Last updated on 2026-03-31 23:56:44 CEST.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 1.0.11 | 8.70 | 58.36 | 67.06 | WARN | |
| r-devel-linux-x86_64-debian-gcc | 1.1.4 | 12.91 | 173.92 | 186.83 | ERROR | |
| r-devel-linux-x86_64-fedora-clang | 1.1.4 | 33.00 | 390.55 | 423.55 | OK | |
| r-devel-linux-x86_64-fedora-gcc | 1.1.4 | 32.00 | 402.28 | 434.28 | OK | |
| r-devel-macos-arm64 | 1.1.4 | 5.00 | 83.00 | 88.00 | OK | |
| r-devel-windows-x86_64 | 1.0.11 | 10.00 | 75.00 | 85.00 | WARN | |
| r-patched-linux-x86_64 | 1.0.11 | 7.20 | 51.73 | 58.93 | OK | |
| r-release-linux-x86_64 | 1.0.11 | 4.70 | 53.02 | 57.72 | OK | |
| r-release-macos-arm64 | 1.1.4 | 4.00 | 84.00 | 88.00 | OK | |
| r-release-macos-x86_64 | 1.1.4 | 13.00 | 273.00 | 286.00 | OK | |
| r-release-windows-x86_64 | 1.1.4 | 22.00 | 383.00 | 405.00 | OK | |
| r-oldrel-macos-arm64 | 1.0.11 | OK | ||||
| r-oldrel-macos-x86_64 | 1.1.4 | 14.00 | ERROR | |||
| r-oldrel-windows-x86_64 | 1.0.11 | 13.00 | 92.00 | 105.00 | OK |
Version: 1.0.11
Check: dependencies in R code
Result: WARN
Missing or unexported objects:
‘Biostrings::compareStrings’
‘Biostrings::nucleotideSubstitutionMatrix’
‘Biostrings::pairwiseAlignment’
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-windows-x86_64
Version: 1.1.4
Check: tests
Result: ERROR
Running ‘testthat.R’ [70s/86s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> # This file is part of the standard setup for testthat.
> # It is recommended that you do not modify it.
> #
> # Where should you do additional test configuration?
> # Learn more about the roles of various files in:
> # * https://r-pkgs.org/testing-design.html#sec-tests-files-overview
> # * https://testthat.r-lib.org/articles/special-files.html
>
> library(testthat)
> library(PACVr)
>
> test_check("PACVr")
Saving _problems/test-PACVr-9.R
Warning: stack imbalance in '<-', 123 then 125
Warning: stack imbalance in '{', 119 then 121
Warning: stack imbalance in '{', 112 then 114
Warning: stack imbalance in '<-', 105 then 107
Warning: stack imbalance in 'withVisible', 99 then 101
Warning: stack imbalance in '<-', 88 then 90
Warning: stack imbalance in '{', 84 then 86
Saving _problems/test-readingOps-50.R
Saving _problems/test-readingOps-50.R
[ FAIL 3 | WARN 3 | SKIP 0 | PASS 27 ]
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-PACVr.R:9:5'): successful run of `Mitochondrial_Genome.R` ──────
Error in `file(con, "w")`: cannot open the connection
Backtrace:
▆
1. ├─base::suppressMessages(source(usageFileFull)) at test-PACVr.R:9:5
2. │ └─base::withCallingHandlers(...)
3. ├─base::source(usageFileFull)
4. │ ├─base::withVisible(eval(ei, envir))
5. │ └─base::eval(ei, envir)
6. │ └─base::eval(ei, envir)
7. └─PACVr::PACVr.complete(...)
8. └─GBKData$new(gbkFile, analysisSpecs)
9. └─PACVr (local) initialize(...)
10. └─PACVr:::PACVr.read.gb(gbkFile)
11. └─PACVr:::read.gbWithHandling(gbkRaw)
12. └─base::tryCatch(...)
13. └─base (local) tryCatchList(expr, classes, parentenv, handlers)
14. └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
15. └─value[[3L]](cond)
16. └─PACVr:::read.gbOnFix(gbkRaw, count)
17. └─PACVr:::fixGbkChar(gbkRaw)
18. └─base::writeLines(gbkCharFixed, gbkFileFixed)
19. └─base::file(con, "w")
── Error ('test-readingOps.R:50:5'): successful parsing of `MG936619/MG936619.gb` ──
Error in `file(con, "w")`: cannot open the connection
Backtrace:
▆
1. └─PACVr:::PACVr.read.gb(gbkFileFull) at test-readingOps.R:50:5
2. └─PACVr:::read.gbWithHandling(gbkRaw)
3. └─base::tryCatch(...)
4. └─base (local) tryCatchList(expr, classes, parentenv, handlers)
5. └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
6. └─value[[3L]](cond)
7. └─PACVr:::read.gbOnFix(gbkRaw, count)
8. └─PACVr:::fixGbkChar(gbkRaw)
9. └─base::writeLines(gbkCharFixed, gbkFileFixed)
10. └─base::file(con, "w")
── Error ('test-readingOps.R:50:5'): successful parsing of `MG936619/MG936619.gb` ──
Error in `file(con, "w")`: cannot open the connection
Backtrace:
▆
1. └─PACVr:::PACVr.read.gb(gbkFileFull) at test-readingOps.R:50:5
2. └─PACVr:::read.gbWithHandling(gbkRaw)
3. └─base::tryCatch(...)
4. └─base (local) tryCatchList(expr, classes, parentenv, handlers)
5. └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
6. └─value[[3L]](cond)
7. └─PACVr:::read.gbOnFix(gbkRaw, count)
8. └─PACVr:::fixGbkChar(gbkRaw)
9. └─base::writeLines(gbkCharFixed, gbkFileFixed)
10. └─base::file(con, "w")
[ FAIL 3 | WARN 3 | SKIP 0 | PASS 27 ]
Error:
! Test failures.
Execution halted
Flavor: r-devel-linux-x86_64-debian-gcc
Version: 1.1.4
Check: package dependencies
Result: ERROR
Package required but not available: ‘pwalign’
See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Flavor: r-oldrel-macos-x86_64