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This page was generated on 2025-10-11 12:03 -0400 (Sat, 11 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: 2025-10-10 13:45 -0400 (Fri, 10 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: 2025-10-10 21:18:09 -0400 (Fri, 10 Oct 2025)
EndedAt: 2025-10-10 21:42:19 -0400 (Fri, 10 Oct 2025)
EllapsedTime: 1449.9 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 290.089  6.172 105.045
write_xl                 222.213  6.093 254.090
rm_diann_contaminants     82.230  0.912  23.475
awblinmod                 41.133  0.095  39.904
read_rnaseq_counts        38.730  1.284  31.904
default_formula           28.535  0.442  18.895
LINMOD                    25.287  0.396  23.663
ftype                     24.514  0.095   8.800
plot_exprs                22.876  1.504  22.458
plot_exprs_per_coef       19.291  0.589  19.820
read_somascan             13.854  0.018  13.497
plot_volcano              13.566  0.215  13.953
analyze                   13.190  0.071  13.163
plot_summary              12.910  0.171  12.989
read_metabolon            12.593  0.048  12.564
plot_densities            11.836  0.694  10.636
read_olink                12.398  0.019   1.711
fit_survival              10.673  0.032  10.709
explore-transforms        10.075  0.069  10.145
fcluster                   9.625  0.013   9.479
plot_detections            7.928  0.226   8.185
read_fragpipe              7.591  0.098   5.768
plot_subgroup_points       7.402  0.132   5.880
subtract_baseline          6.658  0.134   6.347
plot_contrastogram         6.532  0.146   3.065
biplot_covariates          6.624  0.045   6.646
plot_xy_density            6.337  0.037   6.392
log2transform              4.995  0.234   5.229
plot_violins               4.875  0.147   4.998
* 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

##############################################################################
##############################################################################
###
### 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 
267.047   6.400 235.471 

Example timings

autonomics.Rcheck/autonomics-Ex.timings

nameusersystemelapsed
AUTONOMICS_DATASETS0.0010.0000.000
COMPOUNDDISCOVERER_PATTERNS000
LINMOD25.287 0.39623.663
LINMODENGINES000
MAXQUANT_PATTERNS000
TAXON_TO_ORGNAME0.0000.0000.001
TESTS000
X1.1700.0101.144
abstract_fit0.9770.0220.977
add_adjusted_pvalues0.5090.0320.542
add_assay_means0.3300.0200.351
add_facetvars1.3510.0121.343
add_opentargets_by_uniprot0.3680.0030.372
add_psp0.4860.0060.494
add_smiles0.4550.0150.449
all_non_numeric0.5860.0230.609
analysis0.5100.0140.524
analyze13.190 0.07113.163
annotate_maxquant0.8690.0190.888
annotate_uniprot_rest1.2970.1533.592
assert_is_valid_sumexp0.5190.0080.505
awblinmod41.133 0.09539.904
biplot3.7800.0713.830
biplot_corrections3.4170.0063.401
biplot_covariates6.6240.0456.646
block2limma0.0020.0000.001
block2lm0.0030.0000.002
block2lme0.0020.0000.002
block2lmer0.0030.0000.003
block_has_two_levels0.6260.0110.599
center1.8520.0131.861
code4.7260.0204.723
collapsed_entrezg_to_symbol0.9760.0431.018
contrast_subgroup_cols0.5860.0070.571
contrastdt0.5640.0000.564
count_in0.0010.0000.001
counts0.3590.0000.359
counts2cpm0.2990.0000.299
counts2tpm0.2830.0000.284
cpm0.3380.0030.341
create_design0.7310.0050.713
default_formula28.535 0.44218.895
default_geom0.4820.0080.469
default_sfile0.0010.0000.001
demultiplex0.0130.0000.014
densities0.2090.0010.210
dequantify0.0030.0000.002
dequantify_compounddiscoverer0.0010.0000.001
dot-coxph0.3690.0030.372
dot-merge0.0240.0000.024
dot-read_maxquant_proteingroups0.1140.0020.115
download_data000
download_gtf000
download_mcclain210.0010.0000.000
dt2mat0.0030.0000.003
enrichment1.1830.0011.184
entrezg_to_symbol0.1270.0010.128
explore-transforms10.075 0.06910.145
extract_contrast_features4.5340.0144.526
extract_rectangle0.1110.0050.116
factor.vars0.1780.0000.179
factorize0.8280.0040.832
fcluster9.6250.0139.479
fcor1.5370.0311.569
fdata0.5250.0000.526
fdr2p0.9360.0100.924
filter_exprs_replicated_in_some_subgroup1.0290.0100.916
filter_features0.4970.0060.483
filter_medoid0.5530.0010.555
filter_samples0.5300.0030.511
fit_survival10.673 0.03210.709
fits0.3070.0010.308
fix_xlgenes0.0010.0000.001
flevels0.3980.0050.403
fnames0.4580.0050.463
formula2str000
ftype24.514 0.095 8.800
fvalues0.3690.0000.369
fvars0.3650.0010.366
genome_to_orgdb0.0010.0000.000
group_by_level0.0010.0000.000
guess_compounddiscoverer_quantity0.0010.0000.001
guess_fitsep0.4800.0010.482
guess_maxquant_quantity0.0060.0000.006
guess_sep0.4530.0070.439
has_multiple_levels0.050.000.05
hdlproteins0.0400.0030.045
impute3.2120.0073.220
invert_subgroups0.6380.0010.638
is_character_matrix0.1370.0000.137
is_collapsed_subset000
is_compounddiscoverer_output1.7770.0720.264
is_correlation_matrix0.0020.0000.001
is_diann_report1.3590.0250.128
is_fastadt0.2030.0000.060
is_file000
is_fraction0.0010.0000.001
is_fragpipe_tsv0.7870.0140.088
is_imputed0.7380.0050.726
is_maxquant_phosphosites0.6240.0170.074
is_maxquant_proteingroups1.6420.0100.112
is_positive_number0.0010.0000.002
is_scalar_subset0.3390.0010.340
is_sig1.5190.0031.530
is_valid_formula0.0520.0000.055
keep_estimable_features0.8560.0120.823
label2index0.0000.0000.001
list2mat0.0000.0000.001
log2counts0.3590.0010.360
log2cpm0.2900.0010.290
log2diffs0.3130.0010.314
log2proteins0.3230.0010.325
log2sites0.3450.0020.347
log2tpm0.2870.0010.287
log2transform4.9950.2345.229
logical2factor0.0010.0000.002
make_alpha_palette0.5190.0370.534
make_colors0.0090.0010.010
make_volcano_dt0.8980.1021.000
map_fvalues0.3510.0170.368
matrix2sumexp1.0070.0401.013
mclust_breaks0.5010.0440.545
merge_sample_file0.4690.0290.498
merge_sdata0.6180.0810.676
message_df0.0020.0000.002
model_coefs0.7240.0360.737
modelvar4.3970.3194.606
object10.4980.0030.501
order_on_p1.2850.0431.289
overall_parameters0.0260.0010.026
pca3.1440.1683.272
pg_to_canonical0.0050.0000.005
plot_coef_densities1.3080.0311.301
plot_contrast_venn2.3400.0962.285
plot_contrastogram6.5320.1463.065
plot_data1.7780.1571.911
plot_densities11.836 0.69410.636
plot_design0.6790.0360.716
plot_detections7.9280.2268.185
plot_exprs22.876 1.50422.458
plot_exprs_per_coef19.291 0.58919.820
plot_fit_summary2.1850.1082.180
plot_heatmap1.8610.0381.899
plot_matrix0.4900.0060.476
plot_subgroup_points7.4020.1325.880
plot_summary12.910 0.17112.989
plot_venn0.0170.0000.016
plot_venn_heatmap0.0610.0000.061
plot_violins4.8750.1474.998
plot_volcano13.566 0.21513.953
plot_xy_density6.3370.0376.392
preprocess_rnaseq_counts0.2980.0010.299
pull_columns0.0020.0000.002
pvalues_estimable0.0350.0010.041
read_affymetrix000
read_diann_proteingroups290.089 6.172105.045
read_fragpipe7.5910.0985.768
read_maxquant_phosphosites2.6950.0872.783
read_maxquant_proteingroups1.1620.0051.168
read_metabolon12.593 0.04812.564
read_msigdt0.0010.0000.001
read_olink12.398 0.019 1.711
read_rectangles0.1690.0040.174
read_rnaseq_counts38.730 1.28431.904
read_salmon0.0000.0000.001
read_somascan13.854 0.01813.497
read_uniprotdt0.2940.0050.299
reset_fit4.7580.0174.770
rm_diann_contaminants82.230 0.91223.475
rm_missing_in_some_samples0.4810.0100.468
rm_unmatched_samples0.6700.0470.717
sbind4.2930.3574.649
scaledlibsizes0.2940.0030.297
scoremat0.8420.0210.840
slevels0.3820.0020.385
snames0.3870.0140.402
split_extract_fixed0.5640.0090.546
split_samples1.2490.0131.231
stepauc0.3300.0080.338
stri_any_regex000
stri_detect_fixed_in_collapsed0.4110.0050.417
subgroup_matrix0.5670.0360.562
subtract_baseline6.6580.1346.347
sumexp_to_longdt2.8400.0253.074
sumexp_to_tsv0.8130.0130.825
sumexplist_to_longdt2.2520.0322.393
summarize_fit2.8800.0783.326
survobj0.2430.0050.279
svalues0.6340.0050.639
svars0.7280.0030.733
systematic_nas0.8570.0170.874
tag_features1.7880.1002.064
tag_hdlproteins0.8090.0311.045
taxon2org0.0010.0000.001
tpm0.5170.0090.625
uncollapse0.0430.0020.044
values0.7800.0090.790
varlevels_dont_clash0.0280.0010.029
venn_detects0.8250.0060.904
weights0.6150.0040.660
write_xl222.213 6.093254.090
zero_to_na0.0030.0000.003