* using log directory ‘/Users/ripley/R/packages/tests-devel/missCompare.Rcheck’
* using R Under development (unstable) (2026-06-11 r90128)
* using platform: aarch64-apple-darwin25.5.0
* R was compiled by
    Apple clang version 21.0.0 (clang-2100.1.1.101)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Tahoe 26.5.1
* using session charset: UTF-8
* current time: 2026-06-11 12:32:46 UTC
* using option ‘--no-stop-on-test-error’
* 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 ... [10s/10s] OK
* checking installed package size ... OK
* checking package directory ... 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 ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking whether startup messages can be suppressed ... 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 ... [10s/10s] OK
* checking Rd files ... OK
* checking Rd metadata ... 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 ... 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 ... 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
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 ERROR
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=69152 on localhost:11415 at 13:34:08.934
  starting worker pid=69151 on localhost:11415 at 13:34:08.953
  [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=69386 on localhost:11415 at 13:34:11.014
  starting worker pid=69387 on localhost:11415 at 13:34:11.021
  [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 ... [14s/17s] OK
* checking PDF version of manual ... OK
* checking HTML version of manual ... OK
* checking for detritus in the temp directory ... OK
* DONE

Status: 2 ERRORs
See
  ‘/Users/ripley/R/packages/tests-devel/missCompare.Rcheck/00check.log’
for details.

      109.46 real        85.89 user        14.01 sys