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This page was generated on 2025-10-20 12:04 -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 lconway

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: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:autonomics.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings autonomics_1.17.16.tar.gz
StartedAt: 2025-10-19 20:23:26 -0400 (Sun, 19 Oct 2025)
EndedAt: 2025-10-19 20:48:31 -0400 (Sun, 19 Oct 2025)
EllapsedTime: 1504.2 seconds
RetCode: 0
Status:   OK  
CheckDir: autonomics.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:autonomics.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings autonomics_1.17.16.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/autonomics.Rcheck’
* using R version 4.5.1 Patched (2025-09-10 r88807)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Monterey 12.7.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* 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 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                  167.439 11.127 245.889
read_diann_proteingroups  117.691  4.169 130.503
awblinmod                  47.931  0.306  48.538
read_rnaseq_counts         35.811  3.734  40.355
rm_diann_contaminants      27.841  0.487  28.652
LINMOD                     26.783  0.353  27.279
plot_exprs                 22.137  0.216  22.562
plot_exprs_per_coef        21.994  0.216  22.438
default_formula            20.155  0.689  21.010
read_somascan              15.987  0.143  16.308
plot_volcano               15.726  0.127  15.917
analyze                    15.489  0.227  15.817
read_metabolon             15.442  0.181  15.793
plot_summary               15.007  0.203  15.463
fit_survival               13.370  0.156  13.680
explore-transforms         12.586  0.118  12.807
fcluster                   11.839  0.087  12.001
plot_densities             10.495  0.306  14.336
ftype                      10.200  0.286  10.707
read_fragpipe               8.524  0.227   8.877
plot_detections             8.616  0.065   8.796
biplot_covariates           8.358  0.128   8.559
plot_xy_density             7.550  0.060   7.656
plot_subgroup_points        6.692  0.102   6.859
subtract_baseline           6.580  0.135   6.808
log2transform               5.934  0.050   6.031
plot_violins                5.731  0.159   5.940
code                        5.720  0.093   5.858
reset_fit                   5.620  0.144   5.844
sbind                       5.419  0.099   5.614
extract_contrast_features   5.376  0.074   5.486
* 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 running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.22-bioc/meat/autonomics.Rcheck/00check.log’
for details.


Installation output

autonomics.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL autonomics
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/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 (2025-09-10 r88807) -- "Great Square Root"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20

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 
148.133  14.914 250.690 

Example timings

autonomics.Rcheck/autonomics-Ex.timings

nameusersystemelapsed
AUTONOMICS_DATASETS0.0000.0000.001
COMPOUNDDISCOVERER_PATTERNS0.0010.0000.001
LINMOD26.783 0.35327.279
LINMODENGINES000
MAXQUANT_PATTERNS0.0000.0010.001
TAXON_TO_ORGNAME000
TESTS0.0010.0000.001
X1.3810.0581.452
abstract_fit1.1660.0631.237
add_adjusted_pvalues0.5720.0120.588
add_assay_means0.3970.0080.406
add_facetvars1.5740.0711.663
add_opentargets_by_uniprot0.4360.0090.449
add_psp0.5520.0170.570
add_smiles0.5070.0410.550
all_non_numeric0.6520.0040.657
analysis0.4490.0080.459
analyze15.489 0.22715.817
annotate_maxquant1.0580.1091.181
annotate_uniprot_rest0.0810.0131.967
assert_is_valid_sumexp0.7550.0500.814
awblinmod47.931 0.30648.538
biplot4.3890.0754.499
biplot_corrections4.2360.0684.343
biplot_covariates8.3580.1288.559
block2limma0.0030.0010.003
block2lm0.0030.0010.003
block2lme0.0030.0010.003
block2lmer0.0040.0000.005
block_has_two_levels0.8030.0540.869
center2.2360.0312.362
code5.7200.0935.858
collapsed_entrezg_to_symbol1.1420.0961.254
contrast_subgroup_cols0.7720.0620.846
contrastdt0.6900.0060.699
count_in0.0010.0010.002
counts0.4060.0040.414
counts2cpm0.3930.0020.397
counts2tpm0.3510.0030.356
cpm0.3840.0030.388
create_design0.7960.0460.849
default_formula20.155 0.68921.010
default_geom0.6380.0480.693
default_sfile0.0020.0010.002
demultiplex0.0190.0020.020
densities0.2840.0110.298
dequantify0.0030.0010.003
dequantify_compounddiscoverer0.0020.0010.002
dot-coxph0.5710.0620.644
dot-merge0.0310.0020.032
dot-read_maxquant_proteingroups0.1410.0070.149
download_data0.0010.0020.002
download_gtf000
download_mcclain210.0000.0000.001
dt2mat0.0030.0010.004
enrichment1.4210.0151.451
entrezg_to_symbol0.1820.0040.189
explore-transforms12.586 0.11812.807
extract_contrast_features5.3760.0745.486
extract_rectangle0.1750.0530.233
factor.vars0.2130.0010.214
factorize1.0520.0181.078
fcluster11.839 0.08712.001
fcor1.9370.0371.994
fdata0.7410.0180.767
fdr2p1.2190.0631.308
filter_exprs_replicated_in_some_subgroup1.1170.0541.182
filter_features0.6590.0540.722
filter_medoid0.6920.0070.704
filter_samples0.6780.0820.774
fit_survival13.370 0.15613.680
fits0.4970.0050.505
fix_xlgenes0.0020.0000.002
flevels0.4760.0060.485
fnames0.5680.0100.582
formula2str0.0010.0010.000
ftype10.200 0.28610.707
fvalues0.5040.0080.514
fvars0.4750.0070.484
genome_to_orgdb0.0010.0000.001
group_by_level0.0010.0010.002
guess_compounddiscoverer_quantity0.0010.0010.002
guess_fitsep0.6410.0070.651
guess_maxquant_quantity0.0070.0020.009
guess_sep0.5810.0440.627
has_multiple_levels0.0750.0040.078
hdlproteins0.0530.0450.101
impute4.3330.0384.393
invert_subgroups0.7570.0070.768
is_character_matrix0.1640.0010.166
is_collapsed_subset0.0010.0000.000
is_compounddiscoverer_output0.050.030.16
is_correlation_matrix0.0010.0000.002
is_diann_report0.0940.0150.110
is_fastadt0.0720.0020.074
is_file0.0000.0010.001
is_fraction0.0020.0010.002
is_fragpipe_tsv0.0580.0070.065
is_imputed0.8740.0080.885
is_maxquant_phosphosites0.0560.0070.063
is_maxquant_proteingroups0.0560.0080.063
is_positive_number0.0020.0000.002
is_scalar_subset0.3800.0060.387
is_sig1.6630.0131.682
is_valid_formula0.0480.0010.049
keep_estimable_features0.8560.0450.905
label2index0.0010.0000.001
list2mat0.0000.0000.001
log2counts0.4390.0050.444
log2cpm0.3460.0030.349
log2diffs0.3600.0060.366
log2proteins0.3630.0050.369
log2sites0.4170.0050.423
log2tpm0.3760.0030.379
log2transform5.9340.0506.031
logical2factor0.0010.0000.002
make_alpha_palette0.5950.0460.654
make_colors0.0090.0010.011
make_volcano_dt2.1450.0282.178
map_fvalues0.4160.0090.424
matrix2sumexp1.1000.0621.172
mclust_breaks0.6070.0990.714
merge_sample_file0.5320.0110.547
merge_sdata0.6750.0670.749
message_df0.0020.0000.002
model_coefs0.7880.0590.861
modelvar3.4890.0603.567
object10.6000.0040.609
order_on_p1.6170.0611.701
overall_parameters0.0290.0000.030
pca3.8550.0773.960
pg_to_canonical0.0060.0010.006
plot_coef_densities1.5470.0771.651
plot_contrast_venn2.5900.0592.672
plot_contrastogram3.0410.1293.212
plot_data1.8370.0621.927
plot_densities10.495 0.30614.336
plot_design0.6030.0100.683
plot_detections8.6160.0658.796
plot_exprs22.137 0.21622.562
plot_exprs_per_coef21.994 0.21622.438
plot_fit_summary2.2170.3033.679
plot_heatmap1.8590.0352.524
plot_matrix0.5680.0710.694
plot_subgroup_points6.6920.1026.859
plot_summary15.007 0.20315.463
plot_venn0.0160.0030.022
plot_venn_heatmap0.0250.0030.035
plot_violins5.7310.1595.940
plot_volcano15.726 0.12715.917
plot_xy_density7.5500.0607.656
preprocess_rnaseq_counts0.5000.0060.508
pull_columns0.0030.0000.004
pvalues_estimable0.0470.0070.055
read_affymetrix0.0010.0000.000
read_diann_proteingroups117.691 4.169130.503
read_fragpipe8.5240.2278.877
read_maxquant_phosphosites1.7550.0501.833
read_maxquant_proteingroups1.3780.0251.430
read_metabolon15.442 0.18115.793
read_msigdt0.0010.0010.002
read_olink1.6240.0951.794
read_rectangles0.2280.0320.286
read_rnaseq_counts35.811 3.73440.355
read_salmon0.0000.0010.001
read_somascan15.987 0.14316.308
read_uniprotdt0.3480.0530.418
reset_fit5.6200.1445.844
rm_diann_contaminants27.841 0.48728.652
rm_missing_in_some_samples0.6430.0640.729
rm_unmatched_samples0.8390.0230.880
sbind5.4190.0995.614
scaledlibsizes0.4010.0070.417
scoremat1.2200.1121.375
slevels0.4950.0110.525
snames0.6160.0150.681
split_extract_fixed0.6120.0600.683
split_samples1.5950.0611.676
stepauc0.4170.0060.432
stri_any_regex0.0010.0000.002
stri_detect_fixed_in_collapsed0.5210.0110.539
subgroup_matrix0.6530.0560.727
subtract_baseline6.5800.1356.808
sumexp_to_longdt2.2420.1202.400
sumexp_to_tsv0.7120.0130.740
sumexplist_to_longdt2.0180.0352.081
summarize_fit2.2250.0642.318
survobj0.1950.0020.200
svalues0.4980.0100.516
svars0.4890.0090.503
systematic_nas0.7790.0130.804
tag_features1.5030.0571.617
tag_hdlproteins0.6770.0500.743
taxon2org0.0010.0010.001
tpm0.4240.0040.432
uncollapse0.0410.0010.044
values0.6990.0280.742
varlevels_dont_clash0.0240.0010.026
venn_detects0.7260.0130.748
weights0.5140.0060.527
write_xl167.439 11.127245.889
zero_to_na0.0030.0100.049