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###
### Running command:
###
###   /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_1.1.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/MotifPeeker.Rcheck’
* using R version 4.5.0 Patched (2025-04-21 r88169)
* 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 ‘1.1.0’
* 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
Non-topic package-anchored link(s) in Rd file 'pipe.Rd':
  ‘[magrittr:pipe]{%>%}’

See section 'Cross-references' in the 'Writing R Extensions' manual.

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 (function (cond)  : 
  error in evaluating the argument 'x' in selecting a method for function 'bfcrid': Failed to collect lazy table.
Caused by error:
! attempt to write a readonly database
Calls: MotifPeeker ... <Anonymous> -> signal_abort -> signalCondition -> <Anonymous>

Quitting from MotifPeeker.Rmd:56-200 [setup]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error:
! error in evaluating the argument 'x' in selecting a method for function 'bfcrid': Failed to collect lazy table.
Caused by error:
! attempt to write a readonly database
---
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::bfcrpath(bfc, url)
  5. │   └─BiocFileCache::bfcrpath(bfc, url)
  6. │     └─base::vapply(...)
  7. │       └─BiocFileCache (local) FUN(X[[i]], ...)
  8. │         ├─BiocFileCache::bfcrid(bfcquery(x, rname, field = "rname", exact = exact))
  9. │         ├─BiocFileCache::bfcquery(x, rname, field = "rname", exact = exact)
 10. │         └─BiocFileCache::bfcquery(x, rname, field = "rname", exact = exact)
 11. │           ├─base::stopifnot(all(field %in% .get_all_colnames(x)))
 12. │           ├─field %in% .get_all_colnames(x)
 13. │           └─BiocFileCache:::.get_all_colnames(x)
 14. │             ├─base::colnames(.sql_get_resource_table(bfc))
 15. │             │ └─base::is.data.frame(x)
 16. │             └─BiocFileCache:::.sql_get_resource_table(bfc)
 17. │               ├─base::tryCatch(...)
 18. │               │ └─base (local) tryCatchList(expr, classes, parentenv, handlers)
 19. │               └─tbl %>% collect
 20. ├─dplyr::collect(.)
 21. ├─dbplyr:::collect.tbl_sql(.)
 22. │ ├─base::withCallingHandlers(...)
 23. │ ├─dbplyr::db_collect(...)
 24. │ └─dbplyr:::db_collect.DBIConnection(...)
 25. │   ├─DBI::dbSendQuery(con, sql)
 26. │   └─RSQLite::dbSendQuery(con, sql)
 27. │     └─RSQLite (local) .local(conn, statement, ...)
 28. │       ├─methods::new(...)
 29. │       │ ├─methods::initialize(value, ...)
 30. │       │ └─methods::initialize(value, ...)
 31. │       └─RSQLite:::result_create(conn@ptr, statement)
 32. ├─base::.handleSimpleError(...)
 33. │ └─dbplyr (local) h(simpleError(msg, call))
 34. │   └─cli::cli_abort("Failed to collect lazy table.", parent = cnd)
 35. │     └─rlang::abort(...)
 36. │       └─rlang:::signal_abort(cnd, .file)
 37. │         └─base::signalCondition(cnd)
 38. └─base (local) `<fn>`(`<rlng_rrr>`)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Execution halted
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* 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: 1 ERROR, 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.22-bioc/meat/MotifPeeker.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL MotifPeeker
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library’
* installing *source* package ‘MotifPeeker’ ...
** this is package ‘MotifPeeker’ version ‘1.1.0’
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (MotifPeeker)

R version 4.5.0 Patched (2025-04-21 r88169) -- "How About a Twenty-Six"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> desc_path <- list.files("../","^DESCRIPTION$",
+                         full.names = TRUE, recursive = TRUE)[1]
> pkg <- read.dcf(desc_path, fields = "Package")[1]
> library(testthat)
> library(pkg, character.only = TRUE)
> 
> test_check(pkg)
[WARNING] This document format requires a nonempty <title> element.
  Please specify either 'title' or 'pagetitle' in the metadata,
  e.g. by using --metadata pagetitle="..." on the command line.
  Falling back to 'MotifPeeker.knit'
[WARNING] This document format requires a nonempty <title> element.
  Please specify either 'title' or 'pagetitle' in the metadata,
  e.g. by using --metadata pagetitle="..." on the command line.
  Falling back to 'MotifPeeker.knit'
[WARNING] This document format requires a nonempty <title> element.
  Please specify either 'title' or 'pagetitle' in the metadata,
  e.g. by using --metadata pagetitle="..." on the command line.
  Falling back to 'MotifPeeker.knit'
Warning: p-values will be inaccurate if primary and control

Warning: p-values will be inaccurate if primary and control

The output directory '/tmp/Rtmp9lM3FL/tomtom/2/1' already exists.
Its contents will be overwritten.
Processing query 1 out of 1 
# Computing q-values.
#   Estimating pi_0 from all 4692 observed p-values.
#   Estimating pi_0.
# Minimal pi_zero = 1.00096
#   Estimated pi_0=1


The output directory '/tmp/Rtmp9lM3FL/tomtom/1/1' already exists.
Its contents will be overwritten.
Processing query 1 out of 1 
# Computing q-values.
#   Estimating pi_0 from all 4692 observed p-values.
#   Estimating pi_0.
# Minimal pi_zero = 1.00096
#   Estimated pi_0=1

The output directory '/tmp/Rtmp9lM3FL/tomtom/1/2' already exists.
Its contents will be overwritten.
Processing query 1 out of 1 
# Computing q-values.
#   Estimating pi_0 from all 4692 observed p-values.
#   Estimating pi_0.
# Minimal pi_zero = 0.989668
#   Estimated pi_0=0.990885


The output directory '/tmp/Rtmp9lM3FL/tomtom/3/1' already exists.
Its contents will be overwritten.
Processing query 1 out of 1 
# Computing q-values.
#   Estimating pi_0 from all 4692 observed p-values.
#   Estimating pi_0.
# Minimal pi_zero = 1.00288
#   Estimated pi_0=1

The output directory '/tmp/Rtmp9lM3FL/tomtom/3/2' already exists.
Its contents will be overwritten.
Processing query 1 out of 1 
# Computing q-values.
#   Estimating pi_0 from all 4692 observed p-values.
#   Estimating pi_0.
# Minimal pi_zero = 0.99046
#   Estimated pi_0=0.99046


The output directory '/tmp/Rtmp9lM3FL/tomtom/4/1' already exists.
Its contents will be overwritten.
Processing query 1 out of 1 
# Computing q-values.
#   Estimating pi_0 from all 4692 observed p-values.
#   Estimating pi_0.
# Minimal pi_zero = 0.989961
#   Estimated pi_0=0.99008

The output directory '/tmp/Rtmp9lM3FL/tomtom/4/2' already exists.
Its contents will be overwritten.
Processing query 1 out of 1 
# Computing q-values.
#   Estimating pi_0 from all 4692 observed p-values.
#   Estimating pi_0.
# Minimal pi_zero = 0.999983
#   Estimated pi_0=1



### Exp2 {- .unlisted}  
**Reference Experiment Label**: Exp1 (Total Reads: 100)  
**Comparison Experiment Label**: Exp2 (Total Reads: 200)  

## Exp2 {- .unlisted .tabset .tabset-fade .tabset-pills}  
**Reference Experiment Label**: Exp1  
**Comparison Experiment Label**: Exp2  
[ FAIL 0 | WARN 0 | SKIP 2 | PASS 696 ]

══ Skipped tests (2) ═══════════════════════════════════════════════════════════
• On CRAN (2): 'test-check_ENCODE.R:1:1', 'test-check_JASPAR.R:1:1'

[ FAIL 0 | WARN 0 | SKIP 2 | PASS 696 ]
> 
> proc.time()
   user  system elapsed 
191.024  82.072 318.210 
Error while shutting down parallel: unable to terminate some child processes