- using R version 4.5.2 Patched (2026-01-31 r89382)
- using platform: aarch64-apple-darwin20
- R was compiled by
Apple clang version 16.0.0 (clang-1600.0.26.6)
GNU Fortran (GCC) 14.2.0
- running under: macOS Ventura 13.7.8
- using session charset: UTF-8
- checking for file ‘BET/DESCRIPTION’ ... OK
- checking extension type ... Package
- this is package ‘BET’ version ‘0.6.0’
- 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 ‘BET’ can be installed ... [6s/6s] OK
See the install log for details.
- used C++ compiler: ‘Apple clang version 14.0.3 (clang-1403.0.22.14.1)’
- used SDK: ‘MacOSX11.3.1.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 ... [0s/0s] OK
- checking whether the package can be loaded with stated dependencies ... [0s/0s] OK
- checking whether the package can be unloaded cleanly ... [0s/0s] OK
- checking whether the namespace can be loaded with stated dependencies ... [0s/0s] OK
- checking whether the namespace can be unloaded cleanly ... [0s/0s] OK
- checking loading without being on the library search path ... [0s/0s] 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 ... [2s/2s] OK
- checking Rd files ... [0s/0s] 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 ... [0s/0s] 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 $(LAPACK_LIBS) ... OK
- checking use of PKG_*FLAGS in Makefiles ... OK
- checking compiled code ... OK
- checking examples ... [1s/1s] OK
- checking for unstated dependencies in ‘tests’ ... OK
- checking tests ... [1s/1s] ERROR
Running ‘regression.R’ [0s/0s]
Running the tests in ‘tests/regression.R’ failed.
Complete output:
> # Small, deterministic/frozen-fixture tests; no full study or benchmark.
> library(BET)
> stopifnot(as.character(packageVersion("BET")) == "0.6.0")
> fixtures <- readRDS("fixtures/inputs.rds")
> expected <- readRDS("fixtures/expected_054.rds")
> api <- readRDS("fixtures/api_054.rds")
> checks <- 0L
> ok <- function(x) {stopifnot(isTRUE(x));checks <<- checks+1L;invisible(TRUE)}
> error <- function(expr, pattern=NULL) {
+ ans <- tryCatch({force(expr);NULL},error=function(e)e)
+ ok(inherits(ans,"error"))
+ if (!is.null(pattern)) ok(grepl(pattern,conditionMessage(ans),fixed=TRUE))
+ }
> inside <- function(name) getFromNamespace(paste0(".beast_asym_",name),"BET")
> RNGkind("Mersenne-Twister","Inversion","Rejection")
> for (id in names(fixtures)) {
+ f <- fixtures[[id]]; X <- f$X
+ for (name in names(api)) {
+ fun <- getExportedValue("BET",name)
+ ok(identical(formals(fun),api[[name]]$formals))
+ ok(identical(deparse(body(fun),width.cutoff=500L),api[[name]]$body))
+ }
+ set.seed(f$statistic_seed)
+ fit <- BEAST(X,3,subsample.percent=f$fraction,B=f$B,lambda=f$lambda,
+ index=list(1L,2L),method="stat")
+ after <- .Random.seed
+ ok(identical(fit,expected[[id]]$BEAST))
+ set.seed(f$statistic_seed)
+ repeat_fit <- BEAST(X,3,subsample.percent=f$fraction,B=f$B,lambda=f$lambda,
+ index=list(1L,2L),method="stat")
+ ok(identical(fit,repeat_fit) && identical(.Random.seed,after))
+ ok(identical(MaxBET(X,3,index=list(1L,2L)),expected[[id]]$MaxBET))
+ ok(identical(MaxBETs(X,3,index=list(1L,2L)),expected[[id]]$MaxBETs))
+ ok(identical(cell.counts(X,3),expected[[id]]$cell.counts))
+ ok(identical(symm(X,3,print.sample.size=FALSE),expected[[id]]$symm))
+ ok(identical(get.signs(X,3),expected[[id]]$get.signs))
+ }
Error in ok(identical(fit, expected[[id]]$BEAST)) : isTRUE(x) is not TRUE
Calls: ok -> stopifnot
Execution halted
- checking PDF version of manual ... [6s/6s] OK
- DONE
Status: 1 ERROR