• using R Under development (unstable) (2025-09-10 r88809)
• using platform: x86_64-pc-linux-gnu
• R was compiled by     Debian clang version 19.1.7 (3+b2)     Debian flang-new version 19.1.7 (3+b2)
• running under: Debian GNU/Linux forky/sid
• using session charset: UTF-8
• checking for file ‘PopPsiSeqR/DESCRIPTION’ ... OK
• checking extension type ... Package
• this is package ‘PopPsiSeqR’ version ‘1.0.0’
• package encoding: UTF-8
• checking CRAN incoming feasibility ... [1s/2s] 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 serialization versions ... OK
• checking whether package ‘PopPsiSeqR’ 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 ... [3s/4s] OK
• checking whether the package can be loaded with stated dependencies ... [3s/4s] OK
• checking whether the package can be unloaded cleanly ... [3s/3s] OK
• checking whether the namespace can be loaded with stated dependencies ... [3s/3s] OK
• checking whether the namespace can be unloaded cleanly ... [3s/4s] OK
• checking loading without being on the library search path ... [3s/5s] 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 ... [15s/20s] 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 ... [3s/5s] OK
• checking for unstated dependencies in ‘tests’ ... OK
• checking tests ... [28s/35s] ERROR   Running ‘testthat.R’ [28s/34s] 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(PopPsiSeqR)   >   > test_check("PopPsiSeqR")   [ FAIL 2 | WARN 1 | SKIP 0 | PASS 9 ]      ══ Failed tests ════════════════════════════════════════════════════════════════   ── Failure ('test-plot.R:26:5'): returns a plot ────────────────────────────────   Expected `mock.plot <- windowedFrequencyShift.plotter(mock_data)` to run without any errors.   i Actually got a <simpleError> with text:     invalid class "GGbio" object: invalid object for slot "ggplot" in class "GGbio": got class "ggplot2::ggplot", should be or extend class "gg_OR_NULL"   ── Error ('test-plot.R:27:5'): returns a plot ──────────────────────────────────   Error in `eval(code, test_env)`: object 'mock.plot' not found   Backtrace:       ▆    1. ├─testthat::expect_true(ggplot2::is.ggplot(mock.plot@ggplot)) at test-plot.R:27:5    2. │ └─testthat::quasi_label(enquo(object), label, arg = "object")    3. │ └─rlang::eval_bare(expr, quo_get_env(quo))    4. └─ggplot2::is.ggplot(mock.plot@ggplot)    5. └─ggplot2::is_ggplot(x)    6. └─S7::S7_inherits(x, class_ggplot)      [ FAIL 2 | WARN 1 | SKIP 0 | PASS 9 ]   Error: Test failures   Execution halted
• checking for unstated dependencies in vignettes ... OK
• checking package vignettes ... OK
• checking re-building of vignette outputs ... [27s/34s] ERROR Error(s) in re-building vignettes:   ... --- re-building ‘PopPsiSeq_and_Helpers.Rmd’ using rmarkdown Quitting from PopPsiSeq_and_Helpers.Rmd:120-124 [unnamed-chunk-7] ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ <error/rlang_error> Error in `validObject()`: ! invalid class "GGbio" object: invalid object for slot "ggplot" in class "GGbio": got class "ggplot2::ggplot", should be or extend class "gg_OR_NULL" --- Backtrace:      x   1. +-ggplot2::autoplot(...)   2. \-ggbio::autoplot(...)   3. \-ggbio (local) .local(object, ...)   4. +-BiocGenerics::do.call(ggplot, c(list(data = object), list(aes.res)))   5. +-base::do.call(ggplot, c(list(data = object), list(aes.res)))   6. +-ggplot2 (local) `<fn>`(data = `<GRanges>`, `<ggplt2::>`)   7. \-ggbio:::ggplot.Vector(data = `<GRanges>`, `<ggplt2::>`)   8. \-ggbio::GGbio(gg, data = data)   9. +-BiocGenerics::do.call(...)  10. +-base::do.call(...)  11. \-methods (local) `<fn>`(...)  12. +-methods::initialize(value, ...)  13. \-methods::initialize(value, ...)  14. \-methods::validObject(.Object) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error: processing vignette 'PopPsiSeq_and_Helpers.Rmd' failed with diagnostics: invalid class "GGbio" object: invalid object for slot "ggplot" in class "GGbio": got class "ggplot2::ggplot", should be or extend class "gg_OR_NULL" --- failed re-building ‘PopPsiSeq_and_Helpers.Rmd’ SUMMARY: processing the following file failed:   ‘PopPsiSeq_and_Helpers.Rmd’ Error: Vignette re-building failed. Execution halted
• checking PDF version of manual ... [5s/8s] OK
• checking HTML version of manual ... [0s/0s] OK
• checking for non-standard things in the check directory ... OK
• DONE

Status: 2 ERRORs