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This page was generated on 2025-10-08 12:52 -0400 (Wed, 08 Oct 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" 4854
lconwaymacOS 12.7.1 Montereyx86_644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4641
kjohnson3macOS 13.7.7 Venturaarm644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4586
taishanLinux (openEuler 24.03 LTS)aarch644.5.0 (2025-04-11) -- "How About a Twenty-Six" 4584
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 1.17.16  (landing page)
Aditya Bhagwat
Snapshot Date: 2025-10-07 13:45 -0400 (Tue, 07 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  YES
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  YES
kjohnson3macOS 13.7.7 Ventura / arm64  OK    OK    OK    OK  YES
taishanLinux (openEuler 24.03 LTS) / aarch64  OK    OK    OK  


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: 1.17.16
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: 2025-10-07 18:17:32 -0400 (Tue, 07 Oct 2025)
EndedAt: 2025-10-07 18:24:09 -0400 (Tue, 07 Oct 2025)
EllapsedTime: 397.0 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_1.17.16.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: 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 13.7.7
* 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                 51.796  2.199  56.563
read_diann_proteingroups 34.216  0.948  35.997
awblinmod                12.591  0.079  13.221
read_rnaseq_counts        9.715  0.709  10.751
rm_diann_contaminants     7.175  0.202   7.312
LINMOD                    7.150  0.094   7.615
default_formula           6.163  0.183   6.401
plot_exprs                5.963  0.028   6.290
plot_exprs_per_coef       5.602  0.031   5.809
* 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-arm64/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: 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 
 52.952   3.320  57.453 

Example timings

autonomics.Rcheck/autonomics-Ex.timings

nameusersystemelapsed
AUTONOMICS_DATASETS0.0000.0000.001
COMPOUNDDISCOVERER_PATTERNS000
LINMOD7.1500.0947.615
LINMODENGINES000
MAXQUANT_PATTERNS000
TAXON_TO_ORGNAME000
TESTS000
X0.3460.0140.361
abstract_fit0.2910.0150.306
add_adjusted_pvalues0.1580.0030.163
add_assay_means0.1010.0010.103
add_facetvars0.3880.0160.406
add_opentargets_by_uniprot0.1200.0020.124
add_psp0.1510.0030.154
add_smiles0.1470.0140.161
all_non_numeric0.1590.0010.160
analysis0.1160.0020.122
analyze4.0120.0564.138
annotate_maxquant0.3230.0240.372
annotate_uniprot_rest0.0320.0062.199
assert_is_valid_sumexp0.2410.0140.274
awblinmod12.591 0.07913.221
biplot1.1520.0181.181
biplot_corrections1.0500.0141.080
biplot_covariates2.1070.0182.173
block2limma0.0010.0000.001
block2lm0.0010.0000.001
block2lme000
block2lmer0.0000.0010.002
block_has_two_levels0.2120.0150.230
center0.5500.0050.558
code1.3630.0161.388
collapsed_entrezg_to_symbol0.3320.0180.362
contrast_subgroup_cols0.2070.0150.264
contrastdt0.1810.0010.183
count_in0.0010.0000.001
counts0.0920.0000.095
counts2cpm0.0980.0010.100
counts2tpm0.0800.0010.081
cpm0.0980.0010.098
create_design0.2040.0130.217
default_formula6.1630.1836.401
default_geom0.1460.0140.245
default_sfile0.0010.0000.001
demultiplex0.0040.0000.004
densities0.0650.0020.069
dequantify0.0000.0000.001
dequantify_compounddiscoverer0.0000.0000.001
dot-coxph0.1280.0120.149
dot-merge0.0120.0010.032
dot-read_maxquant_proteingroups0.0470.0020.049
download_data000
download_gtf000
download_mcclain210.0000.0010.000
dt2mat0.0010.0000.002
enrichment0.3310.0040.348
entrezg_to_symbol0.0510.0020.055
explore-transforms2.9630.0273.074
extract_contrast_features1.3610.0361.447
extract_rectangle0.0430.0140.061
factor.vars0.0490.0000.049
factorize0.2460.0040.258
fcluster2.8430.0172.909
fcor0.4920.0100.502
fdata0.1540.0020.156
fdr2p0.2840.0130.298
filter_exprs_replicated_in_some_subgroup0.2870.0150.301
filter_features0.1470.0130.160
filter_medoid0.1590.0020.160
filter_samples0.1770.0140.191
fit_survival3.3320.0563.519
fits0.0890.0000.090
fix_xlgenes0.0010.0000.001
flevels0.1210.0010.129
fnames0.1440.0020.146
formula2str000
ftype2.5620.1052.884
fvalues0.1240.0020.126
fvars0.1220.0020.125
genome_to_orgdb000
group_by_level0.0010.0000.000
guess_compounddiscoverer_quantity000
guess_fitsep0.1650.0020.167
guess_maxquant_quantity0.0020.0010.002
guess_sep0.1450.0120.158
has_multiple_levels0.0160.0010.016
hdlproteins0.0220.0100.037
impute1.0670.0091.104
invert_subgroups0.1840.0020.186
is_character_matrix0.040.000.04
is_collapsed_subset0.0000.0000.001
is_compounddiscoverer_output0.0270.0060.064
is_correlation_matrix000
is_diann_report0.0480.0050.046
is_fastadt0.0200.0000.026
is_file000
is_fraction0.0010.0000.000
is_fragpipe_tsv0.0350.0040.043
is_imputed0.2430.0030.256
is_maxquant_phosphosites0.0280.0020.029
is_maxquant_proteingroups0.0250.0020.030
is_positive_number0.0010.0000.000
is_scalar_subset0.0940.0010.095
is_sig0.4140.0020.427
is_valid_formula0.0130.0010.014
keep_estimable_features0.2240.0150.244
label2index0.0000.0000.001
list2mat0.0010.0000.000
log2counts0.1150.0010.116
log2cpm0.0860.0010.086
log2diffs0.0910.0010.093
log2proteins0.0930.0020.103
log2sites0.1170.0010.120
log2tpm0.0880.0010.097
log2transform1.5790.0151.645
logical2factor0.0010.0000.001
make_alpha_palette0.1620.0150.210
make_colors0.0040.0000.005
make_volcano_dt0.3240.0060.332
map_fvalues0.1150.0020.118
matrix2sumexp0.3200.0150.352
mclust_breaks0.2090.0200.238
merge_sample_file0.1580.0040.169
merge_sdata0.2320.0180.257
message_df0.0010.0000.001
model_coefs0.2360.0150.336
modelvar1.1000.0201.234
object10.1760.0020.195
order_on_p0.4460.0150.512
overall_parameters0.0090.0000.012
pca1.0700.0191.187
pg_to_canonical0.0020.0000.002
plot_coef_densities0.4340.0150.509
plot_contrast_venn0.6890.0190.779
plot_contrastogram0.9850.0391.139
plot_data0.5450.0180.614
plot_densities3.7910.0894.389
plot_design0.2110.0020.219
plot_detections2.2110.0102.339
plot_exprs5.9630.0286.290
plot_exprs_per_coef5.6020.0315.809
plot_fit_summary0.6430.0250.710
plot_heatmap0.5770.0030.608
plot_matrix0.1490.0150.169
plot_subgroup_points1.7510.0201.827
plot_summary3.8300.0224.054
plot_venn0.0120.0010.013
plot_venn_heatmap0.0090.0000.008
plot_violins1.5460.0371.707
plot_volcano4.0780.0304.429
plot_xy_density1.9890.0092.045
preprocess_rnaseq_counts0.1050.0010.106
pull_columns0.0010.0010.001
pvalues_estimable0.0120.0010.014
read_affymetrix0.0000.0000.001
read_diann_proteingroups34.216 0.94835.997
read_fragpipe1.8920.0482.010
read_maxquant_phosphosites0.4780.0060.503
read_maxquant_proteingroups0.3730.0070.391
read_metabolon3.7580.0543.875
read_msigdt0.0000.0000.001
read_olink0.5140.0200.541
read_rectangles0.0640.0070.071
read_rnaseq_counts 9.715 0.70910.751
read_salmon0.0000.0000.001
read_somascan4.0050.0084.247
read_uniprotdt0.1000.0060.107
reset_fit1.4270.0531.558
rm_diann_contaminants7.1750.2027.312
rm_missing_in_some_samples0.1430.0190.166
rm_unmatched_samples0.1880.0060.203
sbind1.1780.0051.210
scaledlibsizes0.1450.0150.160
scoremat0.2330.0130.258
slevels0.1510.0030.181
snames0.1260.0020.173
split_extract_fixed0.1470.0150.175
split_samples0.3620.0140.376
stepauc0.0930.0000.094
stri_any_regex000
stri_detect_fixed_in_collapsed0.1250.0010.131
subgroup_matrix0.1520.0140.170
subtract_baseline1.4260.0261.498
sumexp_to_longdt0.5640.0270.649
sumexp_to_tsv0.1380.0020.139
sumexplist_to_longdt0.4670.0050.482
summarize_fit0.4750.0170.525
survobj0.0630.0000.063
svalues0.1250.0010.136
svars0.1180.0020.119
systematic_nas0.1720.0020.176
tag_features0.3390.0110.361
tag_hdlproteins0.1940.0130.213
taxon2org0.0010.0000.001
tpm0.1210.0010.126
uncollapse0.0080.0010.010
values0.1250.0020.130
varlevels_dont_clash0.0090.0000.013
venn_detects0.1550.0030.183
weights0.1220.0000.145
write_xl51.796 2.19956.563
zero_to_na0.0010.0010.000