* using log directory ‘/data/localhost/ripley/R/packages/tests-donttest/SVG.Rcheck’
* using R Under development (unstable) (2026-08-25 r90448)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (GCC) 16.1.1 20260515 (Red Hat 16.1.1-2)
    GNU Fortran (GCC) 16.1.1 20260515 (Red Hat 16.1.1-2)
* running under: Fedora Linux 44 (Server Edition)
* using session charset: UTF-8
* current time: 2026-08-26 15:18:43 UTC
* checking for file ‘SVG/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘SVG’ version ‘1.0.0’
* 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 ‘SVG’ can be installed ... [24s/50s] OK
* used C compiler: ‘gcc (GCC) 16.2.1 20260819 (Red Hat 16.2.1-2)’
* used C++ compiler: ‘g++ (GCC) 16.2.1 20260819 (Red Hat 16.2.1-2)’
* checking package directory ... OK
* checking ‘build’ 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 whether startup messages can be suppressed ... 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 ... [6s/13s] 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 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 use of SHLIB_OPENMP_*FLAGS in Makefiles ... OK
* checking pragmas in C/C++ headers and code ... OK
* checking compilation flags used ... OK
* checking compiled code ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking examples with --run-donttest ... [5s/10s] ERROR
Running examples in ‘SVG-Ex.R’ failed
The error most likely occurred in:

> ### Name: CalSVG_nnSVG
> ### Title: nnSVG: Nearest-Neighbor Gaussian Process SVG Detection
> ### Aliases: CalSVG_nnSVG
> 
> ### ** Examples
> 
> # Load example data
> data(example_svg_data)
> expr <- example_svg_data$logcounts[1:10, ]  # Small subset
> coords <- example_svg_data$spatial_coords
> 
> ## No test: 
> # Basic usage (requires BRISC package)
> if (requireNamespace("BRISC", quietly = TRUE)) {
+     results <- CalSVG_nnSVG(expr, coords, verbose = FALSE)
+     head(results)
+ }
Warning in BRISC::BRISC_estimation(coords = coords_scaled, y = y, x = X,  :
  The ordering of inputs x (covariates) and y (response) in BRISC_estimation has been changed BRISC 1.0.0 onwards.
Please check the new documentation with ?BRISC_estimation.

 *** caught segfault ***
address 0x1, cause 'memory not mapped'

Traceback:
 1: BRISC::BRISC_estimation(coords = coords_scaled, y = y, x = X,     n.neighbors = n_neighbors, n_omp = 1, order = order, cov.model = cov_model,     search.type = "tree", verbose = FALSE, ordering = ordering,     neighbor = neighbor_info)
 2: doTryCatch(return(expr), name, parentenv, handler)
 3: tryCatchOne(expr, names, parentenv, handlers[[1L]])
 4: tryCatchList(expr, classes, parentenv, handlers)
 5: tryCatch({    brisc_out <- BRISC::BRISC_estimation(coords = coords_scaled,         y = y, x = X, n.neighbors = n_neighbors, n_omp = 1, order = order,         cov.model = cov_model, search.type = "tree", verbose = FALSE,         ordering = ordering, neighbor = neighbor_info)    list(sigma.sq = brisc_out$Theta["sigma.sq"], tau.sq = brisc_out$Theta["tau.sq"],         phi = brisc_out$Theta["phi"], loglik = brisc_out$log_likelihood,         success = TRUE)}, error = function(e) {    list(sigma.sq = NA, tau.sq = NA, phi = NA, loglik = NA, success = FALSE)})
 6: system.time({    result <- tryCatch({        brisc_out <- BRISC::BRISC_estimation(coords = coords_scaled,             y = y, x = X, n.neighbors = n_neighbors, n_omp = 1,             order = order, cov.model = cov_model, search.type = "tree",             verbose = FALSE, ordering = ordering, neighbor = neighbor_info)        list(sigma.sq = brisc_out$Theta["sigma.sq"], tau.sq = brisc_out$Theta["tau.sq"],             phi = brisc_out$Theta["phi"], loglik = brisc_out$log_likelihood,             success = TRUE)    }, error = function(e) {        list(sigma.sq = NA, tau.sq = NA, phi = NA, loglik = NA,             success = FALSE)    })})
 7: fit_one_gene(i)
 8: FUN(X[[i]], ...)
 9: lapply(seq_len(n_genes), function(i) {    result <- fit_one_gene(i)    if (verbose && n_genes > 50)         setTxtProgressBar(pb, i)    return(result)})
10: CalSVG_nnSVG(expr, coords, verbose = FALSE)
An irrecoverable exception occurred. R is aborting now ...
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... [14s/30s] OK
* checking PDF version of manual ... [5s/10s] OK
* checking HTML 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/localhost/ripley/R/packages/tests-donttest/SVG.Rcheck/00check.log’
for details.

Command exited with non-zero status 1
Time 2:58.37, 74.49 + 10.43