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This page was generated on 2025-09-25 12:03 -0400 (Thu, 25 Sep 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" 4831
lconwaymacOS 12.7.1 Montereyx86_644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4618
kjohnson3macOS 13.7.7 Venturaarm644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4562
taishanLinux (openEuler 24.03 LTS)aarch644.5.0 (2025-04-11) -- "How About a Twenty-Six" 4560
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 1.17.1  (landing page)
Aditya Bhagwat
Snapshot Date: 2025-09-24 13:45 -0400 (Wed, 24 Sep 2025)
git_url: https://git.bioconductor.org/packages/autonomics
git_branch: devel
git_last_commit: f77ea54
git_last_commit_date: 2025-09-23 05:37:31 -0400 (Tue, 23 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 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: 1.17.1
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_1.17.1.tar.gz
StartedAt: 2025-09-24 21:08:04 -0400 (Wed, 24 Sep 2025)
EndedAt: 2025-09-24 21:28:04 -0400 (Wed, 24 Sep 2025)
EllapsedTime: 1199.5 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_1.17.1.tar.gz
###
##############################################################################
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* 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 ‘1.17.1’
* 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 250.815  4.284  99.877
rm_diann_contaminants     86.427  1.492  23.928
awblinmod                 42.747  0.595  41.850
read_rnaseq_counts        37.016  1.727  32.685
plot_exprs                26.015  1.032  23.117
LINMOD                    25.376  0.812  24.264
default_formula           24.549  0.562  18.696
plot_exprs_per_coef       20.146  0.444  20.484
ftype                     16.905  0.397   9.251
read_somascan             15.704  0.410  15.665
plot_volcano              15.814  0.144  15.912
analyze                   13.624  0.371  13.911
plot_summary              13.709  0.130  13.749
read_metabolon            13.182  0.261  13.409
plot_densities            12.379  0.162  10.353
read_olink                12.037  0.039   1.795
explore-transforms        10.954  0.066  11.021
fit_survival              10.663  0.093  10.760
plot_contrastogram        10.128  0.115   3.049
fcluster                   9.403  0.152   9.390
plot_detections            7.611  0.554   8.099
plot_subgroup_points       7.844  0.104   6.246
read_fragpipe              7.288  0.278   5.665
plot_xy_density            7.119  0.081   7.218
biplot_covariates          6.904  0.148   7.029
plot_violins               5.807  0.030   5.818
reset_fit                  5.528  0.017   5.526
subtract_baseline          5.294  0.107   4.784
* 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 ‘1.17.1’
** 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 
259.677   4.934 223.361 

Example timings

autonomics.Rcheck/autonomics-Ex.timings

nameusersystemelapsed
AUTONOMICS_DATASETS0.0010.0000.000
COMPOUNDDISCOVERER_PATTERNS000
LINMOD25.376 0.81224.264
LINMODENGINES000
MAXQUANT_PATTERNS000
TAXON_TO_ORGNAME000
TESTS000
X1.2850.3751.619
abstract_fit1.0350.0611.057
add_adjusted_pvalues0.5230.0530.577
add_assay_means0.3470.0240.371
add_facetvars1.4450.0611.466
add_opentargets_by_uniprot0.3780.0130.393
add_psp0.4950.0300.527
add_smiles0.4860.0340.495
all_non_numeric0.5970.0500.648
analysis0.4990.0270.526
analyze13.624 0.37113.911
annotate_maxquant0.8900.0540.945
annotate_uniprot_rest1.4060.0903.045
assert_is_valid_sumexp0.5450.0210.536
awblinmod42.747 0.59541.850
biplot3.7950.0553.809
biplot_corrections3.5160.0863.567
biplot_covariates6.9040.1487.029
block2limma0.0020.0000.002
block2lm0.0030.0000.003
block2lme0.0010.0000.002
block2lmer0.0030.0000.003
block_has_two_levels0.6700.0450.677
center1.9240.0101.931
code4.8920.0074.876
collapsed_entrezg_to_symbol0.9800.0451.026
contrast_subgroup_cols0.5790.0050.563
contrastdt0.3670.0000.368
count_in0.0010.0000.001
counts0.3270.0000.327
counts2cpm0.3530.0000.352
counts2tpm0.2750.0010.276
cpm0.3230.0020.326
create_design0.7210.0090.709
default_formula24.549 0.56218.696
default_geom0.5580.0090.533
default_sfile0.0020.0000.001
demultiplex0.0150.0000.014
densities0.2070.0020.209
dequantify0.0020.0000.003
dequantify_compounddiscoverer0.0010.0000.001
dot-coxph0.3730.0090.382
dot-merge0.0190.0010.019
dot-read_maxquant_proteingroups0.1130.0020.116
download_data0.0000.0000.001
download_gtf0.0010.0000.000
download_mcclain210.0000.0000.001
dt2mat0.0040.0000.003
enrichment1.1620.0011.163
entrezg_to_symbol0.1370.0010.138
explore-transforms10.954 0.06611.021
extract_contrast_features4.3690.0424.389
extract_rectangle0.1140.0040.118
factor.vars0.1890.0010.190
factorize0.7720.0360.809
fcluster9.4030.1529.390
fcor1.5350.0241.560
fdata0.5830.0050.588
fdr2p0.9420.0150.933
filter_exprs_replicated_in_some_subgroup1.0850.0311.030
filter_features0.5480.0360.544
filter_medoid0.6480.0580.706
filter_samples0.5250.0160.501
fit_survival10.663 0.09310.760
fits0.3250.0050.329
fix_xlgenes0.0010.0010.002
flevels0.4150.0040.419
fnames0.4190.0020.421
formula2str000
ftype16.905 0.397 9.251
fvalues0.4360.0000.436
fvars0.3910.0030.394
genome_to_orgdb0.0000.0000.001
group_by_level0.0010.0000.001
guess_compounddiscoverer_quantity0.0010.0000.001
guess_fitsep0.4730.0050.478
guess_maxquant_quantity0.0060.0000.005
guess_sep0.5290.0060.511
has_multiple_levels0.0530.0030.056
hdlproteins0.0380.0110.052
impute3.4490.0083.458
invert_subgroups0.5990.0140.613
is_character_matrix0.1430.0000.143
is_collapsed_subset0.0010.0000.001
is_correlation_matrix0.0020.0000.001
is_diann_report4.6080.1270.630
is_fastadt0.0570.0010.057
is_file0.0010.0000.000
is_fraction0.0010.0000.001
is_imputed0.6410.0010.643
is_positive_number0.0010.0000.002
is_scalar_subset0.2900.0020.292
is_sig1.3120.0001.312
is_valid_formula0.0410.0000.041
keep_estimable_features0.8250.0230.768
label2index0.0010.0000.000
list2mat0.0010.0000.000
log2counts0.2800.0010.281
log2cpm0.2760.0000.276
log2diffs0.2800.0040.284
log2proteins0.3530.0010.354
log2sites0.3120.0000.311
log2tpm0.3080.0000.309
log2transform4.8570.1214.981
logical2factor0.0020.0000.002
make_alpha_palette0.4940.0260.497
make_colors0.010.000.01
make_volcano_dt0.8610.0100.876
map_fvalues0.3530.0000.353
matrix2sumexp0.9550.0100.943
mclust_breaks0.4770.0540.531
merge_sample_file0.4450.0090.454
merge_sdata0.5730.0190.567
message_df0.0020.0000.002
model_coefs0.6930.0080.679
modelvar3.1910.0153.131
object10.4810.0010.482
order_on_p1.2900.0031.263
overall_parameters0.0270.0010.027
pca3.2950.0203.285
pg_to_canonical0.0050.0000.005
plot_coef_densities1.3360.0101.320
plot_contrast_venn2.2580.0222.209
plot_contrastogram10.128 0.115 3.049
plot_data1.5470.0281.553
plot_densities12.379 0.16210.353
plot_design0.8420.0370.888
plot_detections7.6110.5548.099
plot_exprs26.015 1.03223.117
plot_exprs_per_coef20.146 0.44420.484
plot_fit_summary2.3000.0142.259
plot_heatmap1.9790.0181.997
plot_matrix0.6100.0040.597
plot_subgroup_points7.8440.1046.246
plot_summary13.709 0.13013.749
plot_venn0.0180.0000.017
plot_venn_heatmap0.0250.0010.027
plot_violins5.8070.0305.818
plot_volcano15.814 0.14415.912
plot_xy_density7.1190.0817.218
preprocess_rnaseq_counts0.4550.0210.482
pull_columns0.0030.0000.002
pvalues_estimable0.0390.0000.039
read_affymetrix000
read_diann_proteingroups250.815 4.284 99.877
read_fragpipe7.2880.2785.665
read_maxquant_phosphosites1.5020.0981.600
read_maxquant_proteingroups1.2170.0711.289
read_metabolon13.182 0.26113.409
read_msigdt0.0000.0000.001
read_olink12.037 0.039 1.795
read_rectangles0.1680.0110.179
read_rnaseq_counts37.016 1.72732.685
read_salmon000
read_somascan15.704 0.41015.665
read_uniprotdt0.3460.0060.352
reset_fit5.5280.0175.526
rm_diann_contaminants86.427 1.49223.928
rm_missing_in_some_samples0.5110.0040.491
rm_unmatched_samples0.6540.0020.656
sbind4.3110.0234.334
scaledlibsizes0.290.000.29
scoremat0.8600.0070.845
slevels0.3780.0010.378
snames0.3700.0050.375
split_extract_fixed0.5370.0010.514
split_samples1.1490.0441.172
stepauc0.2980.0050.303
stri_any_regex000
stri_detect_fixed_in_collapsed0.3200.0090.329
subgroup_matrix0.5410.0130.530
subtract_baseline5.2940.1074.784
sumexp_to_longdt1.9370.0441.884
sumexp_to_tsv0.4840.0060.490
sumexplist_to_longdt1.5400.0061.552
summarize_fit1.7070.0161.663
survobj0.1450.0000.144
svalues0.3830.0050.388
svars0.3980.0020.400
systematic_nas0.5770.0030.580
tag_features0.9200.0220.942
tag_hdlproteins0.5710.0110.582
taxon2org0.0010.0000.001
tpm0.3120.0000.312
uncollapse0.0270.0000.027
values0.4060.0000.405
varlevels_dont_clash0.0190.0000.020
venn_detects0.5830.0020.585
weights0.3220.0000.321
write_xl0.7950.0270.779
zero_to_na0.0020.0000.001