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### Running command:
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###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:tidybulk.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings tidybulk_2.0.1.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/tidybulk.Rcheck’
* using R version 4.5.2 (2025-10-31)
* 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 ‘tidybulk/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘tidybulk’ version ‘2.0.1’
* 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 hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘tidybulk’ 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 whether startup messages can be suppressed ... OK
* checking dependencies in R code ... NOTE
Package in Depends field not imported from: ‘ttservice’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.aggregate_duplicates_se: no visible global function definition for
  ‘where’
aggregate_duplicates,RangedSummarizedExperiment: no visible global
  function definition for ‘where’
aggregate_duplicates,SummarizedExperiment: no visible global function
  definition for ‘where’
Undefined global functions or variables:
  where
* checking Rd files ... NOTE
checkRd: (-1) remove_redundancy-methods.Rd:104-113: Lost braces
   104 | select_closest_pairs = function(df) {
       |                                     ^
checkRd: (-1) remove_redundancy-methods.Rd:106-111: Lost braces
   106 |   while (df |> nrow() > 0) {
       |                            ^
checkRd: (-1) rotate_dimensions-methods.Rd:76-82: Lost braces
    76 | rotation = function(m, d) {
       |                           ^
* 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking LazyData ... 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
test_differential_abundance-methods  139.880  1.402 203.450
test_differential_expression-methods 136.620  1.043 214.309
adjust_abundance-methods              24.185  0.950  38.744
aggregate_duplicates-methods          17.491  0.377  24.007
test_gene_enrichment-methods          12.124  0.812  20.733
describe_transcript-methods            5.895  0.197   8.208
impute_missing_abundance-methods       5.556  0.108   7.637
pivot_transcript-methods               5.452  0.105   7.471
pivot_sample-methods                   5.179  0.091   7.309
remove_redundancy-methods              4.409  0.112   6.068
keep_abundant                          3.959  0.076   5.468
reduce_dimensions-methods              3.659  0.067   5.030
keep_variable-methods                  3.565  0.069   5.045
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’

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### Running command:
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###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL tidybulk
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library’
* installing *source* package ‘tidybulk’ ...
** this is package ‘tidybulk’ version ‘2.0.1’
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
*** copying figures
** 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 (tidybulk)

R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble"
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.

> library(testthat)
> library(tidybulk)
Loading required package: ttservice
========================================
tidybulk version 2.0.1
If you use TIDYBULK in published research, please cite:

Mangiola et al. tidybulk: an R tidy framework for modular 
transcriptomic data analysis. Genome Biology 2021.

This message can be suppressed by:
  suppressPackageStartupMessages(library(tidybulk))
========================================

> 
> test_check("tidybulk")
Found 2 batches
Using null model in ComBat-seq.
Adjusting for 1 covariate(s) or covariate level(s)
Estimating dispersions
Fitting the GLM model
Shrinkage off - using GLM estimates for parameters
Adjusting the data
Found 2 batches
Using null model in ComBat-seq.
Adjusting for 1 covariate(s) or covariate level(s)
Estimating dispersions
Fitting the GLM model
Shrinkage off - using GLM estimates for parameters
Adjusting the data
Found 2 batches
Using null model in ComBat-seq.
Adjusting for 1 covariate(s) or covariate level(s)
Estimating dispersions
Fitting the GLM model
Apply shrinkage - computing posterior estimates for parameters
Using 20 random genes for Monte Carlo integration
Adjusting the data
[1] "MDS result_df colnames: sample, 1, 2"
[1] "MDS result_df colnames: sample, 1, 2"
[1] "Loading MSigDB Gene Sets ... "
[1] "Loaded gene sets for the collection h ..."
[1] "Indexed the collection h ..."
[1] "Created annotation for the collection h ..."
##------ Tue Dec  9 13:37:29 2025 ------##
[1] "Loading MSigDB Gene Sets ... "
[1] "Loaded gene sets for the collection c1 ..."
[1] "Indexed the collection c1 ..."
[1] "Created annotation for the collection c1 ..."
##------ Tue Dec  9 13:37:38 2025 ------##
[1] "Loading MSigDB Gene Sets ... "
[1] "Loaded gene sets for the collection c2 ..."
[1] "Indexed the collection c2 ..."
[1] "Created annotation for the collection c2 ..."
##------ Tue Dec  9 13:37:55 2025 ------##
[1] "Loading MSigDB Gene Sets ... "
[1] "Loaded gene sets for the collection h ..."
[1] "Indexed the collection h ..."
[1] "Created annotation for the collection h ..."
##------ Tue Dec  9 13:38:02 2025 ------##
[1] "Loading MSigDB Gene Sets ... "
[1] "Loaded gene sets for the collection h ..."
[1] "Indexed the collection h ..."
[1] "Created annotation for the collection h ..."
##------ Tue Dec  9 13:38:08 2025 ------##
[1] "Loading MSigDB Gene Sets ... "
[1] "Loaded gene sets for the collection h ..."
[1] "Indexed the collection h ..."
[1] "Created annotation for the collection h ..."
##------ Tue Dec  9 13:38:14 2025 ------##
##------ Tue Dec  9 13:38:14 2025 ------##
##------ Tue Dec  9 13:38:14 2025 ------##
2025-12-09 13:38:35.092 R[82879:107888559] XType: com.apple.fonts is not accessible.
2025-12-09 13:38:35.092 R[82879:107888559] XType: XTFontStaticRegistry is enabled.
##------ Tue Dec  9 13:49:49 2025 ------##
[1] "Loading MSigDB Gene Sets ... "
[1] "Loaded gene sets for the collection h ..."
[1] "Indexed the collection h ..."
[1] "Created annotation for the collection h ..."
##------ Tue Dec  9 13:49:55 2025 ------##
[1] "Loading MSigDB Gene Sets ... "
[1] "Loaded gene sets for the collection h ..."
[1] "Indexed the collection h ..."
[1] "Created annotation for the collection h ..."
##------ Tue Dec  9 13:50:01 2025 ------##
[1] "Loading MSigDB Gene Sets ... "
[1] "Loaded gene sets for the collection h ..."
[1] "Indexed the collection h ..."
[1] "Created annotation for the collection h ..."
##------ Tue Dec  9 13:50:06 2025 ------##
[1] "Loading MSigDB Gene Sets ... "
[1] "Loaded gene sets for the collection h ..."
[1] "Indexed the collection h ..."
[1] "Created annotation for the collection h ..."
##------ Tue Dec  9 13:50:12 2025 ------##
[1] "Loading MSigDB Gene Sets ... "
[1] "Loaded gene sets for the collection h ..."
[1] "Indexed the collection h ..."
[1] "Created annotation for the collection h ..."
##------ Tue Dec  9 13:50:17 2025 ------##
[1] "Loading MSigDB Gene Sets ... "
[1] "Loaded gene sets for the collection h ..."
[1] "Indexed the collection h ..."
[1] "Created annotation for the collection h ..."
##------ Tue Dec  9 13:50:23 2025 ------##
[1] "Loading MSigDB Gene Sets ... "
[1] "Loaded gene sets for the collection h ..."
[1] "Indexed the collection h ..."
[1] "Created annotation for the collection h ..."
##------ Tue Dec  9 13:50:28 2025 ------##