Last updated on 2026-06-27 18:50:18 CEST.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 1.0.3 | 22.83 | 263.98 | 286.81 | ERROR | |
| r-devel-linux-x86_64-debian-gcc | 1.0.3 | 17.25 | 189.45 | 206.70 | ERROR | |
| r-devel-linux-x86_64-fedora-clang | 1.0.3 | 42.00 | 415.49 | 457.49 | ERROR | |
| r-devel-linux-x86_64-fedora-gcc | 1.0.3 | 40.00 | 419.01 | 459.01 | ERROR | |
| r-devel-windows-x86_64 | 1.0.3 | 29.00 | 254.00 | 283.00 | ERROR | |
| r-patched-linux-x86_64 | 1.0.3 | 24.68 | 242.14 | 266.82 | ERROR | |
| r-release-linux-x86_64 | 1.0.3 | 23.57 | 244.91 | 268.48 | 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 | 31.00 | 252.00 | 283.00 | ERROR | |
| 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 | 38.00 | 353.00 | 391.00 | 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-clang, r-devel-linux-x86_64-debian-gcc, r-patched-linux-x86_64, r-release-linux-x86_64
Version: 1.0.3
Check: tests
Result: ERROR
Running ‘testthat.R’ [14s/33s]
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=2319182 on localhost:11051 at 06:09:41.807
starting worker pid=2319183 on localhost:11051 at 06:09:41.915
[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=2321212 on localhost:11051 at 06:09:51.391
starting worker pid=2321213 on localhost:11051 at 06:09:51.538
[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-clang
Version: 1.0.3
Check: tests
Result: ERROR
Running ‘testthat.R’ [10s/25s]
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=3659482 on localhost:11943 at 17:59:39.558
starting worker pid=3659481 on localhost:11943 at 17:59:39.611
[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=3664468 on localhost:11943 at 17:59:46.802
starting worker pid=3664467 on localhost:11943 at 17:59:46.854
[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-release-windows-x86_64, r-oldrel-windows-x86_64
Version: 1.0.3
Check: tests
Result: ERROR
Running ‘testthat.R’ [22s/61s]
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=1647742 on localhost:11094 at 22:40:52.807
starting worker pid=1647741 on localhost:11094 at 22:40:52.838
[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=1649647 on localhost:11094 at 22:41:10.677
starting worker pid=1649646 on localhost:11094 at 22:41:10.913
[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’ [21s/54s]
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=1301800 on localhost:11019 at 21:06:44.198
starting worker pid=1301799 on localhost:11019 at 21:06:44.209
[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=1303802 on localhost:11019 at 21:07:01.666
starting worker pid=1303801 on localhost:11019 at 21:07:01.720
[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=61636 on localhost:11265 at 15:59:49.399
starting worker pid=20708 on localhost:11265 at 15:59:49.441
[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=42092 on localhost:11265 at 15:59:54.751
starting worker pid=22004 on localhost:11265 at 15:59:54.773
[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-windows-x86_64
Version: 1.0.3
Check: tests
Result: ERROR
Running ‘testthat.R’ [13s/26s]
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=2982093 on localhost:11812 at 17:35:12.036
starting worker pid=2982092 on localhost:11812 at 17:35:12.064
[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=2984731 on localhost:11812 at 17:35:19.567
starting worker pid=2984732 on localhost:11812 at 17:35:19.580
[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-patched-linux-x86_64
Version: 1.0.3
Check: tests
Result: ERROR
Running ‘testthat.R’ [13s/33s]
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=3725279 on localhost:11867 at 02:58:42.857
starting worker pid=3725280 on localhost:11867 at 02:58:42.913
[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=3727710 on localhost:11867 at 02:58:53.410
starting worker pid=3727711 on localhost:11867 at 02:58:53.521
[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' [19s]
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=92780 on localhost:11278 at 15:32:09.121
starting worker pid=86584 on localhost:11278 at 15:32:09.126
[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=41352 on localhost:11278 at 15:32:14.071
starting worker pid=91208 on localhost:11278 at 15:32:14.086
[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-windows-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=33012 on localhost:11028 at 19:56:50.374
starting worker pid=47848 on localhost:11028 at 19:56:50.441
[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=103532 on localhost:11028 at 19:56:58.603
starting worker pid=41140 on localhost:11028 at 19:56:58.622
[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