] "Median imputation - in progress"
[1] "Mean imputation - in progress"
[1] "missMDA regularized imputation - in progress"
Saving _problems/test.imp_data-40.R
[1] "Median imputation - in progress"
[1] "Mean imputation - in progress"
[1] "missMDA regularized imputation - in progress"
Saving _problems/test.imp_data-45.R
[1] "ITERATION 1 OF TOTAL 1 - IN PROGRESS"
[1] "random replacement imputation - in progress"
[1] "Median imputation - in progress"
[1] "Mean imputation - in progress"
[1] "missMDA regularized imputation - in progress"
Saving _problems/test.imp_simulation-23.R
[ FAIL 4 | WARN 1 | SKIP 0 | PASS 21 ]
══ Failed tests ════════════════════════════════════════════════════════════════
── Failure ('test.imp_data.R:34:3'): runs OK when all numeric and with scaling ──
`impute_data(small, n.iter = 1, scale = T, sel_method = c(1:16))` threw an error.
Message: infinite or missing values in 'x'
Class: simpleError/error/condition
Backtrace:
▆
1. ├─testthat::expect_error(...) at test.imp_data.R:34:3
2. │ └─testthat:::quasi_capture(...)
3. │ ├─testthat (local) .capture(...)
4. │ │ └─base::withCallingHandlers(...)
5. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
6. └─missCompare::impute_data(small, n.iter = 1, scale = T, sel_method = c(1:16))
7. └─missMDA::estim_ncpPCA(X, ncp.max = ncol(X) - 2)
8. └─missMDA::imputePCA(...)
9. └─missMDA (local) impute(...)
10. └─FactoMineR::svd.triplet(Xhat, row.w = row.w, ncp = ncp)
11. └─irlba::irlba(X, nu = ncp, nv = ncp)
12. └─base::svd(A)
── Failure ('test.imp_data.R:40:3'): runs OK when all numeric and without scaling ──
`suppressWarnings(impute_data(small, n.iter = 1, scale = F, sel_method = c(1:16)))` threw an error.
Message: infinite or missing values in 'x'
Class: simpleError/error/condition
Backtrace:
▆
1. ├─testthat::expect_error(...) at test.imp_data.R:40:3
2. │ └─testthat:::quasi_capture(...)
3. │ ├─testthat (local) .capture(...)
4. │ │ └─base::withCallingHandlers(...)
5. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
6. ├─base::suppressWarnings(...)
7. │ └─base::withCallingHandlers(...)
8. └─missCompare::impute_data(small, n.iter = 1, scale = F, sel_method = c(1:16))
9. └─missMDA::estim_ncpPCA(X, ncp.max = ncol(X) - 2)
10. └─missMDA::imputePCA(...)
11. └─missMDA (local) impute(...)
12. └─FactoMineR::svd.triplet(Xhat, row.w = row.w, ncp = ncp)
13. └─irlba::irlba(X, nu = ncp, nv = ncp)
14. └─base::svd(A)
── Error ('test.imp_data.R:45:1'): (code run outside of `test_that()`) ─────────
Error in `svd(A)`: infinite or missing values in 'x'
Backtrace:
▆
1. └─missCompare::impute_data(...) at test.imp_data.R:45:1
2. └─missMDA::estim_ncpPCA(X, ncp.max = ncol(X) - 2)
3. └─missMDA::imputePCA(...)
4. └─missMDA (local) impute(...)
5. └─FactoMineR::svd.triplet(Xhat, row.w = row.w, ncp = ncp)
6. └─irlba::irlba(X, nu = ncp, nv = ncp)
7. └─base::svd(A)
── Failure ('test.imp_simulation.R:17:3'): simulation runs without errors ──────
`impute_simulated(...)` threw an error.
Message: infinite or missing values in 'x'
Class: simpleError/error/condition
Backtrace:
▆
1. ├─base::suppressWarnings(...) at test.imp_simulation.R:17:3
2. │ └─base::withCallingHandlers(...)
3. ├─testthat::expect_error(...)
4. │ └─testthat:::quasi_capture(...)
5. │ ├─testthat (local) .capture(...)
6. │ │ └─base::withCallingHandlers(...)
7. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
8. └─missCompare::impute_simulated(...)
9. ├─base::as.data.frame(test_missMDA_reg(sim$Simulated_matrix, list = res))
10. └─missCompare::test_missMDA_reg(sim$Simulated_matrix, list = res)
11. ├─utils::capture.output(results <- lapply(list, missMDA_regularized_imp))
12. │ └─base::withVisible(...elt(i))
13. └─base::lapply(list, missMDA_regularized_imp)
14. └─missCompare (local) FUN(X[[i]], ...)
15. └─missMDA::estim_ncpPCA(X, ncp.max = ncol(X) - 2)
16. └─missMDA::imputePCA(...)
17. └─missMDA (local) impute(...)
18. └─FactoMineR::svd.triplet(Xhat, row.w = row.w, ncp = ncp)
19. └─irlba::irlba(X, nu = ncp, nv = ncp)
20. └─base::svd(A)
[ FAIL 4 | WARN 1 | SKIP 0 | PASS 21 ]
Error:
! Test failures.
Execution halted
Flavor: r-devel-windows-x86_64
Version: 1.0.3
Check: tests
Result: ERROR
Running ‘testthat.R’ [14s/32s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> library(testthat)
> library(missCompare)
Attaching package: 'missCompare'
The following object is masked from 'package:stats':
simulate
>
> test_check("missCompare")
[1] "random replacement imputation - in progress"
[1] "mice mixed imputation - in progress"
[1] "mi imputation - in progress"
starting worker pid=441291 on localhost:11780 at 17:17:39.263
starting worker pid=441292 on localhost:11780 at 17:17:39.304
[1] "missForest imputation - in progress"
[1] "Hmisc aregImpute imputation - in progress"
[1] "VIM kNN imputation - in progress"
[1] "random replacement imputation - in progress"
[1] "mice mixed imputation - in progress"
[1] "mi imputation - in progress"
starting worker pid=443316 on localhost:11780 at 17:17:49.290
starting worker pid=443317 on localhost:11780 at 17:17:49.372
[1] "missForest imputation - in progress"
[1] "Hmisc aregImpute imputation - in progress"
[1] "VIM kNN imputation - in progress"
[1] "random replacement imputation - in progress"
[1] "Median imputation - in progress"
[1] "Mean imputation - in progress"
[1] "missMDA regularized imputation - in progress"
Saving _problems/test.imp_data-34.R
[1] "random replacement imputation - in progress"
[1] "Median imputation - in progress"
[1] "Mean imputation - in progress"
[1] "missMDA regularized imputation - in progress"
Saving _problems/test.imp_data-40.R
[1] "Median imputation - in progress"
[1] "Mean imputation - in progress"
[1] "missMDA regularized imputation - in progress"
Saving _problems/test.imp_data-45.R
[1] "ITERATION 1 OF TOTAL 1 - IN PROGRESS"
[1] "random replacement imputation - in progress"
[1] "Median imputation - in progress"
[1] "Mean imputation - in progress"
[1] "missMDA regularized imputation - in progress"
Saving _problems/test.imp_simulation-23.R
[ FAIL 4 | WARN 1 | SKIP 0 | PASS 21 ]
══ Failed tests ════════════════════════════════════════════════════════════════
── Failure ('test.imp_data.R:34:3'): runs OK when all numeric and with scaling ──
`impute_data(small, n.iter = 1, scale = T, sel_method = c(1:16))` threw an error.
Message: infinite or missing values in 'x'
Class: simpleError/error/condition
Backtrace:
▆
1. ├─testthat::expect_error(...) at test.imp_data.R:34:3
2. │ └─testthat:::quasi_capture(...)
3. │ ├─testthat (local) .capture(...)
4. │ │ └─base::withCallingHandlers(...)
5. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
6. └─missCompare::impute_data(small, n.iter = 1, scale = T, sel_method = c(1:16))
7. └─missMDA::estim_ncpPCA(X, ncp.max = ncol(X) - 2)
8. └─missMDA::imputePCA(...)
9. └─missMDA (local) impute(...)
10. └─FactoMineR::svd.triplet(Xhat, row.w = row.w, ncp = ncp)
11. └─irlba::irlba(X, nu = ncp, nv = ncp)
12. └─base::svd(A)
── Failure ('test.imp_data.R:40:3'): runs OK when all numeric and without scaling ──
`suppressWarnings(impute_data(small, n.iter = 1, scale = F, sel_method = c(1:16)))` threw an error.
Message: infinite or missing values in 'x'
Class: simpleError/error/condition
Backtrace:
▆
1. ├─testthat::expect_error(...) at test.imp_data.R:40:3
2. │ └─testthat:::quasi_capture(...)
3. │ ├─testthat (local) .capture(...)
4. │ │ └─base::withCallingHandlers(...)
5. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
6. ├─base::suppressWarnings(...)
7. │ └─base::withCallingHandlers(...)
8. └─missCompare::impute_data(small, n.iter = 1, scale = F, sel_method = c(1:16))
9. └─missMDA::estim_ncpPCA(X, ncp.max = ncol(X) - 2)
10. └─missMDA::imputePCA(...)
11. └─missMDA (local) impute(...)
12. └─FactoMineR::svd.triplet(Xhat, row.w = row.w, ncp = ncp)
13. └─irlba::irlba(X, nu = ncp, nv = ncp)
14. └─base::svd(A)
── Error ('test.imp_data.R:45:1'): (code run outside of `test_that()`) ─────────
Error in `svd(A)`: infinite or missing values in 'x'
Backtrace:
▆
1. └─missCompare::impute_data(...) at test.imp_data.R:45:1
2. └─missMDA::estim_ncpPCA(X, ncp.max = ncol(X) - 2)
3. └─missMDA::imputePCA(...)
4. └─missMDA (local) impute(...)
5. └─FactoMineR::svd.triplet(Xhat, row.w = row.w, ncp = ncp)
6. └─irlba::irlba(X, nu = ncp, nv = ncp)
7. └─base::svd(A)
── Failure ('test.imp_simulation.R:17:3'): simulation runs without errors ──────
`impute_simulated(...)` threw an error.
Message: infinite or missing values in 'x'
Class: simpleError/error/condition
Backtrace:
▆
1. ├─base::suppressWarnings(...) at test.imp_simulation.R:17:3
2. │ └─base::withCallingHandlers(...)
3. ├─testthat::expect_error(...)
4. │ └─testthat:::quasi_capture(...)
5. │ ├─testthat (local) .capture(...)
6. │ │ └─base::withCallingHandlers(...)
7. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
8. └─missCompare::impute_simulated(...)
9. ├─base::as.data.frame(test_missMDA_reg(sim$Simulated_matrix, list = res))
10. └─missCompare::test_missMDA_reg(sim$Simulated_matrix, list = res)
11. ├─utils::capture.output(results <- lapply(list, missMDA_regularized_imp))
12. │ └─base::withVisible(...elt(i))
13. └─base::lapply(list, missMDA_regularized_imp)
14. └─missCompare (local) FUN(X[[i]], ...)
15. └─missMDA::estim_ncpPCA(X, ncp.max = ncol(X) - 2)
16. └─missMDA::imputePCA(...)
17. └─missMDA (local) impute(...)
18. └─FactoMineR::svd.triplet(Xhat, row.w = row.w, ncp = ncp)
19. └─irlba::irlba(X, nu = ncp, nv = ncp)
20. └─base::svd(A)
[ FAIL 4 | WARN 1 | SKIP 0 | PASS 21 ]
Error:
! Test failures.
Execution halted
Flavor: r-release-linux-x86_64
Version: 1.0.3
Check: tests
Result: ERROR
Running 'testthat.R' [29s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
> library(testthat)
> library(missCompare)
Attaching package: 'missCompare'
The following object is masked from 'package:stats':
simulate
>
> test_check("missCompare")
[1] "random replacement imputation - in progress"
[1] "mice mixed imputation - in progress"
[1] "mi imputation - in progress"
starting worker pid=11092 on localhost:11967 at 05:03:57.666
starting worker pid=28380 on localhost:11967 at 05:03:57.732
[1] "missForest imputation - in progress"
[1] "Hmisc aregImpute imputation - in progress"
[1] "VIM kNN imputation - in progress"
[1] "random replacement imputation - in progress"
[1] "mice mixed imputation - in progress"
[1] "mi imputation - in progress"
starting worker pid=66296 on localhost:11967 at 05:04:05.561
starting worker pid=102552 on localhost:11967 at 05:04:05.585
[1] "missForest imputation - in progress"
[1] "Hmisc aregImpute imputation - in progress"
[1] "VIM kNN imputation - in progress"
[1] "random replacement imputation - in progress"
[1] "Median imputation - in progress"
[1] "Mean imputation - in progress"
[1] "missMDA regularized imputation - in progress"
Saving _problems/test.imp_data-34.R
[1] "random replacement imputation - in progress"
[1] "Median imputation - in progress"
[1] "Mean imputation - in progress"
[1] "missMDA regularized imputation - in progress"
Saving _problems/test.imp_data-40.R
[1] "Median imputation - in progress"
[1] "Mean imputation - in progress"
[1] "missMDA regularized imputation - in progress"
Saving _problems/test.imp_data-45.R
[1] "ITERATION 1 OF TOTAL 1 - IN PROGRESS"
[1] "random replacement imputation - in progress"
[1] "Median imputation - in progress"
[1] "Mean imputation - in progress"
[1] "missMDA regularized imputation - in progress"
Saving _problems/test.imp_simulation-23.R
[ FAIL 4 | WARN 1 | SKIP 0 | PASS 21 ]
══ Failed tests ════════════════════════════════════════════════════════════════
── Failure ('test.imp_data.R:34:3'): runs OK when all numeric and with scaling ──
`impute_data(small, n.iter = 1, scale = T, sel_method = c(1:16))` threw an error.
Message: infinite or missing values in 'x'
Class: simpleError/error/condition
Backtrace:
▆
1. ├─testthat::expect_error(...) at test.imp_data.R:34:3
2. │ └─testthat:::quasi_capture(...)
3. │ ├─testthat (local) .capture(...)
4. │ │ └─base::withCallingHandlers(...)
5. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
6. └─missCompare::impute_data(small, n.iter = 1, scale = T, sel_method = c(1:16))
7. └─missMDA::estim_ncpPCA(X, ncp.max = ncol(X) - 2)
8. └─missMDA::imputePCA(...)
9. └─missMDA (local) impute(...)
10. └─FactoMineR::svd.triplet(Xhat, row.w = row.w, ncp = ncp)
11. └─irlba::irlba(X, nu = ncp, nv = ncp)
12. └─base::svd(A)
── Failure ('test.imp_data.R:40:3'): runs OK when all numeric and without scaling ──
`suppressWarnings(impute_data(small, n.iter = 1, scale = F, sel_method = c(1:16)))` threw an error.
Message: infinite or missing values in 'x'
Class: simpleError/error/condition
Backtrace:
▆
1. ├─testthat::expect_error(...) at test.imp_data.R:40:3
2. │ └─testthat:::quasi_capture(...)
3. │ ├─testthat (local) .capture(...)
4. │ │ └─base::withCallingHandlers(...)
5. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
6. ├─base::suppressWarnings(...)
7. │ └─base::withCallingHandlers(...)
8. └─missCompare::impute_data(small, n.iter = 1, scale = F, sel_method = c(1:16))
9. └─missMDA::estim_ncpPCA(X, ncp.max = ncol(X) - 2)
10. └─missMDA::imputePCA(...)
11. └─missMDA (local) impute(...)
12. └─FactoMineR::svd.triplet(Xhat, row.w = row.w, ncp = ncp)
13. └─irlba::irlba(X, nu = ncp, nv = ncp)
14. └─base::svd(A)
── Error ('test.imp_data.R:45:1'): (code run outside of `test_that()`) ─────────
Error in `svd(A)`: infinite or missing values in 'x'
Backtrace:
▆
1. └─missCompare::impute_data(...) at test.imp_data.R:45:1
2. └─missMDA::estim_ncpPCA(X, ncp.max = ncol(X) - 2)
3. └─missMDA::imputePCA(...)
4. └─missMDA (local) impute(...)
5. └─FactoMineR::svd.triplet(Xhat, row.w = row.w, ncp = ncp)
6. └─irlba::irlba(X, nu = ncp, nv = ncp)
7. └─base::svd(A)
── Failure ('test.imp_simulation.R:17:3'): simulation runs without errors ──────
`impute_simulated(...)` threw an error.
Message: infinite or missing values in 'x'
Class: simpleError/error/condition
Backtrace:
▆
1. ├─base::suppressWarnings(...) at test.imp_simulation.R:17:3
2. │ └─base::withCallingHandlers(...)
3. ├─testthat::expect_error(...)
4. │ └─testthat:::quasi_capture(...)
5. │ ├─testthat (local) .capture(...)
6. │ │ └─base::withCallingHandlers(...)
7. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
8. └─missCompare::impute_simulated(...)
9. ├─base::as.data.frame(test_missMDA_reg(sim$Simulated_matrix, list = res))
10. └─missCompare::test_missMDA_reg(sim$Simulated_matrix, list = res)
11. ├─utils::capture.output(results <- lapply(list, missMDA_regularized_imp))
12. │ └─base::withVisible(...elt(i))
13. └─base::lapply(list, missMDA_regularized_imp)
14. └─missCompare (local) FUN(X[[i]], ...)
15. └─missMDA::estim_ncpPCA(X, ncp.max = ncol(X) - 2)
16. └─missMDA::imputePCA(...)
17. └─missMDA (local) impute(...)
18. └─FactoMineR::svd.triplet(Xhat, row.w = row.w, ncp = ncp)
19. └─irlba::irlba(X, nu = ncp, nv = ncp)
20. └─base::svd(A)
[ FAIL 4 | WARN 1 | SKIP 0 | PASS 21 ]
Error:
! Test failures.
Execution halted
Flavor: r-oldrel-windows-x86_64