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This page was generated on 2025-10-13 11:38 -0400 (Mon, 13 Oct 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 (2025-06-13) -- "Great Square Root" 4833
merida1macOS 12.7.5 Montereyx86_644.5.1 RC (2025-06-05 r88288) -- "Great Square Root" 4614
kjohnson1macOS 13.6.6 Venturaarm644.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" 4555
kunpeng2Linux (openEuler 24.03 LTS)aarch64R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" 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 117/2341HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
autonomics 1.16.0  (landing page)
Aditya Bhagwat
Snapshot Date: 2025-10-09 13:40 -0400 (Thu, 09 Oct 2025)
git_url: https://git.bioconductor.org/packages/autonomics
git_branch: RELEASE_3_21
git_last_commit: a47f4df
git_last_commit_date: 2025-04-15 12:21:58 -0400 (Tue, 15 Apr 2025)
nebbiolo1Linux (Ubuntu 24.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 12.7.5 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.6 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published
kunpeng2Linux (openEuler 24.03 LTS) / aarch64  OK    OK    ERROR  


CHECK results for autonomics on merida1

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: 1.16.0
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_1.16.0.tar.gz
StartedAt: 2025-10-10 00:13:15 -0400 (Fri, 10 Oct 2025)
EndedAt: 2025-10-10 00:51:38 -0400 (Fri, 10 Oct 2025)
EllapsedTime: 2302.4 seconds
RetCode: 0
Status:   OK  
CheckDir: autonomics.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### 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_1.16.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/autonomics.Rcheck’
* using R version 4.5.1 RC (2025-06-05 r88288)
* 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 ‘1.16.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... INFO
Imports includes 30 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
read_diann_proteingroups 232.506  4.506 270.063
read_rnaseq_counts        77.163  3.302  85.857
fit_linmod                77.583  0.441  81.795
plot_exprs_per_coef       63.760  0.302  67.599
plot_exprs                61.884  0.274  64.967
rm_diann_contaminants     44.909  0.461  46.034
analyze                   40.393  0.325  41.769
default_formula           40.095  0.484  42.980
read_metabolon            38.896  0.548  44.424
plot_summary              38.197  0.394  42.751
read_somascan             35.719  0.200  37.400
plot_volcano              34.222  0.637  41.752
plot_densities            23.399  0.252  26.287
fcluster                  21.824  0.134  23.362
ftype                     19.840  0.423  21.388
plot_sample_nas           16.542  0.113  18.139
biplot_covariates         16.369  0.100  16.563
extract_coef_features     16.325  0.122  17.290
read_fragpipe             14.682  0.194  18.082
plot_subgroup_points      14.247  0.144  15.475
code                      13.072  0.122  13.418
fit_survival              12.541  0.092  13.214
log2transform             12.368  0.097  13.174
subtract_baseline         12.096  0.159  22.938
plot_violins              11.781  0.384  15.327
reset_fit                 11.793  0.110  11.999
biplot                    10.977  0.119  11.360
plot_joint_density        10.604  0.153  11.373
biplot_corrections         9.916  0.103  10.055
plot_survival              9.780  0.226  12.550
modelvar                   8.871  0.097   9.697
pca                        8.286  0.113   8.853
impute                     8.219  0.055   8.632
plot_contrastogram         6.885  0.180   7.651
plot_heatmap               6.030  0.027   6.403
plot_contrast_venn         5.896  0.079   6.194
plot_fit_summary           5.459  0.093   5.900
sumexp_to_longdt           4.345  0.198   8.524
summarize_fit              4.225  0.105   8.003
sumexplist_to_longdt       3.414  0.041   6.731
* 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-3.21-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 ‘1.16.0’
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** 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 RC (2025-06-05 r88288) -- "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 
284.425  19.372 377.615 

Example timings

autonomics.Rcheck/autonomics-Ex.timings

nameusersystemelapsed
AUTONOMICS_DATASETS0.0000.0010.002
COMPOUNDDISCOVERER_PATTERNS0.0000.0000.001
FITSEP0.0000.0000.001
LINMODENGINES0.0000.0000.001
MAXQUANT_PATTERNS0.0010.0010.001
SURVIVALENGINES000
TAXON_TO_ORGNAME0.0010.0000.002
TESTS0.0000.0010.001
X3.5970.2724.044
abstract_fit4.3370.1724.748
add_adjusted_pvalues1.2870.0351.370
add_assay_means0.8350.0160.884
add_facetvars3.7470.1044.019
add_opentargets_by_uniprot0.8800.0100.986
add_psp1.1390.0241.254
add_smiles1.0690.0661.188
analysis0.8420.0100.896
analyze40.393 0.32541.769
annotate_maxquant1.9220.1232.052
annotate_uniprot_rest0.1470.0201.992
assert_is_valid_sumexp1.2090.0671.296
bin0.8890.0190.911
biplot10.977 0.11911.360
biplot_corrections 9.916 0.10310.055
biplot_covariates16.369 0.10016.563
block2lme0.0060.0020.007
center4.0340.0304.071
code13.072 0.12213.418
coefs1.9250.0712.009
collapsed_entrezg_to_symbol0.0010.0010.001
contrast_subgroup_cols1.3650.0691.458
count_in0.0020.0020.005
counts0.7390.0040.745
counts2cpm0.7330.0040.747
counts2tpm0.6690.0040.697
cpm0.7260.0050.762
create_design1.7520.0881.945
default_formula40.095 0.48442.980
default_geom1.1920.0691.339
default_sfile0.0030.0010.003
demultiplex0.0350.0020.039
dequantify0.0040.0000.006
dequantify_compounddiscoverer0.0030.0010.005
dot-coxph0.9450.0581.077
dot-merge0.0340.0020.039
dot-read_maxquant_proteingroups0.2040.0080.223
download_data0.0000.0010.001
download_gtf0.0000.0000.001
download_mcclain210.0010.0000.001
dt2mat0.0070.0010.008
enrichment4.5010.0174.738
entrezg_to_symbol0.0010.0010.001
extract_coef_features16.325 0.12217.290
extract_rectangle0.2680.0650.345
fcluster21.824 0.13423.362
fcor3.3440.0543.544
fdata1.2700.0351.338
fdr2p2.2570.0752.397
filter_exprs_replicated_in_some_subgroup2.2430.0722.416
filter_features1.1560.0691.280
filter_medoid1.6070.0281.760
filter_samples1.2080.0671.375
fit_linmod77.583 0.44181.795
fit_survival12.541 0.09213.214
fitcoefs2.0270.0692.199
fits1.8050.0691.969
fix_xlgenes0.0030.0010.004
flevels0.9400.0110.996
fnames1.0230.0101.124
formula2str0.0000.0000.001
ftype19.840 0.42321.388
fvalues0.9780.0101.032
fvars0.8860.0090.941
genome_to_orgdb0.0010.0010.001
group_by_level0.0030.0020.004
guess_compounddiscoverer_quantity0.0020.0010.004
guess_fitsep1.0940.0111.188
guess_maxquant_quantity0.0110.0020.014
guess_sep1.1550.0701.566
has_multiple_levels0.1290.0060.149
hdlproteins0.0820.0670.174
impute8.2190.0558.632
invert_subgroups1.5090.0121.590
is_collapsed_subset0.0010.0000.002
is_correlation_matrix0.0020.0010.003
is_diann_report0.3900.0870.554
is_fastadt0.1400.0020.154
is_file0.0000.0010.002
is_fraction0.0040.0020.005
is_imputed1.7230.0121.819
is_positive_number0.0040.0010.006
is_scalar_subset0.7210.0090.769
is_sig4.2700.0214.486
is_valid_formula0.0990.0030.107
keep_connected_blocks1.1260.0671.265
keep_connected_features1.6630.0681.834
keep_replicated_features1.8570.0712.005
label2index0.0020.0010.003
list2mat0.0010.0010.002
log2counts0.7910.0050.874
log2cpm0.7130.0050.801
log2diffs0.7570.0100.827
log2proteins0.6990.0110.738
log2sites0.7030.0070.751
log2tpm0.7720.0050.817
log2transform12.368 0.09713.174
logical2factor0.0020.0010.004
make_alpha_palette1.2100.0691.352
make_colors0.0170.0030.019
make_volcano_dt2.0480.0182.156
map_fvalues0.8780.0150.937
matrix2sumexp2.3770.0742.568
merge_sample_file0.9540.0141.014
merge_sdata1.2710.0961.435
message_df0.0060.0000.006
model_coefs1.7130.0721.890
modelvar8.8710.0979.697
order_on_p2.8180.0743.048
pca8.2860.1138.853
pg_to_canonical0.0140.0010.015
plot_coef_densities3.2130.0743.425
plot_contrast_venn5.8960.0796.194
plot_contrastogram6.8850.1807.651
plot_data3.8200.0844.367
plot_densities23.399 0.25226.287
plot_design1.6570.0141.795
plot_exprs61.884 0.27464.967
plot_exprs_per_coef63.760 0.30267.599
plot_fit_summary5.4590.0935.900
plot_heatmap6.0300.0276.403
plot_joint_density10.604 0.15311.373
plot_matrix1.1810.0761.331
plot_sample_nas16.542 0.11318.139
plot_subgroup_points14.247 0.14415.475
plot_summary38.197 0.39442.751
plot_survival 9.780 0.22612.550
plot_venn0.0070.0020.011
plot_venn_heatmap0.0490.0050.064
plot_violins11.781 0.38415.327
plot_volcano34.222 0.63741.752
preprocess_rnaseq_counts0.6830.0070.783
pull_columns0.0050.0010.006
read_affymetrix0.0000.0010.001
read_diann_proteingroups232.506 4.506270.063
read_fragpipe14.682 0.19418.082
read_maxquant_phosphosites3.2830.0774.207
read_maxquant_proteingroups2.7440.0643.411
read_metabolon38.896 0.54844.424
read_msigdt0.0020.0010.003
read_olink3.1550.1373.729
read_rectangles0.3890.0380.515
read_rnaseq_counts77.163 3.30285.857
read_salmon0.0010.0010.003
read_somascan35.719 0.20037.400
read_uniprotdt0.6130.0520.668
reset_fit11.793 0.11011.999
rm_diann_contaminants44.909 0.46146.034
rm_missing_in_some_samples1.0210.0611.088
rm_unmatched_samples1.2940.0151.310
scaledlibsizes0.6460.0040.651
scoremat2.1290.0752.230
slevels0.8270.0130.845
snames1.1290.1801.316
split_extract_fixed1.1210.0861.231
split_samples2.7200.0964.052
stri_any_regex0.0000.0010.002
stri_detect_fixed_in_collapsed0.7860.0221.526
subgroup_matrix1.3030.0742.573
subtract_baseline12.096 0.15922.938
sumexp_to_longdt4.3450.1988.524
sumexp_to_tsv1.1580.0122.107
sumexplist_to_longdt3.4140.0416.731
summarize_fit4.2250.1058.003
svalues0.8760.0161.650
svars1.0170.0161.891
systematic_nas1.2930.0172.339
tag_features2.2870.0744.265
tag_hdlproteins1.1470.1082.384
taxon2org0.0010.0010.003
tpm0.8470.0521.569
uncollapse0.0610.0050.131
values0.9050.0231.806
varlevels_dont_clash0.0330.0020.054
venn_detects1.0890.0181.898
weights0.4430.0060.548
write_xl0.9970.3192.098
zero_to_na0.0030.0030.005