Aditya Bhagwat
| Snapshot Date: 2025-11-27 13:45 -0500 (Thu, 27 Nov 2025) |
| 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 2025-12-01 12:02 -0500 (Mon, 01 Dec 2025).
| 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" | 4878 |
| merida1 | macOS 12.7.6 Monterey | x86_64 | 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble" | 4610 |
| taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4669 |
| 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 | | ||||||||
| merida1 | macOS 12.7.6 Monterey / x86_64 | OK | OK | TIMEOUT | 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: 2025-11-28 06:44:26 -0000 (Fri, 28 Nov 2025) |
| EndedAt: 2025-11-28 07:25:05 -0000 (Fri, 28 Nov 2025) |
| EllapsedTime: 2439.2 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 239.888 1.627 272.222
awblinmod 63.604 0.295 76.228
read_diann_proteingroups 58.476 0.642 72.661
read_rnaseq_counts 40.595 1.361 61.166
LINMOD 34.557 0.458 40.786
plot_exprs 30.624 0.087 35.918
plot_exprs_per_coef 29.808 0.188 41.254
default_formula 25.480 0.416 31.430
analyze 20.353 0.130 26.059
read_somascan 20.044 0.187 25.385
plot_summary 19.660 0.111 25.057
read_metabolon 19.547 0.075 22.999
plot_volcano 19.340 0.075 20.500
fit_survival 16.036 0.161 19.815
plot_densities 14.954 0.138 21.317
explore-transforms 14.996 0.071 16.251
fcluster 14.004 0.072 18.495
rm_diann_contaminants 12.378 0.088 14.833
ftype 11.288 0.139 13.542
plot_detections 10.722 0.084 11.363
biplot_covariates 10.438 0.044 11.209
plot_xy_density 9.877 0.103 12.441
plot_subgroup_points 8.890 0.032 11.375
read_fragpipe 8.477 0.171 10.586
reset_fit 7.601 0.143 8.644
plot_violins 7.107 0.059 7.520
log2transform 7.086 0.071 7.776
code 7.028 0.055 7.841
subtract_baseline 6.879 0.024 7.012
extract_contrast_features 6.731 0.035 7.307
sbind 6.023 0.012 6.645
biplot 5.799 0.027 6.156
biplot_corrections 5.123 0.036 5.765
modelvar 5.112 0.012 7.037
pca 4.773 0.028 5.261
impute 4.754 0.044 6.183
plot_contrastogram 4.152 0.024 5.294
annotate_uniprot_rest 0.117 0.000 5.086
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’/home/biocbuild/R/R-4.5.0/bin/BATCH: line 60: 3845706 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 | 0.000 | 0.001 | |
| COMPOUNDDISCOVERER_PATTERNS | 0 | 0 | 0 | |
| LINMOD | 34.557 | 0.458 | 40.786 | |
| LINMODENGINES | 0 | 0 | 0 | |
| MAXQUANT_PATTERNS | 0.001 | 0.000 | 0.000 | |
| TAXON_TO_ORGNAME | 0.000 | 0.000 | 0.001 | |
| TESTS | 0 | 0 | 0 | |
| X | 1.715 | 0.012 | 1.732 | |
| abstract_fit | 1.460 | 0.012 | 1.510 | |
| add_adjusted_pvalues | 0.754 | 0.016 | 0.911 | |
| add_assay_means | 0.522 | 0.020 | 0.578 | |
| add_facetvars | 2.154 | 0.004 | 3.062 | |
| add_opentargets_by_uniprot | 0.605 | 0.000 | 1.222 | |
| add_psp | 0.702 | 0.012 | 0.730 | |
| add_smiles | 0.674 | 0.016 | 0.956 | |
| all_non_numeric | 0.815 | 0.004 | 0.822 | |
| analysis | 0.559 | 0.008 | 1.029 | |
| analyze | 20.353 | 0.130 | 26.059 | |
| annotate_maxquant | 1.367 | 0.048 | 1.448 | |
| annotate_uniprot_rest | 0.117 | 0.000 | 5.086 | |
| assert_is_valid_sumexp | 0.769 | 0.008 | 1.348 | |
| awblinmod | 63.604 | 0.295 | 76.228 | |
| biplot | 5.799 | 0.027 | 6.156 | |
| biplot_corrections | 5.123 | 0.036 | 5.765 | |
| biplot_covariates | 10.438 | 0.044 | 11.209 | |
| block2limma | 0.002 | 0.000 | 0.002 | |
| block2lm | 0.004 | 0.000 | 0.004 | |
| block2lme | 0.003 | 0.000 | 0.003 | |
| block2lmer | 0.003 | 0.002 | 0.005 | |
| block_has_two_levels | 0.884 | 0.017 | 0.936 | |
| center | 2.565 | 0.012 | 2.616 | |
| code | 7.028 | 0.055 | 7.841 | |
| collapsed_entrezg_to_symbol | 1.094 | 0.055 | 1.153 | |
| contrast_subgroup_cols | 0.900 | 0.016 | 0.977 | |
| contrastdt | 0.887 | 0.004 | 0.923 | |
| count_in | 0.002 | 0.000 | 0.001 | |
| counts | 0.544 | 0.004 | 0.550 | |
| counts2cpm | 0.465 | 0.000 | 0.507 | |
| counts2tpm | 0.476 | 0.000 | 0.479 | |
| cpm | 0.529 | 0.000 | 0.635 | |
| create_design | 1.100 | 0.064 | 1.267 | |
| default_formula | 25.480 | 0.416 | 31.430 | |
| default_geom | 0.655 | 0.016 | 0.673 | |
| default_sfile | 0.001 | 0.000 | 0.001 | |
| demultiplex | 0.02 | 0.00 | 0.02 | |
| densities | 0.312 | 0.000 | 0.313 | |
| dequantify | 0.003 | 0.000 | 0.003 | |
| dequantify_compounddiscoverer | 0.001 | 0.000 | 0.001 | |
| dot-coxph | 0.515 | 0.028 | 0.588 | |
| dot-merge | 0.028 | 0.000 | 0.028 | |
| dot-read_maxquant_proteingroups | 0.123 | 0.008 | 0.131 | |
| download_data | 0 | 0 | 0 | |
| download_gtf | 0 | 0 | 0 | |
| download_mcclain21 | 0.000 | 0.000 | 0.001 | |
| dt2mat | 0.001 | 0.003 | 0.004 | |
| enrichment | 1.692 | 0.005 | 1.863 | |
| entrezg_to_symbol | 0.170 | 0.004 | 0.175 | |
| explore-transforms | 14.996 | 0.071 | 16.251 | |
| extract_contrast_features | 6.731 | 0.035 | 7.307 | |
| extract_rectangle | 0.148 | 0.000 | 0.148 | |
| factor.vars | 0.251 | 0.000 | 0.310 | |
| factorize | 1.135 | 0.008 | 1.254 | |
| fcluster | 14.004 | 0.072 | 18.495 | |
| fcor | 2.068 | 0.020 | 2.283 | |
| fdata | 0.751 | 0.000 | 0.930 | |
| fdr2p | 1.493 | 0.008 | 2.780 | |
| filter_exprs_replicated_in_some_subgroup | 1.382 | 0.036 | 1.832 | |
| filter_features | 0.801 | 0.032 | 0.952 | |
| filter_medoid | 0.799 | 0.020 | 0.828 | |
| filter_samples | 0.774 | 0.004 | 0.897 | |
| fit_survival | 16.036 | 0.161 | 19.815 | |
| fits | 0.438 | 0.000 | 0.663 | |
| fix_xlgenes | 0.002 | 0.000 | 0.002 | |
| flevels | 0.598 | 0.004 | 0.932 | |
| fnames | 0.584 | 0.004 | 0.591 | |
| formula2str | 0 | 0 | 0 | |
| ftype | 11.288 | 0.139 | 13.542 | |
| fvalues | 0.544 | 0.000 | 0.640 | |
| fvars | 0.514 | 0.007 | 0.523 | |
| genome_to_orgdb | 0.000 | 0.000 | 0.001 | |
| group_by_level | 0.001 | 0.000 | 0.002 | |
| guess_compounddiscoverer_quantity | 0.001 | 0.000 | 0.001 | |
| guess_fitsep | 0.706 | 0.004 | 1.281 | |
| guess_maxquant_quantity | 0.008 | 0.000 | 0.017 | |
| guess_sep | 0.710 | 0.009 | 1.310 | |
| has_multiple_levels | 0.076 | 0.000 | 0.077 | |
| hdlproteins | 0.057 | 0.004 | 0.161 | |
| impute | 4.754 | 0.044 | 6.183 | |
| invert_subgroups | 0.905 | 0.000 | 0.941 | |
| is_character_matrix | 0.200 | 0.004 | 0.204 | |
| is_collapsed_subset | 0 | 0 | 0 | |
| is_compounddiscoverer_output | 0.134 | 0.004 | 0.473 | |
| is_correlation_matrix | 0.001 | 0.000 | 0.006 | |
| is_diann_report | 0.183 | 0.008 | 0.204 | |
| is_fastadt | 0.087 | 0.000 | 0.087 | |
| is_file | 0 | 0 | 0 | |
| is_fraction | 0.002 | 0.000 | 0.002 | |
| is_fragpipe_tsv | 0.123 | 0.000 | 0.124 | |
| is_imputed | 0.963 | 0.004 | 0.982 | |
| is_maxquant_phosphosites | 0.089 | 0.008 | 0.097 | |
| is_maxquant_proteingroups | 0.091 | 0.008 | 0.099 | |
| is_positive_number | 0.002 | 0.000 | 0.002 | |
| is_scalar_subset | 0.478 | 0.000 | 0.908 | |
| is_sig | 2.065 | 0.032 | 3.290 | |
| is_valid_formula | 0.062 | 0.004 | 0.110 | |
| keep_estimable_features | 1.065 | 0.032 | 1.363 | |
| label2index | 0.001 | 0.000 | 0.000 | |
| list2mat | 0.001 | 0.000 | 0.005 | |
| log2counts | 0.451 | 0.004 | 0.712 | |
| log2cpm | 0.503 | 0.000 | 0.504 | |
| log2diffs | 0.440 | 0.004 | 0.876 | |
| log2proteins | 0.426 | 0.008 | 0.593 | |
| log2sites | 0.418 | 0.004 | 0.424 | |
| log2tpm | 0.485 | 0.000 | 0.545 | |
| log2transform | 7.086 | 0.071 | 7.776 | |
| logical2factor | 0.000 | 0.002 | 0.002 | |
| make_alpha_palette | 0.720 | 0.014 | 0.736 | |
| make_colors | 0.011 | 0.000 | 0.011 | |
| make_volcano_dt | 1.259 | 0.008 | 1.405 | |
| map_fvalues | 0.521 | 0.000 | 0.523 | |
| matrix2sumexp | 1.424 | 0.016 | 1.526 | |
| mclust_breaks | 0.709 | 0.024 | 0.759 | |
| merge_sample_file | 0.721 | 0.032 | 0.817 | |
| merge_sdata | 0.716 | 0.028 | 0.746 | |
| message_df | 0.003 | 0.000 | 0.003 | |
| model_coefs | 1.061 | 0.047 | 1.117 | |
| modelvar | 5.112 | 0.012 | 7.037 | |
| object1 | 0.729 | 0.000 | 0.895 | |
| order_on_p | 1.988 | 0.024 | 2.592 | |
| overall_parameters | 0.038 | 0.000 | 0.039 | |
| pca | 4.773 | 0.028 | 5.261 | |
| pg_to_canonical | 0.009 | 0.000 | 0.008 | |
| plot_coef_densities | 1.984 | 0.016 | 2.149 | |
| plot_contrast_venn | 3.534 | 0.027 | 3.942 | |
| plot_contrastogram | 4.152 | 0.024 | 5.294 | |
| plot_data | 2.413 | 0.031 | 2.507 | |
| plot_densities | 14.954 | 0.138 | 21.317 | |
| plot_design | 0.998 | 0.000 | 1.004 | |
| plot_detections | 10.722 | 0.084 | 11.363 | |
| plot_exprs | 30.624 | 0.087 | 35.918 | |
| plot_exprs_per_coef | 29.808 | 0.188 | 41.254 | |
| plot_fit_summary | 3.276 | 0.019 | 4.136 | |
| plot_heatmap | 2.930 | 0.004 | 3.131 | |
| plot_matrix | 0.736 | 0.012 | 0.759 | |
| plot_subgroup_points | 8.890 | 0.032 | 11.375 | |
| plot_summary | 19.660 | 0.111 | 25.057 | |
| plot_venn | 0.018 | 0.000 | 0.019 | |
| plot_venn_heatmap | 0.028 | 0.000 | 0.029 | |
| plot_violins | 7.107 | 0.059 | 7.520 | |
| plot_volcano | 19.340 | 0.075 | 20.500 | |
| plot_xy_density | 9.877 | 0.103 | 12.441 | |
| preprocess_rnaseq_counts | 0.435 | 0.004 | 0.446 | |
| pull_columns | 0.002 | 0.000 | 0.003 | |
| pvalues_estimable | 0.05 | 0.00 | 0.05 | |
| read_affymetrix | 0 | 0 | 0 | |
| read_diann_proteingroups | 58.476 | 0.642 | 72.661 | |
| read_fragpipe | 8.477 | 0.171 | 10.586 | |
| read_maxquant_phosphosites | 2.150 | 0.028 | 3.602 | |
| read_maxquant_proteingroups | 1.679 | 0.004 | 1.759 | |
| read_metabolon | 19.547 | 0.075 | 22.999 | |
| read_msigdt | 0.001 | 0.000 | 0.001 | |
| read_olink | 1.896 | 0.024 | 3.523 | |
| read_rectangles | 0.238 | 0.004 | 0.488 | |
| read_rnaseq_counts | 40.595 | 1.361 | 61.166 | |
| read_salmon | 0 | 0 | 0 | |
| read_somascan | 20.044 | 0.187 | 25.385 | |
| read_uniprotdt | 0.383 | 0.012 | 0.531 | |
| reset_fit | 7.601 | 0.143 | 8.644 | |
| rm_diann_contaminants | 12.378 | 0.088 | 14.833 | |
| rm_missing_in_some_samples | 0.700 | 0.020 | 0.794 | |
| rm_unmatched_samples | 0.876 | 0.000 | 0.907 | |
| sbind | 6.023 | 0.012 | 6.645 | |
| scaledlibsizes | 0.445 | 0.000 | 0.446 | |
| scoremat | 1.288 | 0.016 | 2.203 | |
| slevels | 0.560 | 0.000 | 0.686 | |
| snames | 0.543 | 0.004 | 0.548 | |
| split_extract_fixed | 0.756 | 0.004 | 0.907 | |
| split_samples | 1.683 | 0.008 | 2.552 | |
| stepauc | 0.491 | 0.011 | 0.518 | |
| stri_any_regex | 0 | 0 | 0 | |
| stri_detect_fixed_in_collapsed | 0.423 | 0.036 | 0.459 | |
| subgroup_matrix | 0.687 | 0.016 | 0.704 | |
| subtract_baseline | 6.879 | 0.024 | 7.012 | |
| sumexp_to_longdt | 2.849 | 0.060 | 3.815 | |
| sumexp_to_tsv | 0.670 | 0.004 | 0.675 | |
| sumexplist_to_longdt | 2.067 | 0.016 | 2.200 | |
| summarize_fit | 2.284 | 0.012 | 2.327 | |
| survobj | 0.249 | 0.000 | 0.252 | |
| svalues | 0.544 | 0.000 | 0.615 | |
| svars | 0.554 | 0.008 | 0.718 | |
| systematic_nas | 0.833 | 0.032 | 1.075 | |
| tag_features | 1.313 | 0.008 | 1.381 | |
| tag_hdlproteins | 0.749 | 0.000 | 1.042 | |
| taxon2org | 0.001 | 0.000 | 0.002 | |
| tpm | 0.549 | 0.000 | 0.622 | |
| uncollapse | 0.039 | 0.000 | 0.040 | |
| values | 0.571 | 0.004 | 0.579 | |
| varlevels_dont_clash | 0.027 | 0.004 | 0.031 | |
| venn_detects | 0.793 | 0.000 | 0.953 | |
| weights | 0.530 | 0.000 | 0.534 | |
| write_xl | 239.888 | 1.627 | 272.222 | |
| zero_to_na | 0.001 | 0.000 | 0.002 | |