• using R Under development (unstable) (2025-07-18 r88431)
• using platform: x86_64-pc-linux-gnu
• R was compiled by     gcc (GCC) 15.1.1 20250521 (Red Hat 15.1.1-2)     GNU Fortran (GCC) 15.1.1 20250521 (Red Hat 15.1.1-2)
• running under: Fedora Linux 42 (Workstation Edition)
• using session charset: UTF-8
• using option ‘--no-stop-on-test-error’
• checking for file ‘deepdep/DESCRIPTION’ ... OK
• this is package ‘deepdep’ version ‘0.4.3’
• 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 ‘deepdep’ can be installed ... OK See the install log for details.
• 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 ... OK
• checking whether the package can be loaded with stated dependencies ... OK
• checking whether the package can be unloaded cleanly ... OK
• checking whether the namespace can be loaded with stated dependencies ... OK
• checking whether the namespace can be unloaded cleanly ... OK
• checking loading without being on the library search path ... 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 ... OK
• checking Rd files ... 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 installed files from ‘inst/doc’ ... OK
• checking files in ‘vignettes’ ... OK
• checking examples ... OK
• checking for unstated dependencies in ‘tests’ ... OK
• checking tests ... [16s/25s] ERROR   Running ‘spelling.R’   Running ‘testthat.R’ [15s/23s] Running the tests in ‘tests/testthat.R’ failed. Complete output:   > library(testthat)   > library(deepdep)   >   > test_check("deepdep")   [ FAIL 4 | WARN 0 | SKIP 1 | PASS 21 ]      ══ Skipped tests (1) ═══════════════════════════════════════════════════════════   • On CRAN (1): 'test-plot_downloads.R:8:3'      ══ Failed tests ════════════════════════════════════════════════════════════════   ── Error ('test-deepdep.R:33:5'): obtaining Bioc dependencies returns objects of correct types ──   Error in `value[[3L]](cond)`: incorrect number of dimensions   Backtrace:       ▆    1. ├─vcr::use_cassette(...) at test-deepdep.R:32:3    2. │ └─cassette$call_block(...)    3. └─deepdep (local) deepdep_wrapped(...) at test-deepdep.R:33:5    4. └─base::tryCatch(...) at test-deepdep.R:3:3    5. └─base (local) tryCatchList(expr, classes, parentenv, handlers)    6. └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])    7. └─value[[3L]](cond)   ── Error ('test-deepdep.R:55:5'): packages with no dependencies return empty deepdep object in result ──   Error: parse error: premature EOF                                                                  (right here) ------^      Backtrace:        ▆     1. ├─vcr::use_cassette(...) at test-deepdep.R:54:3     2. │ └─cassette$call_block(...)     3. └─deepdep::deepdep("rlang") at test-deepdep.R:55:5     4. └─deepdep::deepdep(...) at tests/testthat/setup-deepdep.R:6:3     5. └─deepdep::get_dependencies(package, downloads, bioc, local, dependency_type)     6. └─deepdep::get_description(package, bioc, local)     7. └─deepdep:::get_desc_cached(package, "CRAN")     8. └─deepdep:::append_desc_CRAN(package, descs)     9. └─deepdep:::DB(package)    10. └─jsonlite::prettify(ret)    11. └─jsonlite:::reformat(txt, TRUE, indent_string)    12. └─jsonlite:::stop(out[[2]], call. = FALSE)   ── Error ('test-deepdep_declutter.R:2:3'): (code run outside of `test_that()`) ──   Error: parse error: premature EOF                                                                  (right here) ------^      Backtrace:        ▆     1. ├─vcr::use_cassette(...) at test-deepdep_declutter.R:1:1     2. │ └─cassette$call_block(...)     3. └─deepdep::deepdep("R6", depth = 3, dependency_type = "all") at test-deepdep_declutter.R:2:3     4. └─deepdep::deepdep(...) at tests/testthat/setup-deepdep.R:6:3     5. └─deepdep::get_dependencies(package, downloads, bioc, local, dependency_type)     6. └─deepdep::get_description(package, bioc, local)     7. └─deepdep:::get_desc_cached(package, "CRAN")     8. └─deepdep:::append_desc_CRAN(package, descs)     9. └─deepdep:::DB(package)    10. └─jsonlite::prettify(ret)    11. └─jsonlite:::reformat(txt, TRUE, indent_string)    12. └─jsonlite:::stop(out[[2]], call. = FALSE)   ── Error ('test-plot.R:15:3'): (code run outside of `test_that()`) ─────────────   Error: parse error: premature EOF                                                                  (right here) ------^      Backtrace:        ▆     1. ├─vcr::use_cassette(...) at test-plot.R:14:1     2. │ └─cassette$call_block(...)     3. └─deepdep::deepdep("shiny", depth = 2) at test-plot.R:15:3     4. └─deepdep::deepdep(...) at tests/testthat/setup-deepdep.R:6:3     5. └─deepdep::get_dependencies(package, downloads, bioc, local, dependency_type)     6. └─deepdep::get_description(package, bioc, local)     7. └─deepdep:::get_desc_cached(package, "CRAN")     8. └─deepdep:::append_desc_CRAN(package, descs)     9. └─deepdep:::DB(package)    10. └─jsonlite::prettify(ret)    11. └─jsonlite:::reformat(txt, TRUE, indent_string)    12. └─jsonlite:::stop(out[[2]], call. = FALSE)      [ FAIL 4 | WARN 0 | SKIP 1 | PASS 21 ]   Error: Test failures   Execution halted
• checking for unstated dependencies in vignettes ... OK
• checking package vignettes ... OK
• checking re-building of vignette outputs ... [19s/24s] OK
• checking PDF version of manual ... [9s/12s] OK
• checking HTML version of manual ... OK
• checking for non-standard things in the check directory ... OK
• checking for detritus in the temp directory ... OK
• DONE

Status: 1 ERROR