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This page was generated on 2025-08-21 11:40 -0400 (Thu, 21 Aug 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 (2025-06-13) -- "Great Square Root" 4824
merida1macOS 12.7.5 Montereyx86_644.5.1 RC (2025-06-05 r88288) -- "Great Square Root" 4604
kjohnson1macOS 13.6.6 Venturaarm644.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" 4545
kunpeng2Linux (openEuler 24.03 LTS)aarch64R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" 4579
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 1.16.0  (landing page)
Aditya Bhagwat
Snapshot Date: 2025-08-18 13:40 -0400 (Mon, 18 Aug 2025)
git_url: https://git.bioconductor.org/packages/autonomics
git_branch: RELEASE_3_21
git_last_commit: a47f4df
git_last_commit_date: 2025-04-15 12:21:58 -0400 (Tue, 15 Apr 2025)
nebbiolo1Linux (Ubuntu 24.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 12.7.5 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.6 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published
kunpeng2Linux (openEuler 24.03 LTS) / aarch64  OK    OK    OK  


CHECK results for autonomics on kjohnson1

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: 1.16.0
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_1.16.0.tar.gz
StartedAt: 2025-08-19 13:16:44 -0400 (Tue, 19 Aug 2025)
EndedAt: 2025-08-19 13:32:41 -0400 (Tue, 19 Aug 2025)
EllapsedTime: 956.7 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_1.16.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.21-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 13.7.5
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘autonomics/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘autonomics’ version ‘1.16.0’
* 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 98.331  2.604 101.478
read_rnaseq_counts       33.396  1.261  35.609
fit_linmod               31.201  0.300  31.680
plot_exprs_per_coef      22.434  0.170  23.175
plot_exprs               21.407  0.162  22.177
rm_diann_contaminants    19.655  0.505  19.425
default_formula          16.989  0.461  17.091
plot_summary             14.091  0.105  14.395
read_metabolon           14.037  0.115  14.444
analyze                  13.730  0.184  14.000
read_somascan            13.160  0.053  13.334
plot_volcano             11.760  0.115  11.942
ftype                     9.405  0.390  10.102
plot_densities            8.395  0.184   8.814
fcluster                  6.445  0.075   6.560
extract_coef_features     6.377  0.113   6.511
plot_sample_nas           6.366  0.055   6.578
read_fragpipe             5.906  0.144   6.132
fit_survival              5.360  0.060   5.447
code                      5.104  0.084   5.195
biplot_covariates         5.018  0.065   5.096
* 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-3.21-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 ‘1.16.0’
** 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 
161.706   9.097 170.601 

Example timings

autonomics.Rcheck/autonomics-Ex.timings

nameusersystemelapsed
AUTONOMICS_DATASETS0.0000.0000.001
COMPOUNDDISCOVERER_PATTERNS0.0000.0000.001
FITSEP000
LINMODENGINES000
MAXQUANT_PATTERNS000
SURVIVALENGINES0.0000.0010.000
TAXON_TO_ORGNAME000
TESTS000
X2.4790.1072.649
abstract_fit1.6210.1051.769
add_adjusted_pvalues0.5690.0170.590
add_assay_means0.3830.0090.399
add_facetvars1.0720.0631.208
add_opentargets_by_uniprot0.3020.0070.323
add_psp0.5220.0150.552
add_smiles0.4510.0440.512
analysis0.4380.0120.451
analyze13.730 0.18414.000
annotate_maxquant1.1440.1101.288
annotate_uniprot_rest0.1000.0190.616
assert_is_valid_sumexp1.5890.0751.672
bin0.3700.0080.387
biplot4.5580.0954.697
biplot_corrections3.0650.0523.126
biplot_covariates5.0180.0655.096
block2lme0.0040.0000.003
center1.4220.0221.448
code5.1040.0845.195
coefs0.8160.0460.871
collapsed_entrezg_to_symbol000
contrast_subgroup_cols0.5980.0480.650
count_in0.0010.0010.002
counts0.3770.0040.382
counts2cpm0.3030.0030.306
counts2tpm0.3170.0030.322
cpm0.2950.0020.297
create_design0.6980.0470.752
default_formula16.989 0.46117.091
default_geom0.4940.0470.543
default_sfile0.0020.0010.002
demultiplex0.0110.0010.012
dequantify0.0020.0010.002
dequantify_compounddiscoverer0.0010.0000.001
dot-coxph0.4840.0430.558
dot-merge0.0240.0010.024
dot-read_maxquant_proteingroups0.1460.0050.152
download_data0.0010.0010.001
download_gtf000
download_mcclain210.0000.0000.001
dt2mat0.0040.0000.004
enrichment1.7270.0091.743
entrezg_to_symbol0.0000.0000.001
extract_coef_features6.3770.1136.511
extract_rectangle0.1540.0430.199
fcluster6.4450.0756.560
fcor1.1740.0321.220
fdata0.5030.0120.515
fdr2p1.0220.0501.099
filter_exprs_replicated_in_some_subgroup0.9780.0471.034
filter_features0.5500.0440.597
filter_medoid0.7330.0220.768
filter_samples0.5610.0450.614
fit_linmod31.201 0.30031.680
fit_survival5.3600.0605.447
fitcoefs0.9340.0460.985
fits0.8000.0460.848
fix_xlgenes0.0020.0000.003
flevels0.4280.0080.439
fnames0.5610.0080.576
formula2str0.0000.0000.001
ftype 9.405 0.39010.102
fvalues0.4110.0150.433
fvars0.4340.0100.451
genome_to_orgdb0.0010.0000.000
group_by_level0.0010.0010.002
guess_compounddiscoverer_quantity0.0010.0000.001
guess_fitsep0.4760.0070.498
guess_maxquant_quantity0.0050.0010.007
guess_sep0.4990.0430.557
has_multiple_levels0.0580.0020.059
hdlproteins0.0610.0300.098
impute2.8260.0442.985
invert_subgroups0.6080.0120.652
is_collapsed_subset0.0010.0000.000
is_correlation_matrix0.0010.0000.002
is_diann_report0.4540.0610.518
is_fastadt0.0590.0020.061
is_file0.0000.0000.001
is_fraction0.0020.0000.002
is_imputed0.7150.0070.731
is_positive_number0.0020.0000.002
is_scalar_subset0.3200.0060.327
is_sig1.7480.0201.822
is_valid_formula0.0550.0020.070
keep_connected_blocks0.5230.0510.703
keep_connected_features0.7040.0480.772
keep_replicated_features0.8090.0510.905
label2index0.0000.0000.001
list2mat0.0010.0000.001
log2counts0.3210.0040.331
log2cpm0.3190.0040.324
log2diffs0.3610.0090.373
log2proteins0.3220.0070.336
log2sites0.3170.0070.327
log2tpm0.3280.0040.354
log2transform3.8370.0653.987
logical2factor0.0010.0000.002
make_alpha_palette0.5180.0420.567
make_colors0.0140.0020.015
make_volcano_dt0.9230.0120.943
map_fvalues0.3850.0100.403
matrix2sumexp0.9440.0481.031
merge_sample_file0.4500.0090.466
merge_sdata0.5620.0500.618
message_df0.0020.0000.003
model_coefs0.7570.0470.818
modelvar3.5180.0673.704
order_on_p1.0980.0521.175
pca2.9620.0713.175
pg_to_canonical0.0060.0000.008
plot_coef_densities1.3750.0691.488
plot_contrast_venn2.5720.0792.851
plot_contrastogram2.9450.1213.135
plot_data1.2420.0561.314
plot_densities8.3950.1848.814
plot_design0.5950.0090.611
plot_exprs21.407 0.16222.177
plot_exprs_per_coef22.434 0.17023.175
plot_fit_summary2.0660.0542.169
plot_heatmap2.1720.0172.221
plot_joint_density3.0280.0783.267
plot_matrix0.5600.0470.622
plot_sample_nas6.3660.0556.578
plot_subgroup_points4.6710.0694.839
plot_summary14.091 0.10514.395
plot_survival3.5920.0323.661
plot_venn0.0050.0010.006
plot_venn_heatmap0.0240.0020.026
plot_violins3.9120.0894.026
plot_volcano11.760 0.11511.942
preprocess_rnaseq_counts0.5110.0170.530
pull_columns0.0040.0000.004
read_affymetrix000
read_diann_proteingroups 98.331 2.604101.478
read_fragpipe5.9060.1446.132
read_maxquant_phosphosites1.6590.0481.788
read_maxquant_proteingroups1.3170.0331.400
read_metabolon14.037 0.11514.444
read_msigdt0.0010.0010.001
read_olink1.5510.0721.744
read_rectangles0.2130.0260.247
read_rnaseq_counts33.396 1.26135.609
read_salmon0.0010.0000.000
read_somascan13.160 0.05313.334
read_uniprotdt0.3710.0230.422
reset_fit4.7050.0644.809
rm_diann_contaminants19.655 0.50519.425
rm_missing_in_some_samples0.4820.0410.526
rm_unmatched_samples0.6250.0080.634
scaledlibsizes0.3020.0030.305
scoremat0.9820.0451.030
slevels0.3960.0060.403
snames0.3940.0050.400
split_extract_fixed0.5330.0430.578
split_samples1.1720.0461.248
stri_any_regex0.0010.0010.001
stri_detect_fixed_in_collapsed0.3360.0060.343
subgroup_matrix0.4990.0410.544
subtract_baseline4.5530.0834.691
sumexp_to_longdt1.7990.0871.893
sumexp_to_tsv0.6010.0070.610
sumexplist_to_longdt1.5260.0171.544
summarize_fit1.6150.0491.677
svalues0.4710.0060.477
svars0.4030.0060.411
systematic_nas0.4980.0060.506
tag_features1.1490.0331.188
tag_hdlproteins0.5340.0240.566
taxon2org0.0010.0000.001
tpm0.2890.0030.293
uncollapse0.0280.0010.030
values0.5330.0080.547
varlevels_dont_clash0.0270.0010.028
venn_detects0.5540.0100.578
weights0.3150.0030.334
write_xl0.7870.0450.848
zero_to_na0.0010.0010.002