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This page was generated on 2025-09-27 12:04 -0400 (Sat, 27 Sep 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" 4832
lconwaymacOS 12.7.1 Montereyx86_644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4620
kjohnson3macOS 13.7.7 Venturaarm644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4565
taishanLinux (openEuler 24.03 LTS)aarch644.5.0 (2025-04-11) -- "How About a Twenty-Six" 4563
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 116/2334HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
autonomics 1.17.2  (landing page)
Aditya Bhagwat
Snapshot Date: 2025-09-26 13:45 -0400 (Fri, 26 Sep 2025)
git_url: https://git.bioconductor.org/packages/autonomics
git_branch: devel
git_last_commit: b9e7bf3
git_last_commit_date: 2025-09-25 03:15:20 -0400 (Thu, 25 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 autonomics on lconway

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: 1.17.2
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:autonomics.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings autonomics_1.17.2.tar.gz
StartedAt: 2025-09-26 19:30:07 -0400 (Fri, 26 Sep 2025)
EndedAt: 2025-09-26 19:51:21 -0400 (Fri, 26 Sep 2025)
EllapsedTime: 1273.6 seconds
RetCode: 0
Status:   OK  
CheckDir: autonomics.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:autonomics.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings autonomics_1.17.2.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/autonomics.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 ‘autonomics/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘autonomics’ version ‘1.17.2’
* 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 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  117.769  2.386 121.988
awblinmod                  47.065  0.275  47.537
read_rnaseq_counts         36.071  3.421  40.189
LINMOD                     27.031  0.331  27.497
rm_diann_contaminants      26.063  0.578  27.091
plot_exprs                 23.626  0.273  24.322
plot_exprs_per_coef        22.377  0.188  22.703
default_formula            22.066  0.478  22.902
plot_volcano               17.456  0.159  17.753
read_somascan              17.022  0.134  17.337
read_metabolon             15.888  0.276  16.382
analyze                    15.519  0.227  15.831
plot_summary               15.062  0.101  15.222
fit_survival               14.473  0.216  14.808
plot_densities             12.774  0.200  13.046
explore-transforms         12.759  0.110  12.946
fcluster                   11.315  0.082  11.447
ftype                       9.804  0.302  10.175
plot_xy_density             8.091  0.056   8.196
biplot_covariates           8.003  0.081   8.119
plot_detections             7.715  0.040   7.777
read_fragpipe               6.623  0.104   6.874
plot_subgroup_points        6.545  0.073   6.650
subtract_baseline           6.126  0.124   6.305
log2transform               6.131  0.052   6.210
plot_violins                6.020  0.094   6.157
extract_contrast_features   5.938  0.126   6.098
reset_fit                   5.519  0.160   5.794
code                        5.574  0.070   5.673
sbind                       5.194  0.067   5.318
* 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: 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.22-bioc/meat/autonomics.Rcheck/00check.log’
for details.


Installation output

autonomics.Rcheck/00install.out

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


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library’
* installing *source* package ‘autonomics’ ...
** this is package ‘autonomics’ version ‘1.17.2’
** 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 (2025-09-10 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(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 
148.261  16.020 290.186 

Example timings

autonomics.Rcheck/autonomics-Ex.timings

nameusersystemelapsed
AUTONOMICS_DATASETS0.0000.0000.001
COMPOUNDDISCOVERER_PATTERNS000
LINMOD27.031 0.33127.497
LINMODENGINES0.0000.0000.001
MAXQUANT_PATTERNS0.0010.0010.000
TAXON_TO_ORGNAME0.0010.0000.001
TESTS0.0000.0000.001
X1.3630.0731.460
abstract_fit1.1690.0601.247
add_adjusted_pvalues0.6360.0130.654
add_assay_means0.4120.0080.421
add_facetvars1.6980.0601.774
add_opentargets_by_uniprot0.4720.0090.487
add_psp0.5920.0140.611
add_smiles0.5550.0470.605
all_non_numeric0.7140.0040.721
analysis0.4790.0090.491
analyze15.519 0.22715.831
annotate_maxquant1.0550.1001.162
annotate_uniprot_rest0.0890.0142.397
assert_is_valid_sumexp0.7550.0500.811
awblinmod47.065 0.27547.537
biplot4.4180.0784.531
biplot_corrections4.2000.0584.279
biplot_covariates8.0030.0818.119
block2limma0.0020.0000.003
block2lm0.0030.0000.005
block2lme0.0020.0000.002
block2lmer0.0030.0000.004
block_has_two_levels0.7890.0470.844
center2.1720.0232.207
code5.5740.0705.673
collapsed_entrezg_to_symbol1.0420.0781.129
contrast_subgroup_cols0.7520.0540.814
contrastdt0.4300.0030.455
count_in0.0010.0020.002
counts0.3890.0030.396
counts2cpm0.4030.0030.407
counts2tpm0.3370.0020.341
cpm0.3830.0030.386
create_design0.7660.0420.811
default_formula22.066 0.47822.902
default_geom0.6300.0550.695
default_sfile0.0010.0010.003
demultiplex0.0190.0010.021
densities0.2700.0060.278
dequantify0.0020.0000.003
dequantify_compounddiscoverer0.0010.0010.001
dot-coxph0.4870.0540.549
dot-merge0.0270.0010.028
dot-read_maxquant_proteingroups0.1410.0070.148
download_data0.0010.0010.001
download_gtf0.0000.0010.001
download_mcclain21000
dt2mat0.0030.0000.004
enrichment1.3930.0161.418
entrezg_to_symbol0.1830.0060.188
explore-transforms12.759 0.11012.946
extract_contrast_features5.9380.1266.098
extract_rectangle0.1610.0480.214
factor.vars0.1970.0020.199
factorize1.1370.0181.164
fcluster11.315 0.08211.447
fcor1.7230.0331.767
fdata0.5940.0130.610
fdr2p1.0800.0461.133
filter_exprs_replicated_in_some_subgroup1.2010.0491.261
filter_features0.6050.0440.655
filter_medoid0.7100.0070.723
filter_samples0.6360.0440.686
fit_survival14.473 0.21614.808
fits0.3990.0020.403
fix_xlgenes0.0020.0000.002
flevels0.4760.0080.486
fnames0.6800.0100.701
formula2str0.0000.0000.001
ftype 9.804 0.30210.175
fvalues0.4650.0060.473
fvars0.4350.0050.440
genome_to_orgdb0.0010.0010.001
group_by_level0.0020.0010.002
guess_compounddiscoverer_quantity0.0010.0000.001
guess_fitsep0.6090.0070.620
guess_maxquant_quantity0.0060.0020.008
guess_sep0.5700.0480.628
has_multiple_levels0.0700.0020.073
hdlproteins0.0490.0380.089
impute4.0970.0344.148
invert_subgroups0.7330.0080.744
is_character_matrix0.1740.0010.176
is_collapsed_subset0.0010.0000.000
is_correlation_matrix0.0020.0000.001
is_diann_report0.2540.0560.391
is_fastadt0.0600.0020.062
is_file0.0000.0010.001
is_fraction0.0010.0000.001
is_imputed0.9240.0080.938
is_positive_number0.0020.0000.003
is_scalar_subset0.3520.0060.359
is_sig1.6330.0151.657
is_valid_formula0.0430.0010.044
keep_estimable_features0.8680.0450.927
label2index0.0010.0010.001
list2mat0.0010.0000.001
log2counts0.4660.0040.473
log2cpm0.3650.0020.370
log2diffs0.3570.0070.370
log2proteins0.3820.0040.389
log2sites0.4610.0070.471
log2tpm0.3690.0030.376
log2transform6.1310.0526.210
logical2factor0.0020.0000.002
make_alpha_palette0.6270.0450.675
make_colors0.0120.0020.013
make_volcano_dt1.1520.0171.174
map_fvalues0.4830.0070.493
matrix2sumexp1.3290.0601.405
mclust_breaks0.6850.0990.788
merge_sample_file0.5640.0100.575
merge_sdata0.7540.0760.870
message_df0.0030.0000.003
model_coefs0.8690.0610.938
modelvar3.9980.0654.090
object10.5930.0030.598
order_on_p1.5770.0491.633
overall_parameters0.0320.0000.033
pca4.0260.0694.117
pg_to_canonical0.0050.0010.005
plot_coef_densities1.5460.0661.640
plot_contrast_venn2.6320.0572.705
plot_contrastogram3.3960.1203.549
plot_data2.1070.0532.170
plot_densities12.774 0.20013.046
plot_design0.8140.0080.825
plot_detections7.7150.0407.777
plot_exprs23.626 0.27324.322
plot_exprs_per_coef22.377 0.18822.703
plot_fit_summary2.3800.0502.437
plot_heatmap2.2030.0152.227
plot_matrix0.5970.0560.664
plot_subgroup_points6.5450.0736.650
plot_summary15.062 0.10115.222
plot_venn0.0160.0030.020
plot_venn_heatmap0.0300.0030.033
plot_violins6.0200.0946.157
plot_volcano17.456 0.15917.753
plot_xy_density8.0910.0568.196
preprocess_rnaseq_counts0.3990.0040.426
pull_columns0.0030.0000.004
pvalues_estimable0.0470.0050.053
read_affymetrix0.0000.0000.001
read_diann_proteingroups117.769 2.386121.988
read_fragpipe6.6230.1046.874
read_maxquant_phosphosites1.7880.0451.858
read_maxquant_proteingroups1.5630.0241.600
read_metabolon15.888 0.27616.382
read_msigdt0.0020.0000.002
read_olink1.6080.0731.713
read_rectangles0.2240.0290.262
read_rnaseq_counts36.071 3.42140.189
read_salmon000
read_somascan17.022 0.13417.337
read_uniprotdt0.3290.0360.380
reset_fit5.5190.1605.794
rm_diann_contaminants26.063 0.57827.091
rm_missing_in_some_samples0.6850.0800.800
rm_unmatched_samples0.8140.0400.870
sbind5.1940.0675.318
scaledlibsizes0.4540.0080.468
scoremat1.0330.0591.110
slevels0.5460.0100.562
snames0.4790.0100.494
split_extract_fixed0.6150.0510.673
split_samples1.4140.0581.486
stepauc0.4230.0040.430
stri_any_regex0.0000.0010.001
stri_detect_fixed_in_collapsed0.3950.0120.410
subgroup_matrix0.6430.0480.696
subtract_baseline6.1260.1246.305
sumexp_to_longdt2.3980.1472.597
sumexp_to_tsv0.5800.0100.597
sumexplist_to_longdt1.8460.0281.906
summarize_fit1.9680.0592.046
survobj0.2450.0020.249
svalues0.4910.0090.511
svars0.4710.0080.503
systematic_nas0.7300.0120.771
tag_features1.1850.0401.272
tag_hdlproteins0.6320.0440.684
taxon2org0.0010.0000.001
tpm0.5180.0100.534
uncollapse0.0350.0010.038
values0.5250.0130.549
varlevels_dont_clash0.0270.0010.028
venn_detects0.7770.0240.815
weights0.4370.0040.444
write_xl0.8170.0630.898
zero_to_na0.0020.0010.003