Back to Multiple platform build/check report for BioC 3.22:   simplified   long
ABCDEFGHIJKLMNOPQRS[T]UVWXYZ

This page was generated on 2025-09-20 12:05 -0400 (Sat, 20 Sep 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" 4814
lconwaymacOS 12.7.1 Montereyx86_644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4603
kjohnson3macOS 13.7.7 Venturaarm644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4547
taishanLinux (openEuler 24.03 LTS)aarch644.5.0 (2025-04-11) -- "How About a Twenty-Six" 4553
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

Package 2180/2333HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
tidybulk 1.99.4  (landing page)
Stefano Mangiola
Snapshot Date: 2025-09-19 13:45 -0400 (Fri, 19 Sep 2025)
git_url: https://git.bioconductor.org/packages/tidybulk
git_branch: devel
git_last_commit: 6eafc1e
git_last_commit_date: 2025-09-16 04:06:04 -0400 (Tue, 16 Sep 2025)
nebbiolo2Linux (Ubuntu 24.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson3macOS 13.7.7 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published
taishanLinux (openEuler 24.03 LTS) / aarch64  OK    OK    OK  


CHECK results for tidybulk on lconway

To the developers/maintainers of the tidybulk package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/tidybulk.git to reflect on this report. See Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results


Summary

Package: tidybulk
Version: 1.99.4
Command: /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_1.99.4.tar.gz
StartedAt: 2025-09-20 00:32:14 -0400 (Sat, 20 Sep 2025)
EndedAt: 2025-09-20 00:48:53 -0400 (Sat, 20 Sep 2025)
EllapsedTime: 998.9 seconds
RetCode: 0
Status:   OK  
CheckDir: tidybulk.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /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_1.99.4.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/tidybulk.Rcheck’
* using R version 4.5.1 Patched (2025-09-10 r88807)
* 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 ‘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 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  90.809  0.974  92.336
test_differential_expression-methods 89.373  0.904  90.828
adjust_abundance-methods             13.110  0.488  13.698
test_gene_enrichment-methods          8.392  0.626   9.117
aggregate_duplicates-methods          8.336  0.125   8.504
keep_abundant                         5.139  0.105   5.272
* 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: 3 NOTEs
See
  ‘/Users/biocbuild/bbs-3.22-bioc/meat/tidybulk.Rcheck/00check.log’
for details.


Installation output

tidybulk.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL tidybulk
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/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)

Tests output

tidybulk.Rcheck/tests/testthat.Rout


R version 4.5.1 Patched (2025-09-10 r88807) -- "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.

> 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 ..."
##------ Sat Sep 20 00:42:49 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 ..."
##------ Sat Sep 20 00:42:51 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 ..."
##------ Sat Sep 20 00:42:54 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 ..."
##------ Sat Sep 20 00:42:56 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 ..."
##------ Sat Sep 20 00:42:58 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 ..."
##------ Sat Sep 20 00:43:00 2025 ------##
##------ Sat Sep 20 00:43:00 2025 ------##
##------ Sat Sep 20 00:43:00 2025 ------##
2025-09-20 00:43:08.200 R[54600:335710374] XType: com.apple.fonts is not accessible.
2025-09-20 00:43:08.200 R[54600:335710374] XType: XTFontStaticRegistry is enabled.
##------ Sat Sep 20 00:46:41 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 ..."
##------ Sat Sep 20 00:46:43 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 ..."
##------ Sat Sep 20 00:46:45 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 ..."
##------ Sat Sep 20 00:46:47 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 ..."
##------ Sat Sep 20 00:46:49 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 ..."
##------ Sat Sep 20 00:46:51 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 ..."
##------ Sat Sep 20 00:46:53 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 ..."
##------ Sat Sep 20 00:46:55 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 
457.140  27.090 509.111 

Example timings

tidybulk.Rcheck/tidybulk-Ex.timings

nameusersystemelapsed
adjust_abundance-methods13.110 0.48813.698
aggregate_duplicates-methods8.3360.1258.504
as_SummarizedExperiment-methods0.1460.0030.150
as_matrix0.0320.0010.034
cluster_elements-methods1.4750.0211.506
deconvolve_cellularity-methods2.1700.0592.248
describe_transcript-methods3.6370.1023.774
fill_missing_abundance-methods1.5830.0281.622
get_X_cibersort0.0060.0010.008
get_bibliography-methods1.4220.0201.451
identify_abundant-methods3.8900.0713.975
impute_missing_abundance-methods4.1840.0604.272
keep_abundant5.1390.1055.272
keep_variable-methods2.1080.0202.139
log10_reverse_trans000
logit_trans0.2580.0050.265
pivot_sample-methods3.2400.0553.317
pivot_transcript-methods3.4750.0733.575
quantile_normalise_abundance-methods3.6280.0773.731
reduce_dimensions-methods2.0150.0252.051
remove_redundancy-methods2.5200.0622.603
resolve_complete_confounders_of_non_interest000
rotate_dimensions-methods1.9240.0341.977
scale_abundance-methods2.8650.0682.963
scale_x_log10_reverse0.2060.0030.211
scale_y_log10_reverse0.2040.0050.210
test_differential_abundance-methods90.809 0.97492.336
test_differential_expression-methods89.373 0.90490.828
test_gene_enrichment-methods8.3920.6269.117
test_gene_overrepresentation-methods1.5140.0141.540
test_gene_rank-methods1.5070.0181.540