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This page was generated on 2025-09-23 12:03 -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 nebbiolo2

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: /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:autonomics.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings autonomics_1.17.0.tar.gz
StartedAt: 2025-09-22 21:02:59 -0400 (Mon, 22 Sep 2025)
EndedAt: 2025-09-22 21:22:31 -0400 (Mon, 22 Sep 2025)
EllapsedTime: 1171.4 seconds
RetCode: 0
Status:   OK  
CheckDir: autonomics.Rcheck
Warnings: 0

Command output

##############################################################################
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### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:autonomics.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings autonomics_1.17.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/autonomics.Rcheck’
* using R version 4.5.1 Patched (2025-08-23 r88802)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
    GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.3 LTS
* using session charset: UTF-8
* 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 loading without being on the library search path ... 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 396.194  2.085 102.968
rm_diann_contaminants    104.492  1.242  23.687
read_rnaseq_counts        44.614  1.860  38.257
fit_linmod                42.926  0.265  32.202
ftype                     39.204  0.150   9.229
plot_exprs                28.728  0.056  25.191
default_formula           26.375  0.301  17.358
plot_exprs_per_coef       24.915  0.032  24.864
plot_contrastogram        19.639  0.058   3.312
read_somascan             17.873  0.136  17.467
analyze                   16.275  0.238  16.389
read_metabolon            15.821  0.331  16.056
plot_summary              15.266  0.098  15.261
plot_volcano              14.163  0.020  14.096
plot_densities            12.094  0.115   9.967
read_olink                11.916  0.042   1.787
is_diann_report            8.706  0.107   0.696
fcluster                   8.731  0.043   8.623
read_fragpipe              7.644  0.266   5.928
plot_subgroup_points       7.121  0.095   5.647
plot_sample_nas            6.792  0.035   6.803
biplot_covariates          6.518  0.031   6.518
extract_coef_features      6.369  0.022   6.359
subtract_baseline          6.167  0.115   5.145
log2transform              5.850  0.117   5.968
fit_survival               5.372  0.078   5.433
code                       5.147  0.035   5.145
plot_joint_density         4.874  0.153   5.005
* 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 re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.22-bioc/meat/autonomics.Rcheck/00check.log’
for details.


Installation output

autonomics.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD INSTALL autonomics
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.22-bioc/R/site-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 (2025-08-23 r88802) -- "Great Square Root"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu

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 
283.527   9.179 222.726 

Example timings

autonomics.Rcheck/autonomics-Ex.timings

nameusersystemelapsed
AUTONOMICS_DATASETS000
COMPOUNDDISCOVERER_PATTERNS000
FITSEP000
LINMODENGINES000
MAXQUANT_PATTERNS000
SURVIVALENGINES000
TAXON_TO_ORGNAME000
TESTS000
X1.4640.1401.579
abstract_fit1.6690.0501.694
add_adjusted_pvalues0.5450.0110.557
add_assay_means0.3500.0040.354
add_facetvars1.5070.0201.507
add_opentargets_by_uniprot0.3810.0090.393
add_psp0.5150.0090.525
add_smiles0.4330.0050.418
analysis0.3740.0010.376
analyze16.275 0.23816.389
annotate_maxquant0.8490.0300.879
annotate_uniprot_rest0.3350.0302.120
assert_is_valid_sumexp0.5610.0070.529
bin0.3780.0130.391
biplot4.3550.0894.406
biplot_corrections4.3900.1284.479
biplot_covariates6.5180.0316.518
block2lme0.0020.0010.003
center1.7370.0031.741
code5.1470.0355.145
coefs0.7830.0060.751
collapsed_entrezg_to_symbol0.0000.0010.000
contrast_subgroup_cols0.5510.0450.573
count_in0.0010.0000.001
counts0.3140.0210.334
counts2cpm0.2910.0050.296
counts2tpm0.260.000.26
cpm0.3500.0030.353
create_design0.6400.0090.616
default_formula26.375 0.30117.358
default_geom0.4880.0040.470
default_sfile0.0010.0000.001
demultiplex0.0120.0010.013
dequantify0.0020.0000.002
dequantify_compounddiscoverer0.0010.0000.000
dot-coxph0.3720.0060.378
dot-merge0.0160.0000.017
dot-read_maxquant_proteingroups0.1060.0040.110
download_data000
download_gtf000
download_mcclain21000
dt2mat0.0030.0000.002
enrichment1.7310.0011.732
entrezg_to_symbol000
extract_coef_features6.3690.0226.359
extract_rectangle0.1020.0050.108
fcluster8.7310.0438.623
fcor1.3790.0051.384
fdata0.5890.0470.636
fdr2p0.9230.0150.917
filter_exprs_replicated_in_some_subgroup0.9510.0060.902
filter_features0.5020.0060.488
filter_medoid0.6190.0040.625
filter_samples0.5150.0110.498
fit_linmod42.926 0.26532.202
fit_survival5.3720.0785.433
fitcoefs0.8440.0050.827
fits0.7060.0060.690
fix_xlgenes0.0020.0000.002
flevels0.3670.0010.369
fnames0.4680.0030.471
formula2str000
ftype39.204 0.150 9.229
fvalues0.3870.0020.388
fvars0.4080.0020.409
genome_to_orgdb0.0010.0000.000
group_by_level0.0010.0000.001
guess_compounddiscoverer_quantity0.0010.0000.002
guess_fitsep0.4600.0050.465
guess_maxquant_quantity0.0050.0010.006
guess_sep0.5420.0100.521
has_multiple_levels0.0540.0000.054
hdlproteins0.0420.0080.052
impute3.5640.0113.575
invert_subgroups0.6590.0000.658
is_collapsed_subset000
is_correlation_matrix0.0000.0010.001
is_diann_report8.7060.1070.696
is_fastadt0.0650.0010.066
is_file0.0000.0010.001
is_fraction0.0020.0000.002
is_imputed0.7250.0030.729
is_positive_number0.0010.0000.002
is_scalar_subset0.3510.0030.355
is_sig1.7910.0041.796
is_valid_formula0.0420.0000.044
keep_connected_blocks0.8420.0110.526
keep_connected_features2.6960.0140.808
keep_replicated_features0.8940.0110.841
label2index0.0010.0000.000
list2mat0.0010.0000.001
log2counts0.3160.0000.316
log2cpm0.3480.0000.348
log2diffs0.3170.0010.317
log2proteins0.3880.0000.388
log2sites0.3070.0020.308
log2tpm0.3360.0000.336
log2transform5.8500.1175.968
logical2factor0.0010.0000.002
make_alpha_palette0.5090.0080.495
make_colors0.010.000.01
make_volcano_dt0.8740.0010.876
map_fvalues0.3550.0020.357
matrix2sumexp0.9890.0060.973
merge_sample_file0.4180.0020.420
merge_sdata0.5490.0050.531
message_df0.0020.0000.002
model_coefs0.6970.0100.687
modelvar3.5610.0363.541
order_on_p1.1750.0081.162
pca3.4610.0093.448
pg_to_canonical0.0050.0000.005
plot_coef_densities1.3180.0051.302
plot_contrast_venn2.4420.0342.395
plot_contrastogram19.639 0.058 3.312
plot_data1.5820.0061.566
plot_densities12.094 0.115 9.967
plot_design0.7380.0030.741
plot_exprs28.728 0.05625.191
plot_exprs_per_coef24.915 0.03224.864
plot_fit_summary2.2120.0102.124
plot_heatmap2.2930.0052.300
plot_joint_density4.8740.1535.005
plot_matrix0.4610.0100.436
plot_sample_nas6.7920.0356.803
plot_subgroup_points7.1210.0955.647
plot_summary15.266 0.09815.261
plot_survival4.1170.0284.162
plot_venn0.0050.0000.005
plot_venn_heatmap0.0230.0000.023
plot_violins4.7150.0534.745
plot_volcano14.163 0.02014.096
preprocess_rnaseq_counts0.3380.0020.339
pull_columns0.0020.0000.002
read_affymetrix000
read_diann_proteingroups396.194 2.085102.968
read_fragpipe7.6440.2665.928
read_maxquant_phosphosites1.6500.0251.679
read_maxquant_proteingroups1.1500.0191.169
read_metabolon15.821 0.33116.056
read_msigdt0.0010.0000.000
read_olink11.916 0.042 1.787
read_rectangles0.1720.0100.182
read_rnaseq_counts44.614 1.86038.257
read_salmon000
read_somascan17.873 0.13617.467
read_uniprotdt0.2800.0030.283
reset_fit4.9280.0084.842
rm_diann_contaminants104.492 1.242 23.687
rm_missing_in_some_samples0.4880.0680.532
rm_unmatched_samples0.6520.0950.747
scaledlibsizes0.2710.0060.277
scoremat0.9700.0220.967
slevels0.3830.0060.390
snames0.4680.0200.488
split_extract_fixed0.4860.0320.494
split_samples1.3010.0751.360
stri_any_regex0.0000.0000.001
stri_detect_fixed_in_collapsed0.3590.0140.374
subgroup_matrix0.6190.0390.628
subtract_baseline6.1670.1155.145
sumexp_to_longdt2.0320.0942.073
sumexp_to_tsv0.4420.0080.450
sumexplist_to_longdt1.3770.0191.396
summarize_fit1.7720.0151.720
svalues0.4020.0060.407
svars0.4000.0040.404
systematic_nas0.6240.0220.646
tag_features1.0520.0131.066
tag_hdlproteins0.5830.0160.599
taxon2org0.0000.0010.001
tpm0.3040.0030.308
uncollapse0.0270.0000.027
values0.3910.0110.402
varlevels_dont_clash0.0210.0010.022
venn_detects0.5710.0010.572
weights0.2880.0000.288
write_xl0.9790.0561.012
zero_to_na0.0010.0000.001