Last updated on 2026-07-24 20:49:08 CEST.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 0.2.2 | 3.68 | 481.06 | 484.74 | OK | |
| r-devel-linux-x86_64-debian-gcc | 0.2.2 | 3.11 | 338.94 | 342.05 | OK | |
| r-devel-linux-x86_64-fedora-clang | 0.2.2 | 712.80 | OK | |||
| r-devel-linux-x86_64-fedora-gcc | 0.2.2 | 333.77 | OK | |||
| r-devel-windows-x86_64 | 0.2.2 | 7.00 | 553.00 | 560.00 | OK | |
| r-patched-linux-x86_64 | 0.2.2 | 5.20 | 483.32 | 488.52 | OK | |
| r-release-linux-x86_64 | 0.2.2 | 4.06 | 454.45 | 458.51 | OK | |
| r-release-macos-arm64 | 0.2.2 | 1.00 | 306.00 | 307.00 | OK | |
| r-release-macos-x86_64 | 0.2.2 | 3.00 | 661.00 | 664.00 | OK | |
| r-release-windows-x86_64 | 0.2.2 | 5.00 | 554.00 | 559.00 | OK | |
| r-oldrel-macos-arm64 | 0.2.2 | 1.00 | 356.00 | 357.00 | ERROR | |
| r-oldrel-macos-x86_64 | 0.2.2 | 3.00 | 777.00 | 780.00 | ERROR | |
| r-oldrel-windows-x86_64 | 0.2.2 | 6.00 | 651.00 | 657.00 | ERROR |
Version: 0.2.2
Check: examples
Result: ERROR
Running examples in ‘repo.data-Ex.R’ failed
The error most likely occurred in:
> ### Name: bioc_cran_archived
> ### Title: Bioconductor packages using CRAN archived packages
> ### Aliases: bioc_cran_archived
>
> ### ** Examples
>
> bca <- bioc_cran_archived()
Downloading and caching packages available on Bioconductor for this session.
Downloading and caching CRAN's packages database for this session.
Error in bioc[, columns] : incorrect number of dimensions
Calls: bioc_cran_archived -> rbind -> rbind
Execution halted
Flavor: r-oldrel-macos-arm64
Version: 0.2.2
Check: tests
Result: ERROR
Running ‘spelling.R’ [0s/0s]
Running ‘test-actions.R’ [5s/11s]
Running ‘test-alias.R’ [8s/47s]
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
Flavor: r-oldrel-macos-arm64
Version: 0.2.2
Check: re-building of vignette outputs
Result: ERROR
Error(s) in re-building vignettes:
--- re-building ‘repo.data.Rmd’ using knitr
Downloading and caching CRAN aliases for this session.
Quitting from repo.data.Rmd:162-168 [doom]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `bioc[, columns]`:
! incorrect number of dimensions
---
Backtrace:
▆
1. └─repo.data::cran_doom(bioc = TRUE)
2. └─base::rbind(db[, columns], bioc[, columns])
3. └─base::rbind(deparse.level, ...)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'repo.data.Rmd' failed with diagnostics:
incorrect number of dimensions
--- failed re-building ‘repo.data.Rmd’
SUMMARY: processing the following file failed:
‘repo.data.Rmd’
Error: Vignette re-building failed.
Execution halted
Flavor: r-oldrel-macos-arm64
Version: 0.2.2
Check: tests
Result: ERROR
Running ‘spelling.R’ [0s/0s]
Running ‘test-actions.R’ [13s/38s]
Running ‘test-alias.R’ [17s/54s]
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
Flavor: r-oldrel-macos-x86_64
Version: 0.2.2
Check: tests
Result: ERROR
Running 'spelling.R' [0s]
Running 'test-actions.R' [1s]
Running 'test-alias.R' [31s]
Running 'test-bioconductor.R' [5s]
Running 'test-cran_actions.R' [0s]
Running 'test-cran_archive.R' [52s]
Running 'test-cran_doom.R' [23s]
Running 'test-cran_history.R' [0s]
Running 'test-cran_issues.R' [0s]
Running 'test-cran_targets_links.R' [0s]
Running 'test-cran_version.R' [7s]
Running 'test-dates.R' [4s]
Running 'test-help.R' [0s]
Running 'test-links.R' [67s]
Running 'test-maintainers.R' [4s]
Running 'test-package_date.R' [6s]
Running 'test-package_repos.R' [34s]
Running 'test-update_dependencies.R' [61s]
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
Flavor: r-oldrel-windows-x86_64