* using log directory ‘/data/blackswan/ripley/R/packages/tests-devel/VBphenoR.Rcheck’
* using R Under development (unstable) (2025-12-18 r89199)
* 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 ‘VBphenoR/DESCRIPTION’ ... OK
* this is package ‘VBphenoR’ version ‘1.1.0’
* 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 ‘VBphenoR’ 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 ... 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking examples ... OK
* checking examples with --run-donttest ... [157s/158s] ERROR
Running examples in ‘VBphenoR-Ex.R’ failed
The error most likely occurred in:

> ### Name: run_Model
> ### Title: Run the Variational Bayes patient phenotyping model
> ### Aliases: run_Model
> 
> ### ** Examples
> 
> ## No test: 
> ##Example 1: Use the internal Sickle Cell Disease data to find the rare
> ##           phenotype.  SCD is extremely rare so we use DBSCAN to initialise
> ##           the VB GMM. We also use an informative prior for the mixing
> ##           coefficient and stop iterations when the ELBO starts to reverse
> ##           so that we stop when the minor (SCD) component is reached.
> 
> library(data.table)

Attaching package: ‘data.table’

The following object is masked from ‘package:base’:

    %notin%

> 
> # Load the SCD example data supplied with the VBphenoR package
> data(scd_cohort)
> 
> # We will use the SCD biomarkers to discover the SCD latent class.
> # X1 is the data matrix for the VB GMM.
> X1 <- scd_cohort[,.(CBC,RC)]
> 
> # We need to supply DBSCAN hyper-parameters as we will initialise VBphenoR
> # with DBSCAN. See help(DBSCAN) for details of these parameters.
> initParams <- c(0.15, 5)
> names(initParams) <- c('eps','minPts')
> 
> # Set an informative prior for the VB GMM mixing coefficient alpha
> # hyper-parameter
> prior_gmm <- list(
+   alpha = 0.001
+ )
> 
> # Set informative priors for the beta coefficients of the VB logit
> prior_logit <- list(mu=c(1,
+                    mean(scd_cohort$age),
+                    mean(scd_cohort$highrisk),
+                    mean(scd_cohort$CBC),
+                    mean(scd_cohort$RC)),
+               Sigma=diag(1,5))           # Simplest isotropic case
> 
> # X2 is the design matrix for the VB logit
> X2 <- scd_cohort[,.(age,highrisk,CBC,RC)]
> X2[,age:=as.numeric(age)]
> X2[,highrisk:=as.numeric(highrisk)]
> X2[,Intercept:=1]
> setcolorder(X2, c("Intercept","age","highrisk","CBC","RC"))
> 
> # Run the patient phenotyping model
> 
> # Need to state what columns are the biomarkers
> biomarkers <- c('CBC', 'RC')
> set.seed(123)
> 
> pheno_result <- run_Model(biomarkers,
+                         gmm_X=X1, gmm_init="dbscan",
+                         gmm_initParams=initParams,
+                         gmm_maxiters=20, gmm_prior=prior_gmm,
+                         gmm_stopIfELBOReverse=TRUE,
+                         logit_X=X2, logit_prior=prior_logit
+ )
Error in `[.data.table`(logit_dt, , `:=`(log_odds, sum(coeff * .SD)),  : 
  attempt access index 5/5 in VECTOR_ELT
Calls: run_Model -> [ -> [.data.table
Execution halted
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* 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/VBphenoR.Rcheck/00check.log’
for details.

Command exited with non-zero status 1
Time 3:44.58, 206.11 + 16.91