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### Running command:
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###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:MotifPeeker.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings MotifPeeker_0.99.13.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/MotifPeeker.Rcheck’
* using R Under development (unstable) (2025-01-22 r87618)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Monterey 12.7.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘MotifPeeker/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘MotifPeeker’ version ‘0.99.13’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... INFO
Imports includes 25 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘MotifPeeker’ can be installed ... OK
* 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 ... 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 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 cross-references ... NOTE
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  motif_enrichment.Rd: memes
  plot_motif_comparison.Rd: compare_motifs
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
* 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... ERROR
Running examples in ‘MotifPeeker-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: MotifPeeker
> ### Title: Benchmark epigenomic profiling methods using motif enrichment
> ### Aliases: MotifPeeker
> 
> ### ** Examples
> 
> peaks <- list(
+     system.file("extdata", "CTCF_ChIP_peaks.narrowPeak",
+                 package = "MotifPeeker"),
+     system.file("extdata", "CTCF_TIP_peaks.narrowPeak",
+                 package = "MotifPeeker")
+ )
> 
> alignments <- list(
+     system.file("extdata", "CTCF_ChIP_alignment.bam",
+                 package = "MotifPeeker"),
+     system.file("extdata", "CTCF_TIP_alignment.bam",
+                 package = "MotifPeeker")
+ )
> 
> motifs <- list(
+     system.file("extdata", "motif_MA1930.2.jaspar",
+                 package = "MotifPeeker"),
+     system.file("extdata", "motif_MA1102.3.jaspar",
+                 package = "MotifPeeker")
+ )
> 
> if (memes::meme_is_installed()) {
+     MotifPeeker(
+         peak_files = peaks,
+         reference_index = 2,
+         alignment_files = alignments,
+         exp_labels = c("ChIP", "TIP"),
+         exp_type = c("chipseq", "tipseq"),
+         genome_build = "hg38",
+         motif_files = motifs,
+         motif_labels = NULL,
+         cell_counts = NULL,
+         motif_discovery = TRUE,
+         motif_discovery_count = 2,
+         motif_db = NULL,
+         download_buttons = TRUE,
+         out_dir = tempdir(),
+         debug = FALSE,
+         quiet = TRUE,
+         verbose = FALSE
+     )
+ }
Error in `mutate()`:
ℹ In argument: `rpath = unname(bfcrpath(x, rids = rids))`.
Caused by error in `bfcrpath()`:
! all(rids %in% bfcrid(x)) is not TRUE
Backtrace:
     ▆
  1. ├─base::ifelse(is.null(params$motif_db), get_JASPARCORE(), params$motif_db)
  2. ├─MotifPeeker::get_JASPARCORE()
  3. │ └─MotifPeeker:::use_cache(core_url, verbose = verbose)
  4. │   ├─BiocFileCache::bfcinfo(bfc)
  5. │   └─BiocFileCache::bfcinfo(bfc)
  6. │     ├─dplyr::mutate(tbl, rpath = unname(bfcrpath(x, rids = rids)))
  7. │     └─dplyr:::mutate.data.frame(tbl, rpath = unname(bfcrpath(x, rids = rids)))
  8. │       └─dplyr:::mutate_cols(.data, dplyr_quosures(...), by)
  9. │         ├─base::withCallingHandlers(...)
 10. │         └─dplyr:::mutate_col(dots[[i]], data, mask, new_columns)
 11. │           └─mask$eval_all_mutate(quo)
 12. │             └─dplyr (local) eval()
 13. ├─base::unname(bfcrpath(x, rids = rids))
 14. ├─BiocFileCache::bfcrpath(x, rids = rids)
 15. ├─BiocFileCache::bfcrpath(x, rids = rids)
 16. │ └─base::stopifnot(all(rids %in% bfcrid(x)))
 17. │   └─base::stop(simpleError(msg, call = if (p <- sys.parent(1L)) sys.call(p)))
 18. └─dplyr (local) `<fn>`(`<smplErrr>`)
 19.   └─rlang::abort(message, class = error_class, parent = parent, call = error_call)

Quitting from lines 57-200 [setup] (MotifPeeker.Rmd)
Execution halted
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 ERROR
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
   24.   │                 │ │ └─base::eval(call)
   25.   │                 │ └─base::withCallingHandlers(...)
   26.   │                 ├─base::withVisible(eval(expr, envir))
   27.   │                 └─base::eval(expr, envir)
   28.   │                   └─base::eval(expr, envir)
   29.   ├─base::ifelse(is.null(params$motif_db), get_JASPARCORE(), params$motif_db)
   30.   └─MotifPeeker::get_JASPARCORE()
   31.     └─MotifPeeker:::use_cache(core_url, verbose = verbose)
   32.       ├─BiocFileCache::bfcrpath(bfc, url)
   33.       └─BiocFileCache::bfcrpath(bfc, url)
  
  [ FAIL 1 | WARN 0 | SKIP 2 | PASS 216 ]
  Error: Test failures
  Execution halted
  Error while shutting down parallel: unable to terminate some child processes
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 2 ERRORs, 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.21-bioc/meat/MotifPeeker.Rcheck/00check.log’
for details.