Check results for 'PACVr'

using R Under development (unstable) (2026-03-31 r89754)
using platform: x86_64-pc-linux-gnu
R was compiled by gcc-15 (Debian 15.2.0-16) 15.2.0 GNU Fortran (Debian 15.2.0-16) 15.2.0
running under: Debian GNU/Linux forky/sid
using session charset: UTF-8 * current time: 2026-04-01 12:05:13 UTC
checking for file ‘PACVr/DESCRIPTION’ ... OK
this is package ‘PACVr’ version ‘1.1.4’
package encoding: UTF-8
checking CRAN incoming feasibility ... [1s/1s] OK
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 ‘PACVr’ can be installed ... OK See the install log for details.
checking package directory ... OK
checking for future file timestamps ... 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 ... [4s/4s] OK
checking whether the package can be loaded with stated dependencies ... [3s/4s] OK
checking whether the package can be unloaded cleanly ... [3s/6s] OK
checking whether the namespace can be loaded with stated dependencies ... [3s/5s] OK
checking whether the namespace can be unloaded cleanly ... [4s/6s] OK
checking loading without being on the library search path ... [4s/7s] OK
checking whether startup messages can be suppressed ... [4s/6s] OK
checking use of S3 registration ... 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 ... [19s/28s] OK
checking Rd files ... [0s/1s] OK
checking Rd metadata ... OK
checking Rd line widths ... 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 sizes of PDF files under ‘inst/doc’ ... OK
checking installed files from ‘inst/doc’ ... OK
checking files in ‘vignettes’ ... OK
checking examples ... [4s/5s] OK
checking for unstated dependencies in ‘tests’ ... OK
checking tests ... [71s/93s] ERROR Running ‘testthat.R’ [71s/93s] 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
checking for unstated dependencies in vignettes ... OK
checking package vignettes ... OK
checking re-building of vignette outputs ... [3s/5s] OK
checking PDF version of manual ... [3s/5s] OK
checking HTML version of manual ... [0s/0s] OK
checking for non-standard things in the check directory ... OK
DONE

Status: 1 ERROR