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This page was generated on 2025-09-03 12:06 -0400 (Wed, 03 Sep 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 (2025-06-13) -- "Great Square Root" 4826
lconwaymacOS 12.7.1 Montereyx86_644.5.1 (2025-06-13) -- "Great Square Root" 4616
kjohnson3macOS 13.7.7 Venturaarm644.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" 4563
taishanLinux (openEuler 24.03 LTS)aarch644.5.0 (2025-04-11) -- "How About a Twenty-Six" 4541
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 116/2321HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
autonomics 1.17.0  (landing page)
Aditya Bhagwat
Snapshot Date: 2025-09-02 13:45 -0400 (Tue, 02 Sep 2025)
git_url: https://git.bioconductor.org/packages/autonomics
git_branch: devel
git_last_commit: f051989
git_last_commit_date: 2025-04-15 12:21:58 -0400 (Tue, 15 Apr 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: 1.17.0
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_1.17.0.tar.gz
StartedAt: 2025-09-02 18:11:28 -0400 (Tue, 02 Sep 2025)
EndedAt: 2025-09-02 18:16:40 -0400 (Tue, 02 Sep 2025)
EllapsedTime: 311.7 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_1.17.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/autonomics.Rcheck’
* using R version 4.5.1 Patched (2025-06-14 r88325)
* 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 ‘1.17.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... INFO
Imports includes 30 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
read_diann_proteingroups 31.520  1.013  32.790
read_rnaseq_counts       10.336  0.827  11.311
fit_linmod                9.252  0.073   9.538
rm_diann_contaminants     6.869  0.203   7.054
plot_exprs_per_coef       6.534  0.024   6.856
plot_exprs                6.338  0.048   6.521
default_formula           5.554  0.185   5.808
* 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 ‘1.17.0’
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** 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 (2025-06-14 r88325) -- "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 2 | SKIP 0 | PASS 158 ]

[ FAIL 0 | WARN 2 | SKIP 0 | PASS 158 ]
> 
> proc.time()
   user  system elapsed 
 52.604   3.186  57.036 

Example timings

autonomics.Rcheck/autonomics-Ex.timings

nameusersystemelapsed
AUTONOMICS_DATASETS000
COMPOUNDDISCOVERER_PATTERNS000
FITSEP000
LINMODENGINES000
MAXQUANT_PATTERNS000
SURVIVALENGINES0.0000.0000.001
TAXON_TO_ORGNAME000
TESTS0.0000.0010.000
X0.8220.0210.879
abstract_fit0.4880.0260.555
add_adjusted_pvalues0.1790.0050.198
add_assay_means0.1000.0020.102
add_facetvars0.4350.0160.465
add_opentargets_by_uniprot0.1150.0020.120
add_psp0.1560.0040.162
add_smiles0.1350.0130.162
analysis0.1140.0030.116
analyze4.1760.0464.229
annotate_maxquant0.3820.0210.404
annotate_uniprot_rest0.0310.0061.835
assert_is_valid_sumexp0.1590.0140.197
bin0.4510.0050.470
biplot1.3480.0211.419
biplot_corrections0.8720.0150.925
biplot_covariates1.4650.0181.520
block2lme0.0010.0000.001
center0.4260.0060.468
code1.5000.0201.526
coefs0.2350.0140.249
collapsed_entrezg_to_symbol000
contrast_subgroup_cols0.1700.0140.183
count_in000
counts0.1000.0010.101
counts2cpm0.0990.0010.100
counts2tpm0.0880.0010.089
cpm0.0960.0010.096
create_design0.1910.0140.205
default_formula5.5540.1855.808
default_geom0.1640.0140.239
default_sfile000
demultiplex0.0040.0000.003
dequantify0.0010.0000.000
dequantify_compounddiscoverer000
dot-coxph0.1270.0100.137
dot-merge0.0080.0000.007
dot-read_maxquant_proteingroups0.0450.0010.054
download_data0.0000.0010.000
download_gtf000
download_mcclain21000
dt2mat0.0010.0000.001
enrichment0.5190.0020.526
entrezg_to_symbol000
extract_coef_features1.9230.0211.963
extract_rectangle0.0460.0120.058
fcluster1.9210.0301.954
fcor0.3690.0090.380
fdata0.1560.0030.159
fdr2p0.3080.0140.322
filter_exprs_replicated_in_some_subgroup0.2820.0200.311
filter_features0.1670.0190.190
filter_medoid0.2340.0050.239
filter_samples0.1660.0140.195
fit_linmod9.2520.0739.538
fit_survival1.6190.0111.664
fitcoefs0.2800.0130.318
fits0.2690.0140.332
fix_xlgenes0.0000.0000.001
flevels0.1310.0020.141
fnames0.1710.0020.174
formula2str0.0010.0000.000
ftype2.9430.1423.649
fvalues0.1310.0070.148
fvars0.1150.0020.119
genome_to_orgdb000
group_by_level0.0000.0000.001
guess_compounddiscoverer_quantity000
guess_fitsep0.1310.0020.137
guess_maxquant_quantity0.0020.0000.001
guess_sep0.1380.0130.152
has_multiple_levels0.0160.0010.017
hdlproteins0.0200.0100.034
impute0.8550.0110.880
invert_subgroups0.1810.0020.189
is_collapsed_subset000
is_correlation_matrix0.0010.0000.001
is_diann_report0.1660.0160.188
is_fastadt0.0190.0010.028
is_file000
is_fraction0.0010.0000.001
is_imputed0.2020.0030.207
is_positive_number000
is_scalar_subset0.0970.0010.105
is_sig0.4640.0030.475
is_valid_formula0.0130.0000.013
keep_connected_blocks0.1420.0150.162
keep_connected_features0.2000.0160.284
keep_replicated_features0.2210.0140.310
label2index0.0000.0010.000
list2mat000
log2counts0.0900.0000.094
log2cpm0.0950.0000.095
log2diffs0.0890.0020.090
log2proteins0.0900.0010.091
log2sites0.0900.0010.095
log2tpm0.0860.0010.087
log2transform1.0860.0131.114
logical2factor0.0010.0000.001
make_alpha_palette0.1480.0140.162
make_colors0.0040.0000.005
make_volcano_dt0.2520.0030.254
map_fvalues0.1080.0020.110
matrix2sumexp0.2620.0130.277
merge_sample_file0.1360.0030.139
merge_sdata0.1550.0150.176
message_df0.0010.0000.001
model_coefs0.2150.0140.243
modelvar1.0140.0201.052
order_on_p0.3470.0150.376
pca0.8230.0210.883
pg_to_canonical0.0020.0000.002
plot_coef_densities0.3510.0200.420
plot_contrast_venn0.7700.0660.878
plot_contrastogram0.9030.0491.052
plot_data0.3690.0170.392
plot_densities2.4390.0792.652
plot_design0.1790.0030.210
plot_exprs6.3380.0486.521
plot_exprs_per_coef6.5340.0246.856
plot_fit_summary0.5720.0190.698
plot_heatmap0.6400.0030.688
plot_joint_density0.8710.0230.985
plot_matrix0.1450.0150.267
plot_sample_nas1.8120.0151.873
plot_subgroup_points1.3550.0191.495
plot_summary4.2830.0464.640
plot_survival1.0480.0051.131
plot_venn0.0020.0010.002
plot_venn_heatmap0.0070.0000.007
plot_violins1.2210.0341.347
plot_volcano3.5240.0353.801
preprocess_rnaseq_counts0.0820.0010.085
pull_columns0.0010.0000.000
read_affymetrix000
read_diann_proteingroups31.520 1.01332.790
read_fragpipe2.3860.0692.446
read_maxquant_phosphosites0.4470.0090.471
read_maxquant_proteingroups0.3540.0060.363
read_metabolon3.9740.0714.230
read_msigdt000
read_olink0.4750.0250.535
read_rectangles0.0650.0080.077
read_rnaseq_counts10.336 0.82711.311
read_salmon000
read_somascan4.0550.0124.108
read_uniprotdt0.1030.0050.109
reset_fit1.4650.0211.550
rm_diann_contaminants6.8690.2037.054
rm_missing_in_some_samples0.1470.0170.170
rm_unmatched_samples0.1960.0020.198
scaledlibsizes0.0830.0010.084
scoremat0.3070.0160.327
slevels0.1190.0020.122
snames0.1200.0010.121
split_extract_fixed0.1740.0150.192
split_samples0.4000.0310.450
stri_any_regex000
stri_detect_fixed_in_collapsed0.0990.0010.105
subgroup_matrix0.1520.0140.166
subtract_baseline1.4200.0351.483
sumexp_to_longdt0.5990.0250.646
sumexp_to_tsv0.1410.0020.144
sumexplist_to_longdt0.4640.0050.481
summarize_fit0.5400.0170.605
svalues0.1210.0020.126
svars0.1180.0020.121
systematic_nas0.1860.0010.195
tag_features0.4060.0110.421
tag_hdlproteins0.2150.0160.246
taxon2org000
tpm0.0920.0000.095
uncollapse0.0080.0000.009
values0.1220.0020.131
varlevels_dont_clash0.0090.0010.009
venn_detects0.2140.0020.231
weights0.0890.0000.092
write_xl0.2410.0140.282
zero_to_na000