Back to Multiple platform build/check report for BioC 3.22: simplified long |
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This page was generated on 2025-09-29 12:04 -0400 (Mon, 29 Sep 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" | 4833 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4621 |
kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4566 |
taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4563 |
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 116/2334 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
autonomics 1.17.2 (landing page) Aditya Bhagwat
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | OK | ![]() | ||||||||
lconway | macOS 12.7.1 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 | OK | ||||||||||
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: 1.17.2 |
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_1.17.2.tar.gz |
StartedAt: 2025-09-28 19:33:31 -0400 (Sun, 28 Sep 2025) |
EndedAt: 2025-09-28 19:55:11 -0400 (Sun, 28 Sep 2025) |
EllapsedTime: 1299.5 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_1.17.2.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 ‘1.17.2’ * 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 read_diann_proteingroups 116.890 2.331 120.825 awblinmod 47.486 0.256 47.936 read_rnaseq_counts 37.169 3.461 41.572 LINMOD 27.322 0.334 27.812 rm_diann_contaminants 24.865 0.507 25.680 default_formula 22.158 0.486 22.847 plot_exprs_per_coef 22.111 0.155 22.355 plot_exprs 21.376 0.138 21.641 plot_volcano 17.427 0.162 17.753 read_metabolon 16.831 0.238 17.304 read_somascan 16.130 0.178 16.477 analyze 15.585 0.217 15.888 fit_survival 14.753 0.216 15.097 plot_summary 14.824 0.135 15.059 plot_densities 12.878 0.245 13.201 explore-transforms 12.709 0.115 12.918 fcluster 11.199 0.080 11.330 ftype 9.617 0.285 9.953 plot_detections 8.710 0.045 8.781 biplot_covariates 8.114 0.076 8.229 plot_xy_density 8.129 0.058 8.246 read_fragpipe 7.719 0.162 7.990 plot_subgroup_points 6.541 0.085 6.664 subtract_baseline 6.275 0.116 6.455 extract_contrast_features 6.048 0.143 6.255 log2transform 6.130 0.054 6.218 code 5.548 0.066 5.634 plot_violins 5.526 0.083 5.636 sbind 5.474 0.077 5.621 reset_fit 5.265 0.175 5.533 * 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 ‘1.17.2’ ** 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 151.733 17.893 319.896
autonomics.Rcheck/autonomics-Ex.timings
name | user | system | elapsed | |
AUTONOMICS_DATASETS | 0.000 | 0.000 | 0.001 | |
COMPOUNDDISCOVERER_PATTERNS | 0 | 0 | 0 | |
LINMOD | 27.322 | 0.334 | 27.812 | |
LINMODENGINES | 0.000 | 0.001 | 0.001 | |
MAXQUANT_PATTERNS | 0.000 | 0.000 | 0.001 | |
TAXON_TO_ORGNAME | 0 | 0 | 0 | |
TESTS | 0.000 | 0.001 | 0.000 | |
X | 1.380 | 0.056 | 1.448 | |
abstract_fit | 1.120 | 0.051 | 1.181 | |
add_adjusted_pvalues | 0.635 | 0.013 | 0.654 | |
add_assay_means | 0.396 | 0.006 | 0.403 | |
add_facetvars | 1.572 | 0.050 | 1.628 | |
add_opentargets_by_uniprot | 0.454 | 0.008 | 0.465 | |
add_psp | 0.590 | 0.015 | 0.609 | |
add_smiles | 0.538 | 0.038 | 0.578 | |
all_non_numeric | 0.723 | 0.006 | 0.739 | |
analysis | 0.462 | 0.009 | 0.472 | |
analyze | 15.585 | 0.217 | 15.888 | |
annotate_maxquant | 1.036 | 0.111 | 1.159 | |
annotate_uniprot_rest | 0.080 | 0.013 | 2.128 | |
assert_is_valid_sumexp | 0.742 | 0.044 | 0.791 | |
awblinmod | 47.486 | 0.256 | 47.936 | |
biplot | 4.476 | 0.065 | 4.567 | |
biplot_corrections | 4.301 | 0.071 | 4.411 | |
biplot_covariates | 8.114 | 0.076 | 8.229 | |
block2limma | 0.003 | 0.001 | 0.002 | |
block2lm | 0.003 | 0.001 | 0.003 | |
block2lme | 0.003 | 0.001 | 0.004 | |
block2lmer | 0.005 | 0.000 | 0.005 | |
block_has_two_levels | 0.759 | 0.051 | 0.825 | |
center | 2.138 | 0.018 | 2.163 | |
code | 5.548 | 0.066 | 5.634 | |
collapsed_entrezg_to_symbol | 1.110 | 0.080 | 1.196 | |
contrast_subgroup_cols | 0.773 | 0.058 | 0.848 | |
contrastdt | 0.411 | 0.002 | 0.416 | |
count_in | 0.001 | 0.001 | 0.001 | |
counts | 0.399 | 0.004 | 0.406 | |
counts2cpm | 0.391 | 0.004 | 0.396 | |
counts2tpm | 0.339 | 0.003 | 0.342 | |
cpm | 0.400 | 0.003 | 0.406 | |
create_design | 0.807 | 0.045 | 0.856 | |
default_formula | 22.158 | 0.486 | 22.847 | |
default_geom | 0.619 | 0.051 | 0.678 | |
default_sfile | 0.002 | 0.001 | 0.003 | |
demultiplex | 0.020 | 0.001 | 0.021 | |
densities | 0.272 | 0.005 | 0.278 | |
dequantify | 0.002 | 0.001 | 0.003 | |
dequantify_compounddiscoverer | 0.001 | 0.001 | 0.002 | |
dot-coxph | 0.489 | 0.052 | 0.548 | |
dot-merge | 0.032 | 0.001 | 0.033 | |
dot-read_maxquant_proteingroups | 0.123 | 0.006 | 0.129 | |
download_data | 0.000 | 0.000 | 0.001 | |
download_gtf | 0 | 0 | 0 | |
download_mcclain21 | 0.001 | 0.001 | 0.000 | |
dt2mat | 0.003 | 0.001 | 0.004 | |
enrichment | 1.324 | 0.017 | 1.350 | |
entrezg_to_symbol | 0.182 | 0.005 | 0.187 | |
explore-transforms | 12.709 | 0.115 | 12.918 | |
extract_contrast_features | 6.048 | 0.143 | 6.255 | |
extract_rectangle | 0.191 | 0.059 | 0.258 | |
factor.vars | 0.269 | 0.002 | 0.273 | |
factorize | 1.078 | 0.019 | 1.107 | |
fcluster | 11.199 | 0.080 | 11.330 | |
fcor | 1.680 | 0.035 | 1.723 | |
fdata | 0.617 | 0.014 | 0.636 | |
fdr2p | 1.153 | 0.052 | 1.214 | |
filter_exprs_replicated_in_some_subgroup | 1.204 | 0.049 | 1.264 | |
filter_features | 0.568 | 0.047 | 0.622 | |
filter_medoid | 0.693 | 0.007 | 0.704 | |
filter_samples | 0.694 | 0.057 | 0.760 | |
fit_survival | 14.753 | 0.216 | 15.097 | |
fits | 0.478 | 0.003 | 0.487 | |
fix_xlgenes | 0.003 | 0.000 | 0.002 | |
flevels | 0.518 | 0.007 | 0.527 | |
fnames | 0.685 | 0.010 | 0.700 | |
formula2str | 0 | 0 | 0 | |
ftype | 9.617 | 0.285 | 9.953 | |
fvalues | 0.447 | 0.005 | 0.454 | |
fvars | 0.433 | 0.006 | 0.441 | |
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 | 0.621 | 0.008 | 0.631 | |
guess_maxquant_quantity | 0.007 | 0.002 | 0.008 | |
guess_sep | 0.570 | 0.042 | 0.614 | |
has_multiple_levels | 0.069 | 0.001 | 0.070 | |
hdlproteins | 0.049 | 0.036 | 0.090 | |
impute | 4.020 | 0.035 | 4.076 | |
invert_subgroups | 0.744 | 0.008 | 0.756 | |
is_character_matrix | 0.177 | 0.001 | 0.179 | |
is_collapsed_subset | 0.001 | 0.001 | 0.001 | |
is_correlation_matrix | 0.001 | 0.001 | 0.002 | |
is_diann_report | 0.262 | 0.051 | 0.390 | |
is_fastadt | 0.074 | 0.001 | 0.076 | |
is_file | 0.000 | 0.001 | 0.001 | |
is_fraction | 0.001 | 0.001 | 0.002 | |
is_imputed | 0.877 | 0.009 | 0.890 | |
is_positive_number | 0.002 | 0.001 | 0.002 | |
is_scalar_subset | 0.364 | 0.005 | 0.371 | |
is_sig | 1.643 | 0.013 | 1.666 | |
is_valid_formula | 0.046 | 0.001 | 0.047 | |
keep_estimable_features | 0.867 | 0.052 | 0.933 | |
label2index | 0.001 | 0.000 | 0.001 | |
list2mat | 0.001 | 0.000 | 0.001 | |
log2counts | 0.460 | 0.004 | 0.465 | |
log2cpm | 0.378 | 0.002 | 0.383 | |
log2diffs | 0.358 | 0.005 | 0.366 | |
log2proteins | 0.373 | 0.005 | 0.380 | |
log2sites | 0.463 | 0.006 | 0.473 | |
log2tpm | 0.393 | 0.004 | 0.398 | |
log2transform | 6.130 | 0.054 | 6.218 | |
logical2factor | 0.001 | 0.001 | 0.001 | |
make_alpha_palette | 0.637 | 0.048 | 0.691 | |
make_colors | 0.011 | 0.002 | 0.013 | |
make_volcano_dt | 1.154 | 0.018 | 1.178 | |
map_fvalues | 0.501 | 0.008 | 0.513 | |
matrix2sumexp | 1.326 | 0.057 | 1.401 | |
mclust_breaks | 0.683 | 0.105 | 0.799 | |
merge_sample_file | 0.569 | 0.008 | 0.579 | |
merge_sdata | 0.717 | 0.056 | 0.779 | |
message_df | 0.004 | 0.000 | 0.003 | |
model_coefs | 0.845 | 0.059 | 0.945 | |
modelvar | 4.080 | 0.067 | 4.176 | |
object1 | 0.640 | 0.003 | 0.645 | |
order_on_p | 1.638 | 0.053 | 1.701 | |
overall_parameters | 0.032 | 0.001 | 0.033 | |
pca | 4.002 | 0.074 | 4.098 | |
pg_to_canonical | 0.008 | 0.000 | 0.009 | |
plot_coef_densities | 1.675 | 0.049 | 1.737 | |
plot_contrast_venn | 2.714 | 0.059 | 2.789 | |
plot_contrastogram | 3.489 | 0.139 | 3.670 | |
plot_data | 2.081 | 0.060 | 2.161 | |
plot_densities | 12.878 | 0.245 | 13.201 | |
plot_design | 0.824 | 0.012 | 0.840 | |
plot_detections | 8.710 | 0.045 | 8.781 | |
plot_exprs | 21.376 | 0.138 | 21.641 | |
plot_exprs_per_coef | 22.111 | 0.155 | 22.355 | |
plot_fit_summary | 2.392 | 0.075 | 2.490 | |
plot_heatmap | 2.192 | 0.018 | 2.224 | |
plot_matrix | 0.591 | 0.046 | 0.642 | |
plot_subgroup_points | 6.541 | 0.085 | 6.664 | |
plot_summary | 14.824 | 0.135 | 15.059 | |
plot_venn | 0.016 | 0.002 | 0.017 | |
plot_venn_heatmap | 0.022 | 0.001 | 0.023 | |
plot_violins | 5.526 | 0.083 | 5.636 | |
plot_volcano | 17.427 | 0.162 | 17.753 | |
plot_xy_density | 8.129 | 0.058 | 8.246 | |
preprocess_rnaseq_counts | 0.406 | 0.003 | 0.411 | |
pull_columns | 0.002 | 0.001 | 0.003 | |
pvalues_estimable | 0.048 | 0.006 | 0.054 | |
read_affymetrix | 0 | 0 | 0 | |
read_diann_proteingroups | 116.890 | 2.331 | 120.825 | |
read_fragpipe | 7.719 | 0.162 | 7.990 | |
read_maxquant_phosphosites | 2.077 | 0.055 | 2.164 | |
read_maxquant_proteingroups | 1.573 | 0.026 | 1.620 | |
read_metabolon | 16.831 | 0.238 | 17.304 | |
read_msigdt | 0.001 | 0.001 | 0.003 | |
read_olink | 1.713 | 0.086 | 1.857 | |
read_rectangles | 0.228 | 0.031 | 0.265 | |
read_rnaseq_counts | 37.169 | 3.461 | 41.572 | |
read_salmon | 0.000 | 0.001 | 0.001 | |
read_somascan | 16.130 | 0.178 | 16.477 | |
read_uniprotdt | 0.360 | 0.041 | 0.405 | |
reset_fit | 5.265 | 0.175 | 5.533 | |
rm_diann_contaminants | 24.865 | 0.507 | 25.680 | |
rm_missing_in_some_samples | 0.583 | 0.053 | 0.672 | |
rm_unmatched_samples | 0.792 | 0.038 | 0.837 | |
sbind | 5.474 | 0.077 | 5.621 | |
scaledlibsizes | 0.378 | 0.006 | 0.389 | |
scoremat | 1.129 | 0.073 | 1.234 | |
slevels | 0.444 | 0.010 | 0.463 | |
snames | 0.429 | 0.010 | 0.448 | |
split_extract_fixed | 0.659 | 0.084 | 0.785 | |
split_samples | 1.608 | 0.107 | 1.746 | |
stepauc | 0.406 | 0.008 | 0.420 | |
stri_any_regex | 0.001 | 0.002 | 0.002 | |
stri_detect_fixed_in_collapsed | 0.436 | 0.013 | 0.463 | |
subgroup_matrix | 0.756 | 0.065 | 0.832 | |
subtract_baseline | 6.275 | 0.116 | 6.455 | |
sumexp_to_longdt | 2.351 | 0.119 | 2.506 | |
sumexp_to_tsv | 0.609 | 0.009 | 0.623 | |
sumexplist_to_longdt | 1.935 | 0.026 | 1.976 | |
summarize_fit | 2.201 | 0.070 | 2.294 | |
survobj | 0.184 | 0.002 | 0.191 | |
svalues | 0.493 | 0.011 | 0.508 | |
svars | 0.491 | 0.008 | 0.503 | |
systematic_nas | 0.726 | 0.009 | 0.742 | |
tag_features | 1.187 | 0.034 | 1.230 | |
tag_hdlproteins | 0.737 | 0.053 | 0.801 | |
taxon2org | 0.002 | 0.000 | 0.002 | |
tpm | 0.401 | 0.005 | 0.409 | |
uncollapse | 0.035 | 0.002 | 0.037 | |
values | 0.488 | 0.007 | 0.499 | |
varlevels_dont_clash | 0.026 | 0.001 | 0.027 | |
venn_detects | 0.747 | 0.010 | 0.762 | |
weights | 0.401 | 0.004 | 0.408 | |
write_xl | 0.885 | 0.049 | 0.943 | |
zero_to_na | 0.002 | 0.001 | 0.002 | |