* using log directory ‘/Users/ripley/R/packages/tests-devel/MetaHD.Rcheck’
* using R Under development (unstable) (2026-07-08 r90211)
* 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 26.5.2
* using session charset: UTF-8
* current time: 2026-07-08 09:08:51 UTC
* using option ‘--no-stop-on-test-error’
* checking for file ‘MetaHD/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘MetaHD’ version ‘0.1.5’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... INFO
Package suggested but not available for checking: ‘gVenn’
* 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 ‘MetaHD’ can be installed ... [17s/15s] OK
* used C++ compiler: ‘Apple clang version 21.0.0 (clang-2100.1.1.101)’
* used SDK: ‘MacOSX26.5.sdk’
* checking installed package size ... 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 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 ... 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 line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking use of PKG_*FLAGS in Makefiles ... OK
* checking pragmas in C/C++ headers and code ... OK
* checking compilation flags used ... OK
* checking compiled code ... OK
* checking examples ... ERROR
Running examples in ‘MetaHD-Ex.R’ failed
The error most likely occurred in:

> ### Name: plot.MetaHDResult
> ### Title: Plot 'MetaHD' results
> ### Aliases: plot.MetaHDResult
> 
> ### ** Examples
> 
> set.seed(123)
> N <- 100
> truth <- rbinom(N, 1, 0.2)   # 20% of features are true signals
> res <- MetaHDResult(
+   sets = list(
+     method_A = runif(N)^ifelse(truth, 5, 1),
+     method_B = runif(N)^ifelse(truth, 3, 1),
+     method_C = runif(N)^ifelse(truth, 2, 1)
+   ),
+   truth = truth
+ )
> 
> # Example 1: simple UpSet plot 
> plot(res, type = "upset")
> 
> # Example 2: highlights via the `highlight` argument
> plot(res, type = "upset",
+      highlight = list(c("Truth", "method_A", "method_B", "method_C")),
+      highlight.colors = "darkgreen")
> 
> # Example 3: passing in-built queries
> plot(res, type = "upset",
+      queries = list(
+        list(
+          query = UpSetR::intersects,
+          params = list(c("method_A", "method_B", "method_C")),
+          color = "dodgerblue3",
+          active = TRUE,
+          query.name = "Identified by all methods"
+        ),
+        list(
+          query = function(row) {
+            row["method_A"] == 1 && sum(row) < length(row)
+          },
+          color = "orange",
+          active = TRUE,
+          query.name = "Others identified by method_A"
+        )
+      ),
+      show.truth = FALSE)
> 
> # Example 4: ROC curves with AUC values 
> # Requires numeric p-values in sets
> aucs <- plot(res, type = "ROC")
> print(aucs)
 method_A  method_B  method_C 
0.8150407 0.8306233 0.7256098 
> 
> # Example 5: Venn diagram (Tav, 2025)
> # Requires R >= 4.5 and gVenn installed
> plot(res, type = "venn")
Error: Package 'gVenn' is required for Venn diagrams.
It requires R >= 4.5. Install it with:
  BiocManager::install('gVenn')
Execution halted
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’ [91s/91s]
 [91s/92s] OK
* checking PDF version of manual ... OK
* checking HTML version of manual ... OK
* checking for detritus in the temp directory ... OK
* DONE

Status: 1 ERROR
See
  ‘/Users/ripley/R/packages/tests-devel/MetaHD.Rcheck/00check.log’
for details.

      164.68 real       152.54 user         9.38 sys