* using log directory ‘/Volumes/Builds/packages/big-sur-x86_64/results/4.5/repo.data.Rcheck’
* using R version 4.5.2 Patched (2026-01-31 r89382)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Ventura 13.3.1
* using session charset: UTF-8
* checking for file ‘repo.data/DESCRIPTION’ ... OK
* this is package ‘repo.data’ version ‘0.2.2’
* 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 ‘repo.data’ can be installed ... [3s/12s] OK
See 'https://www.r-project.org/nosvn/R.check/r-oldrel-macos-x86_64/repo.data-00install.html' for details.
* checking installed package size ... OK
* 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 ... [0s/1s] OK
* checking whether the package can be loaded with stated dependencies ... [0s/1s] OK
* checking whether the package can be unloaded cleanly ... [0s/1s] OK
* checking whether the namespace can be loaded with stated dependencies ... [0s/1s] OK
* checking whether the namespace can be unloaded cleanly ... [0s/1s] OK
* checking loading without being on the library search path ... [0s/1s] OK
* checking whether startup messages can be suppressed ... [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 ... [5s/10s] 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [23s/72s] OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ... [31s/57s] ERROR
  Running ‘spelling.R’ [0s/0s]
  Running ‘test-actions.R’ [12s/21s]
  Running ‘test-alias.R’ [18s/35s]
Running the tests in ‘tests/test-alias.R’ failed.
Complete output:
  > library("repo.data")
  
  Attaching package: 'repo.data'
  
  The following object is masked from 'package:stats':
  
      alias
  
  > alias_columns <- c("Package", "Source", "Target")
  > pkges <- c("BaseSet", "experDesign")
  > bpkges <- c("tools", "compiler")
  > 
  > # Test that cache works
  > st <- system.time(ca <- cran_alias(pkges))
  Downloading and caching CRAN aliases for this session.
  > repo.data:::no_internet(ca)
  > stopifnot(colnames(ca) == alias_columns)
  > stopifnot(is.data.frame(ca))
  > st1 <- system.time(ca2 <- cran_alias(pkges))
  > stopifnot("Cache didn't work" = st1[[3]] < st[[3]])
  > stopifnot("Cache was not the same" = all.equal(ca, ca2))
  > 
  > clean_cache()
  > st2 <- system.time(ca3 <- cran_alias(pkges))
  Downloading and caching CRAN aliases for this session.
  > repo.data:::no_internet(ca3)
  > stopifnot("Clean cache restores initial state" = st2[[3]] > st1[[3]])
  > stopifnot("Still same result" = all.equal(ca, ca3))
  > 
  > ca <- cran_alias()
  Warning: Packages with targets not present in a OS:
  'sfsmisc'
  > repo.data:::no_internet(ca)
  > stopifnot(colnames(ca) == alias_columns)
  > ca2 <- cran_alias()
  > stopifnot("Cache returns the same for all packages" = all.equal(ca, ca2))
  > 
  > st <- system.time(ba <- base_alias(bpkges))
  Downloading and caching base R's aliases for this session.
  > repo.data:::no_internet(ba)
  > stopifnot(colnames(ba) == alias_columns)
  > stopifnot(is.data.frame(ba))
  > st1 <- system.time(ba2 <- base_alias(bpkges))
  > stopifnot("Cache didn't work" = st1[[3]] < st[[3]])
  > stopifnot("Cache was not the same" = all.equal(ba, ba2))
  > 
  > clean_cache()
  > st2 <- system.time(ba3 <- base_alias(bpkges))
  Downloading and caching base R's aliases for this session.
  > repo.data:::no_internet(ba3)
  > stopifnot("Clean cache restores initial state" = st2[[3]] > st1[[3]])
  > stopifnot("Still same result" = all.equal(ba, ba3))
  > 
  > ba <- base_alias()
  > repo.data:::no_internet(ba)
  > stopifnot(colnames(ba) == alias_columns)
  > ba2 <- base_alias()
  > stopifnot("Cache returns the same for all packages" = all.equal(ba, ba2))
  > 
  > 
  > clean_cache()
  > 
  > oldrepos <- getOption("repos")
  > on.exit(options(oldrepos), add = TRUE)
  > setRepositories(ind = 2, addURLs = c(CRAN = "https://cran.r-project.org"))
  > pkges <- c(pkges, "BioCor")
  > 
  > st <- system.time(ba <- alias(pkges))
  > repo.data:::no_internet(ba)
  > stopifnot(colnames(ba) == alias_columns)
  > st1 <- system.time(ba2 <- alias(pkges))
  > stopifnot("Cache alias didn't work" = any(st1 < st))
  > stopifnot("Alias with cache was not the same" = all.equal(ba, ba2))
  > missing_pkg <- pkges[!pkges %in% ba2$Package]
  > 
  > if (length(missing_pkg)) {
  +   stop(sprintf("All packages are present on alias output: %s", toString(missing_pkg)))
  + }
  Error: All packages are present on alias output: BioCor
  Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... [135s/206s] OK
* checking PDF version of manual ... [7s/10s] OK
* DONE
Status: 1 ERROR

* DONE
* Status: FAILURE
* using check arguments '--no-clean-on-error '
* elapsed time (check, wall clock): 6:49
* result classification: failed check, errors:yes, warnings:no, notes:no