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This page was generated on 2025-10-04 12:05 -0400 (Sat, 04 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: 2025-10-03 13:45 -0400 (Fri, 03 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: 2025-10-03 18:15:16 -0400 (Fri, 03 Oct 2025)
EndedAt: 2025-10-03 18:21:55 -0400 (Fri, 03 Oct 2025)
EllapsedTime: 398.9 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                 52.909  2.129  57.432
read_diann_proteingroups 34.161  0.929  35.579
awblinmod                12.446  0.070  12.830
read_rnaseq_counts        9.853  0.751  10.907
rm_diann_contaminants     7.702  0.228   8.092
LINMOD                    7.153  0.094   7.533
default_formula           6.052  0.206   6.288
plot_exprs                5.901  0.053   6.238
plot_exprs_per_coef       5.536  0.024   5.883
* 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 
 53.400   3.347  58.630 

Example timings

autonomics.Rcheck/autonomics-Ex.timings

nameusersystemelapsed
AUTONOMICS_DATASETS000
COMPOUNDDISCOVERER_PATTERNS000
LINMOD7.1530.0947.533
LINMODENGINES0.0000.0000.001
MAXQUANT_PATTERNS000
TAXON_TO_ORGNAME000
TESTS0.0000.0000.001
X0.3430.0130.357
abstract_fit0.2970.0160.316
add_adjusted_pvalues0.1560.0030.160
add_assay_means0.0980.0010.099
add_facetvars0.3930.0150.415
add_opentargets_by_uniprot0.1230.0010.126
add_psp0.1520.0020.157
add_smiles0.1450.0120.166
all_non_numeric0.1680.0000.169
analysis0.1210.0020.123
analyze3.7660.0503.817
annotate_maxquant0.3100.0240.336
annotate_uniprot_rest0.0310.0061.908
assert_is_valid_sumexp0.2220.0140.236
awblinmod12.446 0.07012.830
biplot1.1170.0211.214
biplot_corrections1.0340.0181.060
biplot_covariates2.0490.0212.076
block2limma000
block2lm0.0010.0000.001
block2lme0.0010.0000.000
block2lmer0.0010.0000.001
block_has_two_levels0.2060.0160.221
center0.5590.0060.567
code1.3910.0151.409
collapsed_entrezg_to_symbol0.3270.0190.347
contrast_subgroup_cols0.2070.0150.225
contrastdt0.1800.0010.180
count_in0.0000.0000.001
counts0.1050.0010.105
counts2cpm0.1000.0010.102
counts2tpm0.0860.0000.087
cpm0.1050.0010.105
create_design0.2120.0150.250
default_formula6.0520.2066.288
default_geom0.1420.0140.158
default_sfile0.0010.0000.000
demultiplex0.0040.0000.003
densities0.0650.0010.065
dequantify0.0010.0000.001
dequantify_compounddiscoverer000
dot-coxph0.1250.0090.136
dot-merge0.0080.0010.009
dot-read_maxquant_proteingroups0.0460.0010.048
download_data0.0000.0010.000
download_gtf000
download_mcclain210.0000.0000.001
dt2mat0.0010.0000.002
enrichment0.3330.0040.346
entrezg_to_symbol0.0480.0010.050
explore-transforms2.9440.0173.038
extract_contrast_features1.3620.0431.407
extract_rectangle0.0440.0130.056
factor.vars0.0510.0000.054
factorize0.2460.0040.251
fcluster2.8680.0162.985
fcor0.4920.0100.508
fdata0.1570.0030.161
fdr2p0.2850.0140.304
filter_exprs_replicated_in_some_subgroup0.3000.0150.323
filter_features0.1560.0140.174
filter_medoid0.1560.0010.168
filter_samples0.1770.0150.198
fit_survival3.2210.0643.321
fits0.0870.0000.087
fix_xlgenes0.0000.0000.001
flevels0.1170.0030.120
fnames0.1290.0020.131
formula2str000
ftype2.5960.1282.838
fvalues0.1210.0020.123
fvars0.1180.0020.137
genome_to_orgdb000
group_by_level0.0000.0010.000
guess_compounddiscoverer_quantity0.0000.0000.001
guess_fitsep0.1610.0010.168
guess_maxquant_quantity0.0010.0000.002
guess_sep0.1420.0140.160
has_multiple_levels0.0160.0010.016
hdlproteins0.0200.0090.033
impute1.0640.0071.093
invert_subgroups0.1840.0010.193
is_character_matrix0.0390.0000.038
is_collapsed_subset000
is_compounddiscoverer_output0.0220.0070.061
is_correlation_matrix0.0010.0000.000
is_diann_report0.0530.0050.057
is_fastadt0.020.000.02
is_file0.0000.0000.001
is_fraction000
is_fragpipe_tsv0.0450.0050.047
is_imputed0.2550.0040.259
is_maxquant_phosphosites0.0330.0030.031
is_maxquant_proteingroups0.0300.0030.027
is_positive_number0.0010.0000.000
is_scalar_subset0.0920.0010.093
is_sig0.4470.0020.450
is_valid_formula0.0140.0000.014
keep_estimable_features0.2330.0140.251
label2index000
list2mat0.0010.0000.001
log2counts0.1290.0000.130
log2cpm0.0870.0000.088
log2diffs0.0930.0010.094
log2proteins0.0910.0010.092
log2sites0.1280.0020.130
log2tpm0.0990.0010.100
log2transform1.5700.0141.609
logical2factor0.0010.0000.001
make_alpha_palette0.1550.0140.176
make_colors0.0040.0000.005
make_volcano_dt0.3060.0080.315
map_fvalues0.1150.0010.117
matrix2sumexp0.3180.0140.340
mclust_breaks0.1930.0200.222
merge_sample_file0.1520.0030.155
merge_sdata0.2090.0180.245
message_df0.0010.0000.001
model_coefs0.2290.0130.258
modelvar1.0450.0181.371
object10.1770.0010.202
order_on_p0.4260.0190.491
overall_parameters0.0080.0010.008
pca1.0630.0191.267
pg_to_canonical0.0010.0000.001
plot_coef_densities0.4260.0150.500
plot_contrast_venn0.6980.0170.781
plot_contrastogram1.0090.0561.181
plot_data0.5540.0180.732
plot_densities3.7600.1214.271
plot_design0.2170.0030.250
plot_detections2.2090.0112.413
plot_exprs5.9010.0536.238
plot_exprs_per_coef5.5360.0245.883
plot_fit_summary0.6680.0180.804
plot_heatmap0.5380.0030.551
plot_matrix0.1460.0140.196
plot_subgroup_points1.7570.0281.860
plot_summary3.7870.0244.048
plot_venn0.0080.0010.009
plot_venn_heatmap0.0080.0000.008
plot_violins1.4810.0361.585
plot_volcano4.1050.0444.374
plot_xy_density1.9030.0091.975
preprocess_rnaseq_counts0.1120.0000.112
pull_columns0.0010.0000.001
pvalues_estimable0.0140.0010.015
read_affymetrix000
read_diann_proteingroups34.161 0.92935.579
read_fragpipe2.0210.0912.072
read_maxquant_phosphosites0.4860.0080.494
read_maxquant_proteingroups0.3980.0060.412
read_metabolon3.9000.0524.105
read_msigdt0.0000.0000.001
read_olink0.5570.0250.662
read_rectangles0.0630.0070.070
read_rnaseq_counts 9.853 0.75110.907
read_salmon000
read_somascan4.1030.0094.332
read_uniprotdt0.1100.0060.120
reset_fit1.4380.0281.611
rm_diann_contaminants7.7020.2288.092
rm_missing_in_some_samples0.1420.0220.168
rm_unmatched_samples0.1910.0040.195
sbind1.1940.0051.208
scaledlibsizes0.1060.0010.107
scoremat0.2460.0210.268
slevels0.2040.0370.285
snames0.1230.0010.144
split_extract_fixed0.1470.0180.166
split_samples0.3660.0210.404
stepauc0.0940.0000.096
stri_any_regex0.0000.0000.001
stri_detect_fixed_in_collapsed0.1250.0010.134
subgroup_matrix0.1610.0240.255
subtract_baseline1.4300.0181.516
sumexp_to_longdt0.5720.0240.790
sumexp_to_tsv0.1390.0020.147
sumexplist_to_longdt0.4650.0060.530
summarize_fit0.4710.0160.511
survobj0.0640.0010.067
svalues0.1190.0010.121
svars0.1180.0010.119
systematic_nas0.1780.0010.180
tag_features0.3370.0080.346
tag_hdlproteins0.1620.0100.172
taxon2org0.0000.0000.001
tpm0.1290.0010.130
uncollapse0.0090.0010.010
values0.1350.0030.138
varlevels_dont_clash0.0090.0000.008
venn_detects0.1500.0030.153
weights0.1180.0010.120
write_xl52.909 2.12957.432
zero_to_na0.0010.0010.002