Last updated on 2026-06-11 14:50:46 CEST.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 1.0.3 | 25.66 | 299.44 | 325.10 | OK | |
| r-devel-linux-x86_64-debian-gcc | 1.0.3 | 17.97 | 215.33 | 233.30 | OK | |
| r-devel-linux-x86_64-fedora-clang | 1.0.3 | 42.00 | 417.58 | 459.58 | ERROR | |
| r-devel-linux-x86_64-fedora-gcc | 1.0.3 | 43.00 | 461.22 | 504.22 | OK | |
| r-devel-windows-x86_64 | 1.0.3 | 29.00 | 308.00 | 337.00 | OK | |
| r-patched-linux-x86_64 | 1.0.3 | 22.95 | 281.30 | 304.25 | OK | |
| r-release-linux-x86_64 | 1.0.3 | 21.58 | 282.35 | 303.93 | OK | |
| 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 | 29.00 | 310.00 | 339.00 | 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 | 39.00 | 426.00 | 465.00 | OK |
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
Flavor: r-devel-linux-x86_64-fedora-clang
Version: 1.0.3
Check: tests
Result: ERROR
Running ‘testthat.R’ [21s/47s]
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=3072066 on localhost:11454 at 10:47:37.125
starting worker pid=3072067 on localhost:11454 at 10:47:37.344
[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=3073355 on localhost:11454 at 10:47:51.536
starting worker pid=3073354 on localhost:11454 at 10:47:51.651
[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