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This page was generated on 2026-02-24 11:57 -0500 (Tue, 24 Feb 2026).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.2 (2025-10-31) -- "[Not] Part in a Rumble" 4891
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Package 119/2361HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
autonomics 1.18.0  (landing page)
Aditya Bhagwat
Snapshot Date: 2026-02-23 13:45 -0500 (Mon, 23 Feb 2026)
git_url: https://git.bioconductor.org/packages/autonomics
git_branch: RELEASE_3_22
git_last_commit: c22fce2
git_last_commit_date: 2025-10-29 11:06:51 -0500 (Wed, 29 Oct 2025)
nebbiolo2Linux (Ubuntu 24.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
See other builds for autonomics in R Universe.


CHECK results for autonomics on nebbiolo2

To the developers/maintainers of the autonomics package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/autonomics.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: autonomics
Version: 1.18.0
Command: /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:autonomics.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings autonomics_1.18.0.tar.gz
StartedAt: 2026-02-23 21:08:29 -0500 (Mon, 23 Feb 2026)
EndedAt: 2026-02-23 21:28:16 -0500 (Mon, 23 Feb 2026)
EllapsedTime: 1187.3 seconds
RetCode: 0
Status:   OK  
CheckDir: autonomics.Rcheck
Warnings: 0

Command output

##############################################################################
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### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:autonomics.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings autonomics_1.18.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/autonomics.Rcheck’
* using R version 4.5.2 (2025-10-31)
* 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 ‘autonomics/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘autonomics’ version ‘1.18.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... INFO
Imports includes 32 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 ... NOTE
Found the following hidden files and directories:
  .BBSoptions
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘autonomics’ 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 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 'reexports.Rd':
  ‘[magrittr:compound]{%<>%}’ ‘[magrittr:pipe]{%>%}’
  ‘[magrittr:aliases]{extract}’

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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                            user system elapsed
write_xl                 157.293  1.168 158.427
read_diann_proteingroups 106.080  0.730 102.300
awblinmod                 43.403  1.005  42.770
read_rnaseq_counts        29.538  1.130  30.526
LINMOD                    24.951  0.537  24.946
rm_diann_contaminants     22.162  0.124  21.076
default_formula           20.025  0.176  19.755
plot_exprs_per_coef       19.289  0.234  19.397
plot_exprs                19.044  0.048  18.932
read_somascan             14.065  0.075  14.089
analyze                   13.008  0.142  13.002
plot_volcano              12.427  0.029  12.344
read_metabolon            12.217  0.045  12.153
plot_summary              12.124  0.011  11.960
plot_densities            10.474  0.119  10.523
explore-transforms        10.330  0.129  10.460
fit_survival              10.239  0.102  10.359
fcluster                   8.646  0.037   8.623
ftype                      7.854  0.037   7.498
plot_detections            6.987  0.005   6.936
biplot_covariates          6.575  0.067   6.605
read_fragpipe              6.531  0.009   6.233
plot_xy_density            5.711  0.020   5.732
plot_subgroup_points       5.234  0.007   5.201
* 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: 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.22-bioc/meat/autonomics.Rcheck/00check.log’
for details.


Installation output

autonomics.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD INSTALL autonomics
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.22-bioc/R/site-library’
* installing *source* package ‘autonomics’ ...
** this is package ‘autonomics’ version ‘1.18.0’
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
Note: wrong number of arguments to 'seq_along' 
Note: wrong number of arguments to 'sqrt' 
** 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 (autonomics)

Tests output

autonomics.Rcheck/tests/testthat.Rout


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-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(autonomics)

Attaching package: 'autonomics'

The following objects are masked from 'package:stats':

    biplot, loadings

The following object is masked from 'package:base':

    beta

> 
> test_check("autonomics")
[ FAIL 0 | WARN 3 | SKIP 0 | PASS 158 ]

[ FAIL 0 | WARN 3 | SKIP 0 | PASS 158 ]
> 
> proc.time()
   user  system elapsed 
140.251   4.219 142.154 

Example timings

autonomics.Rcheck/autonomics-Ex.timings

nameusersystemelapsed
AUTONOMICS_DATASETS0.0000.0000.001
COMPOUNDDISCOVERER_PATTERNS0.0000.0000.001
LINMOD24.951 0.53724.946
LINMODENGINES000
MAXQUANT_PATTERNS000
TAXON_TO_ORGNAME000
TESTS000
X1.1550.0121.145
abstract_fit0.9650.0090.952
add_adjusted_pvalues0.4990.0080.509
add_assay_means0.3580.0160.375
add_facetvars1.3310.0401.350
add_opentargets_by_uniprot0.3950.0050.401
add_psp0.5180.0060.526
add_smiles0.4650.0090.439
all_non_numeric0.5610.0000.561
analysis0.3980.0020.401
analyze13.008 0.14213.002
annotate_maxquant0.9990.0271.027
annotate_uniprot_rest0.2290.0211.638
assert_is_valid_sumexp0.5270.0090.515
awblinmod43.403 1.00542.770
biplot3.6110.0243.613
biplot_corrections3.4690.0793.527
biplot_covariates6.5750.0676.605
block2limma0.0010.0000.002
block2lm0.0020.0000.003
block2lme0.0020.0000.002
block2lmer0.0030.0000.003
block_has_two_levels0.6500.0110.603
center1.7070.0141.719
code4.7560.0714.788
collapsed_entrezg_to_symbol0.8180.0590.878
contrast_subgroup_cols0.6090.0270.613
contrastdt0.5640.0020.566
count_in0.0010.0010.001
counts0.3020.0000.303
counts2cpm0.3290.0000.329
counts2tpm0.2810.0010.282
cpm0.3250.0000.325
create_design0.6620.0090.647
default_formula20.025 0.17619.755
default_geom0.5260.0090.512
default_sfile0.0010.0000.001
demultiplex0.0130.0000.013
densities0.2190.0020.221
dequantify0.0020.0000.002
dequantify_compounddiscoverer0.0010.0000.001
dot-coxph0.3970.0110.409
dot-merge0.0170.0000.017
dot-read_maxquant_proteingroups0.1290.0030.132
download_data000
download_gtf0.0010.0000.000
download_mcclain21000
dt2mat0.0030.0000.002
enrichment2.1540.1362.295
entrezg_to_symbol0.1290.0000.129
explore-transforms10.330 0.12910.460
extract_contrast_features4.2580.0254.260
extract_rectangle0.0990.0070.106
factor.vars0.1650.0010.166
factorize0.7350.0000.735
fcluster8.6460.0378.623
fcor1.4030.0171.420
fdata0.5580.0170.575
fdr2p0.8860.0450.906
filter_exprs_replicated_in_some_subgroup1.0100.0060.953
filter_features0.4950.0110.482
filter_medoid0.6200.0010.621
filter_samples0.4730.0080.458
fit_survival10.239 0.10210.359
fits0.2920.0000.293
fix_xlgenes0.0020.0000.002
flevels0.3890.0020.391
fnames0.4370.0030.440
formula2str0.0010.0000.000
ftype7.8540.0377.498
fvalues0.4070.0010.408
fvars0.4100.0010.412
genome_to_orgdb0.0010.0000.001
group_by_level0.0000.0000.001
guess_compounddiscoverer_quantity0.0010.0000.001
guess_fitsep0.4800.0020.482
guess_maxquant_quantity0.0040.0010.005
guess_sep0.4530.0200.450
has_multiple_levels0.0500.0010.051
hdlproteins0.0390.0030.045
impute3.3970.0223.420
invert_subgroups0.640.000.64
is_character_matrix0.1300.0000.131
is_collapsed_subset000
is_compounddiscoverer_output0.1030.0230.189
is_correlation_matrix0.0010.0000.001
is_diann_report0.1750.0060.121
is_fastadt0.0770.0010.067
is_file000
is_fraction0.0010.0000.002
is_fragpipe_tsv0.1470.0050.096
is_imputed0.6980.0000.688
is_maxquant_phosphosites0.0970.0050.074
is_maxquant_proteingroups0.0960.0020.069
is_positive_number0.0020.0000.001
is_scalar_subset0.3740.0030.377
is_sig1.3650.0001.366
is_valid_formula0.0410.0000.041
keep_estimable_features0.7440.0170.703
label2index0.0010.0000.001
list2mat0.0010.0000.000
log2counts0.2870.0000.287
log2cpm0.3420.0010.344
log2diffs0.3130.0000.312
log2proteins0.3190.0020.321
log2sites0.3090.0010.311
log2tpm0.3390.0000.339
log2transform4.7280.0154.743
logical2factor0.0010.0000.001
make_alpha_palette0.4750.0070.460
make_colors0.0080.0010.009
make_volcano_dt0.8320.0500.883
map_fvalues0.3670.0020.368
matrix2sumexp0.9510.0110.940
mclust_breaks0.4830.0120.495
merge_sample_file0.5520.0000.552
merge_sdata0.5080.0090.495
message_df0.0030.0000.002
model_coefs0.7490.0070.735
modelvar3.2290.0033.169
object10.4970.0190.516
order_on_p1.3360.0491.361
overall_parameters0.0250.0000.026
pca3.2040.0093.182
pg_to_canonical0.0050.0000.005
plot_coef_densities1.2970.0071.281
plot_contrast_venn2.3130.0382.271
plot_contrastogram2.8220.0242.758
plot_data1.5450.0121.535
plot_densities10.474 0.11910.523
plot_design0.7360.0020.739
plot_detections6.9870.0056.936
plot_exprs19.044 0.04818.932
plot_exprs_per_coef19.289 0.23419.397
plot_fit_summary2.0860.0112.044
plot_heatmap1.7920.0401.832
plot_matrix0.4920.0110.462
plot_subgroup_points5.2340.0075.201
plot_summary12.124 0.01111.960
plot_venn0.0160.0000.016
plot_venn_heatmap0.0190.0000.019
plot_violins4.3800.0284.369
plot_volcano12.427 0.02912.344
plot_xy_density5.7110.0205.732
preprocess_rnaseq_counts0.3080.0030.311
pull_columns0.0030.0000.002
pvalues_estimable0.0350.0010.036
read_affymetrix000
read_diann_proteingroups106.08 0.73102.30
read_fragpipe6.5310.0096.233
read_maxquant_phosphosites1.5090.0041.513
read_maxquant_proteingroups1.2360.0331.269
read_metabolon12.217 0.04512.153
read_msigdt0.0010.0000.001
read_olink1.3060.0221.264
read_rectangles0.1650.0030.168
read_rnaseq_counts29.538 1.13030.526
read_salmon000
read_somascan14.065 0.07514.089
read_uniprotdt0.3460.0020.348
reset_fit4.2240.0104.151
rm_diann_contaminants22.162 0.12421.076
rm_missing_in_some_samples0.5050.0070.484
rm_unmatched_samples0.6690.0000.668
sbind4.1640.0684.233
scaledlibsizes0.3050.0030.309
scoremat0.7970.0140.789
slevels0.4310.0020.432
snames0.4890.0000.489
split_extract_fixed0.4930.0050.476
split_samples1.1490.0081.122
stepauc0.3010.0010.303
stri_any_regex000
stri_detect_fixed_in_collapsed0.3530.0010.354
subgroup_matrix0.5410.0050.525
subtract_baseline4.7290.0514.677
sumexp_to_longdt1.9100.0421.837
sumexp_to_tsv0.4620.0030.466
sumexplist_to_longdt1.4710.0031.475
summarize_fit1.6900.0071.581
survobj0.130.000.13
svalues0.3870.0030.390
svars0.3960.0020.398
systematic_nas0.5580.0030.561
tag_features0.9040.0130.917
tag_hdlproteins0.6160.0040.620
taxon2org0.0000.0010.001
tpm0.3050.0000.305
uncollapse0.0210.0000.022
values0.4140.0030.416
varlevels_dont_clash0.0190.0000.019
venn_detects0.5800.0520.632
weights0.3040.0000.304
write_xl157.293 1.168158.427
zero_to_na0.0010.0000.001