- using R version 4.6.1 (2026-06-24)
- using platform: x86_64-pc-linux-gnu
- R was compiled by
gcc-16 (Debian 16.1.0-2) 16.1.0
GNU Fortran (Debian 16.1.0-2) 16.1.0
- running under: Debian GNU/Linux forky/sid
- using session charset: UTF-8
* current time: 2026-06-27 15:36:55 UTC
- checking for file ‘missCompare/DESCRIPTION’ ... OK
- checking extension type ... Package
- this is package ‘missCompare’ version ‘1.0.3’
- package encoding: UTF-8
- checking package namespace information ... OK
- checking package dependencies ... OK
- checking if this is a source package ... OK
- checking if there is a namespace ... OK
- checking for executable files ... OK
- checking for hidden files and directories ... OK
- checking for portable file names ... OK
- checking for sufficient/correct file permissions ... OK
- checking whether package ‘missCompare’ can be installed ... OK
See the install log for details.
- checking package directory ... OK
- checking for future file timestamps ... OK
- checking ‘build’ directory ... OK
- checking DESCRIPTION meta-information ... OK
- checking top-level files ... OK
- checking for left-over files ... OK
- checking index information ... OK
- checking package subdirectories ... OK
- checking code files for non-ASCII characters ... OK
- checking R files for syntax errors ... OK
- checking whether the package can be loaded ... [7s/9s] OK
- checking whether the package can be loaded with stated dependencies ... [7s/10s] OK
- checking whether the package can be unloaded cleanly ... [7s/10s] OK
- checking whether the namespace can be loaded with stated dependencies ... [7s/11s] OK
- checking whether the namespace can be unloaded cleanly ... [7s/9s] OK
- checking loading without being on the library search path ... [8s/11s] OK
- checking whether startup messages can be suppressed ... [8s/10s] OK
- checking use of S3 registration ... OK
- checking dependencies in R code ... OK
- checking S3 generic/method consistency ... OK
- checking replacement functions ... OK
- checking foreign function calls ... OK
- checking R code for possible problems ... [38s/43s] OK
- checking Rd files ... [1s/1s] OK
- checking Rd metadata ... OK
- checking Rd line widths ... OK
- checking Rd cross-references ... OK
- checking for missing documentation entries ... OK
- checking for code/documentation mismatches ... OK
- checking Rd \usage sections ... OK
- checking Rd contents ... OK
- checking for unstated dependencies in examples ... OK
- checking contents of ‘data’ directory ... OK
- checking data for non-ASCII characters ... [0s/0s] OK
- checking LazyData ... OK
- checking data for ASCII and uncompressed saves ... OK
- checking installed files from ‘inst/doc’ ... OK
- checking files in ‘vignettes’ ... OK
- checking examples ... [20s/24s] 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
- checking for unstated dependencies in ‘tests’ ... OK
- checking tests ... [14s/29s] ERROR
Running ‘testthat.R’ [13s/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=4164084 on localhost:11344 at 17:41:10.337
starting worker pid=4164083 on localhost:11344 at 17:41:10.496
[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=4166248 on localhost:11344 at 17:41:19.200
starting worker pid=4166247 on localhost:11344 at 17:41:19.214
[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
- checking for unstated dependencies in vignettes ... OK
- checking package vignettes ... OK
- checking re-building of vignette outputs ... [25s/30s] OK
- checking PDF version of manual ... [6s/8s] OK
- checking HTML version of manual ... [3s/4s] OK
- checking for non-standard things in the check directory ... OK
- DONE
Status: 2 ERRORs