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This page was generated on 2025-09-23 12:05 -0400 (Tue, 23 Sep 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" 4816
lconwaymacOS 12.7.1 Montereyx86_644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4605
kjohnson3macOS 13.7.7 Venturaarm644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4549
taishanLinux (openEuler 24.03 LTS)aarch644.5.0 (2025-04-11) -- "How About a Twenty-Six" 4560
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 116/2334HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
autonomics 1.17.0  (landing page)
Aditya Bhagwat
Snapshot Date: 2025-09-22 13:45 -0400 (Mon, 22 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: 2025-09-22 18:14:53 -0400 (Mon, 22 Sep 2025)
EndedAt: 2025-09-22 18:20:27 -0400 (Mon, 22 Sep 2025)
EllapsedTime: 333.9 seconds
RetCode: 0
Status:   OK  
CheckDir: autonomics.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### 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 (2025-09-10 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 ‘1.17.0’
* 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 31.197  0.918  32.472
read_rnaseq_counts       11.384  0.723  12.440
fit_linmod                9.631  0.073  10.543
rm_diann_contaminants     7.513  0.269   7.974
plot_exprs                7.216  0.072   7.705
plot_exprs_per_coef       7.081  0.031   7.578
default_formula           6.074  0.179   6.342
analyze                   4.924  0.070   5.043
read_somascan             4.866  0.010   5.098
* 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 (2025-09-10 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 
 54.287   3.293  59.606 

Example timings

autonomics.Rcheck/autonomics-Ex.timings

nameusersystemelapsed
AUTONOMICS_DATASETS0.0000.0000.001
COMPOUNDDISCOVERER_PATTERNS000
FITSEP000
LINMODENGINES0.0000.0000.001
MAXQUANT_PATTERNS0.0000.0010.000
SURVIVALENGINES000
TAXON_TO_ORGNAME0.0000.0000.001
TESTS000
X0.4580.0580.538
abstract_fit0.4830.0200.505
add_adjusted_pvalues0.1750.0040.185
add_assay_means0.1110.0030.118
add_facetvars0.4470.0220.474
add_opentargets_by_uniprot0.1200.0020.130
add_psp0.1580.0030.163
add_smiles0.1320.0150.147
analysis0.1120.0020.115
analyze4.9240.0705.043
annotate_maxquant0.3190.0230.344
annotate_uniprot_rest0.0410.0082.233
assert_is_valid_sumexp0.1670.0130.191
bin0.1260.0030.138
biplot1.3360.0191.458
biplot_corrections1.4850.0201.579
biplot_covariates1.9440.0162.058
block2lme0.0010.0000.002
center0.5400.0040.555
code1.4770.0171.582
coefs0.2360.0130.340
collapsed_entrezg_to_symbol000
contrast_subgroup_cols0.1810.0130.290
count_in0.0000.0000.001
counts0.0990.0000.106
counts2cpm0.1210.0010.131
counts2tpm0.0890.0010.090
cpm0.0880.0000.089
create_design0.2110.0150.289
default_formula6.0740.1796.342
default_geom0.1430.0130.155
default_sfile0.0000.0010.001
demultiplex0.0040.0000.004
dequantify0.0010.0000.001
dequantify_compounddiscoverer0.0000.0000.001
dot-coxph0.1440.0120.163
dot-merge0.0070.0010.008
dot-read_maxquant_proteingroups0.0460.0010.056
download_data000
download_gtf000
download_mcclain210.0000.0000.001
dt2mat0.0010.0000.001
enrichment0.5130.0090.525
entrezg_to_symbol000
extract_coef_features1.7950.0161.818
extract_rectangle0.0420.0130.054
fcluster2.7000.0152.747
fcor0.5310.0210.571
fdata0.1540.0040.157
fdr2p0.2900.0140.323
filter_exprs_replicated_in_some_subgroup0.2850.0150.355
filter_features0.1660.0130.243
filter_medoid0.2170.0050.231
filter_samples0.1690.0140.208
fit_linmod 9.631 0.07310.543
fit_survival1.6600.0141.674
fitcoefs0.2690.0130.283
fits0.2300.0140.248
fix_xlgenes0.0000.0000.001
flevels0.1270.0020.129
fnames0.1570.0010.159
formula2str000
ftype2.6820.1273.229
fvalues0.1220.0030.123
fvars0.1440.0020.146
genome_to_orgdb000
group_by_level0.0010.0010.001
guess_compounddiscoverer_quantity000
guess_fitsep0.1310.0010.134
guess_maxquant_quantity0.0010.0010.002
guess_sep0.1660.0160.198
has_multiple_levels0.0160.0000.018
hdlproteins0.0190.0080.029
impute1.1230.0071.162
invert_subgroups0.2120.0010.223
is_collapsed_subset000
is_correlation_matrix0.0010.0000.001
is_diann_report0.1680.0170.203
is_fastadt0.0190.0010.021
is_file000
is_fraction0.0000.0000.001
is_imputed0.2300.0020.231
is_positive_number0.0010.0000.000
is_scalar_subset0.1150.0020.121
is_sig0.5330.0030.544
is_valid_formula0.0130.0000.016
keep_connected_blocks0.1800.0140.220
keep_connected_features0.6660.0230.871
keep_replicated_features0.2310.0210.341
label2index000
list2mat0.0000.0000.001
log2counts0.1090.0090.126
log2cpm0.0860.0010.086
log2diffs0.0910.0020.094
log2proteins0.0910.0020.096
log2sites0.0950.0020.107
log2tpm0.1070.0010.108
log2transform1.4370.0131.502
logical2factor0.0000.0000.001
make_alpha_palette0.1580.0140.196
make_colors0.0040.0010.004
make_volcano_dt0.2370.0010.238
map_fvalues0.1050.0020.107
matrix2sumexp0.2940.0140.362
merge_sample_file0.1410.0030.158
merge_sdata0.1520.0150.206
message_df0.0010.0000.001
model_coefs0.2040.0120.250
modelvar1.0160.0181.110
order_on_p0.3530.0160.405
pca0.9990.0191.102
pg_to_canonical0.0010.0000.002
plot_coef_densities0.3840.0140.457
plot_contrast_venn0.6840.0170.788
plot_contrastogram0.9100.0521.170
plot_data0.5200.0170.546
plot_densities2.9730.0793.227
plot_design0.2180.0020.228
plot_exprs7.2160.0727.705
plot_exprs_per_coef7.0810.0317.578
plot_fit_summary0.6500.0170.817
plot_heatmap0.6840.0030.727
plot_joint_density1.2630.0341.394
plot_matrix0.1520.0140.255
plot_sample_nas2.2000.0132.336
plot_subgroup_points1.9130.0412.105
plot_summary4.7260.0274.968
plot_survival1.1960.0071.248
plot_venn0.0010.0000.002
plot_venn_heatmap0.0070.0010.007
plot_violins1.6110.0471.745
plot_volcano4.4080.0344.795
preprocess_rnaseq_counts0.0840.0010.085
pull_columns0.0010.0010.001
read_affymetrix000
read_diann_proteingroups31.197 0.91832.472
read_fragpipe2.0900.0552.229
read_maxquant_phosphosites0.4560.0060.500
read_maxquant_proteingroups0.3680.0050.399
read_metabolon4.5390.0404.713
read_msigdt0.0000.0010.000
read_olink0.5370.0230.573
read_rectangles0.0610.0080.069
read_rnaseq_counts11.384 0.72312.440
read_salmon000
read_somascan4.8660.0105.098
read_uniprotdt0.1020.0070.110
reset_fit1.5510.0211.733
rm_diann_contaminants7.5130.2697.974
rm_missing_in_some_samples0.1420.0180.193
rm_unmatched_samples0.1780.0030.184
scaledlibsizes0.0800.0010.081
scoremat0.2850.0240.351
slevels0.1200.0030.128
snames0.1250.0020.129
split_extract_fixed0.1600.0150.212
split_samples0.3380.0170.380
stri_any_regex000
stri_detect_fixed_in_collapsed0.1110.0020.116
subgroup_matrix0.1550.0160.627
subtract_baseline1.4710.0311.655
sumexp_to_longdt0.5250.0300.628
sumexp_to_tsv0.1590.0020.167
sumexplist_to_longdt0.4640.0080.534
summarize_fit0.4890.0200.612
svalues0.1200.0030.129
svars0.1360.0040.153
systematic_nas0.1510.0020.171
tag_features0.3650.0160.406
tag_hdlproteins0.1680.0150.190
taxon2org0.0000.0000.001
tpm0.0960.0010.100
uncollapse0.0150.0010.016
values0.1520.0020.161
varlevels_dont_clash0.010.000.01
venn_detects0.1730.0040.181
weights0.0910.0030.127
write_xl0.2190.0180.286
zero_to_na0.0000.0010.001