- 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/7s] OK
See the install log 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/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 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/1s] 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/84s] OK
- checking for unstated dependencies in ‘tests’ ... OK
- checking tests ... [29s/55s] ERROR
Running ‘spelling.R’ [0s/0s]
Running ‘test-actions.R’ [12s/23s]
Running ‘test-alias.R’ [17s/31s]
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 ... [126s/311s] OK
- checking PDF version of manual ... [7s/16s] OK
- DONE
Status: 1 ERROR