Aditya Bhagwat
| Snapshot Date: 2025-10-17 13:45 -0400 (Fri, 17 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) |
| Back to Multiple platform build/check report for BioC 3.22: simplified long |
|
This page was generated on 2025-10-18 12:07 -0400 (Sat, 18 Oct 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" | 4887 |
| lconway | macOS 12.7.6 Monterey | x86_64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4677 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4622 |
| taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4632 |
| 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 118/2353 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| autonomics 1.17.16 (landing page) Aditya Bhagwat
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| lconway | macOS 12.7.6 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson3 | macOS 13.7.7 Ventura / arm64 | OK | 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: 1.17.16 |
| 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: 2025-10-17 06:07:27 -0000 (Fri, 17 Oct 2025) |
| EndedAt: 2025-10-17 06:49:27 -0000 (Fri, 17 Oct 2025) |
| EllapsedTime: 2520.0 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_1.17.16.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 239.918 2.513 247.482
awblinmod 60.075 0.744 61.730
read_rnaseq_counts 41.211 1.259 49.067
read_diann_proteingroups 39.055 0.423 43.688
LINMOD 34.913 0.649 37.402
plot_exprs 30.553 0.195 32.848
plot_exprs_per_coef 29.286 0.075 32.071
default_formula 26.174 0.319 27.104
read_metabolon 21.596 0.227 22.746
analyze 20.536 0.176 20.856
read_somascan 20.392 0.240 22.130
plot_volcano 20.184 0.087 22.825
plot_summary 19.819 0.116 21.357
fit_survival 16.027 0.115 16.644
explore-transforms 15.096 0.004 15.611
plot_densities 14.477 0.039 16.923
fcluster 13.775 0.036 13.908
ftype 12.157 0.123 12.671
plot_detections 10.643 0.040 10.868
biplot_covariates 10.063 0.020 10.340
plot_xy_density 9.393 0.052 10.421
read_fragpipe 8.911 0.008 9.463
plot_subgroup_points 8.856 0.060 11.319
rm_diann_contaminants 8.527 0.056 8.760
subtract_baseline 7.655 0.063 8.118
plot_violins 7.352 0.040 8.949
extract_contrast_features 7.320 0.035 7.464
log2transform 7.235 0.032 7.395
reset_fit 6.733 0.043 6.805
code 6.763 0.012 6.815
sbind 6.211 0.032 6.665
modelvar 5.734 0.148 6.123
biplot 5.401 0.060 5.475
impute 5.075 0.000 5.375
biplot_corrections 5.027 0.016 5.125
pca 4.874 0.095 5.450
plot_contrastogram 4.080 0.100 5.210
annotate_uniprot_rest 1.069 0.191 6.879
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’/home/biocbuild/R/R-4.5.0/bin/BATCH: line 60: 1082670 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 ‘1.17.16’ ** 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)
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 | 0.001 | 0.000 | 0.001 | |
| COMPOUNDDISCOVERER_PATTERNS | 0 | 0 | 0 | |
| LINMOD | 34.913 | 0.649 | 37.402 | |
| LINMODENGINES | 0 | 0 | 0 | |
| MAXQUANT_PATTERNS | 0 | 0 | 0 | |
| TAXON_TO_ORGNAME | 0.001 | 0.000 | 0.000 | |
| TESTS | 0 | 0 | 0 | |
| X | 1.732 | 0.023 | 1.769 | |
| abstract_fit | 1.452 | 0.020 | 1.477 | |
| add_adjusted_pvalues | 0.813 | 0.036 | 1.115 | |
| add_assay_means | 0.510 | 0.004 | 0.516 | |
| add_facetvars | 2.177 | 0.020 | 2.203 | |
| add_opentargets_by_uniprot | 0.546 | 0.016 | 0.568 | |
| add_psp | 0.739 | 0.008 | 0.752 | |
| add_smiles | 0.703 | 0.016 | 0.720 | |
| all_non_numeric | 0.862 | 0.012 | 0.877 | |
| analysis | 0.642 | 0.008 | 0.652 | |
| analyze | 20.536 | 0.176 | 20.856 | |
| annotate_maxquant | 1.230 | 0.024 | 1.421 | |
| annotate_uniprot_rest | 1.069 | 0.191 | 6.879 | |
| assert_is_valid_sumexp | 0.699 | 0.071 | 0.773 | |
| awblinmod | 60.075 | 0.744 | 61.730 | |
| biplot | 5.401 | 0.060 | 5.475 | |
| biplot_corrections | 5.027 | 0.016 | 5.125 | |
| biplot_covariates | 10.063 | 0.020 | 10.340 | |
| block2limma | 0.002 | 0.000 | 0.003 | |
| block2lm | 0.004 | 0.000 | 0.004 | |
| block2lme | 0.003 | 0.000 | 0.003 | |
| block2lmer | 0.005 | 0.000 | 0.005 | |
| block_has_two_levels | 0.911 | 0.008 | 0.924 | |
| center | 2.602 | 0.008 | 2.616 | |
| code | 6.763 | 0.012 | 6.815 | |
| collapsed_entrezg_to_symbol | 1.216 | 0.048 | 1.318 | |
| contrast_subgroup_cols | 0.805 | 0.016 | 0.823 | |
| contrastdt | 0.820 | 0.004 | 0.826 | |
| count_in | 0.001 | 0.000 | 0.002 | |
| counts | 0.537 | 0.008 | 0.557 | |
| counts2cpm | 0.434 | 0.000 | 0.437 | |
| counts2tpm | 0.411 | 0.000 | 0.412 | |
| cpm | 0.470 | 0.000 | 0.471 | |
| create_design | 1.005 | 0.000 | 1.010 | |
| default_formula | 26.174 | 0.319 | 27.104 | |
| default_geom | 0.722 | 0.012 | 0.742 | |
| default_sfile | 0.002 | 0.000 | 0.002 | |
| demultiplex | 0.020 | 0.000 | 0.021 | |
| densities | 0.318 | 0.000 | 0.320 | |
| dequantify | 0.003 | 0.000 | 0.003 | |
| dequantify_compounddiscoverer | 0.002 | 0.000 | 0.002 | |
| dot-coxph | 0.515 | 0.028 | 0.552 | |
| dot-merge | 0.028 | 0.000 | 0.027 | |
| dot-read_maxquant_proteingroups | 0.136 | 0.003 | 0.140 | |
| download_data | 0.001 | 0.000 | 0.001 | |
| download_gtf | 0 | 0 | 0 | |
| download_mcclain21 | 0 | 0 | 0 | |
| dt2mat | 0.005 | 0.000 | 0.005 | |
| enrichment | 1.734 | 0.001 | 1.754 | |
| entrezg_to_symbol | 0.181 | 0.000 | 0.181 | |
| explore-transforms | 15.096 | 0.004 | 15.611 | |
| extract_contrast_features | 7.320 | 0.035 | 7.464 | |
| extract_rectangle | 0.149 | 0.012 | 0.162 | |
| factor.vars | 0.275 | 0.000 | 0.276 | |
| factorize | 1.243 | 0.008 | 1.378 | |
| fcluster | 13.775 | 0.036 | 13.908 | |
| fcor | 2.135 | 0.032 | 2.172 | |
| fdata | 0.708 | 0.000 | 0.710 | |
| fdr2p | 1.437 | 0.004 | 1.493 | |
| filter_exprs_replicated_in_some_subgroup | 1.378 | 0.012 | 1.394 | |
| filter_features | 0.697 | 0.008 | 0.717 | |
| filter_medoid | 0.877 | 0.000 | 0.880 | |
| filter_samples | 0.855 | 0.008 | 1.335 | |
| fit_survival | 16.027 | 0.115 | 16.644 | |
| fits | 0.439 | 0.000 | 0.442 | |
| fix_xlgenes | 0.002 | 0.000 | 0.002 | |
| flevels | 0.536 | 0.004 | 0.542 | |
| fnames | 0.661 | 0.000 | 0.666 | |
| formula2str | 0.001 | 0.000 | 0.000 | |
| ftype | 12.157 | 0.123 | 12.671 | |
| fvalues | 0.520 | 0.000 | 0.521 | |
| fvars | 0.529 | 0.000 | 0.574 | |
| genome_to_orgdb | 0.001 | 0.000 | 0.001 | |
| group_by_level | 0.002 | 0.000 | 0.002 | |
| guess_compounddiscoverer_quantity | 0.001 | 0.000 | 0.001 | |
| guess_fitsep | 0.735 | 0.000 | 0.756 | |
| guess_maxquant_quantity | 0.007 | 0.000 | 0.007 | |
| guess_sep | 0.676 | 0.000 | 0.679 | |
| has_multiple_levels | 0.083 | 0.000 | 0.083 | |
| hdlproteins | 0.059 | 0.001 | 0.177 | |
| impute | 5.075 | 0.000 | 5.375 | |
| invert_subgroups | 0.996 | 0.004 | 1.015 | |
| is_character_matrix | 0.236 | 0.000 | 0.237 | |
| is_collapsed_subset | 0 | 0 | 0 | |
| is_compounddiscoverer_output | 0.078 | 0.003 | 0.287 | |
| is_correlation_matrix | 0.002 | 0.000 | 0.002 | |
| is_diann_report | 0.093 | 0.000 | 0.158 | |
| is_fastadt | 0.094 | 0.000 | 0.191 | |
| is_file | 0.000 | 0.000 | 0.001 | |
| is_fraction | 0.002 | 0.000 | 0.002 | |
| is_fragpipe_tsv | 0.104 | 0.001 | 0.160 | |
| is_imputed | 1.091 | 0.000 | 1.288 | |
| is_maxquant_phosphosites | 0.071 | 0.000 | 0.065 | |
| is_maxquant_proteingroups | 0.053 | 0.004 | 0.057 | |
| is_positive_number | 0.002 | 0.000 | 0.002 | |
| is_scalar_subset | 0.435 | 0.000 | 0.521 | |
| is_sig | 2.152 | 0.007 | 2.243 | |
| is_valid_formula | 0.072 | 0.000 | 0.072 | |
| keep_estimable_features | 1.146 | 0.016 | 1.194 | |
| label2index | 0.000 | 0.000 | 0.001 | |
| list2mat | 0.001 | 0.000 | 0.001 | |
| log2counts | 0.548 | 0.004 | 0.571 | |
| log2cpm | 0.466 | 0.000 | 0.620 | |
| log2diffs | 0.478 | 0.004 | 0.547 | |
| log2proteins | 0.459 | 0.004 | 0.464 | |
| log2sites | 0.606 | 0.000 | 1.009 | |
| log2tpm | 0.478 | 0.000 | 0.660 | |
| log2transform | 7.235 | 0.032 | 7.395 | |
| logical2factor | 0.002 | 0.000 | 0.001 | |
| make_alpha_palette | 0.680 | 0.020 | 0.705 | |
| make_colors | 0.007 | 0.004 | 0.011 | |
| make_volcano_dt | 1.250 | 0.008 | 1.307 | |
| map_fvalues | 0.544 | 0.000 | 0.545 | |
| matrix2sumexp | 1.489 | 0.008 | 1.553 | |
| mclust_breaks | 0.696 | 0.019 | 0.719 | |
| merge_sample_file | 0.642 | 0.004 | 0.648 | |
| merge_sdata | 0.848 | 0.008 | 0.858 | |
| message_df | 0.003 | 0.000 | 0.003 | |
| model_coefs | 1.051 | 0.004 | 1.070 | |
| modelvar | 5.734 | 0.148 | 6.123 | |
| object1 | 0.671 | 0.000 | 1.019 | |
| order_on_p | 1.981 | 0.008 | 2.284 | |
| overall_parameters | 0.042 | 0.000 | 0.076 | |
| pca | 4.874 | 0.095 | 5.450 | |
| pg_to_canonical | 0.008 | 0.000 | 0.009 | |
| plot_coef_densities | 1.912 | 0.024 | 1.956 | |
| plot_contrast_venn | 3.476 | 0.012 | 3.626 | |
| plot_contrastogram | 4.08 | 0.10 | 5.21 | |
| plot_data | 2.396 | 0.004 | 2.965 | |
| plot_densities | 14.477 | 0.039 | 16.923 | |
| plot_design | 1.146 | 0.008 | 1.157 | |
| plot_detections | 10.643 | 0.040 | 10.868 | |
| plot_exprs | 30.553 | 0.195 | 32.848 | |
| plot_exprs_per_coef | 29.286 | 0.075 | 32.071 | |
| plot_fit_summary | 3.133 | 0.024 | 3.211 | |
| plot_heatmap | 2.658 | 0.000 | 2.769 | |
| plot_matrix | 0.657 | 0.016 | 0.674 | |
| plot_subgroup_points | 8.856 | 0.060 | 11.319 | |
| plot_summary | 19.819 | 0.116 | 21.357 | |
| plot_venn | 0.018 | 0.000 | 0.018 | |
| plot_venn_heatmap | 0.030 | 0.000 | 0.031 | |
| plot_violins | 7.352 | 0.040 | 8.949 | |
| plot_volcano | 20.184 | 0.087 | 22.825 | |
| plot_xy_density | 9.393 | 0.052 | 10.421 | |
| preprocess_rnaseq_counts | 0.456 | 0.004 | 0.462 | |
| pull_columns | 0.003 | 0.000 | 0.003 | |
| pvalues_estimable | 0.055 | 0.000 | 0.056 | |
| read_affymetrix | 0 | 0 | 0 | |
| read_diann_proteingroups | 39.055 | 0.423 | 43.688 | |
| read_fragpipe | 8.911 | 0.008 | 9.463 | |
| read_maxquant_phosphosites | 2.141 | 0.024 | 2.190 | |
| read_maxquant_proteingroups | 1.776 | 0.007 | 1.994 | |
| read_metabolon | 21.596 | 0.227 | 22.746 | |
| read_msigdt | 0.001 | 0.000 | 0.002 | |
| read_olink | 1.933 | 0.027 | 2.071 | |
| read_rectangles | 0.245 | 0.000 | 0.247 | |
| read_rnaseq_counts | 41.211 | 1.259 | 49.067 | |
| read_salmon | 0 | 0 | 0 | |
| read_somascan | 20.392 | 0.240 | 22.130 | |
| read_uniprotdt | 0.451 | 0.000 | 0.452 | |
| reset_fit | 6.733 | 0.043 | 6.805 | |
| rm_diann_contaminants | 8.527 | 0.056 | 8.760 | |
| rm_missing_in_some_samples | 0.726 | 0.016 | 0.743 | |
| rm_unmatched_samples | 1.044 | 0.004 | 1.106 | |
| sbind | 6.211 | 0.032 | 6.665 | |
| scaledlibsizes | 0.529 | 0.000 | 0.567 | |
| scoremat | 1.216 | 0.020 | 1.275 | |
| slevels | 0.643 | 0.000 | 0.680 | |
| snames | 0.583 | 0.004 | 0.745 | |
| split_extract_fixed | 0.786 | 0.044 | 0.832 | |
| split_samples | 1.843 | 0.064 | 1.911 | |
| stepauc | 0.533 | 0.000 | 0.536 | |
| stri_any_regex | 0.000 | 0.001 | 0.001 | |
| stri_detect_fixed_in_collapsed | 0.483 | 0.003 | 0.487 | |
| subgroup_matrix | 0.767 | 0.020 | 0.790 | |
| subtract_baseline | 7.655 | 0.063 | 8.118 | |
| sumexp_to_longdt | 2.713 | 0.012 | 2.811 | |
| sumexp_to_tsv | 0.688 | 0.004 | 0.779 | |
| sumexplist_to_longdt | 2.164 | 0.048 | 2.674 | |
| summarize_fit | 2.412 | 0.048 | 2.485 | |
| survobj | 0.208 | 0.000 | 0.209 | |
| svalues | 0.559 | 0.004 | 0.564 | |
| svars | 0.570 | 0.004 | 0.635 | |
| systematic_nas | 0.803 | 0.007 | 0.814 | |
| tag_features | 1.238 | 0.016 | 1.337 | |
| tag_hdlproteins | 0.756 | 0.020 | 0.783 | |
| taxon2org | 0.002 | 0.000 | 0.001 | |
| tpm | 0.473 | 0.000 | 0.474 | |
| uncollapse | 0.042 | 0.000 | 0.049 | |
| values | 0.573 | 0.000 | 0.750 | |
| varlevels_dont_clash | 0.028 | 0.000 | 0.028 | |
| venn_detects | 0.818 | 0.008 | 0.935 | |
| weights | 0.476 | 0.008 | 0.557 | |
| write_xl | 239.918 | 2.513 | 247.482 | |
| zero_to_na | 0.002 | 0.000 | 0.002 | |