Back to Multiple platform build/check report for BioC 3.23:   simplified   long
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This page was generated on 2025-12-06 11:35 -0500 (Sat, 06 Dec 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.3 LTS)x86_64R Under development (unstable) (2025-10-20 r88955) -- "Unsuffered Consequences" 4869
kjohnson3macOS 13.7.7 Venturaarm64R Under development (unstable) (2025-11-04 r88984) -- "Unsuffered Consequences" 4576
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 121/2331HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
autonomics 1.19.0  (landing page)
Aditya Bhagwat
Snapshot Date: 2025-12-05 13:40 -0500 (Fri, 05 Dec 2025)
git_url: https://git.bioconductor.org/packages/autonomics
git_branch: devel
git_last_commit: 9fc1276
git_last_commit_date: 2025-10-29 11:06:51 -0500 (Wed, 29 Oct 2025)
nebbiolo1Linux (Ubuntu 24.04.3 LTS) / x86_64  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


CHECK results for autonomics on kjohnson3

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: 1.19.0
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_1.19.0.tar.gz
StartedAt: 2025-12-05 18:30:17 -0500 (Fri, 05 Dec 2025)
EndedAt: 2025-12-05 18:37:43 -0500 (Fri, 05 Dec 2025)
EllapsedTime: 446.3 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_1.19.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.23-bioc/meat/autonomics.Rcheck’
* using R Under development (unstable) (2025-11-04 r88984)
* using platform: aarch64-apple-darwin20
* R was compiled by
    Apple clang version 16.0.0 (clang-1600.0.26.6)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Ventura 13.7.8
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘autonomics/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘autonomics’ version ‘1.19.0’
* 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                 58.329  2.698  66.054
read_diann_proteingroups 35.910  0.879  38.617
awblinmod                13.584  0.092  14.784
read_rnaseq_counts       10.304  0.776  12.115
LINMOD                    7.752  0.104   8.760
rm_diann_contaminants     7.406  0.255   8.428
default_formula           6.651  0.303   7.327
plot_exprs                6.116  0.051   6.638
plot_exprs_per_coef       5.916  0.030   6.344
* 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-3.23-bioc/meat/autonomics.Rcheck/00check.log’
for details.


Installation output

autonomics.Rcheck/00install.out

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


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library’
* installing *source* package ‘autonomics’ ...
** this is package ‘autonomics’ version ‘1.19.0’
** 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 Under development (unstable) (2025-11-04 r88984) -- "Unsuffered Consequences"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: aarch64-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 
 55.536   3.501  62.646 

Example timings

autonomics.Rcheck/autonomics-Ex.timings

nameusersystemelapsed
AUTONOMICS_DATASETS000
COMPOUNDDISCOVERER_PATTERNS000
LINMOD7.7520.1048.760
LINMODENGINES000
MAXQUANT_PATTERNS0.0000.0000.001
TAXON_TO_ORGNAME000
TESTS000
X0.3710.0170.427
abstract_fit0.3100.0180.353
add_adjusted_pvalues0.1650.0040.197
add_assay_means0.1260.0030.141
add_facetvars0.4310.0180.497
add_opentargets_by_uniprot0.1340.0020.151
add_psp0.1640.0040.197
add_smiles0.1540.0160.213
all_non_numeric0.1800.0000.204
analysis0.1290.0020.135
analyze4.2280.0534.683
annotate_maxquant0.3400.0280.389
annotate_uniprot_rest0.1110.0073.708
assert_is_valid_sumexp0.1780.0160.207
awblinmod13.584 0.09214.784
biplot1.2180.0231.325
biplot_corrections1.1040.0221.245
biplot_covariates2.2290.0192.367
block2limma0.0010.0000.000
block2lm0.0010.0000.001
block2lme0.0010.0000.001
block2lmer0.0010.0010.001
block_has_two_levels0.2250.0170.266
center0.6000.0060.640
code1.4890.0201.662
collapsed_entrezg_to_symbol0.3430.0210.387
contrast_subgroup_cols0.2130.0170.237
contrastdt0.1950.0020.215
count_in0.0010.0000.001
counts0.1000.0010.106
counts2cpm0.1110.0010.122
counts2tpm0.0890.0010.092
cpm0.1110.0010.124
create_design0.2430.0190.295
default_formula6.6510.3037.327
default_geom0.1670.0160.203
default_sfile0.0000.0010.001
demultiplex0.0040.0000.004
densities0.0790.0050.089
dequantify0.0010.0010.002
dequantify_compounddiscoverer000
dot-coxph0.1340.0180.167
dot-merge0.0090.0010.010
dot-read_maxquant_proteingroups0.0470.0030.051
download_data0.0000.0000.001
download_gtf000
download_mcclain210.0010.0000.001
dt2mat0.0010.0010.002
enrichment0.3610.0030.401
entrezg_to_symbol0.0490.0020.052
explore-transforms3.0990.0333.273
extract_contrast_features1.3810.0211.479
extract_rectangle0.0480.0150.068
factor.vars0.0540.0000.059
factorize0.2260.0030.246
fcluster2.9900.0193.259
fcor0.5050.0120.558
fdata0.1750.0030.187
fdr2p0.3040.0150.362
filter_exprs_replicated_in_some_subgroup0.3140.0180.433
filter_features0.1590.0150.231
filter_medoid0.1970.0020.224
filter_samples0.1700.0160.240
fit_survival3.4540.0543.806
fits0.0950.0000.098
fix_xlgenes0.0000.0000.001
flevels0.1330.0020.144
fnames0.1670.0030.190
formula2str0.0000.0000.001
ftype2.6150.1243.214
fvalues0.1230.0020.130
fvars0.1250.0020.133
genome_to_orgdb000
group_by_level000
guess_compounddiscoverer_quantity0.0010.0000.000
guess_fitsep0.1540.0020.158
guess_maxquant_quantity0.0020.0010.003
guess_sep0.1570.0160.195
has_multiple_levels0.0160.0010.017
hdlproteins0.0210.0140.038
impute1.0580.0101.179
invert_subgroups0.2180.0020.229
is_character_matrix0.0420.0000.045
is_collapsed_subset0.0000.0010.000
is_compounddiscoverer_output0.0300.0080.063
is_correlation_matrix000
is_diann_report0.0530.0050.055
is_fastadt0.0210.0010.022
is_file0.0000.0000.001
is_fraction0.0010.0000.006
is_fragpipe_tsv0.0340.0040.036
is_imputed0.2470.0020.270
is_maxquant_phosphosites0.0340.0030.035
is_maxquant_proteingroups0.0290.0040.033
is_positive_number0.0010.0000.000
is_scalar_subset0.1070.0020.122
is_sig0.4380.0030.474
is_valid_formula0.0150.0000.016
keep_estimable_features0.2290.0150.268
label2index000
list2mat0.0000.0000.001
log2counts0.1230.0010.125
log2cpm0.1090.0010.111
log2diffs0.0990.0020.100
log2proteins0.0980.0020.108
log2sites0.0960.0010.104
log2tpm0.1210.0010.142
log2transform1.5900.0131.745
logical2factor0.0010.0000.001
make_alpha_palette0.1970.0160.249
make_colors0.0050.0010.006
make_volcano_dt0.2480.0020.255
map_fvalues0.1160.0020.123
matrix2sumexp0.3980.0210.461
mclust_breaks0.2460.0210.276
merge_sample_file0.1680.0040.179
merge_sdata0.1890.0290.274
message_df0.0010.0000.001
model_coefs0.2800.0190.380
modelvar1.0590.0191.171
object10.1980.0010.204
order_on_p0.4440.0180.552
overall_parameters0.0110.0000.012
pca1.0790.0211.181
pg_to_canonical0.0010.0000.001
plot_coef_densities0.4580.0200.505
plot_contrast_venn0.7780.0190.904
plot_contrastogram1.0090.0491.174
plot_data0.5720.0210.670
plot_densities3.9300.1114.422
plot_design0.2110.0020.226
plot_detections2.2210.0122.355
plot_exprs6.1160.0516.638
plot_exprs_per_coef5.9160.0306.344
plot_fit_summary0.6810.0240.771
plot_heatmap0.6000.0040.630
plot_matrix0.1600.0160.191
plot_subgroup_points1.8160.0221.951
plot_summary3.9580.0254.290
plot_venn0.0090.0000.011
plot_venn_heatmap0.0070.0010.009
plot_violins1.5350.0431.705
plot_volcano4.2610.0564.891
plot_xy_density2.0170.0112.214
preprocess_rnaseq_counts0.1000.0000.108
pull_columns0.0010.0000.001
pvalues_estimable0.0110.0010.012
read_affymetrix000
read_diann_proteingroups35.910 0.87938.617
read_fragpipe2.1350.0622.286
read_maxquant_phosphosites0.5310.0120.599
read_maxquant_proteingroups0.4100.0070.499
read_metabolon4.1080.0354.537
read_msigdt000
read_olink0.6050.0560.693
read_rectangles0.0660.0070.077
read_rnaseq_counts10.304 0.77612.115
read_salmon000
read_somascan4.4180.0244.802
read_uniprotdt0.1040.0090.137
reset_fit1.3700.0371.599
rm_diann_contaminants7.4060.2558.428
rm_missing_in_some_samples0.1950.0210.250
rm_unmatched_samples0.2240.0100.266
sbind1.3990.0271.551
scaledlibsizes0.1150.0020.125
scoremat0.3340.0210.409
slevels0.1390.0040.165
snames0.1700.0030.199
split_extract_fixed0.1650.0160.210
split_samples0.3990.0220.466
stepauc0.0990.0010.110
stri_any_regex0.0000.0010.002
stri_detect_fixed_in_collapsed0.1460.0020.164
subgroup_matrix0.1780.0170.237
subtract_baseline1.7420.0331.968
sumexp_to_longdt0.6870.0430.790
sumexp_to_tsv0.1470.0020.159
sumexplist_to_longdt0.5070.0080.598
summarize_fit0.5870.0190.710
survobj0.0470.0000.051
svalues0.1430.0030.157
svars0.1310.0020.144
systematic_nas0.1920.0020.212
tag_features0.3830.0320.446
tag_hdlproteins0.2740.0180.306
taxon2org0.0000.0000.001
tpm0.1000.0000.101
uncollapse0.0100.0000.015
values0.1370.0020.148
varlevels_dont_clash0.010.000.01
venn_detects0.2030.0020.218
weights0.1090.0010.121
write_xl58.329 2.69866.054
zero_to_na0.0000.0000.001