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This page was generated on 2025-10-20 12:03 -0400 (Mon, 20 Oct 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" 4887
lconwaymacOS 12.7.6 Montereyx86_644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4677
kjohnson3macOS 13.7.7 Venturaarm644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4622
taishanLinux (openEuler 24.03 LTS)aarch644.5.0 (2025-04-11) -- "How About a Twenty-Six" 4632
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 118/2353HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
autonomics 1.17.16  (landing page)
Aditya Bhagwat
Snapshot Date: 2025-10-19 13:45 -0400 (Sun, 19 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 12.7.6 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    TIMEOUT  


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: 2025-10-19 21:08:55 -0400 (Sun, 19 Oct 2025)
EndedAt: 2025-10-19 21:27:51 -0400 (Sun, 19 Oct 2025)
EllapsedTime: 1136.9 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
###
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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 ‘1.17.16’
* 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
write_xl                 157.004  1.197 158.235
read_diann_proteingroups  93.847  0.999  90.452
awblinmod                 38.412  0.143  37.639
read_rnaseq_counts        27.320  0.899  28.050
LINMOD                    22.903  0.386  22.764
rm_diann_contaminants     20.489  0.140  19.313
plot_exprs                19.207  0.105  19.125
plot_exprs_per_coef       18.525  0.011  18.393
default_formula           17.383  0.400  17.391
plot_volcano              12.554  0.091  12.590
analyze                   12.563  0.072  12.512
read_metabolon            12.429  0.010  12.303
read_somascan             12.379  0.000  12.269
plot_summary              12.259  0.025  12.191
fit_survival               9.801  0.032   9.837
explore-transforms         9.181  0.152   9.334
plot_densities             9.213  0.035   9.113
fcluster                   8.588  0.020   8.540
ftype                      7.855  0.072   7.525
plot_detections            6.968  0.053   6.934
biplot_covariates          6.563  0.347   6.886
plot_xy_density            5.751  0.008   5.760
read_fragpipe              5.702  0.042   5.445
plot_subgroup_points       5.544  0.013   5.480
* 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 
138.377   3.343 139.140 

Example timings

autonomics.Rcheck/autonomics-Ex.timings

nameusersystemelapsed
AUTONOMICS_DATASETS000
COMPOUNDDISCOVERER_PATTERNS000
LINMOD22.903 0.38622.764
LINMODENGINES0.0000.0010.000
MAXQUANT_PATTERNS0.0000.0000.001
TAXON_TO_ORGNAME000
TESTS000
X1.1580.0181.138
abstract_fit0.9860.0140.969
add_adjusted_pvalues0.4800.0100.491
add_assay_means0.3160.0060.322
add_facetvars1.3230.0061.299
add_opentargets_by_uniprot0.3650.0230.389
add_psp0.4640.0380.505
add_smiles0.4480.0280.439
all_non_numeric0.5330.0010.534
analysis0.4160.0060.423
analyze12.563 0.07212.512
annotate_maxquant0.8220.0390.861
annotate_uniprot_rest1.2010.0862.851
assert_is_valid_sumexp0.5180.0040.499
awblinmod38.412 0.14337.639
biplot3.9670.0253.959
biplot_corrections3.7060.0093.692
biplot_covariates6.5630.3476.886
block2limma0.0010.0010.002
block2lm0.0030.0000.002
block2lme0.0020.0000.001
block2lmer0.0030.0000.003
block_has_two_levels0.6210.0280.613
center1.8230.0791.900
code4.6100.0404.638
collapsed_entrezg_to_symbol0.8860.0520.939
contrast_subgroup_cols0.5670.0180.549
contrastdt0.5570.0110.567
count_in0.0010.0000.001
counts0.3420.0000.343
counts2cpm0.2980.0020.299
counts2tpm0.2730.0010.274
cpm0.3270.0070.334
create_design0.6770.0210.676
default_formula17.383 0.40017.391
default_geom0.4620.0060.446
default_sfile0.0010.0010.001
demultiplex0.0130.0000.013
densities0.2040.0030.207
dequantify0.0020.0000.002
dequantify_compounddiscoverer0.0010.0000.001
dot-coxph0.3440.0050.350
dot-merge0.0180.0010.019
dot-read_maxquant_proteingroups0.1080.0010.109
download_data000
download_gtf000
download_mcclain21000
dt2mat0.0030.0000.003
enrichment1.1180.0011.119
entrezg_to_symbol0.1210.0030.124
explore-transforms9.1810.1529.334
extract_contrast_features4.2560.0344.262
extract_rectangle0.1010.0120.113
factor.vars0.1730.0050.179
factorize0.7660.0170.783
fcluster8.5880.0208.540
fcor1.3860.0081.396
fdata0.4850.0030.488
fdr2p0.8820.0040.865
filter_exprs_replicated_in_some_subgroup1.0030.0020.900
filter_features0.4840.0030.465
filter_medoid0.5110.0020.513
filter_samples0.5110.0050.494
fit_survival9.8010.0329.837
fits0.280.000.28
fix_xlgenes0.0020.0000.002
flevels0.3590.0040.363
fnames0.4340.0030.437
formula2str000
ftype7.8550.0727.525
fvalues0.3680.0000.368
fvars0.3580.0010.359
genome_to_orgdb000
group_by_level0.0010.0000.000
guess_compounddiscoverer_quantity0.0010.0000.001
guess_fitsep0.4570.0000.457
guess_maxquant_quantity0.0050.0010.005
guess_sep0.4680.0050.434
has_multiple_levels0.0490.0010.050
hdlproteins0.0350.0050.044
impute3.2520.0033.255
invert_subgroups0.6470.0000.648
is_character_matrix0.1310.0000.132
is_collapsed_subset0.0000.0000.001
is_compounddiscoverer_output0.0690.0220.175
is_correlation_matrix0.0010.0000.001
is_diann_report0.1240.0020.096
is_fastadt0.0630.0000.058
is_file000
is_fraction0.0010.0000.001
is_fragpipe_tsv0.0920.0020.066
is_imputed0.6840.0000.679
is_maxquant_phosphosites0.0810.0030.062
is_maxquant_proteingroups0.0810.0010.057
is_positive_number0.0020.0000.002
is_scalar_subset0.2850.0020.286
is_sig1.3040.0041.308
is_valid_formula0.040.000.04
keep_estimable_features0.7710.0030.691
label2index0.0010.0000.000
list2mat0.0010.0000.001
log2counts0.3280.0000.328
log2cpm0.2740.0000.273
log2diffs0.2890.0000.289
log2proteins0.2850.0020.288
log2sites0.3280.0010.330
log2tpm0.2760.0000.277
log2transform4.5470.0074.555
logical2factor0.0010.0000.002
make_alpha_palette0.4720.0070.457
make_colors0.0080.0010.009
make_volcano_dt0.7860.0010.787
map_fvalues0.3540.0020.355
matrix2sumexp0.9320.0060.916
mclust_breaks0.4780.0170.495
merge_sample_file0.4390.0000.439
merge_sdata0.5630.0070.549
message_df0.0020.0000.002
model_coefs0.6710.0050.654
modelvar4.0780.0774.085
object10.4450.0000.445
order_on_p1.2130.0071.182
overall_parameters0.0260.0000.026
pca2.9460.0272.935
pg_to_canonical0.0050.0000.005
plot_coef_densities1.2360.0061.205
plot_contrast_venn2.2050.0102.067
plot_contrastogram2.6290.0082.569
plot_data1.5250.0081.502
plot_densities9.2130.0359.113
plot_design0.6740.0020.676
plot_detections6.9680.0536.934
plot_exprs19.207 0.10519.125
plot_exprs_per_coef18.525 0.01118.393
plot_fit_summary2.1530.0092.049
plot_heatmap1.7420.0031.745
plot_matrix0.5200.0070.488
plot_subgroup_points5.5440.0135.480
plot_summary12.259 0.02512.191
plot_venn0.0150.0010.016
plot_venn_heatmap0.0190.0010.020
plot_violins4.4090.0204.407
plot_volcano12.554 0.09112.590
plot_xy_density5.7510.0085.760
preprocess_rnaseq_counts0.3240.0010.325
pull_columns0.0020.0000.002
pvalues_estimable0.0340.0000.034
read_affymetrix000
read_diann_proteingroups93.847 0.99990.452
read_fragpipe5.7020.0425.445
read_maxquant_phosphosites1.4340.0041.437
read_maxquant_proteingroups1.1650.0021.167
read_metabolon12.429 0.01012.303
read_msigdt0.0010.0000.001
read_olink1.2680.0151.213
read_rectangles1.2550.0361.290
read_rnaseq_counts27.320 0.89928.050
read_salmon000
read_somascan12.379 0.00012.269
read_uniprotdt0.2790.0020.281
reset_fit4.4870.0084.378
rm_diann_contaminants20.489 0.14019.313
rm_missing_in_some_samples0.4880.0080.468
rm_unmatched_samples0.6490.0010.651
sbind4.0430.0044.047
scaledlibsizes0.2910.0000.291
scoremat0.8540.0070.824
slevels0.3720.0000.372
snames0.3820.0000.382
split_extract_fixed0.5480.0060.514
split_samples1.2110.0601.230
stepauc0.3090.0040.313
stri_any_regex000
stri_detect_fixed_in_collapsed0.3270.0030.330
subgroup_matrix0.5640.0070.532
subtract_baseline4.7070.0124.649
sumexp_to_longdt1.8730.0111.779
sumexp_to_tsv0.4390.0220.460
sumexplist_to_longdt1.4180.0331.451
summarize_fit1.7230.0081.609
survobj0.1320.0000.131
svalues0.3650.0020.366
svars0.3650.0030.368
systematic_nas0.5780.0010.579
tag_features1.0440.0091.053
tag_hdlproteins0.5590.0020.562
taxon2org0.0010.0010.001
tpm0.2900.0020.292
uncollapse0.0260.0000.026
values0.4530.0020.455
varlevels_dont_clash0.0190.0000.019
venn_detects0.5060.0020.508
weights0.2980.0000.298
write_xl157.004 1.197158.235
zero_to_na0.0020.0000.001