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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_1.1.3.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/MotifPeeker.Rcheck’
* using R version 4.5.1 (2025-06-13)
* 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 ‘1.1.3’
* 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.
* 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 ... OK
Examples with CPU (user + system) or elapsed time > 5s
                     user system elapsed
MotifPeeker       122.003 69.879 191.508
motif_enrichment    5.469  8.041  13.786
motif_similarity    6.450  1.163   6.809
find_motifs         1.869  0.419   5.872
get_df_enrichment   0.228  0.232  40.119
* 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 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 ‘1.1.3’
** 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 4.5.1 (2025-06-13) -- "Great Square Root"
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/RtmpjGyNdS/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/RtmpjGyNdS/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 = 0.999884
#   Estimated pi_0=0.999884

The output directory '/tmp/RtmpjGyNdS/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 = 1.00417
#   Estimated pi_0=1


The output directory '/tmp/RtmpjGyNdS/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/RtmpjGyNdS/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/RtmpjGyNdS/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/RtmpjGyNdS/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


Hello world
Hello world

### 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 697 ]

══ 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 697 ]
> 
> proc.time()
   user  system elapsed 
203.244  92.544 347.191 
Error while shutting down parallel: unable to terminate some child processes