Back to Multiple platform build/check report for BioC 3.23:   simplified   long
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This page was generated on 2025-12-09 11:35 -0500 (Tue, 09 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: 2025-12-08 13:40 -0500 (Mon, 08 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: 2025-12-08 18:30:26 -0500 (Mon, 08 Dec 2025)
EndedAt: 2025-12-08 18:37:51 -0500 (Mon, 08 Dec 2025)
EllapsedTime: 445.3 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                 57.511  2.922  64.617
read_diann_proteingroups 35.883  0.888  39.155
awblinmod                13.509  0.091  15.209
read_rnaseq_counts       10.201  0.840  11.705
rm_diann_contaminants     7.752  0.176   8.477
LINMOD                    7.774  0.106   8.729
plot_exprs                6.575  0.033   7.114
default_formula           6.226  0.225   6.793
plot_exprs_per_coef       6.353  0.047   6.947
* 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

##############################################################################
##############################################################################
###
### 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 
 56.089   3.548  63.858 

Example timings

autonomics.Rcheck/autonomics-Ex.timings

nameusersystemelapsed
AUTONOMICS_DATASETS0.0000.0010.000
COMPOUNDDISCOVERER_PATTERNS000
LINMOD7.7740.1068.729
LINMODENGINES000
MAXQUANT_PATTERNS000
TAXON_TO_ORGNAME000
TESTS000
X0.3940.0180.458
abstract_fit0.3280.0180.374
add_adjusted_pvalues0.1620.0040.185
add_assay_means0.1330.0020.145
add_facetvars0.4440.0170.479
add_opentargets_by_uniprot0.1390.0030.153
add_psp0.1760.0040.188
add_smiles0.1570.0150.207
all_non_numeric0.1910.0000.201
analysis0.1330.0010.145
analyze4.3120.0514.720
annotate_maxquant0.3370.0250.392
annotate_uniprot_rest0.0570.0103.402
assert_is_valid_sumexp0.2560.0180.313
awblinmod13.509 0.09115.209
biplot1.2070.0221.327
biplot_corrections1.1370.0171.186
biplot_covariates2.2360.0222.350
block2limma0.0010.0000.001
block2lm0.0010.0000.001
block2lme0.0010.0000.001
block2lmer0.0010.0010.001
block_has_two_levels0.2180.0170.269
center0.5880.0050.599
code1.5000.0211.566
collapsed_entrezg_to_symbol0.3750.0280.417
contrast_subgroup_cols0.2120.0180.237
contrastdt0.1720.0010.176
count_in0.0010.0000.000
counts0.1310.0010.133
counts2cpm0.1080.0010.117
counts2tpm0.0890.0010.090
cpm0.1050.0010.105
create_design0.2400.0150.267
default_formula6.2260.2256.793
default_geom0.1590.0170.190
default_sfile000
demultiplex0.0040.0010.005
densities0.0650.0010.071
dequantify000
dequantify_compounddiscoverer000
dot-coxph0.1310.0100.151
dot-merge0.0090.0010.009
dot-read_maxquant_proteingroups0.0470.0020.050
download_data000
download_gtf000
download_mcclain210.0000.0000.001
dt2mat0.0010.0010.001
enrichment0.3650.0040.386
entrezg_to_symbol0.0550.0020.065
explore-transforms3.2190.0843.529
extract_contrast_features1.3900.0181.519
extract_rectangle0.0490.0150.070
factor.vars0.0580.0010.065
factorize0.2680.0040.288
fcluster3.0320.0183.241
fcor0.5120.0130.552
fdata0.1650.0030.181
fdr2p0.3270.0170.408
filter_exprs_replicated_in_some_subgroup0.2960.0150.350
filter_features0.2010.0150.224
filter_medoid0.1750.0020.178
filter_samples0.1900.0150.241
fit_survival3.8100.0324.088
fits0.0850.0000.092
fix_xlgenes0.0000.0000.001
flevels0.1400.0030.155
fnames0.1310.0020.144
formula2str000
ftype2.4600.1382.907
fvalues0.1260.0010.135
fvars0.1210.0020.127
genome_to_orgdb0.0000.0010.000
group_by_level0.0010.0000.000
guess_compounddiscoverer_quantity0.0000.0000.001
guess_fitsep0.1510.0020.167
guess_maxquant_quantity0.0010.0010.002
guess_sep0.1490.0140.209
has_multiple_levels0.0180.0010.018
hdlproteins0.0210.0140.037
impute1.0330.0121.117
invert_subgroups0.2020.0020.216
is_character_matrix0.0470.0010.054
is_collapsed_subset000
is_compounddiscoverer_output0.0290.0080.086
is_correlation_matrix0.0010.0000.000
is_diann_report0.0530.0050.053
is_fastadt0.0190.0010.020
is_file000
is_fraction0.0000.0000.001
is_fragpipe_tsv0.0490.0040.049
is_imputed0.2200.0020.223
is_maxquant_phosphosites0.0330.0040.031
is_maxquant_proteingroups0.0330.0040.039
is_positive_number0.0010.0000.001
is_scalar_subset0.1110.0020.118
is_sig0.4170.0030.436
is_valid_formula0.0130.0010.012
keep_estimable_features0.2310.0160.282
label2index000
list2mat000
log2counts0.0960.0000.101
log2cpm0.1130.0020.134
log2diffs0.0960.0020.106
log2proteins0.0960.0010.108
log2sites0.0960.0020.105
log2tpm0.0920.0000.096
log2transform1.6320.0521.901
logical2factor000
make_alpha_palette0.1600.0160.189
make_colors0.0050.0010.006
make_volcano_dt0.2660.0020.280
map_fvalues0.1110.0020.115
matrix2sumexp0.3490.0160.399
mclust_breaks0.2090.0210.244
merge_sample_file0.1580.0030.167
merge_sdata0.2170.0230.293
message_df0.0010.0000.001
model_coefs0.2450.0160.274
modelvar1.0420.0191.140
object10.1630.0010.170
order_on_p0.4230.0170.503
overall_parameters0.0090.0000.010
pca1.0570.0261.171
pg_to_canonical0.0010.0000.002
plot_coef_densities0.4310.0190.504
plot_contrast_venn0.7440.0210.876
plot_contrastogram0.9750.0601.137
plot_data0.5670.0190.633
plot_densities3.4050.1073.766
plot_design0.2280.0020.233
plot_detections2.4070.0112.511
plot_exprs6.5750.0337.114
plot_exprs_per_coef6.3530.0476.947
plot_fit_summary0.7080.0180.775
plot_heatmap0.6450.0040.684
plot_matrix0.1640.0140.191
plot_subgroup_points1.9210.0232.092
plot_summary4.2170.0264.581
plot_venn0.0080.0000.010
plot_venn_heatmap0.0080.0010.008
plot_violins2.0360.0472.198
plot_volcano3.8620.0374.237
plot_xy_density1.8370.0112.005
preprocess_rnaseq_counts0.1070.0010.139
pull_columns0.0010.0000.001
pvalues_estimable0.0110.0020.012
read_affymetrix000
read_diann_proteingroups35.883 0.88839.155
read_fragpipe2.5930.0682.773
read_maxquant_phosphosites0.5040.0120.531
read_maxquant_proteingroups0.4010.0060.434
read_metabolon3.9130.0304.255
read_msigdt0.0000.0000.001
read_olink0.5230.0240.591
read_rectangles0.0690.0080.081
read_rnaseq_counts10.201 0.84011.705
read_salmon000
read_somascan4.0060.0114.311
read_uniprotdt0.1030.0090.114
reset_fit1.4100.0291.596
rm_diann_contaminants7.7520.1768.477
rm_missing_in_some_samples0.1600.0170.212
rm_unmatched_samples0.2180.0020.260
sbind1.4560.0401.674
scaledlibsizes0.1000.0010.104
scoremat0.2980.0160.391
slevels0.1300.0020.154
snames0.1300.0020.137
split_extract_fixed0.1980.0160.265
split_samples0.4130.0160.465
stepauc0.1070.0010.109
stri_any_regex000
stri_detect_fixed_in_collapsed0.1070.0020.119
subgroup_matrix0.2280.0200.278
subtract_baseline1.6870.0201.883
sumexp_to_longdt0.6250.0260.729
sumexp_to_tsv0.1980.0030.220
sumexplist_to_longdt0.5440.0060.579
summarize_fit0.5420.0180.640
survobj0.0480.0000.051
svalues0.1840.0020.199
svars0.1400.0020.153
systematic_nas0.1950.0020.213
tag_features0.4660.0140.503
tag_hdlproteins0.2110.0130.235
taxon2org000
tpm0.1120.0000.124
uncollapse0.0100.0010.011
values0.1400.0020.158
varlevels_dont_clash0.0100.0000.011
venn_detects0.2110.0020.234
weights0.1060.0000.116
write_xl57.511 2.92264.617
zero_to_na0.0010.0010.003