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This page was generated on 2025-09-26 12:03 -0400 (Fri, 26 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" 4619
kjohnson3macOS 13.7.7 Venturaarm644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4563
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: 2025-09-25 13:45 -0400 (Thu, 25 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  YES
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  YES
kjohnson3macOS 13.7.7 Ventura / arm64  OK    OK    OK    OK  YES
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: 1.17.2
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_1.17.2.tar.gz
StartedAt: 2025-09-25 21:06:04 -0400 (Thu, 25 Sep 2025)
EndedAt: 2025-09-25 21:26:28 -0400 (Thu, 25 Sep 2025)
EllapsedTime: 1224.4 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_1.17.2.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 ‘1.17.2’
* 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 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 258.531  5.590 106.216
rm_diann_contaminants    108.279  1.455  23.416
awblinmod                 42.513  0.168  41.293
read_rnaseq_counts        38.802  2.058  35.102
ftype                     38.430  0.248  10.470
default_formula           28.788  0.492  19.362
plot_exprs                26.409  0.457  22.830
LINMOD                    26.191  0.446  24.656
plot_exprs_per_coef       22.316  0.336  22.594
plot_contrastogram        18.123  0.242   3.888
plot_volcano              16.497  0.459  16.874
plot_summary              16.204  0.423  16.502
read_somascan             15.214  0.202  15.068
read_metabolon            14.496  0.168  14.582
analyze                   13.933  0.125  13.926
plot_densities            13.013  0.254  11.216
explore-transforms        11.727  0.027  11.756
fit_survival              11.088  0.034  11.125
fcluster                   9.747  0.035   9.592
plot_subgroup_points       8.860  0.292   7.355
plot_detections            8.236  0.149   8.344
read_fragpipe              7.638  0.079   5.802
plot_xy_density            7.455  0.212   7.709
biplot_covariates          7.202  0.027   7.207
is_diann_report            6.759  0.130   0.685
plot_violins               6.238  0.063   6.278
subtract_baseline          6.000  0.180   5.387
log2transform              5.042  0.378   5.441
code                       5.068  0.019   5.057
* 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 ‘1.17.2’
** 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 (2025-08-23 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 
259.061   9.626 221.836 

Example timings

autonomics.Rcheck/autonomics-Ex.timings

nameusersystemelapsed
AUTONOMICS_DATASETS0.0000.0010.000
COMPOUNDDISCOVERER_PATTERNS000
LINMOD26.191 0.44624.656
LINMODENGINES000
MAXQUANT_PATTERNS000
TAXON_TO_ORGNAME000
TESTS000
X1.2150.0181.209
abstract_fit1.0660.0051.037
add_adjusted_pvalues0.5190.0040.523
add_assay_means0.3550.0090.364
add_facetvars1.4250.0371.423
add_opentargets_by_uniprot0.3740.0070.382
add_psp0.4980.0090.508
add_smiles0.4780.0040.445
all_non_numeric0.5870.0000.587
analysis0.4740.0060.480
analyze13.933 0.12513.926
annotate_maxquant0.8870.0190.906
annotate_uniprot_rest1.3240.0953.312
assert_is_valid_sumexp0.5850.0290.575
awblinmod42.513 0.16841.293
biplot4.1270.0604.165
biplot_corrections3.6600.0123.635
biplot_covariates7.2020.0277.207
block2limma0.0020.0000.003
block2lm0.0020.0010.003
block2lme0.0010.0010.003
block2lmer0.0040.0000.005
block_has_two_levels0.7090.0180.689
center2.0450.0072.050
code5.0680.0195.057
collapsed_entrezg_to_symbol1.0250.0391.064
contrast_subgroup_cols0.6560.0050.639
contrastdt0.3680.0000.368
count_in0.0010.0000.001
counts0.3310.0000.331
counts2cpm0.3610.0010.361
counts2tpm0.3050.0010.306
cpm0.3660.0010.367
create_design0.7320.0100.704
default_formula28.788 0.49219.362
default_geom0.5810.0190.574
default_sfile0.0020.0000.001
demultiplex0.0150.0000.014
densities0.2150.0010.215
dequantify0.0030.0000.003
dequantify_compounddiscoverer0.0010.0000.001
dot-coxph0.3940.0070.401
dot-merge0.0220.0000.022
dot-read_maxquant_proteingroups0.1170.0000.116
download_data000
download_gtf000
download_mcclain21000
dt2mat0.0030.0000.003
enrichment1.2240.0021.226
entrezg_to_symbol0.1550.0020.157
explore-transforms11.727 0.02711.756
extract_contrast_features4.7580.0054.740
extract_rectangle0.1080.0090.117
factor.vars0.1750.0010.176
factorize0.8000.0060.806
fcluster9.7470.0359.592
fcor1.5160.0141.530
fdata0.5840.0050.589
fdr2p1.0010.0070.984
filter_exprs_replicated_in_some_subgroup1.0950.0061.025
filter_features0.5740.0050.554
filter_medoid0.6390.0010.639
filter_samples0.5500.0040.514
fit_survival11.088 0.03411.125
fits0.3030.0000.304
fix_xlgenes0.0010.0000.002
flevels0.4010.0020.404
fnames0.4330.0010.434
formula2str000
ftype38.430 0.24810.470
fvalues0.4140.0000.414
fvars0.3860.0010.386
genome_to_orgdb0.0010.0000.001
group_by_level0.0010.0000.001
guess_compounddiscoverer_quantity0.0010.0000.001
guess_fitsep0.4420.0310.473
guess_maxquant_quantity0.0050.0010.006
guess_sep0.5030.0200.499
has_multiple_levels0.0530.0000.054
hdlproteins0.0380.0120.053
impute3.4000.0133.413
invert_subgroups0.6040.0030.607
is_character_matrix0.1420.0000.143
is_collapsed_subset000
is_correlation_matrix0.0010.0000.001
is_diann_report6.7590.1300.685
is_fastadt0.0630.0010.063
is_file0.0010.0010.001
is_fraction0.0010.0000.002
is_imputed0.6900.0020.692
is_positive_number0.0010.0000.001
is_scalar_subset0.2920.0030.296
is_sig1.2980.0021.301
is_valid_formula0.0410.0000.041
keep_estimable_features0.8750.0160.909
label2index0.0010.0000.001
list2mat0.0010.0000.001
log2counts0.3160.0020.326
log2cpm0.3130.0110.324
log2diffs0.2990.0050.304
log2proteins0.3560.0330.396
log2sites0.2940.0240.318
log2tpm0.2910.0160.307
log2transform5.0420.3785.441
logical2factor0.0020.0000.002
make_alpha_palette0.5110.0150.493
make_colors0.0090.0000.010
make_volcano_dt0.8600.0330.893
map_fvalues0.3750.0190.393
matrix2sumexp1.0230.1151.097
mclust_breaks0.5020.0680.571
merge_sample_file0.4800.0180.498
merge_sdata0.6810.0270.680
message_df0.0020.0000.002
model_coefs0.7050.0140.697
modelvar3.5280.2023.732
object10.5490.0280.577
order_on_p1.4830.0641.521
overall_parameters0.0370.0000.037
pca3.6150.1643.752
pg_to_canonical0.0050.0010.005
plot_coef_densities1.5100.0251.498
plot_contrast_venn2.4960.0132.376
plot_contrastogram18.123 0.242 3.888
plot_data1.7570.0461.781
plot_densities13.013 0.25411.216
plot_design0.7650.0130.778
plot_detections8.2360.1498.344
plot_exprs26.409 0.45722.830
plot_exprs_per_coef22.316 0.33622.594
plot_fit_summary2.4870.0162.451
plot_heatmap2.1530.0052.158
plot_matrix0.6910.0080.673
plot_subgroup_points8.8600.2927.355
plot_summary16.204 0.42316.502
plot_venn0.0170.0010.018
plot_venn_heatmap0.0270.0010.029
plot_violins6.2380.0636.278
plot_volcano16.497 0.45916.874
plot_xy_density7.4550.2127.709
preprocess_rnaseq_counts0.4820.0090.492
pull_columns0.0030.0000.003
pvalues_estimable0.0430.0020.045
read_affymetrix000
read_diann_proteingroups258.531 5.590106.216
read_fragpipe7.6380.0795.802
read_maxquant_phosphosites1.6280.0231.652
read_maxquant_proteingroups1.3840.0521.436
read_metabolon14.496 0.16814.582
read_msigdt0.0010.0000.001
read_olink3.8290.0391.567
read_rectangles0.1790.0110.190
read_rnaseq_counts38.802 2.05835.102
read_salmon000
read_somascan15.214 0.20215.068
read_uniprotdt0.3050.0120.317
reset_fit4.6570.0304.557
rm_diann_contaminants108.279 1.455 23.416
rm_missing_in_some_samples0.4940.0400.509
rm_unmatched_samples0.6800.0740.754
sbind4.2200.2014.432
scaledlibsizes0.3250.0250.363
scoremat0.9200.0310.937
slevels0.4000.0140.413
snames0.3890.0050.393
split_extract_fixed0.5440.0160.532
split_samples1.1670.0221.164
stepauc0.3110.0060.317
stri_any_regex0.0010.0000.000
stri_detect_fixed_in_collapsed0.3440.0040.347
subgroup_matrix0.6860.0150.689
subtract_baseline6.0000.1805.387
sumexp_to_longdt1.9270.0261.941
sumexp_to_tsv0.6220.0000.622
sumexplist_to_longdt1.6060.0121.625
summarize_fit1.6840.0211.643
survobj0.1500.0010.151
svalues0.3800.0030.382
svars0.3990.0030.420
systematic_nas0.6440.0020.650
tag_features0.9590.0200.981
tag_hdlproteins0.5990.0210.621
taxon2org0.0000.0010.001
tpm0.3180.0010.319
uncollapse0.0290.0000.029
values0.4200.0070.427
varlevels_dont_clash0.0230.0000.023
venn_detects0.5960.0010.598
weights0.3150.0000.314
write_xl0.8120.0600.846
zero_to_na0.0010.0000.001