* using log directory ‘/data/blackswan/ripley/R/packages/tests-devel/easy.glmnet.Rcheck’
* using R Under development (unstable) (2025-11-16 r89026)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (GCC) 14.2.1 20240912 (Red Hat 14.2.1-3)
    GNU Fortran (GCC) 14.2.1 20240912 (Red Hat 14.2.1-3)
* running under: Fedora Linux 40 (Workstation Edition)
* using session charset: UTF-8
* checking for file ‘easy.glmnet/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘easy.glmnet’ version ‘1.0’
* 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 ‘easy.glmnet’ can be installed ... OK
* checking package 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 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 ... [13s/14s] OK
* checking Rd files ... 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 examples ... [13s/16s] OK
* checking examples with --run-donttest ... [9s/12s] ERROR
Running examples in ‘easy.glmnet-Ex.R’ failed
The error most likely occurred in:

> ### Name: impute.glmnet.matrix_fit
> ### Title: Impute missing variables in a glmnet matrix multiple times
> ### Aliases: impute.glmnet.matrix impute.glmnet.matrix_fit
> 
> ### ** Examples
> 
> # Quick example
> 
> # Create random x with missing values
> x = matrix(rnorm(300), ncol = 3)
> x = x + rnorm(1) * x[,sample(1:3)] + rnorm(1) * x[,sample(1:3)]
> x[sample(1:300, 30)] = NA
> 
> # Impute missing values
> m_impute = impute.glmnet.matrix_fit(x, ncores = 2)
[impute.glmnet.matrix_fit] Estimating imputation models (it can take time!)...
[impute.glmnet.matrix_fit] Running time: 2.928725 seconds
> x_imputed = impute.glmnet.matrix(m_impute, x)
[impute.glmnet.matrix] Imputing missing values...
[impute.glmnet.matrix] Running time: 0.01952028 seconds
> 
> 
> # Complete example (it might take some time even if the example is simple...)
> ## No test: 
>   # Create random x (predictors) and y (binary)
>   x = matrix(rnorm(4000), ncol = 20)
>   x = x + rnorm(1) * x[,sample(1:20)] + rnorm(1) * x[,sample(1:20)]
>   y = 1 * (plogis(x[,1] - x[,2] + rnorm(200, 0, 0.1)) > 0.5)
>   
>   # Make some x missing values
>   x[sample(1:4000, 400)] = NA
>   
>   # Predict y via cross-validation, including imputations
>   fit_fun = function (x_training, y_training) {
+     m = list(
+       impute = impute.glmnet.matrix_fit(x_training, ncores = pmax(1, parallel::detectCores() - 2)),
+       lasso = list()
+     )
+     x_imputed = impute.glmnet.matrix(m$impute, x_training)
+     for (imp in 1:length(x_imputed)) {
+       m$lasso[[imp]] = glmnet_fit(x_imputed[[imp]], y_training, family = "binomial")
+     }
+     m
+   }
>   predict_fun = function (m, x_test) {
+     x_imputed = impute.glmnet.matrix(m$impute, x_test)
+     y_pred = NULL
+     for (imp in 1:length(x_imputed)) {
+       y_pred = cbind(y_pred, glmnet_predict(m$lasso[[imp]], x_imputed[[imp]]))
+     }
+     apply(y_pred, 1, mean)
+   }
>   # Only 2 folds to ensure the example runs quickly
>   res = cv(x, y, family = "binomial", fit_fun = fit_fun, predict_fun = predict_fun, nfolds = 2)
[cv] Simple cross-validation
[cv] Fold 1  - Training
[impute.glmnet.matrix_fit] Estimating imputation models (it can take time!)...
Error in .check_ncores(length(names)) : 30 simultaneous processes spawned
Calls: cv ... impute.glmnet.matrix_fit -> makeCluster -> makePSOCKcluster -> .check_ncores
Execution halted
* checking PDF version of manual ... OK
* checking for non-standard things in the check directory ... OK
* checking for detritus in the temp directory ... OK
* checking for new files in some other directories ... OK
* DONE

Status: 1 ERROR
See
  ‘/data/blackswan/ripley/R/packages/tests-devel/easy.glmnet.Rcheck/00check.log’
for details.

Command exited with non-zero status 1
Time 1:59.72, 90.36 + 20.77