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This page was generated on 2025-10-07 12:03 -0400 (Tue, 07 Oct 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" 4853
lconwaymacOS 12.7.1 Montereyx86_644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4640
kjohnson3macOS 13.7.7 Venturaarm644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4585
taishanLinux (openEuler 24.03 LTS)aarch644.5.0 (2025-04-11) -- "How About a Twenty-Six" 4584
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 117/2341HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
autonomics 1.17.16  (landing page)
Aditya Bhagwat
Snapshot Date: 2025-10-06 13:45 -0400 (Mon, 06 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: 2025-10-06 21:07:21 -0400 (Mon, 06 Oct 2025)
EndedAt: 2025-10-06 21:31:00 -0400 (Mon, 06 Oct 2025)
EllapsedTime: 1418.8 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 403.033  2.437 108.240
write_xl                 209.475  9.914 244.481
rm_diann_contaminants    107.610  0.860  24.357
awblinmod                 41.020  0.070  39.818
read_rnaseq_counts        35.531  1.846  31.162
ftype                     37.135  0.106   8.831
LINMOD                    24.540  0.514  23.409
default_formula           24.182  0.377  18.011
plot_exprs                24.092  0.093  20.331
plot_exprs_per_coef       19.683  0.151  19.789
plot_contrastogram        13.945  0.081   3.043
read_somascan             13.815  0.205  13.530
plot_volcano              13.402  0.141  13.489
plot_summary              13.298  0.024  13.180
analyze                   13.020  0.105  13.036
read_metabolon            12.504  0.225  12.604
plot_densities            11.315  0.067   9.459
fit_survival              10.489  0.028  10.521
explore-transforms         9.830  0.006   9.838
fcluster                   9.292  0.011   9.168
read_fragpipe              7.736  0.457   6.334
plot_subgroup_points       7.254  0.077   6.193
plot_detections            7.171  0.129   7.209
biplot_covariates          6.652  0.034   6.664
plot_xy_density            6.194  0.010   6.204
read_olink                 6.014  0.046   1.492
subtract_baseline          5.871  0.028   5.121
* 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 
252.393   8.425 223.174 

Example timings

autonomics.Rcheck/autonomics-Ex.timings

nameusersystemelapsed
AUTONOMICS_DATASETS000
COMPOUNDDISCOVERER_PATTERNS000
LINMOD24.540 0.51423.409
LINMODENGINES000
MAXQUANT_PATTERNS000
TAXON_TO_ORGNAME000
TESTS000
X1.1820.0091.156
abstract_fit1.0340.0201.015
add_adjusted_pvalues0.5130.0110.525
add_assay_means0.3370.0020.339
add_facetvars1.4090.0051.392
add_opentargets_by_uniprot0.3820.0020.386
add_psp0.4870.0130.501
add_smiles0.4580.0070.444
all_non_numeric0.5770.0000.578
analysis0.4500.0040.454
analyze13.020 0.10513.036
annotate_maxquant0.9030.0200.924
annotate_uniprot_rest1.4460.0963.202
assert_is_valid_sumexp0.5570.0070.526
awblinmod41.020 0.07039.818
biplot3.6790.0123.668
biplot_corrections3.3240.0063.308
biplot_covariates6.6520.0346.664
block2limma0.0020.0000.001
block2lm0.0030.0000.002
block2lme0.0020.0000.002
block2lmer0.0030.0000.003
block_has_two_levels0.6660.0100.607
center1.8400.0051.834
code4.6190.0054.599
collapsed_entrezg_to_symbol0.8540.0420.895
contrast_subgroup_cols0.5650.0080.543
contrastdt0.5580.0010.560
count_in0.0010.0000.001
counts0.3230.0000.323
counts2cpm0.2720.0000.273
counts2tpm0.2630.0010.264
cpm0.3070.0010.308
create_design0.6580.0080.645
default_formula24.182 0.37718.011
default_geom0.4770.0030.458
default_sfile0.0010.0000.002
demultiplex0.0130.0000.013
densities0.2040.0000.204
dequantify0.0030.0000.003
dequantify_compounddiscoverer0.0010.0000.001
dot-coxph0.3650.0060.371
dot-merge0.0200.0000.021
dot-read_maxquant_proteingroups0.1160.0010.116
download_data0.0010.0000.000
download_gtf000
download_mcclain210.0010.0000.000
dt2mat0.0030.0000.004
enrichment1.1270.0031.131
entrezg_to_symbol0.1380.0000.138
explore-transforms9.8300.0069.838
extract_contrast_features4.3760.0094.353
extract_rectangle0.1040.0050.109
factor.vars0.1640.0010.165
factorize0.7670.0030.770
fcluster9.2920.0119.168
fcor1.4750.0101.486
fdata0.4890.0030.492
fdr2p0.9490.0040.913
filter_exprs_replicated_in_some_subgroup1.0690.0250.966
filter_features0.5120.0050.478
filter_medoid0.5530.0040.557
filter_samples0.5590.0040.522
fit_survival10.489 0.02810.521
fits0.2960.0000.295
fix_xlgenes0.0020.0000.001
flevels0.3840.0030.387
fnames0.4520.0000.452
formula2str000
ftype37.135 0.106 8.831
fvalues0.3650.0010.366
fvars0.3560.0020.358
genome_to_orgdb0.0000.0000.001
group_by_level0.0010.0000.001
guess_compounddiscoverer_quantity0.0010.0000.001
guess_fitsep0.4680.0020.469
guess_maxquant_quantity0.0060.0000.005
guess_sep0.4600.0100.448
has_multiple_levels0.0510.0000.051
hdlproteins0.0380.0030.044
impute3.3280.0093.339
invert_subgroups0.6670.0020.670
is_character_matrix0.1430.0000.143
is_collapsed_subset0.0000.0000.001
is_compounddiscoverer_output1.7550.0690.271
is_correlation_matrix0.0010.0000.001
is_diann_report3.3670.0200.236
is_fastadt0.2010.0010.085
is_file0.0010.0000.000
is_fraction0.0010.0010.002
is_fragpipe_tsv1.4740.0210.108
is_imputed0.7540.0030.742
is_maxquant_phosphosites1.7370.0130.143
is_maxquant_proteingroups1.7390.0110.132
is_positive_number0.0010.0000.002
is_scalar_subset0.2910.0010.292
is_sig1.3470.0011.348
is_valid_formula0.0420.0000.042
keep_estimable_features0.7570.0030.700
label2index0.0000.0000.001
list2mat0.0000.0000.001
log2counts0.3430.0020.345
log2cpm0.3030.0010.304
log2diffs0.3080.0030.311
log2proteins0.2940.0010.295
log2sites0.3480.0010.349
log2tpm0.2920.0000.293
log2transform4.7480.0864.835
logical2factor0.0010.0000.002
make_alpha_palette0.5140.0450.518
make_colors0.010.000.01
make_volcano_dt0.8540.0750.930
map_fvalues0.3560.0110.367
matrix2sumexp1.0130.0371.010
mclust_breaks0.4920.0310.523
merge_sample_file0.4540.0100.464
merge_sdata0.6070.0620.646
message_df0.0020.0000.002
model_coefs0.7340.0420.744
modelvar4.3780.2154.542
object10.5180.0080.526
order_on_p1.3550.0191.365
overall_parameters0.0260.0010.027
pca3.1160.1273.221
pg_to_canonical0.0060.0000.005
plot_coef_densities1.2810.0381.295
plot_contrast_venn2.1790.0132.113
plot_contrastogram13.945 0.081 3.043
plot_data1.6470.0231.650
plot_densities11.315 0.067 9.459
plot_design0.6910.0320.723
plot_detections7.1710.1297.209
plot_exprs24.092 0.09320.331
plot_exprs_per_coef19.683 0.15119.789
plot_fit_summary2.1620.0122.082
plot_heatmap1.9140.0061.940
plot_matrix0.4950.0100.466
plot_subgroup_points7.2540.0776.193
plot_summary13.298 0.02413.180
plot_venn0.0160.0000.016
plot_venn_heatmap0.0530.0010.054
plot_violins4.5970.0304.605
plot_volcano13.402 0.14113.489
plot_xy_density6.1940.0106.204
preprocess_rnaseq_counts0.3110.0000.310
pull_columns0.0020.0000.002
pvalues_estimable0.0350.0000.035
read_affymetrix000
read_diann_proteingroups403.033 2.437108.240
read_fragpipe7.7360.4576.334
read_maxquant_phosphosites2.6520.2152.867
read_maxquant_proteingroups1.1390.0241.164
read_metabolon12.504 0.22512.604
read_msigdt0.0000.0000.001
read_olink6.0140.0461.492
read_rectangles0.1700.0040.174
read_rnaseq_counts35.531 1.84631.162
read_salmon000
read_somascan13.815 0.20513.530
read_uniprotdt0.2830.0060.289
reset_fit4.5570.0334.508
rm_diann_contaminants107.610 0.860 24.357
rm_missing_in_some_samples0.5020.0060.484
rm_unmatched_samples0.6830.0030.686
sbind4.5380.0454.621
scaledlibsizes0.2870.0000.286
scoremat0.8610.0070.846
slevels0.3690.0060.374
snames0.3820.0010.383
split_extract_fixed0.5410.0060.525
split_samples1.2210.0071.255
stepauc0.3040.0010.304
stri_any_regex0.0010.0000.000
stri_detect_fixed_in_collapsed0.3840.0010.385
subgroup_matrix0.6500.0050.633
subtract_baseline5.8710.0285.121
sumexp_to_longdt2.0080.0242.027
sumexp_to_tsv0.5600.0030.567
sumexplist_to_longdt1.4420.0071.449
summarize_fit1.7650.0101.669
survobj0.1340.0000.133
svalues0.3820.0020.384
svars0.4710.0020.559
systematic_nas0.5340.0010.536
tag_features1.4160.0411.461
tag_hdlproteins0.6270.0650.700
taxon2org0.0010.0000.001
tpm0.3700.0410.412
uncollapse0.0360.0040.040
values0.6270.0900.717
varlevels_dont_clash0.0240.0010.025
venn_detects0.5750.0130.588
weights0.4560.0220.478
write_xl209.475 9.914244.481
zero_to_na0.0020.0000.003