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This page was generated on 2025-10-08 12:53 -0400 (Wed, 08 Oct 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" 4854
lconwaymacOS 12.7.1 Montereyx86_644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4641
kjohnson3macOS 13.7.7 Venturaarm644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4586
taishanLinux (openEuler 24.03 LTS)aarch644.5.0 (2025-04-11) -- "How About a Twenty-Six" 4584
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 1.17.16  (landing page)
Aditya Bhagwat
Snapshot Date: 2025-10-07 13:45 -0400 (Tue, 07 Oct 2025)
git_url: https://git.bioconductor.org/packages/autonomics
git_branch: devel
git_last_commit: ca513f9
git_last_commit_date: 2025-10-03 08:57:56 -0400 (Fri, 03 Oct 2025)
nebbiolo2Linux (Ubuntu 24.04.3 LTS) / x86_64  OK    OK    OK  YES
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  YES
kjohnson3macOS 13.7.7 Ventura / arm64  OK    OK    OK    OK  YES
taishanLinux (openEuler 24.03 LTS) / aarch64  OK    OK    OK  


CHECK results for autonomics on taishan

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.
- See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host.

raw results


Summary

Package: autonomics
Version: 1.17.16
Command: /home/biocbuild/R/R/bin/R CMD check --install=check:autonomics.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings autonomics_1.17.16.tar.gz
StartedAt: 2025-10-07 04:26:01 -0000 (Tue, 07 Oct 2025)
EndedAt: 2025-10-07 04:49:18 -0000 (Tue, 07 Oct 2025)
EllapsedTime: 1396.7 seconds
RetCode: 0
Status:   OK  
CheckDir: autonomics.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD check --install=check:autonomics.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings autonomics_1.17.16.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/autonomics.Rcheck’
* using R version 4.5.0 (2025-04-11)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
    aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0
    GNU Fortran (GCC) 14.2.0
* running under: openEuler 24.03 (LTS)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘autonomics/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘autonomics’ version ‘1.17.16’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... INFO
Imports includes 32 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
write_xl                  233.854  1.408 235.914
awblinmod                  56.465  0.354  56.962
read_rnaseq_counts         40.636  0.824  41.652
read_diann_proteingroups   35.950  0.463  36.161
LINMOD                     33.840  0.546  34.477
plot_exprs                 28.609  0.167  28.860
plot_exprs_per_coef        27.409  0.088  27.565
default_formula            24.872  0.434  25.230
analyze                    19.128  0.842  20.538
read_somascan              19.197  0.024  19.271
plot_volcano               18.628  0.052  18.729
plot_summary               17.860  0.163  18.073
read_metabolon             17.872  0.071  17.985
fit_survival               14.626  0.040  14.731
explore-transforms         14.142  0.048  14.240
plot_densities             13.948  0.056  14.036
fcluster                   12.787  0.048  12.872
ftype                      11.311  0.144  11.453
plot_detections            10.194  0.008  10.231
biplot_covariates           9.598  0.028   9.657
plot_xy_density             8.692  0.016   8.737
read_fragpipe               8.513  0.096   8.476
plot_subgroup_points        8.220  0.016   8.258
rm_diann_contaminants       8.007  0.076   7.996
subtract_baseline           6.904  0.036   6.950
log2transform               6.861  0.016   6.900
plot_violins                6.762  0.080   6.858
reset_fit                   6.623  0.028   6.660
code                        6.627  0.000   6.645
extract_contrast_features   6.237  0.020   6.276
sbind                       5.953  0.004   5.972
modelvar                    5.540  0.108   5.659
biplot                      5.275  0.024   5.313
annotate_uniprot_rest       1.018  0.044   9.593
* 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
  ‘/home/biocbuild/bbs-3.22-bioc/meat/autonomics.Rcheck/00check.log’
for details.


Installation output

autonomics.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD INSTALL autonomics
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/R/R-4.5.0/site-library’
* installing *source* package ‘autonomics’ ...
** this is package ‘autonomics’ version ‘1.17.16’
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
Note: wrong number of arguments to 'seq_along' 
Note: wrong number of arguments to 'sqrt' 
** 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 4.5.0 (2025-04-11) -- "How About a Twenty-Six"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: aarch64-unknown-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 
182.025   3.497 184.933 

Example timings

autonomics.Rcheck/autonomics-Ex.timings

nameusersystemelapsed
AUTONOMICS_DATASETS0.0000.0000.001
COMPOUNDDISCOVERER_PATTERNS0.0010.0000.000
LINMOD33.840 0.54634.477
LINMODENGINES000
MAXQUANT_PATTERNS000
TAXON_TO_ORGNAME0.0000.0000.001
TESTS000
X1.7120.0361.751
abstract_fit1.4270.0191.449
add_adjusted_pvalues0.7150.0320.753
add_assay_means0.4770.0120.491
add_facetvars1.9570.0442.004
add_opentargets_by_uniprot0.5160.0080.532
add_psp0.6860.0070.699
add_smiles0.6410.0040.643
all_non_numeric0.8160.0040.823
analysis0.6270.0080.638
analyze19.128 0.84220.538
annotate_maxquant1.2260.0731.344
annotate_uniprot_rest1.0180.0449.593
assert_is_valid_sumexp0.6790.0160.694
awblinmod56.465 0.35456.962
biplot5.2750.0245.313
biplot_corrections4.7960.0634.873
biplot_covariates9.5980.0289.657
block2limma0.0030.0000.002
block2lm0.0040.0000.004
block2lme0.0030.0000.002
block2lmer0.0050.0000.005
block_has_two_levels0.8660.0160.880
center2.5160.0202.543
code6.6270.0006.645
collapsed_entrezg_to_symbol1.2230.0321.259
contrast_subgroup_cols0.8170.0240.841
contrastdt0.8460.0040.853
count_in0.0020.0000.001
counts0.4950.0000.497
counts2cpm0.4500.0000.451
counts2tpm0.4060.0040.412
cpm0.4540.0000.456
create_design0.9520.0120.964
default_formula24.872 0.43425.230
default_geom0.6360.0160.651
default_sfile0.0020.0000.001
demultiplex0.0190.0000.020
densities0.2990.0000.301
dequantify0.0030.0000.003
dequantify_compounddiscoverer0.0020.0000.001
dot-coxph0.4930.0120.507
dot-merge0.0270.0000.027
dot-read_maxquant_proteingroups0.1250.0040.129
download_data0.0010.0000.000
download_gtf000
download_mcclain21000
dt2mat0.0040.0000.004
enrichment1.6160.0001.624
entrezg_to_symbol0.1740.0040.178
explore-transforms14.142 0.04814.240
extract_contrast_features6.2370.0206.276
extract_rectangle0.1430.0040.147
factor.vars0.2440.0000.246
factorize1.1140.0001.118
fcluster12.787 0.04812.872
fcor2.0230.0042.034
fdata0.6940.0000.696
fdr2p1.2790.0161.297
filter_exprs_replicated_in_some_subgroup1.3080.0121.319
filter_features0.6600.0080.668
filter_medoid0.7790.0000.784
filter_samples0.7070.0160.723
fit_survival14.626 0.04014.731
fits0.4210.0040.426
fix_xlgenes0.0020.0000.002
flevels0.5120.0110.526
fnames0.6420.0040.648
formula2str000
ftype11.311 0.14411.453
fvalues0.5100.0040.517
fvars0.4950.0080.505
genome_to_orgdb0.0000.0000.001
group_by_level0.0010.0000.001
guess_compounddiscoverer_quantity0.0010.0000.001
guess_fitsep0.6610.0040.668
guess_maxquant_quantity0.0070.0000.007
guess_sep0.6190.0000.619
has_multiple_levels0.0720.0000.072
hdlproteins0.0460.0040.062
impute4.6230.0084.647
invert_subgroups0.8980.0040.905
is_character_matrix0.1920.0000.193
is_collapsed_subset000
is_compounddiscoverer_output0.0490.0120.104
is_correlation_matrix0.0020.0000.001
is_diann_report0.0830.0040.065
is_fastadt0.0850.0000.086
is_file000
is_fraction0.0020.0000.002
is_fragpipe_tsv0.0960.0000.069
is_imputed1.0080.0161.027
is_maxquant_phosphosites0.0620.0040.054
is_maxquant_proteingroups0.0610.0000.049
is_positive_number0.0020.0000.002
is_scalar_subset0.4150.0000.417
is_sig1.8960.0041.906
is_valid_formula0.0590.0000.060
keep_estimable_features0.9850.0120.996
label2index0.0010.0000.000
list2mat0.0010.0000.001
log2counts0.4940.0000.497
log2cpm0.4190.0000.421
log2diffs0.4050.0040.411
log2proteins0.4020.0000.403
log2sites0.4870.0000.489
log2tpm0.4190.0000.420
log2transform6.8610.0166.900
logical2factor0.0020.0000.002
make_alpha_palette0.6770.0120.688
make_colors0.0060.0050.011
make_volcano_dt1.1880.0021.194
map_fvalues0.5250.0080.534
matrix2sumexp1.3890.0041.395
mclust_breaks0.6860.0230.712
merge_sample_file0.6520.0040.658
merge_sdata0.8030.0200.823
message_df0.0020.0000.002
model_coefs1.0560.0161.073
modelvar5.5400.1085.659
object10.6290.0000.630
order_on_p1.7100.0161.729
overall_parameters0.0360.0000.036
pca4.2930.0604.363
pg_to_canonical0.0080.0000.008
plot_coef_densities1.8640.0161.883
plot_contrast_venn3.0070.0003.006
plot_contrastogram3.9970.0564.073
plot_data2.4380.0122.454
plot_densities13.948 0.05614.036
plot_design0.9360.0000.939
plot_detections10.194 0.00810.231
plot_exprs28.609 0.16728.860
plot_exprs_per_coef27.409 0.08827.565
plot_fit_summary2.9700.0242.997
plot_heatmap2.6630.0082.678
plot_matrix0.6810.0080.689
plot_subgroup_points8.2200.0168.258
plot_summary17.860 0.16318.073
plot_venn0.0140.0040.018
plot_venn_heatmap0.0270.0000.028
plot_violins6.7620.0806.858
plot_volcano18.628 0.05218.729
plot_xy_density8.6920.0168.737
preprocess_rnaseq_counts0.4260.0000.427
pull_columns0.0030.0000.003
pvalues_estimable0.050.000.05
read_affymetrix000
read_diann_proteingroups35.950 0.46336.161
read_fragpipe8.5130.0968.476
read_maxquant_phosphosites1.9500.0081.963
read_maxquant_proteingroups1.5960.0281.628
read_metabolon17.872 0.07117.985
read_msigdt0.0010.0000.001
read_olink1.8400.0161.844
read_rectangles0.2320.0040.237
read_rnaseq_counts40.636 0.82441.652
read_salmon000
read_somascan19.197 0.02419.271
read_uniprotdt0.3870.0080.396
reset_fit6.6230.0286.660
rm_diann_contaminants8.0070.0767.996
rm_missing_in_some_samples0.6900.0200.709
rm_unmatched_samples0.9580.0360.998
sbind5.9530.0045.972
scaledlibsizes0.4820.0040.486
scoremat1.1260.0121.137
slevels0.6040.0000.606
snames0.5500.0000.551
split_extract_fixed0.7040.0280.731
split_samples1.6930.0591.754
stepauc0.4810.0000.482
stri_any_regex0.0000.0000.001
stri_detect_fixed_in_collapsed0.5480.0040.554
subgroup_matrix0.7180.0160.733
subtract_baseline6.9040.0366.950
sumexp_to_longdt2.6290.0202.649
sumexp_to_tsv0.6750.0080.684
sumexplist_to_longdt2.0720.0042.082
summarize_fit2.3860.0282.414
survobj0.1990.0000.199
svalues0.5640.0000.565
svars0.6030.0000.605
systematic_nas0.7650.0160.783
tag_features1.2700.0361.310
tag_hdlproteins0.7710.0040.777
taxon2org0.0020.0000.001
tpm0.4550.0040.460
uncollapse0.0420.0000.043
values0.5560.0080.566
varlevels_dont_clash0.0280.0000.029
venn_detects0.8190.0040.825
weights0.4530.0000.454
write_xl233.854 1.408235.914
zero_to_na0.0020.0000.002