| Back to Build/check report for BioC 3.22: simplified long |
|
This page was generated on 2026-02-27 11:57 -0500 (Fri, 27 Feb 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" | 4891 |
| 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 | |||||||||
| See other builds for autonomics in R Universe. | ||||||||||||||
|
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. |
| Package: autonomics |
| Version: 1.18.0 |
| Command: /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:autonomics.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings autonomics_1.18.0.tar.gz |
| StartedAt: 2026-02-26 21:09:22 -0500 (Thu, 26 Feb 2026) |
| EndedAt: 2026-02-26 21:30:07 -0500 (Thu, 26 Feb 2026) |
| EllapsedTime: 1245.2 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: autonomics.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:autonomics.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings autonomics_1.18.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/autonomics.Rcheck’
* using R version 4.5.2 (2025-10-31)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.3 LTS
* using session charset: UTF-8
* 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 157.989 1.470 159.514
read_diann_proteingroups 106.320 2.010 103.637
awblinmod 43.890 0.222 43.039
read_rnaseq_counts 29.527 1.770 31.137
LINMOD 25.630 0.551 25.596
rm_diann_contaminants 22.342 0.341 21.409
default_formula 22.325 0.186 22.059
plot_exprs 19.841 0.250 19.978
plot_exprs_per_coef 19.828 0.075 19.782
analyze 13.761 0.171 13.804
read_somascan 12.648 0.164 12.740
plot_summary 12.466 0.013 12.329
explore-transforms 12.021 0.335 12.359
plot_volcano 12.175 0.036 12.160
read_metabolon 12.079 0.025 11.973
fit_survival 11.911 0.038 11.955
plot_densities 11.262 0.240 11.370
fcluster 10.321 0.014 10.263
ftype 8.964 0.057 8.729
plot_detections 7.348 0.068 7.326
biplot_covariates 6.951 0.097 7.017
read_fragpipe 6.521 0.024 6.277
plot_xy_density 6.091 0.002 6.094
plot_subgroup_points 5.277 0.010 5.232
log2transform 5.105 0.007 5.113
* 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 re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE
Status: 2 NOTEs
See
‘/home/biocbuild/bbs-3.22-bioc/meat/autonomics.Rcheck/00check.log’
for details.
autonomics.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD INSTALL autonomics ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.22-bioc/R/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
R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-pc-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
142.011 4.098 143.480
autonomics.Rcheck/autonomics-Ex.timings
| name | user | system | elapsed | |
| AUTONOMICS_DATASETS | 0 | 0 | 0 | |
| COMPOUNDDISCOVERER_PATTERNS | 0 | 0 | 0 | |
| LINMOD | 25.630 | 0.551 | 25.596 | |
| LINMODENGINES | 0 | 0 | 0 | |
| MAXQUANT_PATTERNS | 0.001 | 0.001 | 0.000 | |
| TAXON_TO_ORGNAME | 0 | 0 | 0 | |
| TESTS | 0 | 0 | 0 | |
| X | 1.198 | 0.020 | 1.197 | |
| abstract_fit | 1.044 | 0.007 | 1.027 | |
| add_adjusted_pvalues | 0.569 | 0.006 | 0.576 | |
| add_assay_means | 0.359 | 0.001 | 0.360 | |
| add_facetvars | 1.424 | 0.008 | 1.395 | |
| add_opentargets_by_uniprot | 0.428 | 0.002 | 0.431 | |
| add_psp | 0.515 | 0.006 | 0.522 | |
| add_smiles | 0.476 | 0.009 | 0.446 | |
| all_non_numeric | 0.581 | 0.000 | 0.581 | |
| analysis | 0.410 | 0.001 | 0.411 | |
| analyze | 13.761 | 0.171 | 13.804 | |
| annotate_maxquant | 1.004 | 0.035 | 1.039 | |
| annotate_uniprot_rest | 0.371 | 0.021 | 1.952 | |
| assert_is_valid_sumexp | 0.552 | 0.011 | 0.541 | |
| awblinmod | 43.890 | 0.222 | 43.039 | |
| biplot | 3.817 | 0.009 | 3.803 | |
| biplot_corrections | 3.487 | 0.006 | 3.471 | |
| biplot_covariates | 6.951 | 0.097 | 7.017 | |
| block2limma | 0.001 | 0.000 | 0.001 | |
| block2lm | 0.003 | 0.000 | 0.003 | |
| block2lme | 0.002 | 0.000 | 0.002 | |
| block2lmer | 0.004 | 0.000 | 0.004 | |
| block_has_two_levels | 0.663 | 0.015 | 0.642 | |
| center | 1.864 | 0.005 | 1.867 | |
| code | 4.980 | 0.007 | 4.965 | |
| collapsed_entrezg_to_symbol | 0.928 | 0.070 | 0.999 | |
| contrast_subgroup_cols | 0.694 | 0.009 | 0.681 | |
| contrastdt | 0.625 | 0.001 | 0.626 | |
| count_in | 0.001 | 0.000 | 0.001 | |
| counts | 0.343 | 0.001 | 0.344 | |
| counts2cpm | 0.333 | 0.000 | 0.333 | |
| counts2tpm | 0.294 | 0.000 | 0.294 | |
| cpm | 0.361 | 0.000 | 0.361 | |
| create_design | 0.735 | 0.001 | 0.712 | |
| default_formula | 22.325 | 0.186 | 22.059 | |
| default_geom | 0.593 | 0.007 | 0.577 | |
| default_sfile | 0.002 | 0.000 | 0.002 | |
| demultiplex | 0.017 | 0.000 | 0.017 | |
| densities | 0.238 | 0.001 | 0.239 | |
| dequantify | 0.003 | 0.000 | 0.003 | |
| dequantify_compounddiscoverer | 0.002 | 0.000 | 0.001 | |
| dot-coxph | 0.456 | 0.006 | 0.461 | |
| dot-merge | 0.019 | 0.000 | 0.020 | |
| dot-read_maxquant_proteingroups | 0.136 | 0.000 | 0.136 | |
| download_data | 0 | 0 | 0 | |
| download_gtf | 0 | 0 | 0 | |
| download_mcclain21 | 0 | 0 | 0 | |
| dt2mat | 0.003 | 0.000 | 0.002 | |
| enrichment | 1.277 | 0.000 | 1.277 | |
| entrezg_to_symbol | 0.173 | 0.001 | 0.174 | |
| explore-transforms | 12.021 | 0.335 | 12.359 | |
| extract_contrast_features | 4.713 | 0.005 | 4.696 | |
| extract_rectangle | 0.107 | 0.010 | 0.117 | |
| factor.vars | 0.174 | 0.000 | 0.175 | |
| factorize | 0.819 | 0.002 | 0.821 | |
| fcluster | 10.321 | 0.014 | 10.263 | |
| fcor | 1.542 | 0.004 | 1.547 | |
| fdata | 0.636 | 0.004 | 0.640 | |
| fdr2p | 0.962 | 0.004 | 0.929 | |
| filter_exprs_replicated_in_some_subgroup | 1.098 | 0.014 | 1.002 | |
| filter_features | 0.572 | 0.010 | 0.540 | |
| filter_medoid | 0.642 | 0.008 | 0.651 | |
| filter_samples | 0.550 | 0.012 | 0.521 | |
| fit_survival | 11.911 | 0.038 | 11.955 | |
| fits | 0.439 | 0.000 | 0.441 | |
| fix_xlgenes | 0.003 | 0.000 | 0.002 | |
| flevels | 0.445 | 0.001 | 0.445 | |
| fnames | 0.496 | 0.002 | 0.498 | |
| formula2str | 0.000 | 0.000 | 0.001 | |
| ftype | 8.964 | 0.057 | 8.729 | |
| fvalues | 0.487 | 0.000 | 0.486 | |
| fvars | 0.488 | 0.000 | 0.488 | |
| genome_to_orgdb | 0.001 | 0.000 | 0.001 | |
| group_by_level | 0.002 | 0.000 | 0.001 | |
| guess_compounddiscoverer_quantity | 0.001 | 0.000 | 0.001 | |
| guess_fitsep | 0.485 | 0.001 | 0.486 | |
| guess_maxquant_quantity | 0.005 | 0.000 | 0.006 | |
| guess_sep | 0.539 | 0.005 | 0.518 | |
| has_multiple_levels | 0.06 | 0.00 | 0.06 | |
| hdlproteins | 0.046 | 0.009 | 0.059 | |
| impute | 3.714 | 0.007 | 3.721 | |
| invert_subgroups | 0.662 | 0.001 | 0.663 | |
| is_character_matrix | 0.165 | 0.000 | 0.164 | |
| is_collapsed_subset | 0.001 | 0.000 | 0.001 | |
| is_compounddiscoverer_output | 0.107 | 0.040 | 0.217 | |
| is_correlation_matrix | 0.002 | 0.000 | 0.002 | |
| is_diann_report | 0.163 | 0.007 | 0.133 | |
| is_fastadt | 0.091 | 0.000 | 0.087 | |
| is_file | 0.001 | 0.000 | 0.000 | |
| is_fraction | 0.002 | 0.000 | 0.001 | |
| is_fragpipe_tsv | 0.109 | 0.003 | 0.079 | |
| is_imputed | 0.788 | 0.000 | 0.783 | |
| is_maxquant_phosphosites | 0.096 | 0.004 | 0.074 | |
| is_maxquant_proteingroups | 0.092 | 0.005 | 0.069 | |
| is_positive_number | 0.001 | 0.000 | 0.001 | |
| is_scalar_subset | 0.331 | 0.001 | 0.332 | |
| is_sig | 1.562 | 0.005 | 1.568 | |
| is_valid_formula | 0.047 | 0.000 | 0.047 | |
| keep_estimable_features | 0.944 | 0.002 | 0.855 | |
| label2index | 0.001 | 0.000 | 0.001 | |
| list2mat | 0.001 | 0.000 | 0.001 | |
| log2counts | 0.304 | 0.001 | 0.305 | |
| log2cpm | 0.320 | 0.001 | 0.321 | |
| log2diffs | 0.451 | 0.000 | 0.450 | |
| log2proteins | 0.345 | 0.001 | 0.345 | |
| log2sites | 0.337 | 0.001 | 0.337 | |
| log2tpm | 0.319 | 0.000 | 0.319 | |
| log2transform | 5.105 | 0.007 | 5.113 | |
| logical2factor | 0.000 | 0.001 | 0.001 | |
| make_alpha_palette | 0.526 | 0.006 | 0.502 | |
| make_colors | 0.01 | 0.00 | 0.01 | |
| make_volcano_dt | 0.914 | 0.000 | 0.914 | |
| map_fvalues | 0.394 | 0.000 | 0.394 | |
| matrix2sumexp | 1.093 | 0.008 | 1.059 | |
| mclust_breaks | 0.528 | 0.016 | 0.544 | |
| merge_sample_file | 0.657 | 0.003 | 0.660 | |
| merge_sdata | 0.569 | 0.011 | 0.540 | |
| message_df | 0.003 | 0.000 | 0.002 | |
| model_coefs | 0.876 | 0.003 | 0.845 | |
| modelvar | 3.634 | 0.010 | 3.574 | |
| object1 | 0.631 | 0.010 | 0.641 | |
| order_on_p | 1.491 | 0.003 | 1.453 | |
| overall_parameters | 0.026 | 0.000 | 0.026 | |
| pca | 3.540 | 0.013 | 3.528 | |
| pg_to_canonical | 0.008 | 0.000 | 0.008 | |
| plot_coef_densities | 1.485 | 0.010 | 1.461 | |
| plot_contrast_venn | 2.706 | 0.019 | 2.562 | |
| plot_contrastogram | 3.210 | 0.022 | 3.141 | |
| plot_data | 2.024 | 0.008 | 2.009 | |
| plot_densities | 11.262 | 0.240 | 11.370 | |
| plot_design | 0.764 | 0.003 | 0.767 | |
| plot_detections | 7.348 | 0.068 | 7.326 | |
| plot_exprs | 19.841 | 0.250 | 19.978 | |
| plot_exprs_per_coef | 19.828 | 0.075 | 19.782 | |
| plot_fit_summary | 2.040 | 0.013 | 1.999 | |
| plot_heatmap | 1.756 | 0.001 | 1.758 | |
| plot_matrix | 0.501 | 0.005 | 0.485 | |
| plot_subgroup_points | 5.277 | 0.010 | 5.232 | |
| plot_summary | 12.466 | 0.013 | 12.329 | |
| plot_venn | 0.016 | 0.000 | 0.016 | |
| plot_venn_heatmap | 0.021 | 0.000 | 0.022 | |
| plot_violins | 4.453 | 0.064 | 4.495 | |
| plot_volcano | 12.175 | 0.036 | 12.160 | |
| plot_xy_density | 6.091 | 0.002 | 6.094 | |
| preprocess_rnaseq_counts | 0.296 | 0.001 | 0.297 | |
| pull_columns | 0.002 | 0.000 | 0.002 | |
| pvalues_estimable | 0.031 | 0.001 | 0.032 | |
| read_affymetrix | 0 | 0 | 0 | |
| read_diann_proteingroups | 106.320 | 2.010 | 103.637 | |
| read_fragpipe | 6.521 | 0.024 | 6.277 | |
| read_maxquant_phosphosites | 1.571 | 0.005 | 1.577 | |
| read_maxquant_proteingroups | 2.374 | 0.144 | 2.518 | |
| read_metabolon | 12.079 | 0.025 | 11.973 | |
| read_msigdt | 0.000 | 0.000 | 0.001 | |
| read_olink | 1.314 | 0.011 | 1.261 | |
| read_rectangles | 0.166 | 0.003 | 0.169 | |
| read_rnaseq_counts | 29.527 | 1.770 | 31.137 | |
| read_salmon | 0 | 0 | 0 | |
| read_somascan | 12.648 | 0.164 | 12.740 | |
| read_uniprotdt | 0.322 | 0.007 | 0.329 | |
| reset_fit | 4.521 | 0.093 | 4.496 | |
| rm_diann_contaminants | 22.342 | 0.341 | 21.409 | |
| rm_missing_in_some_samples | 0.477 | 0.006 | 0.453 | |
| rm_unmatched_samples | 0.649 | 0.005 | 0.654 | |
| sbind | 4.020 | 0.025 | 4.046 | |
| scaledlibsizes | 0.295 | 0.000 | 0.295 | |
| scoremat | 0.848 | 0.013 | 0.838 | |
| slevels | 0.410 | 0.013 | 0.424 | |
| snames | 0.476 | 0.005 | 0.482 | |
| split_extract_fixed | 0.479 | 0.010 | 0.467 | |
| split_samples | 1.196 | 0.006 | 1.166 | |
| stepauc | 0.376 | 0.022 | 0.398 | |
| stri_any_regex | 0.000 | 0.000 | 0.001 | |
| stri_detect_fixed_in_collapsed | 0.351 | 0.025 | 0.377 | |
| subgroup_matrix | 0.573 | 0.014 | 0.564 | |
| subtract_baseline | 4.851 | 0.093 | 4.889 | |
| sumexp_to_longdt | 1.809 | 0.029 | 1.779 | |
| sumexp_to_tsv | 0.553 | 0.002 | 0.555 | |
| sumexplist_to_longdt | 1.532 | 0.009 | 1.541 | |
| summarize_fit | 1.756 | 0.012 | 1.700 | |
| survobj | 0.142 | 0.000 | 0.142 | |
| svalues | 0.415 | 0.003 | 0.418 | |
| svars | 0.484 | 0.004 | 0.488 | |
| systematic_nas | 0.549 | 0.001 | 0.550 | |
| tag_features | 1.218 | 0.032 | 1.250 | |
| tag_hdlproteins | 0.533 | 0.005 | 0.538 | |
| taxon2org | 0.001 | 0.000 | 0.001 | |
| tpm | 0.403 | 0.002 | 0.405 | |
| uncollapse | 0.027 | 0.000 | 0.026 | |
| values | 0.453 | 0.001 | 0.453 | |
| varlevels_dont_clash | 0.023 | 0.000 | 0.022 | |
| venn_detects | 0.541 | 0.002 | 0.543 | |
| weights | 0.417 | 0.000 | 0.417 | |
| write_xl | 157.989 | 1.470 | 159.514 | |
| zero_to_na | 0.002 | 0.000 | 0.001 | |