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This page was generated on 2026-02-28 11:57 -0500 (Sat, 28 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: 2026-02-27 13:45 -0500 (Fri, 27 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: 2026-02-27 21:16:37 -0500 (Fri, 27 Feb 2026)
EndedAt: 2026-02-27 21:36:39 -0500 (Fri, 27 Feb 2026)
EllapsedTime: 1202.2 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                 165.457  1.324 166.810
read_diann_proteingroups 109.963  0.796 105.909
awblinmod                 42.494  0.226  41.096
read_rnaseq_counts        30.171  1.771  31.736
LINMOD                    24.097  0.429  23.881
rm_diann_contaminants     22.924  0.148  21.736
plot_exprs                20.428  0.209  20.542
default_formula           20.110  0.084  19.737
plot_exprs_per_coef       18.672  0.068  18.631
read_somascan             15.163  0.310  15.386
analyze                   12.995  0.049  12.962
plot_summary              12.758  0.030  12.673
read_metabolon            12.606  0.007  12.462
plot_volcano              12.525  0.041  12.511
fit_survival              10.574  0.007  10.597
explore-transforms        10.416  0.127  10.545
plot_densities             9.807  0.034   9.722
fcluster                   9.620  0.018   9.578
ftype                      7.946  0.049   7.697
read_fragpipe              7.727  0.064   7.507
plot_detections            7.371  0.005   7.328
biplot_covariates          6.452  0.010   6.432
plot_xy_density            6.280  0.057   6.337
plot_subgroup_points       5.540  0.005   5.463
* 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 
142.319   3.786 143.904 

Example timings

autonomics.Rcheck/autonomics-Ex.timings

nameusersystemelapsed
AUTONOMICS_DATASETS000
COMPOUNDDISCOVERER_PATTERNS000
LINMOD24.097 0.42923.881
LINMODENGINES0.0010.0000.000
MAXQUANT_PATTERNS000
TAXON_TO_ORGNAME0.0010.0000.000
TESTS000
X1.1450.0041.127
abstract_fit0.9680.0100.954
add_adjusted_pvalues0.4960.0110.509
add_assay_means0.3620.0030.366
add_facetvars1.2950.0081.281
add_opentargets_by_uniprot0.4000.0000.401
add_psp0.4970.0100.507
add_smiles0.4340.0030.415
all_non_numeric0.5510.0010.550
analysis0.3960.0020.397
analyze12.995 0.04912.962
annotate_maxquant0.9630.0401.003
annotate_uniprot_rest0.3840.0272.269
assert_is_valid_sumexp0.5410.0130.514
awblinmod42.494 0.22641.096
biplot3.6760.0103.664
biplot_corrections3.2740.0043.255
biplot_covariates6.4520.0106.432
block2limma0.0020.0000.001
block2lm0.0020.0000.002
block2lme0.0020.0000.002
block2lmer0.0030.0000.003
block_has_two_levels0.6260.0070.593
center1.6930.0061.696
code4.6910.0064.674
collapsed_entrezg_to_symbol0.8300.0380.868
contrast_subgroup_cols0.6560.0070.637
contrastdt0.5680.0010.569
count_in0.0000.0000.001
counts0.3290.0000.330
counts2cpm0.3550.0000.355
counts2tpm0.2850.0000.285
cpm0.3350.0110.346
create_design0.6600.0080.645
default_formula20.110 0.08419.737
default_geom0.5210.0090.506
default_sfile0.0010.0000.002
demultiplex0.0140.0000.013
densities0.2190.0020.220
dequantify0.0030.0000.003
dequantify_compounddiscoverer0.0010.0000.002
dot-coxph0.4050.0080.415
dot-merge0.0180.0000.017
dot-read_maxquant_proteingroups0.1350.0010.137
download_data0.0010.0000.000
download_gtf000
download_mcclain210.0010.0000.000
dt2mat0.0030.0000.003
enrichment2.1490.0352.184
entrezg_to_symbol0.1250.0000.125
explore-transforms10.416 0.12710.545
extract_contrast_features4.3500.0064.333
extract_rectangle0.1060.0080.114
factor.vars0.1750.0000.174
factorize0.7540.0030.757
fcluster9.6200.0189.578
fcor1.3880.0101.398
fdata0.5550.0040.559
fdr2p0.8640.0070.848
filter_exprs_replicated_in_some_subgroup0.9580.0090.903
filter_features0.5000.0070.482
filter_medoid0.5590.0020.562
filter_samples0.4880.0080.473
fit_survival10.574 0.00710.597
fits0.3830.0000.385
fix_xlgenes0.0020.0000.002
flevels0.4130.0020.416
fnames0.4950.0000.497
formula2str000
ftype7.9460.0497.697
fvalues0.460.000.46
fvars0.4030.0030.406
genome_to_orgdb0.0010.0000.000
group_by_level0.0010.0000.001
guess_compounddiscoverer_quantity0.0010.0000.001
guess_fitsep0.4470.0010.449
guess_maxquant_quantity0.0060.0000.005
guess_sep0.5130.0060.495
has_multiple_levels0.0550.0000.056
hdlproteins0.0400.0020.045
impute3.3490.0053.354
invert_subgroups0.6780.0000.678
is_character_matrix0.1350.0000.134
is_collapsed_subset000
is_compounddiscoverer_output0.0980.0340.190
is_correlation_matrix0.0010.0000.001
is_diann_report0.1890.0050.126
is_fastadt0.0840.0000.073
is_file0.0000.0010.001
is_fraction0.0010.0000.001
is_fragpipe_tsv0.1500.0030.096
is_imputed0.7220.0010.715
is_maxquant_phosphosites0.1010.0030.076
is_maxquant_proteingroups0.0960.0040.070
is_positive_number0.0020.0000.001
is_scalar_subset0.3720.0020.375
is_sig1.3680.0051.374
is_valid_formula0.0420.0000.042
keep_estimable_features0.7500.0050.706
label2index000
list2mat0.0010.0000.000
log2counts0.3430.0000.343
log2cpm0.2880.0000.287
log2diffs0.3100.0010.311
log2proteins0.3260.0020.327
log2sites0.3250.0010.326
log2tpm0.4160.0000.417
log2transform4.8770.0074.885
logical2factor0.0010.0000.002
make_alpha_palette0.5400.0090.524
make_colors0.010.000.01
make_volcano_dt0.7920.0000.792
map_fvalues0.4280.0000.428
matrix2sumexp0.9910.0040.966
mclust_breaks0.5030.0080.511
merge_sample_file0.5140.0010.515
merge_sdata0.5940.0050.561
message_df0.0020.0000.002
model_coefs0.7270.0090.696
modelvar3.3360.0043.243
object10.5120.0000.512
order_on_p1.2930.0041.276
overall_parameters0.0240.0000.023
pca3.0750.0123.051
pg_to_canonical0.0040.0000.005
plot_coef_densities1.3260.0041.291
plot_contrast_venn2.4340.0062.285
plot_contrastogram2.8300.0212.759
plot_data1.7550.0281.753
plot_densities9.8070.0349.722
plot_design0.7930.0000.794
plot_detections7.3710.0057.328
plot_exprs20.428 0.20920.542
plot_exprs_per_coef18.672 0.06818.631
plot_fit_summary2.1820.0152.084
plot_heatmap1.8700.0011.870
plot_matrix0.5240.0070.490
plot_subgroup_points5.5400.0055.463
plot_summary12.758 0.03012.673
plot_venn0.0150.0010.017
plot_venn_heatmap0.0200.0010.021
plot_violins4.5520.0274.556
plot_volcano12.525 0.04112.511
plot_xy_density6.2800.0576.337
preprocess_rnaseq_counts0.3380.0000.339
pull_columns0.0020.0000.002
pvalues_estimable0.0380.0030.041
read_affymetrix0.0000.0000.001
read_diann_proteingroups109.963 0.796105.909
read_fragpipe7.7270.0647.507
read_maxquant_phosphosites1.5350.0031.538
read_maxquant_proteingroups1.2360.0061.242
read_metabolon12.606 0.00712.462
read_msigdt0.0010.0000.000
read_olink1.4290.0091.355
read_rectangles0.1800.0070.187
read_rnaseq_counts30.171 1.77131.736
read_salmon000
read_somascan15.163 0.31015.386
read_uniprotdt0.3380.0060.345
reset_fit4.6470.1154.642
rm_diann_contaminants22.924 0.14821.736
rm_missing_in_some_samples0.5880.0060.561
rm_unmatched_samples0.5990.0010.599
sbind4.2180.0174.236
scaledlibsizes0.3790.0090.389
scoremat0.8530.0070.835
slevels0.480.000.48
snames0.4280.0040.432
split_extract_fixed0.5090.0070.492
split_samples1.3820.0051.362
stepauc0.3350.0150.350
stri_any_regex0.0010.0000.001
stri_detect_fixed_in_collapsed0.4140.0060.420
subgroup_matrix0.6240.0130.600
subtract_baseline4.9150.0704.929
sumexp_to_longdt1.9160.0191.876
sumexp_to_tsv0.4830.0030.485
sumexplist_to_longdt1.6130.0521.665
summarize_fit1.8680.0161.757
survobj0.1390.0000.139
svalues0.4640.0040.468
svars0.4380.0010.439
systematic_nas0.5490.0010.550
tag_features1.0830.0551.139
tag_hdlproteins0.5410.0120.553
taxon2org0.0010.0000.001
tpm0.4420.0180.460
uncollapse0.0260.0000.027
values0.4540.0020.456
varlevels_dont_clash0.0290.0010.029
venn_detects0.5430.0000.543
weights0.3880.0000.387
write_xl165.457 1.324166.810
zero_to_na0.0010.0000.002