Back to Multiple platform build/check report for BioC 3.22: simplified long |
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This page was generated on 2025-10-20 12:04 -0400 (Mon, 20 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. |
Package: autonomics |
Version: 1.17.16 |
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:autonomics.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings autonomics_1.17.16.tar.gz |
StartedAt: 2025-10-19 20:23:26 -0400 (Sun, 19 Oct 2025) |
EndedAt: 2025-10-19 20:48:31 -0400 (Sun, 19 Oct 2025) |
EllapsedTime: 1504.2 seconds |
RetCode: 0 |
Status: OK |
CheckDir: autonomics.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:autonomics.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings autonomics_1.17.16.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/autonomics.Rcheck’ * using R version 4.5.1 Patched (2025-09-10 r88807) * using platform: x86_64-apple-darwin20 * R was compiled by Apple clang version 14.0.0 (clang-1400.0.29.202) GNU Fortran (GCC) 14.2.0 * running under: macOS Monterey 12.7.6 * 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 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 167.439 11.127 245.889 read_diann_proteingroups 117.691 4.169 130.503 awblinmod 47.931 0.306 48.538 read_rnaseq_counts 35.811 3.734 40.355 rm_diann_contaminants 27.841 0.487 28.652 LINMOD 26.783 0.353 27.279 plot_exprs 22.137 0.216 22.562 plot_exprs_per_coef 21.994 0.216 22.438 default_formula 20.155 0.689 21.010 read_somascan 15.987 0.143 16.308 plot_volcano 15.726 0.127 15.917 analyze 15.489 0.227 15.817 read_metabolon 15.442 0.181 15.793 plot_summary 15.007 0.203 15.463 fit_survival 13.370 0.156 13.680 explore-transforms 12.586 0.118 12.807 fcluster 11.839 0.087 12.001 plot_densities 10.495 0.306 14.336 ftype 10.200 0.286 10.707 read_fragpipe 8.524 0.227 8.877 plot_detections 8.616 0.065 8.796 biplot_covariates 8.358 0.128 8.559 plot_xy_density 7.550 0.060 7.656 plot_subgroup_points 6.692 0.102 6.859 subtract_baseline 6.580 0.135 6.808 log2transform 5.934 0.050 6.031 plot_violins 5.731 0.159 5.940 code 5.720 0.093 5.858 reset_fit 5.620 0.144 5.844 sbind 5.419 0.099 5.614 extract_contrast_features 5.376 0.074 5.486 * 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 ‘/Users/biocbuild/bbs-3.22-bioc/meat/autonomics.Rcheck/00check.log’ for details.
autonomics.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL autonomics ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/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
R version 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" Copyright (C) 2025 The R Foundation for Statistical Computing Platform: x86_64-apple-darwin20 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 148.133 14.914 250.690
autonomics.Rcheck/autonomics-Ex.timings
name | user | system | elapsed | |
AUTONOMICS_DATASETS | 0.000 | 0.000 | 0.001 | |
COMPOUNDDISCOVERER_PATTERNS | 0.001 | 0.000 | 0.001 | |
LINMOD | 26.783 | 0.353 | 27.279 | |
LINMODENGINES | 0 | 0 | 0 | |
MAXQUANT_PATTERNS | 0.000 | 0.001 | 0.001 | |
TAXON_TO_ORGNAME | 0 | 0 | 0 | |
TESTS | 0.001 | 0.000 | 0.001 | |
X | 1.381 | 0.058 | 1.452 | |
abstract_fit | 1.166 | 0.063 | 1.237 | |
add_adjusted_pvalues | 0.572 | 0.012 | 0.588 | |
add_assay_means | 0.397 | 0.008 | 0.406 | |
add_facetvars | 1.574 | 0.071 | 1.663 | |
add_opentargets_by_uniprot | 0.436 | 0.009 | 0.449 | |
add_psp | 0.552 | 0.017 | 0.570 | |
add_smiles | 0.507 | 0.041 | 0.550 | |
all_non_numeric | 0.652 | 0.004 | 0.657 | |
analysis | 0.449 | 0.008 | 0.459 | |
analyze | 15.489 | 0.227 | 15.817 | |
annotate_maxquant | 1.058 | 0.109 | 1.181 | |
annotate_uniprot_rest | 0.081 | 0.013 | 1.967 | |
assert_is_valid_sumexp | 0.755 | 0.050 | 0.814 | |
awblinmod | 47.931 | 0.306 | 48.538 | |
biplot | 4.389 | 0.075 | 4.499 | |
biplot_corrections | 4.236 | 0.068 | 4.343 | |
biplot_covariates | 8.358 | 0.128 | 8.559 | |
block2limma | 0.003 | 0.001 | 0.003 | |
block2lm | 0.003 | 0.001 | 0.003 | |
block2lme | 0.003 | 0.001 | 0.003 | |
block2lmer | 0.004 | 0.000 | 0.005 | |
block_has_two_levels | 0.803 | 0.054 | 0.869 | |
center | 2.236 | 0.031 | 2.362 | |
code | 5.720 | 0.093 | 5.858 | |
collapsed_entrezg_to_symbol | 1.142 | 0.096 | 1.254 | |
contrast_subgroup_cols | 0.772 | 0.062 | 0.846 | |
contrastdt | 0.690 | 0.006 | 0.699 | |
count_in | 0.001 | 0.001 | 0.002 | |
counts | 0.406 | 0.004 | 0.414 | |
counts2cpm | 0.393 | 0.002 | 0.397 | |
counts2tpm | 0.351 | 0.003 | 0.356 | |
cpm | 0.384 | 0.003 | 0.388 | |
create_design | 0.796 | 0.046 | 0.849 | |
default_formula | 20.155 | 0.689 | 21.010 | |
default_geom | 0.638 | 0.048 | 0.693 | |
default_sfile | 0.002 | 0.001 | 0.002 | |
demultiplex | 0.019 | 0.002 | 0.020 | |
densities | 0.284 | 0.011 | 0.298 | |
dequantify | 0.003 | 0.001 | 0.003 | |
dequantify_compounddiscoverer | 0.002 | 0.001 | 0.002 | |
dot-coxph | 0.571 | 0.062 | 0.644 | |
dot-merge | 0.031 | 0.002 | 0.032 | |
dot-read_maxquant_proteingroups | 0.141 | 0.007 | 0.149 | |
download_data | 0.001 | 0.002 | 0.002 | |
download_gtf | 0 | 0 | 0 | |
download_mcclain21 | 0.000 | 0.000 | 0.001 | |
dt2mat | 0.003 | 0.001 | 0.004 | |
enrichment | 1.421 | 0.015 | 1.451 | |
entrezg_to_symbol | 0.182 | 0.004 | 0.189 | |
explore-transforms | 12.586 | 0.118 | 12.807 | |
extract_contrast_features | 5.376 | 0.074 | 5.486 | |
extract_rectangle | 0.175 | 0.053 | 0.233 | |
factor.vars | 0.213 | 0.001 | 0.214 | |
factorize | 1.052 | 0.018 | 1.078 | |
fcluster | 11.839 | 0.087 | 12.001 | |
fcor | 1.937 | 0.037 | 1.994 | |
fdata | 0.741 | 0.018 | 0.767 | |
fdr2p | 1.219 | 0.063 | 1.308 | |
filter_exprs_replicated_in_some_subgroup | 1.117 | 0.054 | 1.182 | |
filter_features | 0.659 | 0.054 | 0.722 | |
filter_medoid | 0.692 | 0.007 | 0.704 | |
filter_samples | 0.678 | 0.082 | 0.774 | |
fit_survival | 13.370 | 0.156 | 13.680 | |
fits | 0.497 | 0.005 | 0.505 | |
fix_xlgenes | 0.002 | 0.000 | 0.002 | |
flevels | 0.476 | 0.006 | 0.485 | |
fnames | 0.568 | 0.010 | 0.582 | |
formula2str | 0.001 | 0.001 | 0.000 | |
ftype | 10.200 | 0.286 | 10.707 | |
fvalues | 0.504 | 0.008 | 0.514 | |
fvars | 0.475 | 0.007 | 0.484 | |
genome_to_orgdb | 0.001 | 0.000 | 0.001 | |
group_by_level | 0.001 | 0.001 | 0.002 | |
guess_compounddiscoverer_quantity | 0.001 | 0.001 | 0.002 | |
guess_fitsep | 0.641 | 0.007 | 0.651 | |
guess_maxquant_quantity | 0.007 | 0.002 | 0.009 | |
guess_sep | 0.581 | 0.044 | 0.627 | |
has_multiple_levels | 0.075 | 0.004 | 0.078 | |
hdlproteins | 0.053 | 0.045 | 0.101 | |
impute | 4.333 | 0.038 | 4.393 | |
invert_subgroups | 0.757 | 0.007 | 0.768 | |
is_character_matrix | 0.164 | 0.001 | 0.166 | |
is_collapsed_subset | 0.001 | 0.000 | 0.000 | |
is_compounddiscoverer_output | 0.05 | 0.03 | 0.16 | |
is_correlation_matrix | 0.001 | 0.000 | 0.002 | |
is_diann_report | 0.094 | 0.015 | 0.110 | |
is_fastadt | 0.072 | 0.002 | 0.074 | |
is_file | 0.000 | 0.001 | 0.001 | |
is_fraction | 0.002 | 0.001 | 0.002 | |
is_fragpipe_tsv | 0.058 | 0.007 | 0.065 | |
is_imputed | 0.874 | 0.008 | 0.885 | |
is_maxquant_phosphosites | 0.056 | 0.007 | 0.063 | |
is_maxquant_proteingroups | 0.056 | 0.008 | 0.063 | |
is_positive_number | 0.002 | 0.000 | 0.002 | |
is_scalar_subset | 0.380 | 0.006 | 0.387 | |
is_sig | 1.663 | 0.013 | 1.682 | |
is_valid_formula | 0.048 | 0.001 | 0.049 | |
keep_estimable_features | 0.856 | 0.045 | 0.905 | |
label2index | 0.001 | 0.000 | 0.001 | |
list2mat | 0.000 | 0.000 | 0.001 | |
log2counts | 0.439 | 0.005 | 0.444 | |
log2cpm | 0.346 | 0.003 | 0.349 | |
log2diffs | 0.360 | 0.006 | 0.366 | |
log2proteins | 0.363 | 0.005 | 0.369 | |
log2sites | 0.417 | 0.005 | 0.423 | |
log2tpm | 0.376 | 0.003 | 0.379 | |
log2transform | 5.934 | 0.050 | 6.031 | |
logical2factor | 0.001 | 0.000 | 0.002 | |
make_alpha_palette | 0.595 | 0.046 | 0.654 | |
make_colors | 0.009 | 0.001 | 0.011 | |
make_volcano_dt | 2.145 | 0.028 | 2.178 | |
map_fvalues | 0.416 | 0.009 | 0.424 | |
matrix2sumexp | 1.100 | 0.062 | 1.172 | |
mclust_breaks | 0.607 | 0.099 | 0.714 | |
merge_sample_file | 0.532 | 0.011 | 0.547 | |
merge_sdata | 0.675 | 0.067 | 0.749 | |
message_df | 0.002 | 0.000 | 0.002 | |
model_coefs | 0.788 | 0.059 | 0.861 | |
modelvar | 3.489 | 0.060 | 3.567 | |
object1 | 0.600 | 0.004 | 0.609 | |
order_on_p | 1.617 | 0.061 | 1.701 | |
overall_parameters | 0.029 | 0.000 | 0.030 | |
pca | 3.855 | 0.077 | 3.960 | |
pg_to_canonical | 0.006 | 0.001 | 0.006 | |
plot_coef_densities | 1.547 | 0.077 | 1.651 | |
plot_contrast_venn | 2.590 | 0.059 | 2.672 | |
plot_contrastogram | 3.041 | 0.129 | 3.212 | |
plot_data | 1.837 | 0.062 | 1.927 | |
plot_densities | 10.495 | 0.306 | 14.336 | |
plot_design | 0.603 | 0.010 | 0.683 | |
plot_detections | 8.616 | 0.065 | 8.796 | |
plot_exprs | 22.137 | 0.216 | 22.562 | |
plot_exprs_per_coef | 21.994 | 0.216 | 22.438 | |
plot_fit_summary | 2.217 | 0.303 | 3.679 | |
plot_heatmap | 1.859 | 0.035 | 2.524 | |
plot_matrix | 0.568 | 0.071 | 0.694 | |
plot_subgroup_points | 6.692 | 0.102 | 6.859 | |
plot_summary | 15.007 | 0.203 | 15.463 | |
plot_venn | 0.016 | 0.003 | 0.022 | |
plot_venn_heatmap | 0.025 | 0.003 | 0.035 | |
plot_violins | 5.731 | 0.159 | 5.940 | |
plot_volcano | 15.726 | 0.127 | 15.917 | |
plot_xy_density | 7.550 | 0.060 | 7.656 | |
preprocess_rnaseq_counts | 0.500 | 0.006 | 0.508 | |
pull_columns | 0.003 | 0.000 | 0.004 | |
pvalues_estimable | 0.047 | 0.007 | 0.055 | |
read_affymetrix | 0.001 | 0.000 | 0.000 | |
read_diann_proteingroups | 117.691 | 4.169 | 130.503 | |
read_fragpipe | 8.524 | 0.227 | 8.877 | |
read_maxquant_phosphosites | 1.755 | 0.050 | 1.833 | |
read_maxquant_proteingroups | 1.378 | 0.025 | 1.430 | |
read_metabolon | 15.442 | 0.181 | 15.793 | |
read_msigdt | 0.001 | 0.001 | 0.002 | |
read_olink | 1.624 | 0.095 | 1.794 | |
read_rectangles | 0.228 | 0.032 | 0.286 | |
read_rnaseq_counts | 35.811 | 3.734 | 40.355 | |
read_salmon | 0.000 | 0.001 | 0.001 | |
read_somascan | 15.987 | 0.143 | 16.308 | |
read_uniprotdt | 0.348 | 0.053 | 0.418 | |
reset_fit | 5.620 | 0.144 | 5.844 | |
rm_diann_contaminants | 27.841 | 0.487 | 28.652 | |
rm_missing_in_some_samples | 0.643 | 0.064 | 0.729 | |
rm_unmatched_samples | 0.839 | 0.023 | 0.880 | |
sbind | 5.419 | 0.099 | 5.614 | |
scaledlibsizes | 0.401 | 0.007 | 0.417 | |
scoremat | 1.220 | 0.112 | 1.375 | |
slevels | 0.495 | 0.011 | 0.525 | |
snames | 0.616 | 0.015 | 0.681 | |
split_extract_fixed | 0.612 | 0.060 | 0.683 | |
split_samples | 1.595 | 0.061 | 1.676 | |
stepauc | 0.417 | 0.006 | 0.432 | |
stri_any_regex | 0.001 | 0.000 | 0.002 | |
stri_detect_fixed_in_collapsed | 0.521 | 0.011 | 0.539 | |
subgroup_matrix | 0.653 | 0.056 | 0.727 | |
subtract_baseline | 6.580 | 0.135 | 6.808 | |
sumexp_to_longdt | 2.242 | 0.120 | 2.400 | |
sumexp_to_tsv | 0.712 | 0.013 | 0.740 | |
sumexplist_to_longdt | 2.018 | 0.035 | 2.081 | |
summarize_fit | 2.225 | 0.064 | 2.318 | |
survobj | 0.195 | 0.002 | 0.200 | |
svalues | 0.498 | 0.010 | 0.516 | |
svars | 0.489 | 0.009 | 0.503 | |
systematic_nas | 0.779 | 0.013 | 0.804 | |
tag_features | 1.503 | 0.057 | 1.617 | |
tag_hdlproteins | 0.677 | 0.050 | 0.743 | |
taxon2org | 0.001 | 0.001 | 0.001 | |
tpm | 0.424 | 0.004 | 0.432 | |
uncollapse | 0.041 | 0.001 | 0.044 | |
values | 0.699 | 0.028 | 0.742 | |
varlevels_dont_clash | 0.024 | 0.001 | 0.026 | |
venn_detects | 0.726 | 0.013 | 0.748 | |
weights | 0.514 | 0.006 | 0.527 | |
write_xl | 167.439 | 11.127 | 245.889 | |
zero_to_na | 0.003 | 0.010 | 0.049 | |