Check results for 'PopPsiSeqR'

using R version 4.4.1 (2024-06-14)
using platform: x86_64-apple-darwin20
R was compiled by Apple clang version 14.0.0 (clang-1400.0.29.202) GNU Fortran (GCC) 12.2.0
running under: macOS Ventura 13.3.1
using session charset: UTF-8
checking for file ‘PopPsiSeqR/DESCRIPTION’ ... OK
checking extension type ... Package
this is package ‘PopPsiSeqR’ version ‘1.0.2’
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 ‘PopPsiSeqR’ can be installed ... [6s/15s] OK See the install log for details.
checking installed package size ... OK
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 ... [2s/4s] OK
checking whether the package can be loaded with stated dependencies ... [1s/3s] OK
checking whether the package can be unloaded cleanly ... [1s/4s] OK
checking whether the namespace can be loaded with stated dependencies ... [1s/4s] OK
checking whether the namespace can be unloaded cleanly ... [2s/5s] OK
checking loading without being on the library search path ... [2s/4s] 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 ... [4s/13s] OK
checking Rd files ... [0s/1s] OK
checking Rd metadata ... 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 ... [2s/4s] OK
checking for unstated dependencies in ‘tests’ ... OK
checking tests ... [18s/48s] ERROR Running ‘testthat.R’ [18s/48s] 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") Saving _problems/test-plot-26.R Saving _problems/test-plot-27.R [ FAIL 2 | WARN 3 | SKIP 0 | PASS 11 ] ══ Failed tests ════════════════════════════════════════════════════════════════ ── Failure ('test-plot.R:26:5'): returns a plot ──────────────────────────────── Expected `mock.plot <- windowedFrequencyShift.plotter(mock_data)` not to throw any errors. Actually got a <simpleError> with message: 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) 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 3 | SKIP 0 | PASS 11 ] Error: ! Test failures. Execution halted
checking for unstated dependencies in vignettes ... OK
checking package vignettes ... OK
checking re-building of vignette outputs ... [28s/74s] 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 ... [6s/13s] OK
DONE Status: 2 ERRORs
using check arguments '--no-clean-on-error '