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###
### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:tidybulk.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings tidybulk_1.99.4.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/tidybulk.Rcheck’
* using R version 4.5.1 Patched (2025-08-23 r88802)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
    GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.3 LTS
* using session charset: UTF-8
* checking for file ‘tidybulk/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘tidybulk’ version ‘1.99.4’
* 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 loading without being on the library search path ... 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  86.117  0.668  86.790
test_differential_expression-methods 82.578  0.614  83.192
adjust_abundance-methods             12.120  0.574  12.695
aggregate_duplicates-methods          7.409  0.295   7.705
test_gene_enrichment-methods          5.784  0.124   5.913
* 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 re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.22-bioc/meat/tidybulk.Rcheck/00check.log’
for details.

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### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD INSTALL tidybulk
###
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* installing to library ‘/home/biocbuild/bbs-3.22-bioc/R/site-library’
* installing *source* package ‘tidybulk’ ...
** this is package ‘tidybulk’ version ‘1.99.4’
** 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 4.5.1 Patched (2025-08-23 r88802) -- "Great Square Root"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu

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 1.99.4
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 ..."
##------ Wed Sep 17 05:04:48 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 ..."
##------ Wed Sep 17 05:04:52 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 ..."
##------ Wed Sep 17 05:04:54 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 ..."
##------ Wed Sep 17 05:04:58 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 ..."
##------ Wed Sep 17 05:04:59 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 ..."
##------ Wed Sep 17 05:05:01 2025 ------##
##------ Wed Sep 17 05:05:01 2025 ------##
##------ Wed Sep 17 05:05:01 2025 ------##
##------ Wed Sep 17 05:09:17 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 ..."
##------ Wed Sep 17 05:09:19 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 ..."
##------ Wed Sep 17 05:09:21 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 ..."
##------ Wed Sep 17 05:09:23 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 ..."
##------ Wed Sep 17 05:09:25 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 ..."
##------ Wed Sep 17 05:09:27 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 ..."
##------ Wed Sep 17 05:09:29 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 ..."
##------ Wed Sep 17 05:09:30 2025 ------##
 @Article{tidybulk,
  title = {tidybulk: an R tidy framework for modular transcriptomic data analysis},
  author = {Stefano Mangiola and Ramyar Molania and Ruining Dong and Maria A. Doyle & Anthony T. Papenfuss},
  journal = {Genome Biology},
  year = {2021},
  volume = {22},
  number = {42},
  url = {https://genomebiology.biomedcentral.com/articles/10.1186/s13059-020-02233-7},
  }
@article{wickham2019welcome,
  title={Welcome to the Tidyverse},
  author={Wickham, Hadley and Averick, Mara and Bryan, Jennifer and Chang, Winston and McGowan, Lucy D'Agostino and Francois, Romain and Grolemund, Garrett and Hayes, Alex and Henry, Lionel and Hester, Jim and others},
  journal={Journal of Open Source Software},
  volume={4},
  number={43},
  pages={1686},
  year={2019}
	}
[ FAIL 0 | WARN 83 | SKIP 45 | PASS 209 ]

══ Skipped tests (45) ══════════════════════════════════════════════════════════
• DBSCAN clustering not supported (1): 'test-clustering.R:33:3'
• DESeq2 has parameter compatibility issues (1):
  'test-differential-analysis.R:40:3'
• EGSEA test failed: ERROR: One of the base methods failed on this dataset
  (camera). (1): 'test-gene-enrichment.R:208:5'
• EGSEA test failed: ERROR: One of the base methods failed on this dataset
  (roast). (11): 'test-gene-enrichment.R:71:5', 'test-gene-enrichment.R:123:5',
  'test-gene-enrichment.R:167:5', 'test-gene-enrichment.R:249:5',
  'test-gene-enrichment.R:323:5', 'test-gene-enrichment.R:364:5',
  'test-gene-enrichment.R:405:5', 'test-gene-enrichment.R:447:5',
  'test-gene-enrichment.R:488:5', 'test-gene-enrichment.R:529:5',
  'test-gene-enrichment.R:570:5'
• EPIC requires additional Bioconductor packages (1):
  'test-cellularity-analysis.R:54:3'
• GLMMSeq random effects requires more samples than available in airway dataset
  (2): 'test-bulk_methods_SummarizedExperiment.R:398:3',
  'test-bulk_methods_SummarizedExperiment.R:429:3'
• SNN clustering has Matrix package compatibility issues (1):
  'test-clustering.R:23:3'
• UMAP requires more samples than available in airway dataset (1):
  'test-bulk_methods_SummarizedExperiment.R:579:3'
• UMAP requires more samples than available in test data (1):
  'test-dimensionality-reduction.R:33:3'
• aggregate_duplicates requires non-NA transcript values (1):
  'test-data-transformation.R:155:3'
• as_SummarizedExperiment not applicable for SummarizedExperiment input (1):
  'test-data-transformation.R:161:3'
• as_matrix not implemented for SummarizedExperiment (1):
  'test-data-transformation.R:149:3'
• bibliography function not available (1): 'test-utility-functions.R:89:3'
• cibersort function not available (1): 'test-cellularity-analysis.R:66:3'
• deconvolve_cellularity requires specific gene signatures not compatible with
  airway dataset (1): 'test-bulk_methods_SummarizedExperiment.R:231:3'
• describe_transcript has parameter compatibility issues (1):
  'test-utility-functions.R:19:3'
• differential abundance logFC expectations need to be recalibrated for airway
  dataset (2): 'test-bulk_methods_SummarizedExperiment.R:246:3',
  'test-bulk_methods_SummarizedExperiment.R:301:3'
• distance method not supported for remove_redundancy (1):
  'test-dimensionality-reduction.R:57:3'
• empty test (1): 'test-tximeta_GRnges_IRanges.R:7:1'
• fill_missing_abundance not implemented for SummarizedExperiment (1):
  'test-abundance-normalization.R:67:3'
• filterByExpr function is not exported (2): 'test-filtering-selection.R:49:3',
  'test-filtering-selection.R:54:3'
• glmmSeq function not available (1): 'test-differential-analysis.R:115:3'
• hierarchical clustering not supported (1): 'test-clustering.R:28:3'
• resolve_complete_confounders_of_non_interest has formula compatibility issues
  (1): 'test-utility-functions.R:32:3'
• rotate_dimensions has column name compatibility issues (1):
  'test-dimensionality-reduction.R:39:3'
• tSNE requires more samples than available in airway dataset (1):
  'test-bulk_methods_SummarizedExperiment.R:566:3'
• tSNE requires more samples than available in test data (1):
  'test-dimensionality-reduction.R:28:3'
• test_gene_overrepresentation has filter method compatibility issues (1):
  'test-gene-enrichment.R:580:3'
• tidySummarizedExperiment has coercion compatibility issues (1):
  'test-validation-utilities.R:47:3'
• validation functions not available (3): 'test-validation-utilities.R:13:3',
  'test-validation-utilities.R:18:3', 'test-validation-utilities.R:23:3'

[ FAIL 0 | WARN 83 | SKIP 45 | PASS 209 ]
> 
> proc.time()
   user  system elapsed 
471.116  18.099 499.209