missCompare

Intuitive Missing Data Imputation Framework

v1.0.3 · Dec 1, 2020 · MIT + file LICENSE

Description

Offers a convenient pipeline to test and compare various missing data imputation algorithms on simulated and real data. These include simpler methods, such as mean and median imputation and random replacement, but also include more sophisticated algorithms already implemented in popular R packages, such as 'mi', described by Su et al. (2011) <doi:10.18637/jss.v045.i02>; 'mice', described by van Buuren and Groothuis-Oudshoorn (2011) <doi:10.18637/jss.v045.i03>; 'missForest', described by Stekhoven and Buhlmann (2012) <doi:10.1093/bioinformatics/btr597>; 'missMDA', described by Josse and Husson (2016) <doi:10.18637/jss.v070.i01>; and 'pcaMethods', described by Stacklies et al. (2007) <doi:10.1093/bioinformatics/btm069>. The central assumption behind 'missCompare' is that structurally different datasets (e.g. larger datasets with a large number of correlated variables vs. smaller datasets with non correlated variables) will benefit differently from different missing data imputation algorithms. 'missCompare' takes measurements of your dataset and sets up a sandbox to try a curated list of standard and sophisticated missing data imputation algorithms and compares them assuming custom missingness patterns. 'missCompare' will also impute your real-life dataset for you after the selection of the best performing algorithm in the simulations. The package also provides various post-imputation diagnostics and visualizations to help you assess imputation performance.

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Flavor	Status	Time
r-devel-linux-x86_64-debian-clang	ERROR	286.8s
r-devel-linux-x86_64-debian-gcc	ERROR	205.9s
r-devel-linux-x86_64-fedora-clang	ERROR	457.5s
r-devel-linux-x86_64-fedora-gcc	ERROR	459s
r-devel-windows-x86_64	ERROR	283s
r-oldrel-macos-arm64	OK
r-oldrel-macos-x86_64	OK	307s
r-oldrel-windows-x86_64	ERROR	391s
r-patched-linux-x86_64	ERROR	266.8s
r-release-linux-x86_64	ERROR
r-release-macos-arm64	OK	86s
r-release-macos-x86_64	OK	357s
r-release-windows-x86_64	ERROR	283s

Check details (18 non-OK)

ERROR r-devel-linux-x86_64-debian-clang

examples

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

ERROR r-devel-linux-x86_64-debian-clang

tests

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"
  
...[truncated]...
al) .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

ERROR r-devel-linux-x86_64-debian-gcc

examples

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

ERROR r-devel-linux-x86_64-debian-gcc

tests

Running ‘testthat.R’ [10s/22s]
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=412175 on localhost:11535 at 17:58:31.187
  starting worker pid=412174 on localhost:11535 at 17:58:31.250
  [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=414982 on localhost:11535 at 17:58:37.645
  starting worker pid=414981 on localhost:11535 at 17:58:37.645
  [1] "missForest imputation - in progress"
  [1] 
...[truncated]...
al) .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

ERROR r-devel-linux-x86_64-fedora-clang

examples

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

ERROR r-devel-linux-x86_64-fedora-clang

tests

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"
  
...[truncated]...
al) .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

ERROR r-devel-linux-x86_64-fedora-gcc

examples

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

ERROR r-devel-linux-x86_64-fedora-gcc

tests

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"
  
...[truncated]...
al) .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

ERROR r-devel-windows-x86_64

examples

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

ERROR r-devel-windows-x86_64

tests

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 a
...[truncated]...
al) .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

ERROR r-oldrel-windows-x86_64

examples

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

ERROR r-oldrel-windows-x86_64

tests

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 
...[truncated]...
al) .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

ERROR r-patched-linux-x86_64

examples

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

ERROR r-patched-linux-x86_64

tests

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"
  
...[truncated]...
al) .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

ERROR r-release-linux-x86_64

examples

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

ERROR r-release-linux-x86_64

tests

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"
  
...[truncated]...
al) .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

ERROR r-release-windows-x86_64

examples

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

ERROR r-release-windows-x86_64

tests

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 a
...[truncated]...
al) .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

Additional Issues

M1mac Details →

Check History

ERROR 11 OK · 0 NOTE · 0 WARNING · 2 ERROR · 0 FAILURE Jun 12, 2026

ERROR r-devel-linux-x86_64-fedora-clang

examples

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_mi
...[truncated]...
M(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

ERROR r-devel-linux-x86_64-fedora-gcc

examples

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_mi
...[truncated]...
M(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

OK 13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE Jun 9, 2026

ERROR 12 OK · 0 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE Jun 8, 2026

ERROR r-devel-linux-x86_64-debian-gcc

package dependencies

Packages required but not available: 'Hmisc', 'mice', 'missMDA', 'VIM'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.

OK 13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE May 2, 2026

ERROR 11 OK · 0 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE Apr 25, 2026

ERROR r-release-macos-x86_64

package dependencies

Packages required but not available: 'mice', 'missMDA'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.

OK 14 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE Mar 30, 2026

ERROR 13 OK · 0 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE Mar 27, 2026

ERROR r-devel-linux-x86_64-fedora-clang

whether package can be installed

Installation failed.
See ‘/data/gannet/ripley/R/packages/tests-clang/missCompare.Rcheck/00install.out’ for details.

OK 14 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE Mar 10, 2026

Dependency Network

Version History

3 tracked

new 1.0.3 Mar 10, 2026

updated 1.0.3 ← 1.0.1 diff Nov 30, 2020

new 1.0.1 Feb 4, 2019