revdep/problems.md

In igordot/msigdbr: MSigDB Gene Sets for Multiple Organisms in a Tidy Data Format

pairedGSEA

• Version: 1.8.0
• GitHub: https://github.com/shdam/pairedGSEA
• Source code: https://github.com/cran/pairedGSEA
• Date/Publication: 2025-04-15
• Number of recursive dependencies: 168

Run revdepcheck::revdep_details(, "pairedGSEA") for more info

Newly broken

• R CMD check timed out

ReducedExperiment

• Version: 0.99.6
• GitHub: https://github.com/jackgisby/ReducedExperiment
• Source code: https://github.com/cran/ReducedExperiment
• Date/Publication: 2025-01-15
• Number of recursive dependencies: 219

Run revdepcheck::revdep_details(, "ReducedExperiment") for more info

Newly broken

• R CMD check timed out

Newly fixed

• checking tests ... ``` Running ‘testthat.R’ ERROR Running the tests in ‘tests/testthat.R’ failed. Last 13 lines of output: |=================================== | 50% | |======================================================================| 100% [ FAIL 1 | WARN 1 | SKIP 0 | PASS 584 ]

  ══ Failed tests ════════════════════════════════════════════════════════════════ ── Failure ('test_features.R:85:5'): Get MSGIDB data ─────────────────────────── nrow(t2g) > 1e+05 is not TRUE

  actual: FALSE expected: TRUE

  [ FAIL 1 | WARN 1 | SKIP 0 | PASS 584 ] Error: Test failures Execution halted ```

• checking running R code from vignettes ... ``` ‘ReducedExperiment.Rmd’ using ‘UTF-8’... failed ERROR Errors in running code in vignettes: when running code in ‘ReducedExperiment.Rmd’ ... > ggplot(module_1_enrich[1:15, ], aes(-log10(p.adjust),

  • reorder(substr(ID, 1, 45), -log10(p.adjust)))) + geom_point(pch = 21,
  • size = 3) .... [TRUNCATED]

  When sourcing ‘ReducedExperiment.R’: Error: Problem while computing aesthetics. ℹ Error occurred in the 1st layer. Caused by error in log10(): ! non-numeric argument to mathematical function Execution halted ```

In both

• checking dependencies in R code ... NOTE Unexported objects imported by ':::' calls: ‘BiocGenerics:::replaceSlots’ ‘SummarizedExperiment:::.SummarizedExperiment.charbound’ See the note in ?`:::` about the use of this operator.

igordot/msigdbr documentation built on June 15, 2025, 4:29 a.m.