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This page was generated on 2025-10-06 12:05 -0400 (Mon, 06 Oct 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" 4853
lconwaymacOS 12.7.1 Montereyx86_644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4640
kjohnson3macOS 13.7.7 Venturaarm644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4585
taishanLinux (openEuler 24.03 LTS)aarch644.5.0 (2025-04-11) -- "How About a Twenty-Six" 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 117/2341HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
autonomics 1.17.16  (landing page)
Aditya Bhagwat
Snapshot Date: 2025-10-05 13:45 -0400 (Sun, 05 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 12.7.1 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    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: 2025-10-05 18:20:11 -0400 (Sun, 05 Oct 2025)
EndedAt: 2025-10-05 18:26:52 -0400 (Sun, 05 Oct 2025)
EllapsedTime: 400.8 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                 51.770  2.306  56.965
read_diann_proteingroups 34.191  0.824  35.320
awblinmod                12.558  0.092  13.455
read_rnaseq_counts        9.995  0.754  11.079
rm_diann_contaminants     7.361  0.198   7.458
LINMOD                    7.265  0.109   8.227
default_formula           6.178  0.208   6.595
plot_exprs                5.923  0.031   6.269
plot_exprs_per_coef       5.697  0.031   5.950
* 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 
 52.073   3.392  57.086 

Example timings

autonomics.Rcheck/autonomics-Ex.timings

nameusersystemelapsed
AUTONOMICS_DATASETS0.0000.0010.000
COMPOUNDDISCOVERER_PATTERNS0.0000.0000.001
LINMOD7.2650.1098.227
LINMODENGINES000
MAXQUANT_PATTERNS000
TAXON_TO_ORGNAME0.0010.0000.001
TESTS000
X0.3590.0170.408
abstract_fit0.3040.0220.364
add_adjusted_pvalues0.1780.0050.203
add_assay_means0.1050.0030.115
add_facetvars0.4050.0180.500
add_opentargets_by_uniprot0.1280.0020.165
add_psp0.1620.0050.208
add_smiles0.1480.0140.213
all_non_numeric0.1730.0010.184
analysis0.1290.0020.135
analyze4.0310.0474.341
annotate_maxquant0.3130.0220.336
annotate_uniprot_rest0.0320.0072.277
assert_is_valid_sumexp0.2320.0150.283
awblinmod12.558 0.09213.455
biplot1.1450.0211.265
biplot_corrections1.0520.0171.145
biplot_covariates2.0960.0192.245
block2limma0.0010.0010.001
block2lm0.0010.0000.001
block2lme0.0000.0000.006
block2lmer0.0010.0010.002
block_has_two_levels0.2110.0180.305
center0.5720.0110.676
code1.4380.0241.636
collapsed_entrezg_to_symbol0.3310.0200.378
contrast_subgroup_cols0.2010.0160.250
contrastdt0.1760.0010.179
count_in0.0010.0010.001
counts0.1010.0010.133
counts2cpm0.1040.0010.118
counts2tpm0.0850.0010.095
cpm0.1020.0010.110
create_design0.2120.0200.258
default_formula6.1780.2086.595
default_geom0.1480.0150.188
default_sfile0.0010.0000.001
demultiplex0.0040.0000.006
densities0.0710.0020.081
dequantify0.0010.0000.005
dequantify_compounddiscoverer0.0000.0010.001
dot-coxph0.1250.0100.167
dot-merge0.0070.0000.009
dot-read_maxquant_proteingroups0.0460.0010.056
download_data0.0000.0010.000
download_gtf000
download_mcclain21000
dt2mat0.0010.0000.001
enrichment0.3370.0040.374
entrezg_to_symbol0.0480.0020.050
explore-transforms2.9220.0303.066
extract_contrast_features1.3850.0341.472
extract_rectangle0.0430.0140.058
factor.vars0.0500.0000.051
factorize0.2440.0040.256
fcluster2.8740.0143.021
fcor0.5060.0090.531
fdata0.1570.0020.164
fdr2p0.2910.0150.333
filter_exprs_replicated_in_some_subgroup0.2970.0150.359
filter_features0.1530.0140.177
filter_medoid0.1580.0010.169
filter_samples0.1760.0140.259
fit_survival3.3010.0543.504
fits0.0880.0000.091
fix_xlgenes0.0010.0000.001
flevels0.1190.0030.122
fnames0.1480.0030.160
formula2str000
ftype2.5610.1093.320
fvalues0.1170.0020.118
fvars0.1160.0010.124
genome_to_orgdb000
group_by_level0.0010.0010.001
guess_compounddiscoverer_quantity000
guess_fitsep0.1640.0010.175
guess_maxquant_quantity0.0020.0010.002
guess_sep0.1520.0130.231
has_multiple_levels0.0160.0000.017
hdlproteins0.0200.0160.037
impute1.0700.0111.239
invert_subgroups0.1870.0010.197
is_character_matrix0.0390.0000.040
is_collapsed_subset0.0000.0000.001
is_compounddiscoverer_output0.0260.0060.074
is_correlation_matrix0.0010.0000.001
is_diann_report0.0550.0040.065
is_fastadt0.0190.0000.020
is_file0.0000.0000.001
is_fraction000
is_fragpipe_tsv0.0450.0040.055
is_imputed0.2370.0020.259
is_maxquant_phosphosites0.0350.0020.041
is_maxquant_proteingroups0.0310.0030.030
is_positive_number000
is_scalar_subset0.0900.0010.093
is_sig0.4160.0020.444
is_valid_formula0.0130.0000.013
keep_estimable_features0.2250.0150.406
label2index000
list2mat000
log2counts0.1190.0010.131
log2cpm0.0880.0010.089
log2diffs0.0920.0010.093
log2proteins0.0920.0020.094
log2sites0.1340.0020.138
log2tpm0.1030.0010.113
log2transform1.6110.0141.671
logical2factor0.0010.0010.000
make_alpha_palette0.1620.0150.189
make_colors0.0050.0010.005
make_volcano_dt0.3190.0060.353
map_fvalues0.1330.0030.140
matrix2sumexp0.3300.0170.389
mclust_breaks0.2230.0230.249
merge_sample_file0.1600.0030.173
merge_sdata0.2040.0170.238
message_df0.0010.0000.001
model_coefs0.2410.0150.298
modelvar1.0200.0171.116
object10.1660.0010.180
order_on_p0.4210.0190.503
overall_parameters0.0100.0010.009
pca1.0650.0211.167
pg_to_canonical0.0010.0000.002
plot_coef_densities0.4310.0150.533
plot_contrast_venn0.7080.0201.064
plot_contrastogram1.0080.0381.170
plot_data0.5690.0220.682
plot_densities3.7040.0923.938
plot_design0.2120.0020.215
plot_detections2.1440.0112.242
plot_exprs5.9230.0316.269
plot_exprs_per_coef5.6970.0315.950
plot_fit_summary0.6450.0210.737
plot_heatmap0.5610.0030.576
plot_matrix0.1480.0140.241
plot_subgroup_points1.6840.0231.766
plot_summary3.8350.0244.119
plot_venn0.0090.0000.010
plot_venn_heatmap0.0120.0010.013
plot_violins1.5530.0331.727
plot_volcano4.0430.0314.199
plot_xy_density1.9940.0092.052
preprocess_rnaseq_counts0.0980.0010.098
pull_columns0.0010.0000.001
pvalues_estimable0.0110.0010.012
read_affymetrix000
read_diann_proteingroups34.191 0.82435.320
read_fragpipe1.9060.0592.011
read_maxquant_phosphosites0.4780.0080.493
read_maxquant_proteingroups0.3940.0070.423
read_metabolon3.8350.0774.100
read_msigdt0.0010.0010.001
read_olink0.4760.0190.556
read_rectangles0.0650.0070.083
read_rnaseq_counts 9.995 0.75411.079
read_salmon000
read_somascan3.9690.0094.218
read_uniprotdt0.1010.0070.122
reset_fit1.4350.0331.533
rm_diann_contaminants7.3610.1987.458
rm_missing_in_some_samples0.1470.0150.162
rm_unmatched_samples0.2010.0050.215
sbind1.2080.0081.256
scaledlibsizes0.1470.0100.164
scoremat0.2380.0170.302
slevels0.1460.0040.152
snames0.1220.0020.125
split_extract_fixed0.1490.0230.188
split_samples0.3550.0150.375
stepauc0.0960.0000.099
stri_any_regex0.0000.0000.001
stri_detect_fixed_in_collapsed0.1240.0010.126
subgroup_matrix0.1530.0170.172
subtract_baseline1.4180.0221.510
sumexp_to_longdt0.5670.0330.672
sumexp_to_tsv0.1400.0020.148
sumexplist_to_longdt0.4600.0080.531
summarize_fit0.4700.0190.503
survobj0.0620.0000.062
svalues0.1210.0020.123
svars0.1250.0020.128
systematic_nas0.1740.0030.177
tag_features0.3400.0100.351
tag_hdlproteins0.1650.0140.181
taxon2org000
tpm0.1270.0010.128
uncollapse0.0090.0010.010
values0.1310.0020.132
varlevels_dont_clash0.0090.0000.010
venn_detects0.1570.0020.159
weights0.1210.0010.123
write_xl51.770 2.30656.965
zero_to_na0.0000.0010.002