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This page was generated on 2025-10-13 12:03 -0400 (Mon, 13 Oct 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" 4864
lconwaymacOS 12.7.1 Montereyx86_644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4652
kjohnson3macOS 13.7.7 Venturaarm644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4597
taishanLinux (openEuler 24.03 LTS)aarch644.5.0 (2025-04-11) -- "How About a Twenty-Six" 4586
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 117/2346HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
autonomics 1.17.16  (landing page)
Aditya Bhagwat
Snapshot Date: 2025-10-12 13:45 -0400 (Sun, 12 Oct 2025)
git_url: https://git.bioconductor.org/packages/autonomics
git_branch: devel
git_last_commit: ca513f9
git_last_commit_date: 2025-10-03 08:57:56 -0400 (Fri, 03 Oct 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 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: 1.17.16
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_1.17.16.tar.gz
StartedAt: 2025-10-12 21:05:21 -0400 (Sun, 12 Oct 2025)
EndedAt: 2025-10-12 21:28:43 -0400 (Sun, 12 Oct 2025)
EllapsedTime: 1401.7 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_1.17.16.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/autonomics.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 ‘autonomics/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘autonomics’ version ‘1.17.16’
* 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
read_diann_proteingroups 397.564  3.948 109.726
write_xl                 199.937  1.602 216.801
rm_diann_contaminants    102.491  0.342  23.605
awblinmod                 40.894  0.124  39.700
read_rnaseq_counts        38.128  1.273  30.478
ftype                     30.014  0.408   9.059
LINMOD                    27.464  0.562  26.013
default_formula           27.068  0.390  18.410
plot_exprs                23.225  0.129  20.212
plot_exprs_per_coef       19.341  0.029  19.310
plot_contrastogram        15.284  0.068   3.170
read_somascan             14.165  0.134  13.875
analyze                   13.461  0.205  13.521
plot_volcano              12.959  0.073  12.979
read_metabolon            12.703  0.278  12.912
plot_summary              12.675  0.080  12.652
plot_densities            12.414  0.195  10.432
read_olink                12.032  0.031   1.816
fit_survival              10.960  0.227  11.188
explore-transforms        10.084  0.349  10.435
fcluster                   9.654  0.227   9.723
read_fragpipe              7.077  0.421   5.712
plot_subgroup_points       7.285  0.035   5.750
plot_detections            6.990  0.059   6.977
biplot_covariates          6.674  0.026   6.679
plot_xy_density            6.097  0.040   6.138
subtract_baseline          5.652  0.013   4.805
log2transform              4.917  0.157   5.075
* 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 ‘1.17.16’
** 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 4.5.1 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(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 
253.990   8.197 226.155 

Example timings

autonomics.Rcheck/autonomics-Ex.timings

nameusersystemelapsed
AUTONOMICS_DATASETS0.0010.0000.000
COMPOUNDDISCOVERER_PATTERNS000
LINMOD27.464 0.56226.013
LINMODENGINES0.0010.0000.000
MAXQUANT_PATTERNS000
TAXON_TO_ORGNAME0.0010.0000.001
TESTS000
X1.2460.0171.241
abstract_fit1.0690.0091.055
add_adjusted_pvalues0.5550.0090.565
add_assay_means0.3480.0020.350
add_facetvars1.4770.0091.464
add_opentargets_by_uniprot0.3730.0050.379
add_psp0.5050.0130.519
add_smiles0.4490.0080.436
all_non_numeric0.6020.0000.603
analysis0.5030.0130.516
analyze13.461 0.20513.521
annotate_maxquant0.8720.0190.891
annotate_uniprot_rest1.2220.0962.883
assert_is_valid_sumexp0.5410.0280.546
awblinmod40.894 0.12439.700
biplot3.7400.0163.717
biplot_corrections3.4810.0513.501
biplot_covariates6.6740.0266.679
block2limma0.0020.0000.001
block2lm0.0030.0000.002
block2lme0.0020.0000.002
block2lmer0.0030.0000.003
block_has_two_levels0.6630.0040.629
center1.8650.0041.866
code4.6600.0104.648
collapsed_entrezg_to_symbol1.0010.1001.102
contrast_subgroup_cols0.5780.0230.578
contrastdt0.5810.0120.592
count_in0.0010.0000.000
counts0.3470.0020.349
counts2cpm0.2920.0000.293
counts2tpm0.2810.0000.282
cpm0.3370.0000.337
create_design0.6980.0070.682
default_formula27.068 0.39018.410
default_geom0.4740.0100.464
default_sfile0.0010.0010.002
demultiplex0.0130.0010.013
densities0.2050.0000.205
dequantify0.0020.0000.002
dequantify_compounddiscoverer0.0010.0000.001
dot-coxph0.3640.0050.369
dot-merge0.0180.0010.018
dot-read_maxquant_proteingroups0.1110.0010.112
download_data0.0000.0000.001
download_gtf000
download_mcclain210.0000.0000.001
dt2mat0.0020.0000.003
enrichment1.1400.0011.141
entrezg_to_symbol0.1480.0010.149
explore-transforms10.084 0.34910.435
extract_contrast_features4.3600.0384.378
extract_rectangle0.1040.0080.112
factor.vars0.1660.0010.167
factorize0.8040.0090.813
fcluster9.6540.2279.723
fcor1.4730.0671.543
fdata0.5200.0460.566
fdr2p0.9620.0701.008
filter_exprs_replicated_in_some_subgroup1.0130.0130.967
filter_features0.5040.0100.492
filter_medoid0.5430.0030.547
filter_samples0.5540.0070.537
fit_survival10.960 0.22711.188
fits0.3050.0070.312
fix_xlgenes0.0020.0000.002
flevels0.4050.0280.434
fnames0.5010.0290.529
formula2str000
ftype30.014 0.408 9.059
fvalues0.4010.0110.413
fvars0.3690.0030.372
genome_to_orgdb0.0010.0000.001
group_by_level0.0010.0000.001
guess_compounddiscoverer_quantity0.0010.0000.001
guess_fitsep0.4730.0070.480
guess_maxquant_quantity0.0060.0000.005
guess_sep0.4900.0310.491
has_multiple_levels0.0530.0010.055
hdlproteins0.0400.0120.056
impute3.4170.1723.589
invert_subgroups0.6780.0490.727
is_character_matrix0.1360.0040.141
is_collapsed_subset0.0000.0000.001
is_compounddiscoverer_output1.8010.0890.265
is_correlation_matrix0.0000.0010.001
is_diann_report4.7050.0350.274
is_fastadt0.1830.0110.075
is_file0.0010.0000.000
is_fraction0.0010.0000.001
is_fragpipe_tsv1.4850.0120.109
is_imputed0.7600.0700.817
is_maxquant_phosphosites0.7310.0150.087
is_maxquant_proteingroups0.5190.0150.066
is_positive_number0.0020.0000.002
is_scalar_subset0.2880.0050.293
is_sig1.3420.0271.369
is_valid_formula0.0410.0000.041
keep_estimable_features0.7490.0090.712
label2index0.0010.0000.001
list2mat0.0010.0000.001
log2counts0.3360.0000.336
log2cpm0.2820.0010.284
log2diffs0.2950.0020.296
log2proteins0.3000.0020.302
log2sites0.3580.0120.370
log2tpm0.2940.0010.295
log2transform4.9170.1575.075
logical2factor0.0000.0010.001
make_alpha_palette0.4980.0090.484
make_colors0.0090.0010.010
make_volcano_dt0.8150.0080.823
map_fvalues0.3520.0030.355
matrix2sumexp0.9720.0060.955
mclust_breaks0.4860.0330.519
merge_sample_file0.4440.0110.455
merge_sdata0.6170.0220.607
message_df0.0020.0000.002
model_coefs0.7360.0080.713
modelvar4.4340.1584.512
object10.5520.0210.573
order_on_p1.2900.0221.290
overall_parameters0.0290.0010.030
pca3.0830.0903.151
pg_to_canonical0.0040.0010.005
plot_coef_densities1.2420.0341.257
plot_contrast_venn2.1910.0102.130
plot_contrastogram15.284 0.068 3.170
plot_data1.6820.0091.704
plot_densities12.414 0.19510.432
plot_design0.6370.0050.642
plot_detections6.9900.0596.977
plot_exprs23.225 0.12920.212
plot_exprs_per_coef19.341 0.02919.310
plot_fit_summary2.0570.0162.016
plot_heatmap1.7940.0031.797
plot_matrix0.6420.0090.640
plot_subgroup_points7.2850.0355.750
plot_summary12.675 0.08012.652
plot_venn0.0160.0000.016
plot_venn_heatmap0.020.000.02
plot_violins4.6900.0204.688
plot_volcano12.959 0.07312.979
plot_xy_density6.0970.0406.138
preprocess_rnaseq_counts0.3520.0010.353
pull_columns0.0030.0000.002
pvalues_estimable0.0370.0000.038
read_affymetrix000
read_diann_proteingroups397.564 3.948109.726
read_fragpipe7.0770.4215.712
read_maxquant_phosphosites1.4300.0671.499
read_maxquant_proteingroups1.1810.1001.282
read_metabolon12.703 0.27812.912
read_msigdt0.0010.0000.001
read_olink12.032 0.031 1.816
read_rectangles0.1910.0020.196
read_rnaseq_counts38.128 1.27330.478
read_salmon000
read_somascan14.165 0.13413.875
read_uniprotdt0.2830.0070.290
reset_fit4.8210.0154.751
rm_diann_contaminants102.491 0.342 23.605
rm_missing_in_some_samples0.4690.0070.452
rm_unmatched_samples0.6320.0030.635
sbind3.9200.0033.939
scaledlibsizes0.3680.0000.375
scoremat0.8440.0100.832
slevels0.4150.0010.423
snames0.4140.0010.421
split_extract_fixed0.4700.0060.450
split_samples1.1090.0091.097
stepauc0.3850.0010.387
stri_any_regex0.0010.0000.001
stri_detect_fixed_in_collapsed0.3100.0030.313
subgroup_matrix0.4880.0070.466
subtract_baseline5.6520.0134.805
sumexp_to_longdt1.7920.0101.750
sumexp_to_tsv0.4610.0020.463
sumexplist_to_longdt1.5200.0071.543
summarize_fit1.8200.0071.798
survobj0.1330.0010.133
svalues0.4000.0010.405
svars0.3910.0000.392
systematic_nas0.5360.0010.537
tag_features0.9100.0030.913
tag_hdlproteins0.5540.0010.555
taxon2org0.0010.0000.001
tpm0.3140.0000.314
uncollapse0.0260.0000.026
values0.3920.0000.392
varlevels_dont_clash0.020.000.02
venn_detects0.5570.0030.560
weights0.3020.0020.304
write_xl199.937 1.602216.801
zero_to_na0.0010.0000.001