Back to Multiple platform build/check report for BioC 3.22:   simplified   long
[A]BCDEFGHIJKLMNOPQRSTUVWXYZ

This page was generated on 2025-09-23 12:04 -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 lconway

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 19:23:14 -0400 (Mon, 22 Sep 2025)
EndedAt: 2025-09-22 19:43:12 -0400 (Mon, 22 Sep 2025)
EllapsedTime: 1198.2 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: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Monterey 12.7.6
* 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 115.314  2.039 118.550
read_rnaseq_counts        43.189  3.493  47.440
fit_linmod                37.292  0.297  37.770
plot_exprs                28.740  0.246  29.133
plot_exprs_per_coef       28.253  0.172  28.561
rm_diann_contaminants     25.759  0.523  26.562
default_formula           19.665  0.332  20.154
read_somascan             19.585  0.159  19.945
read_metabolon            19.246  0.220  19.687
analyze                   18.294  0.208  18.590
plot_summary              18.159  0.114  18.344
plot_volcano              16.065  0.127  16.263
plot_densities            12.193  0.206  12.469
fcluster                  10.518  0.076  10.630
ftype                     10.116  0.278  10.488
biplot_covariates          8.077  0.086   8.209
plot_sample_nas            8.083  0.071   8.198
extract_coef_features      7.467  0.082   7.597
read_fragpipe              7.314  0.117   7.504
plot_subgroup_points       7.045  0.103   7.190
fit_survival               6.446  0.064   6.543
reset_fit                  6.343  0.101   6.519
subtract_baseline          6.187  0.127   6.447
code                       5.970  0.075   6.076
log2transform              5.927  0.056   6.026
plot_violins               5.704  0.089   5.813
biplot                     5.184  0.073   5.288
biplot_corrections         5.127  0.069   5.218
* 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-x86_64/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: x86_64-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 
159.226  10.942 231.697 

Example timings

autonomics.Rcheck/autonomics-Ex.timings

nameusersystemelapsed
AUTONOMICS_DATASETS0.0010.0000.001
COMPOUNDDISCOVERER_PATTERNS0.0000.0010.001
FITSEP0.0000.0010.001
LINMODENGINES000
MAXQUANT_PATTERNS000
SURVIVALENGINES0.0010.0000.001
TAXON_TO_ORGNAME000
TESTS0.0000.0000.001
X1.7650.1461.925
abstract_fit1.9700.0852.072
add_adjusted_pvalues0.6610.0190.687
add_assay_means0.4370.0100.451
add_facetvars1.8450.0621.919
add_opentargets_by_uniprot0.4790.0090.494
add_psp0.6080.0160.628
add_smiles0.5340.0450.583
analysis0.4140.0070.424
analyze18.294 0.20818.590
annotate_maxquant1.0510.1071.171
annotate_uniprot_rest0.0910.0141.979
assert_is_valid_sumexp0.6280.0430.675
bin0.4410.0100.452
biplot5.1840.0735.288
biplot_corrections5.1270.0695.218
biplot_covariates8.0770.0868.209
block2lme0.0040.0010.005
center2.0330.0212.066
code5.9700.0756.076
coefs0.8830.0390.925
collapsed_entrezg_to_symbol0.0010.0000.001
contrast_subgroup_cols0.6420.0490.695
count_in0.0010.0010.003
counts0.3830.0030.390
counts2cpm0.4420.0030.446
counts2tpm0.3470.0030.351
cpm0.3670.0030.378
create_design0.8060.0530.876
default_formula19.665 0.33220.154
default_geom0.5440.0440.595
default_sfile0.0020.0010.002
demultiplex0.0170.0010.018
dequantify0.0030.0010.003
dequantify_compounddiscoverer0.0010.0010.002
dot-coxph0.4940.0500.549
dot-merge0.0240.0010.025
dot-read_maxquant_proteingroups0.1300.0060.137
download_data0.0000.0010.001
download_gtf000
download_mcclain210.0010.0000.001
dt2mat0.0030.0010.004
enrichment1.9710.0101.989
entrezg_to_symbol0.0000.0000.001
extract_coef_features7.4670.0827.597
extract_rectangle0.1520.0460.206
fcluster10.518 0.07610.630
fcor1.7500.0421.801
fdata0.5750.0140.590
fdr2p1.0330.0391.075
filter_exprs_replicated_in_some_subgroup1.0720.0621.159
filter_features0.6210.0390.663
filter_medoid0.8580.0220.884
filter_samples0.5900.0420.637
fit_linmod37.292 0.29737.770
fit_survival6.4460.0646.543
fitcoefs1.0250.0441.075
fits0.8760.0440.926
fix_xlgenes0.0020.0000.002
flevels0.5200.0090.535
fnames0.5900.0120.608
formula2str000
ftype10.116 0.27810.488
fvalues0.4520.0070.461
fvars0.5190.0070.530
genome_to_orgdb0.0000.0010.001
group_by_level0.0010.0010.002
guess_compounddiscoverer_quantity0.0010.0000.002
guess_fitsep0.4990.0060.508
guess_maxquant_quantity0.0070.0020.009
guess_sep0.6210.0460.673
has_multiple_levels0.0690.0040.077
hdlproteins0.0500.0290.083
impute4.3740.0444.454
invert_subgroups0.8880.0090.904
is_collapsed_subset0.0000.0010.001
is_correlation_matrix0.0010.0000.001
is_diann_report0.2600.0510.391
is_fastadt0.0640.0010.066
is_file0.0000.0000.001
is_fraction0.0020.0000.002
is_imputed0.8620.0070.874
is_positive_number0.0010.0000.002
is_scalar_subset0.4810.0050.492
is_sig2.2940.0142.325
is_valid_formula0.0660.0020.068
keep_connected_blocks0.7330.0780.840
keep_connected_features1.8600.0791.959
keep_replicated_features0.9440.0551.013
label2index0.0010.0000.001
list2mat0.0000.0000.001
log2counts0.4130.0080.427
log2cpm0.4040.0050.412
log2diffs0.4220.0070.433
log2proteins0.4210.0070.430
log2sites0.3990.0080.408
log2tpm0.4560.0040.464
log2transform5.9270.0566.026
logical2factor0.0010.0000.001
make_alpha_palette0.6240.0430.670
make_colors0.0110.0020.012
make_volcano_dt1.0490.0141.071
map_fvalues0.4910.0100.506
matrix2sumexp1.2180.0641.302
merge_sample_file0.5230.0090.534
merge_sdata0.5870.0530.644
message_df0.0020.0000.003
model_coefs0.8450.0540.918
modelvar4.1530.0744.264
order_on_p1.4360.0541.502
pca4.2830.0724.389
pg_to_canonical0.0050.0000.005
plot_coef_densities1.6750.0451.730
plot_contrast_venn2.8760.0632.961
plot_contrastogram3.6150.1663.846
plot_data2.2230.0652.313
plot_densities12.193 0.20612.469
plot_design0.8770.0090.889
plot_exprs28.740 0.24629.133
plot_exprs_per_coef28.253 0.17228.561
plot_fit_summary2.5710.0562.639
plot_heatmap2.6990.0162.723
plot_joint_density4.7240.0784.821
plot_matrix0.5800.0430.627
plot_sample_nas8.0830.0718.198
plot_subgroup_points7.0450.1037.190
plot_summary18.159 0.11418.344
plot_survival4.5110.0304.556
plot_venn0.0050.0020.007
plot_venn_heatmap0.0240.0020.026
plot_violins5.7040.0895.813
plot_volcano16.065 0.12716.263
preprocess_rnaseq_counts0.3510.0030.359
pull_columns0.0030.0010.003
read_affymetrix0.0000.0000.001
read_diann_proteingroups115.314 2.039118.550
read_fragpipe7.3140.1177.504
read_maxquant_phosphosites1.7640.0361.815
read_maxquant_proteingroups1.4370.0231.468
read_metabolon19.246 0.22019.687
read_msigdt0.0010.0010.001
read_olink1.8630.0902.104
read_rectangles0.2370.0310.280
read_rnaseq_counts43.189 3.49347.440
read_salmon0.0010.0010.002
read_somascan19.585 0.15919.945
read_uniprotdt0.4460.0400.491
reset_fit6.3430.1016.519
rm_diann_contaminants25.759 0.52326.562
rm_missing_in_some_samples0.5640.0500.623
rm_unmatched_samples0.8050.0180.829
scaledlibsizes0.3700.0060.379
scoremat1.1890.0611.275
slevels0.4800.0210.508
snames0.4950.0110.513
split_extract_fixed0.6560.0590.726
split_samples1.4480.0641.529
stri_any_regex0.0000.0020.003
stri_detect_fixed_in_collapsed0.4080.0090.434
subgroup_matrix0.6370.0540.705
subtract_baseline6.1870.1276.447
sumexp_to_longdt2.1250.1952.404
sumexp_to_tsv0.6480.0150.686
sumexplist_to_longdt1.7880.0321.905
summarize_fit1.8200.0721.924
svalues0.4580.0110.485
svars0.5030.0100.558
systematic_nas0.6270.0100.650
tag_features1.2920.0451.380
tag_hdlproteins0.6230.0380.671
taxon2org0.0010.0010.001
tpm0.3810.0060.391
uncollapse0.0380.0030.040
values1.6040.0641.686
varlevels_dont_clash0.0270.0010.028
venn_detects0.6640.0270.702
weights0.4060.0050.415
write_xl0.8800.0610.953
zero_to_na0.0010.0010.003