Aditya Bhagwat
| Snapshot Date: 2026-01-01 13:45 -0500 (Thu, 01 Jan 2026) |
| git_url: https://git.bioconductor.org/packages/autonomics |
| git_branch: RELEASE_3_22 |
| git_last_commit: c22fce2 |
| git_last_commit_date: 2025-10-29 11:06:51 -0500 (Wed, 29 Oct 2025) |
| Back to Multiple platform build/check report for BioC 3.22: simplified long |
|
This page was generated on 2026-01-05 11:58 -0500 (Mon, 05 Jan 2026).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble" | 4883 |
| taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4671 |
| 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 119/2361 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| autonomics 1.18.0 (landing page) Aditya Bhagwat
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| taishan | Linux (openEuler 24.03 LTS) / aarch64 | OK | OK | TIMEOUT | ||||||||||
|
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. |
| Package: autonomics |
| Version: 1.18.0 |
| 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_1.18.0.tar.gz |
| StartedAt: 2026-01-02 06:53:01 -0000 (Fri, 02 Jan 2026) |
| EndedAt: 2026-01-02 07:35:10 -0000 (Fri, 02 Jan 2026) |
| EllapsedTime: 2529.5 seconds |
| RetCode: None |
| Status: TIMEOUT |
| CheckDir: autonomics.Rcheck |
| Warnings: NA |
##############################################################################
##############################################################################
###
### 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_1.18.0.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 ‘1.18.0’
* 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 227.224 1.658 229.913
awblinmod 60.233 0.211 60.646
read_diann_proteingroups 59.633 0.629 62.767
read_rnaseq_counts 40.519 0.563 43.041
LINMOD 33.436 0.610 34.165
plot_exprs 29.756 0.115 31.147
plot_exprs_per_coef 28.395 0.115 28.892
default_formula 25.785 0.430 26.561
plot_summary 19.487 0.147 20.113
analyze 18.405 0.076 18.524
read_somascan 18.289 0.116 18.828
read_metabolon 17.970 0.156 18.190
plot_volcano 17.879 0.075 19.050
explore-transforms 15.257 0.148 15.469
fit_survival 14.886 0.127 15.061
plot_densities 14.806 0.142 15.432
rm_diann_contaminants 13.496 0.223 14.104
fcluster 13.163 0.024 13.407
ftype 11.294 0.128 11.430
plot_detections 10.698 0.136 11.116
biplot_covariates 9.589 0.004 9.618
read_fragpipe 8.568 0.024 8.491
plot_xy_density 8.504 0.024 10.391
plot_subgroup_points 8.383 0.036 8.471
log2transform 6.976 0.028 7.295
subtract_baseline 6.744 0.032 6.795
reset_fit 6.451 0.087 6.769
extract_contrast_features 6.448 0.044 6.514
code 6.398 0.016 6.428
plot_violins 6.323 0.072 6.410
sbind 5.530 0.012 5.557
biplot 5.129 0.024 5.163
plot_contrastogram 4.245 0.036 5.404
annotate_uniprot_rest 0.113 0.004 5.305
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’/home/biocbuild/R/R-4.5.0/bin/BATCH: line 60: 1706408 Killed ${R_HOME}/bin/R -f ${in} ${opts} ${R_BATCH_OPTIONS} > ${out} 2>&1
ERROR
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
> 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")
* 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 ...
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 ‘1.18.0’ ** 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)
autonomics.Rcheck/tests/testthat.Rout.fail
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")
autonomics.Rcheck/autonomics-Ex.timings
| name | user | system | elapsed | |
| AUTONOMICS_DATASETS | 0.000 | 0.001 | 0.000 | |
| COMPOUNDDISCOVERER_PATTERNS | 0 | 0 | 0 | |
| LINMOD | 33.436 | 0.610 | 34.165 | |
| LINMODENGINES | 0.001 | 0.000 | 0.000 | |
| MAXQUANT_PATTERNS | 0 | 0 | 0 | |
| TAXON_TO_ORGNAME | 0 | 0 | 0 | |
| TESTS | 0.001 | 0.000 | 0.000 | |
| X | 1.654 | 0.016 | 1.674 | |
| abstract_fit | 1.372 | 0.004 | 1.379 | |
| add_adjusted_pvalues | 0.650 | 0.012 | 0.667 | |
| add_assay_means | 0.478 | 0.008 | 0.487 | |
| add_facetvars | 1.857 | 0.016 | 1.877 | |
| add_opentargets_by_uniprot | 0.523 | 0.004 | 0.533 | |
| add_psp | 0.630 | 0.040 | 0.675 | |
| add_smiles | 0.640 | 0.016 | 0.657 | |
| all_non_numeric | 0.773 | 0.024 | 0.798 | |
| analysis | 0.500 | 0.008 | 0.508 | |
| analyze | 18.405 | 0.076 | 18.524 | |
| annotate_maxquant | 1.354 | 0.055 | 1.579 | |
| annotate_uniprot_rest | 0.113 | 0.004 | 5.305 | |
| assert_is_valid_sumexp | 0.737 | 0.008 | 0.749 | |
| awblinmod | 60.233 | 0.211 | 60.646 | |
| biplot | 5.129 | 0.024 | 5.163 | |
| biplot_corrections | 4.749 | 0.028 | 4.980 | |
| biplot_covariates | 9.589 | 0.004 | 9.618 | |
| block2limma | 0.003 | 0.000 | 0.002 | |
| block2lm | 0.004 | 0.000 | 0.004 | |
| block2lme | 0.003 | 0.000 | 0.003 | |
| block2lmer | 0.006 | 0.000 | 0.005 | |
| block_has_two_levels | 0.843 | 0.008 | 0.849 | |
| center | 2.492 | 0.020 | 2.520 | |
| code | 6.398 | 0.016 | 6.428 | |
| collapsed_entrezg_to_symbol | 1.089 | 0.056 | 1.147 | |
| contrast_subgroup_cols | 0.752 | 0.020 | 0.773 | |
| contrastdt | 0.775 | 0.000 | 0.777 | |
| count_in | 0.000 | 0.001 | 0.002 | |
| counts | 0.475 | 0.003 | 0.480 | |
| counts2cpm | 0.410 | 0.000 | 0.412 | |
| counts2tpm | 0.431 | 0.000 | 0.431 | |
| cpm | 0.446 | 0.000 | 0.448 | |
| create_design | 1.002 | 0.011 | 1.017 | |
| default_formula | 25.785 | 0.430 | 26.561 | |
| default_geom | 0.685 | 0.004 | 0.721 | |
| default_sfile | 0.002 | 0.000 | 0.002 | |
| demultiplex | 0.021 | 0.000 | 0.021 | |
| densities | 0.310 | 0.000 | 0.311 | |
| dequantify | 0.003 | 0.000 | 0.003 | |
| dequantify_compounddiscoverer | 0.002 | 0.000 | 0.002 | |
| dot-coxph | 0.522 | 0.000 | 0.576 | |
| dot-merge | 0.027 | 0.000 | 0.033 | |
| dot-read_maxquant_proteingroups | 0.129 | 0.000 | 0.130 | |
| download_data | 0 | 0 | 0 | |
| download_gtf | 0 | 0 | 0 | |
| download_mcclain21 | 0.001 | 0.000 | 0.001 | |
| dt2mat | 0.004 | 0.000 | 0.004 | |
| enrichment | 1.745 | 0.007 | 1.783 | |
| entrezg_to_symbol | 0.172 | 0.004 | 0.177 | |
| explore-transforms | 15.257 | 0.148 | 15.469 | |
| extract_contrast_features | 6.448 | 0.044 | 6.514 | |
| extract_rectangle | 0.125 | 0.024 | 0.150 | |
| factor.vars | 0.251 | 0.000 | 0.252 | |
| factorize | 1.089 | 0.008 | 1.124 | |
| fcluster | 13.163 | 0.024 | 13.407 | |
| fcor | 2.039 | 0.012 | 2.100 | |
| fdata | 0.737 | 0.024 | 0.763 | |
| fdr2p | 1.219 | 0.016 | 1.237 | |
| filter_exprs_replicated_in_some_subgroup | 1.317 | 0.012 | 1.330 | |
| filter_features | 0.677 | 0.012 | 0.692 | |
| filter_medoid | 0.827 | 0.000 | 0.830 | |
| filter_samples | 0.682 | 0.000 | 0.688 | |
| fit_survival | 14.886 | 0.127 | 15.061 | |
| fits | 0.429 | 0.012 | 0.443 | |
| fix_xlgenes | 0.002 | 0.000 | 0.002 | |
| flevels | 0.514 | 0.016 | 0.531 | |
| fnames | 0.588 | 0.012 | 0.603 | |
| formula2str | 0 | 0 | 0 | |
| ftype | 11.294 | 0.128 | 11.430 | |
| fvalues | 0.520 | 0.004 | 0.526 | |
| fvars | 0.548 | 0.004 | 0.554 | |
| genome_to_orgdb | 0.001 | 0.000 | 0.001 | |
| group_by_level | 0.001 | 0.000 | 0.001 | |
| guess_compounddiscoverer_quantity | 0.001 | 0.000 | 0.001 | |
| guess_fitsep | 0.625 | 0.004 | 0.631 | |
| guess_maxquant_quantity | 0.006 | 0.000 | 0.007 | |
| guess_sep | 0.695 | 0.008 | 0.781 | |
| has_multiple_levels | 0.063 | 0.012 | 0.075 | |
| hdlproteins | 0.057 | 0.004 | 0.071 | |
| impute | 4.815 | 0.035 | 4.956 | |
| invert_subgroups | 0.936 | 0.016 | 0.956 | |
| is_character_matrix | 0.201 | 0.000 | 0.201 | |
| is_collapsed_subset | 0.001 | 0.000 | 0.001 | |
| is_compounddiscoverer_output | 0.095 | 0.024 | 0.203 | |
| is_correlation_matrix | 0.001 | 0.000 | 0.001 | |
| is_diann_report | 0.166 | 0.012 | 0.179 | |
| is_fastadt | 0.080 | 0.004 | 0.084 | |
| is_file | 0 | 0 | 0 | |
| is_fraction | 0.002 | 0.000 | 0.002 | |
| is_fragpipe_tsv | 0.124 | 0.004 | 0.129 | |
| is_imputed | 0.911 | 0.008 | 0.921 | |
| is_maxquant_phosphosites | 0.095 | 0.000 | 0.095 | |
| is_maxquant_proteingroups | 0.087 | 0.004 | 0.091 | |
| is_positive_number | 0.002 | 0.000 | 0.002 | |
| is_scalar_subset | 0.466 | 0.000 | 0.468 | |
| is_sig | 1.846 | 0.015 | 1.892 | |
| is_valid_formula | 0.113 | 0.000 | 0.113 | |
| keep_estimable_features | 1.044 | 0.004 | 1.054 | |
| label2index | 0.001 | 0.000 | 0.001 | |
| list2mat | 0.000 | 0.000 | 0.001 | |
| log2counts | 0.432 | 0.004 | 0.469 | |
| log2cpm | 0.479 | 0.000 | 0.490 | |
| log2diffs | 0.429 | 0.004 | 0.435 | |
| log2proteins | 0.408 | 0.008 | 0.417 | |
| log2sites | 0.418 | 0.008 | 0.426 | |
| log2tpm | 0.413 | 0.008 | 0.422 | |
| log2transform | 6.976 | 0.028 | 7.295 | |
| logical2factor | 0.002 | 0.000 | 0.002 | |
| make_alpha_palette | 0.704 | 0.012 | 0.773 | |
| make_colors | 0.011 | 0.000 | 0.012 | |
| make_volcano_dt | 1.251 | 0.004 | 1.259 | |
| map_fvalues | 0.484 | 0.000 | 0.490 | |
| matrix2sumexp | 1.356 | 0.012 | 1.671 | |
| mclust_breaks | 0.688 | 0.028 | 0.718 | |
| merge_sample_file | 0.720 | 0.008 | 0.925 | |
| merge_sdata | 0.741 | 0.016 | 0.763 | |
| message_df | 0.003 | 0.000 | 0.003 | |
| model_coefs | 0.988 | 0.012 | 1.020 | |
| modelvar | 4.512 | 0.012 | 4.598 | |
| object1 | 0.670 | 0.000 | 0.741 | |
| order_on_p | 1.885 | 0.031 | 2.488 | |
| overall_parameters | 0.034 | 0.008 | 0.042 | |
| pca | 4.655 | 0.076 | 4.743 | |
| pg_to_canonical | 0.008 | 0.000 | 0.008 | |
| plot_coef_densities | 1.973 | 0.004 | 1.983 | |
| plot_contrast_venn | 3.444 | 0.036 | 3.489 | |
| plot_contrastogram | 4.245 | 0.036 | 5.404 | |
| plot_data | 2.477 | 0.020 | 2.579 | |
| plot_densities | 14.806 | 0.142 | 15.432 | |
| plot_design | 1.079 | 0.015 | 1.114 | |
| plot_detections | 10.698 | 0.136 | 11.116 | |
| plot_exprs | 29.756 | 0.115 | 31.147 | |
| plot_exprs_per_coef | 28.395 | 0.115 | 28.892 | |
| plot_fit_summary | 3.047 | 0.020 | 3.077 | |
| plot_heatmap | 2.720 | 0.004 | 2.734 | |
| plot_matrix | 0.666 | 0.007 | 0.676 | |
| plot_subgroup_points | 8.383 | 0.036 | 8.471 | |
| plot_summary | 19.487 | 0.147 | 20.113 | |
| plot_venn | 0.014 | 0.004 | 0.018 | |
| plot_venn_heatmap | 0.027 | 0.000 | 0.027 | |
| plot_violins | 6.323 | 0.072 | 6.410 | |
| plot_volcano | 17.879 | 0.075 | 19.050 | |
| plot_xy_density | 8.504 | 0.024 | 10.391 | |
| preprocess_rnaseq_counts | 0.420 | 0.000 | 0.438 | |
| pull_columns | 0.002 | 0.000 | 0.003 | |
| pvalues_estimable | 0.049 | 0.000 | 0.049 | |
| read_affymetrix | 0 | 0 | 0 | |
| read_diann_proteingroups | 59.633 | 0.629 | 62.767 | |
| read_fragpipe | 8.568 | 0.024 | 8.491 | |
| read_maxquant_phosphosites | 2.054 | 0.020 | 2.080 | |
| read_maxquant_proteingroups | 1.626 | 0.000 | 1.643 | |
| read_metabolon | 17.970 | 0.156 | 18.190 | |
| read_msigdt | 0.001 | 0.000 | 0.001 | |
| read_olink | 1.909 | 0.024 | 2.316 | |
| read_rectangles | 0.246 | 0.004 | 0.251 | |
| read_rnaseq_counts | 40.519 | 0.563 | 43.041 | |
| read_salmon | 0 | 0 | 0 | |
| read_somascan | 18.289 | 0.116 | 18.828 | |
| read_uniprotdt | 0.444 | 0.000 | 0.506 | |
| reset_fit | 6.451 | 0.087 | 6.769 | |
| rm_diann_contaminants | 13.496 | 0.223 | 14.104 | |
| rm_missing_in_some_samples | 0.690 | 0.008 | 0.704 | |
| rm_unmatched_samples | 0.919 | 0.000 | 0.922 | |
| sbind | 5.530 | 0.012 | 5.557 | |
| scaledlibsizes | 0.420 | 0.000 | 0.421 | |
| scoremat | 1.105 | 0.008 | 1.112 | |
| slevels | 0.498 | 0.000 | 0.499 | |
| snames | 0.527 | 0.000 | 0.528 | |
| split_extract_fixed | 0.680 | 0.016 | 0.698 | |
| split_samples | 1.611 | 0.008 | 1.623 | |
| stepauc | 0.429 | 0.004 | 0.434 | |
| stri_any_regex | 0.001 | 0.000 | 0.001 | |
| stri_detect_fixed_in_collapsed | 0.452 | 0.000 | 0.453 | |
| subgroup_matrix | 0.741 | 0.012 | 0.756 | |
| subtract_baseline | 6.744 | 0.032 | 6.795 | |
| sumexp_to_longdt | 2.492 | 0.016 | 2.515 | |
| sumexp_to_tsv | 0.667 | 0.008 | 0.677 | |
| sumexplist_to_longdt | 2.174 | 0.036 | 2.427 | |
| summarize_fit | 2.324 | 0.024 | 2.355 | |
| survobj | 0.193 | 0.004 | 0.197 | |
| svalues | 0.532 | 0.004 | 0.537 | |
| svars | 0.527 | 0.000 | 0.529 | |
| systematic_nas | 0.800 | 0.000 | 0.803 | |
| tag_features | 1.211 | 0.016 | 1.231 | |
| tag_hdlproteins | 0.805 | 0.036 | 0.844 | |
| taxon2org | 0.001 | 0.000 | 0.002 | |
| tpm | 0.448 | 0.000 | 0.449 | |
| uncollapse | 0.038 | 0.000 | 0.038 | |
| values | 0.556 | 0.000 | 0.559 | |
| varlevels_dont_clash | 0.027 | 0.003 | 0.030 | |
| venn_detects | 0.793 | 0.008 | 0.803 | |
| weights | 0.447 | 0.000 | 0.448 | |
| write_xl | 227.224 | 1.658 | 229.913 | |
| zero_to_na | 0.002 | 0.000 | 0.002 | |