* using log directory ‘/data/blackswan/ripley/R/packages/tests-devel/squeezy.Rcheck’
* using R Under development (unstable) (2025-08-07 r88529)
* 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 ‘squeezy/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘squeezy’ version ‘1.1-1’
* checking package namespace information ... OK
* checking package dependencies ... INFO
Package suggested but not available for checking: ‘ecpc’
* 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 ‘squeezy’ 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 ... [10s/11s] 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 ... OK
* checking examples with --run-donttest ... ERROR
Running examples in ‘squeezy-Ex.R’ failed
The error most likely occurred in:

> ### Name: squeezy
> ### Title: Fit a group-adaptive elastic net penalised linear or logistic
> ###   model
> ### Aliases: squeezy
> 
> ### ** Examples
> 
> 
> #####################
> # Simulate toy data #
> #####################
> p<-100 #number of covariates
> n<-50 #sample size training data set
> n2<-100 #sample size test data set
> G<- 5 #number of groups
> 
> taugrp <- rep(c(0.05,0.1,0.2,0.5,1),each=p/G) #ridge prior variance
> groupIndex <- rep(1:G,each=p/G) #groups for co-data
> groupset <- lapply(1:G,function(x){which(groupIndex==x)}) #group set with each element one group
> sigmasq <- 2 #linear regression noise
> lambda1 <- sqrt(taugrp/2) #corresponding lasso penalty
> #A Laplace(0,b) variate can also be generated as the difference of two i.i.d.
> #Exponential(1/b) random variables
> betas <-   rexp(p, 1/lambda1) -  rexp(p, 1/lambda1) #regression coefficients
> X <- matrix(rnorm(n*p),n,p) #simulate training data
> Y <- rnorm(n,X%*%betas,sd=sqrt(sigmasq))
> X2 <- matrix(rnorm(n*p),n,p) #simulate test data
> Y2 <- rnorm(n,X2%*%betas,sd=sqrt(sigmasq))
> 
> ###############
> # Fit squeezy #
> ###############
> #may be fit directly..
> res.squeezy <- squeezy(Y,X,groupset=groupset,Y2=Y2,X2=X2,
+                        model="linear",alpha=0.5)
> 
> ## No test: 
>   #..or with ecpc-fit as initialisation
>   if(requireNamespace("ecpc")){
+     res.ecpc <- ecpc::ecpc(Y,X, #observed data and response to train model
+                      groupsets=list(groupset), #informative co-data group set
+                      Y2=Y2,X2=X2, #test data
+                      model="linear",
+                      hypershrinkage="none",postselection = FALSE)
+     res.squeezy <- squeezy(Y,X, #observed data and response to train model
+                            groupset=groupset, #informative co-data group set
+                            Y2=Y2,X2=X2, #test data
+                            fit.ecpc = res.ecpc, #ecpc-fit for initial values
+                            model="linear", #type of model for the response
+                            alpha=0.5) #elastic net mixing parameter
+   }
Loading required namespace: ecpc
Failed with error:  ‘there is no package called ‘ecpc’’
> ## End(No test)
> 
> 
> summary(res.squeezy$betaApprox) #estimated elastic net regression coefficients
    Min.  1st Qu.   Median     Mean  3rd Qu.     Max. 
-1.34782 -0.06646  0.00000  0.04430  0.22840  1.77463 
> summary(res.squeezy$betaMR) #estimated multi-ridge regression coefficients
    Min.  1st Qu.   Median     Mean  3rd Qu.     Max. 
-1.30934 -0.15625  0.02994  0.02994  0.23418  1.68304 
> res.squeezy$lambdaApprox #estimated group elastic net penalties
[1] 0.17914345 0.11962280 0.16282082 0.03789987 0.14757408
> res.squeezy$tauMR #multi-ridge group variances
[1] 0.1004952 0.1721318 0.1143743 0.7155714 0.1304843
> res.squeezy$MSEApprox #MSE group-elastic net model
[1] 8.575667
> res.squeezy$MSEMR #MSE group-ridge model
[1] 8.654213
> 
> #once fit, quickly find model fit for different values of alpha:
> res.squeezy2 <- squeezy(Y,X, #observed data and response to train model
+                         groupset=groupset, #informative co-data groupset
+                         Y2=Y2,X2=X2, #test data
+                         lambdas = res.squeezy$lambdaMR, #fix lambdas at multi-ridge estimate
+                         model="linear", #type of model for the response
+                         alpha=0.9) #elastic net mixing parameter
> 
> ## No test: 
>   #Select single-group model or multi-group model based on best mAIC
>   res.squeezy <- squeezy(Y,X, #observed data and response to train model
+                          groupset=groupset, #informative co-data group set
+                          Y2=Y2,X2=X2, #test data
+                          fit.ecpc = res.ecpc, #ecpc-fit for initial values
+                          model="linear", #type of model for the response
+                          alpha=0.5, #elastic net mixing parameter
+                          selectAIC = TRUE,resultsAICboth = TRUE)
Error: object 'res.ecpc' not found
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/squeezy.Rcheck/00check.log’
for details.

Command exited with non-zero status 1
Time 2:14.97, 80.56 + 53.57