Back to Multiple platform build/check report for BioC 3.22: simplified long |
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This page was generated on 2025-10-18 12:04 -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. |
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: 2025-10-17 20:16:51 -0400 (Fri, 17 Oct 2025) |
EndedAt: 2025-10-17 20:42:02 -0400 (Fri, 17 Oct 2025) |
EllapsedTime: 1511.0 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 173.515 11.247 254.738 read_diann_proteingroups 117.651 3.850 127.954 awblinmod 48.420 0.295 49.007 read_rnaseq_counts 35.969 3.792 40.909 rm_diann_contaminants 26.818 0.529 27.660 LINMOD 25.764 0.346 26.268 plot_exprs 22.498 0.233 23.033 plot_exprs_per_coef 22.014 0.198 22.376 default_formula 19.758 0.630 20.568 read_somascan 16.105 0.148 16.420 plot_volcano 16.057 0.166 16.306 read_metabolon 15.582 0.190 15.967 analyze 15.224 0.234 15.575 plot_summary 14.878 0.118 15.063 fit_survival 13.114 0.122 13.316 explore-transforms 12.992 0.124 13.211 fcluster 11.952 0.098 12.142 plot_densities 10.391 0.418 12.357 ftype 9.283 0.302 9.675 read_fragpipe 8.335 0.205 8.651 biplot_covariates 8.282 0.080 8.413 plot_xy_density 7.978 0.066 8.100 plot_detections 7.944 0.060 8.077 plot_subgroup_points 6.542 0.145 6.935 subtract_baseline 6.239 0.146 6.462 code 5.740 0.092 5.971 plot_violins 5.609 0.117 5.769 reset_fit 5.414 0.152 5.657 extract_contrast_features 5.341 0.101 5.485 log2transform 5.214 0.045 5.286 sbind 5.010 0.102 5.244 * 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 139.173 19.606 272.143
autonomics.Rcheck/autonomics-Ex.timings
name | user | system | elapsed | |
AUTONOMICS_DATASETS | 0.000 | 0.001 | 0.001 | |
COMPOUNDDISCOVERER_PATTERNS | 0.000 | 0.001 | 0.001 | |
LINMOD | 25.764 | 0.346 | 26.268 | |
LINMODENGINES | 0 | 0 | 0 | |
MAXQUANT_PATTERNS | 0.000 | 0.000 | 0.001 | |
TAXON_TO_ORGNAME | 0.000 | 0.000 | 0.001 | |
TESTS | 0.000 | 0.001 | 0.001 | |
X | 1.305 | 0.047 | 1.359 | |
abstract_fit | 1.144 | 0.051 | 1.203 | |
add_adjusted_pvalues | 0.565 | 0.013 | 0.582 | |
add_assay_means | 0.351 | 0.007 | 0.359 | |
add_facetvars | 1.449 | 0.049 | 1.503 | |
add_opentargets_by_uniprot | 0.421 | 0.007 | 0.432 | |
add_psp | 0.557 | 0.014 | 0.574 | |
add_smiles | 0.525 | 0.054 | 0.601 | |
all_non_numeric | 0.727 | 0.005 | 0.736 | |
analysis | 0.420 | 0.007 | 0.428 | |
analyze | 15.224 | 0.234 | 15.575 | |
annotate_maxquant | 1.027 | 0.108 | 1.146 | |
annotate_uniprot_rest | 0.081 | 0.012 | 2.073 | |
assert_is_valid_sumexp | 0.750 | 0.049 | 0.810 | |
awblinmod | 48.420 | 0.295 | 49.007 | |
biplot | 4.443 | 0.074 | 4.556 | |
biplot_corrections | 4.238 | 0.063 | 4.338 | |
biplot_covariates | 8.282 | 0.080 | 8.413 | |
block2limma | 0.002 | 0.000 | 0.003 | |
block2lm | 0.003 | 0.000 | 0.004 | |
block2lme | 0.003 | 0.000 | 0.003 | |
block2lmer | 0.004 | 0.001 | 0.005 | |
block_has_two_levels | 0.753 | 0.046 | 0.804 | |
center | 2.302 | 0.032 | 2.356 | |
code | 5.740 | 0.092 | 5.971 | |
collapsed_entrezg_to_symbol | 1.104 | 0.098 | 1.222 | |
contrast_subgroup_cols | 0.792 | 0.057 | 0.861 | |
contrastdt | 0.731 | 0.011 | 0.748 | |
count_in | 0.001 | 0.001 | 0.002 | |
counts | 0.395 | 0.005 | 0.405 | |
counts2cpm | 0.422 | 0.006 | 0.430 | |
counts2tpm | 0.358 | 0.005 | 0.381 | |
cpm | 0.448 | 0.006 | 0.461 | |
create_design | 0.842 | 0.051 | 0.900 | |
default_formula | 19.758 | 0.630 | 20.568 | |
default_geom | 0.521 | 0.042 | 0.568 | |
default_sfile | 0.001 | 0.000 | 0.002 | |
demultiplex | 0.015 | 0.001 | 0.016 | |
densities | 0.260 | 0.007 | 0.270 | |
dequantify | 0.003 | 0.001 | 0.004 | |
dequantify_compounddiscoverer | 0.001 | 0.000 | 0.002 | |
dot-coxph | 0.454 | 0.057 | 0.533 | |
dot-merge | 0.026 | 0.001 | 0.027 | |
dot-read_maxquant_proteingroups | 0.118 | 0.006 | 0.124 | |
download_data | 0.000 | 0.000 | 0.001 | |
download_gtf | 0 | 0 | 0 | |
download_mcclain21 | 0.000 | 0.001 | 0.001 | |
dt2mat | 0.003 | 0.001 | 0.004 | |
enrichment | 1.383 | 0.017 | 1.408 | |
entrezg_to_symbol | 0.205 | 0.006 | 0.211 | |
explore-transforms | 12.992 | 0.124 | 13.211 | |
extract_contrast_features | 5.341 | 0.101 | 5.485 | |
extract_rectangle | 0.153 | 0.046 | 0.205 | |
factor.vars | 0.195 | 0.001 | 0.196 | |
factorize | 0.954 | 0.017 | 0.981 | |
fcluster | 11.952 | 0.098 | 12.142 | |
fcor | 2.000 | 0.042 | 2.063 | |
fdata | 0.640 | 0.017 | 0.662 | |
fdr2p | 1.109 | 0.053 | 1.172 | |
filter_exprs_replicated_in_some_subgroup | 1.039 | 0.050 | 1.100 | |
filter_features | 0.636 | 0.041 | 0.682 | |
filter_medoid | 0.651 | 0.005 | 0.659 | |
filter_samples | 0.586 | 0.044 | 0.635 | |
fit_survival | 13.114 | 0.122 | 13.316 | |
fits | 1.392 | 0.011 | 1.409 | |
fix_xlgenes | 0.002 | 0.001 | 0.002 | |
flevels | 0.470 | 0.007 | 0.479 | |
fnames | 0.576 | 0.009 | 0.590 | |
formula2str | 0.001 | 0.000 | 0.001 | |
ftype | 9.283 | 0.302 | 9.675 | |
fvalues | 0.461 | 0.007 | 0.470 | |
fvars | 0.450 | 0.009 | 0.462 | |
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 | 0.507 | 0.007 | 0.517 | |
guess_maxquant_quantity | 0.005 | 0.002 | 0.007 | |
guess_sep | 0.574 | 0.042 | 0.620 | |
has_multiple_levels | 0.062 | 0.003 | 0.066 | |
hdlproteins | 0.049 | 0.037 | 0.097 | |
impute | 3.681 | 0.036 | 3.737 | |
invert_subgroups | 0.738 | 0.008 | 0.749 | |
is_character_matrix | 0.160 | 0.001 | 0.161 | |
is_collapsed_subset | 0 | 0 | 0 | |
is_compounddiscoverer_output | 0.049 | 0.033 | 0.165 | |
is_correlation_matrix | 0.001 | 0.001 | 0.001 | |
is_diann_report | 0.090 | 0.014 | 0.105 | |
is_fastadt | 0.065 | 0.001 | 0.067 | |
is_file | 0.001 | 0.000 | 0.000 | |
is_fraction | 0.001 | 0.001 | 0.002 | |
is_fragpipe_tsv | 0.056 | 0.008 | 0.065 | |
is_imputed | 0.728 | 0.007 | 0.738 | |
is_maxquant_phosphosites | 0.053 | 0.007 | 0.061 | |
is_maxquant_proteingroups | 0.054 | 0.007 | 0.063 | |
is_positive_number | 0.002 | 0.000 | 0.002 | |
is_scalar_subset | 0.334 | 0.005 | 0.338 | |
is_sig | 1.465 | 0.013 | 1.484 | |
is_valid_formula | 0.053 | 0.001 | 0.054 | |
keep_estimable_features | 0.834 | 0.044 | 0.886 | |
label2index | 0.001 | 0.000 | 0.001 | |
list2mat | 0.000 | 0.001 | 0.001 | |
log2counts | 0.334 | 0.003 | 0.339 | |
log2cpm | 0.347 | 0.003 | 0.351 | |
log2diffs | 0.372 | 0.007 | 0.381 | |
log2proteins | 0.342 | 0.006 | 0.348 | |
log2sites | 0.349 | 0.005 | 0.357 | |
log2tpm | 0.358 | 0.003 | 0.363 | |
log2transform | 5.214 | 0.045 | 5.286 | |
logical2factor | 0.002 | 0.000 | 0.003 | |
make_alpha_palette | 0.551 | 0.046 | 0.603 | |
make_colors | 0.010 | 0.001 | 0.011 | |
make_volcano_dt | 0.953 | 0.012 | 0.971 | |
map_fvalues | 0.418 | 0.011 | 0.432 | |
matrix2sumexp | 1.162 | 0.055 | 1.241 | |
mclust_breaks | 0.568 | 0.097 | 0.670 | |
merge_sample_file | 0.705 | 0.049 | 0.761 | |
merge_sdata | 0.594 | 0.066 | 0.670 | |
message_df | 0.003 | 0.000 | 0.003 | |
model_coefs | 0.775 | 0.045 | 0.825 | |
modelvar | 3.493 | 0.075 | 3.602 | |
object1 | 0.599 | 0.005 | 0.607 | |
order_on_p | 1.494 | 0.063 | 1.578 | |
overall_parameters | 0.023 | 0.000 | 0.024 | |
pca | 3.993 | 0.074 | 4.096 | |
pg_to_canonical | 0.007 | 0.001 | 0.008 | |
plot_coef_densities | 1.563 | 0.057 | 1.637 | |
plot_contrast_venn | 2.636 | 0.063 | 2.723 | |
plot_contrastogram | 3.133 | 0.125 | 3.289 | |
plot_data | 1.433 | 0.075 | 1.984 | |
plot_densities | 10.391 | 0.418 | 12.357 | |
plot_design | 0.727 | 0.011 | 0.770 | |
plot_detections | 7.944 | 0.060 | 8.077 | |
plot_exprs | 22.498 | 0.233 | 23.033 | |
plot_exprs_per_coef | 22.014 | 0.198 | 22.376 | |
plot_fit_summary | 2.355 | 0.062 | 2.568 | |
plot_heatmap | 1.639 | 0.021 | 2.185 | |
plot_matrix | 0.565 | 0.101 | 0.965 | |
plot_subgroup_points | 6.542 | 0.145 | 6.935 | |
plot_summary | 14.878 | 0.118 | 15.063 | |
plot_venn | 0.019 | 0.002 | 0.021 | |
plot_venn_heatmap | 0.027 | 0.002 | 0.029 | |
plot_violins | 5.609 | 0.117 | 5.769 | |
plot_volcano | 16.057 | 0.166 | 16.306 | |
plot_xy_density | 7.978 | 0.066 | 8.100 | |
preprocess_rnaseq_counts | 0.396 | 0.005 | 0.404 | |
pull_columns | 0.003 | 0.000 | 0.004 | |
pvalues_estimable | 0.051 | 0.006 | 0.056 | |
read_affymetrix | 0.001 | 0.000 | 0.000 | |
read_diann_proteingroups | 117.651 | 3.850 | 127.954 | |
read_fragpipe | 8.335 | 0.205 | 8.651 | |
read_maxquant_phosphosites | 1.813 | 0.047 | 1.884 | |
read_maxquant_proteingroups | 1.536 | 0.032 | 1.587 | |
read_metabolon | 15.582 | 0.190 | 15.967 | |
read_msigdt | 0.001 | 0.001 | 0.002 | |
read_olink | 1.576 | 0.080 | 1.714 | |
read_rectangles | 0.244 | 0.030 | 0.287 | |
read_rnaseq_counts | 35.969 | 3.792 | 40.909 | |
read_salmon | 0.000 | 0.001 | 0.001 | |
read_somascan | 16.105 | 0.148 | 16.420 | |
read_uniprotdt | 0.366 | 0.053 | 0.433 | |
reset_fit | 5.414 | 0.152 | 5.657 | |
rm_diann_contaminants | 26.818 | 0.529 | 27.660 | |
rm_missing_in_some_samples | 0.598 | 0.073 | 0.699 | |
rm_unmatched_samples | 0.835 | 0.036 | 0.886 | |
sbind | 5.010 | 0.102 | 5.244 | |
scaledlibsizes | 0.354 | 0.006 | 0.367 | |
scoremat | 0.979 | 0.059 | 1.056 | |
slevels | 0.459 | 0.013 | 0.482 | |
snames | 0.458 | 0.011 | 0.476 | |
split_extract_fixed | 0.642 | 0.058 | 0.718 | |
split_samples | 1.452 | 0.063 | 1.533 | |
stepauc | 0.379 | 0.007 | 0.392 | |
stri_any_regex | 0.000 | 0.001 | 0.001 | |
stri_detect_fixed_in_collapsed | 0.380 | 0.008 | 0.393 | |
subgroup_matrix | 0.671 | 0.052 | 0.738 | |
subtract_baseline | 6.239 | 0.146 | 6.462 | |
sumexp_to_longdt | 2.316 | 0.185 | 2.657 | |
sumexp_to_tsv | 0.600 | 0.013 | 0.617 | |
sumexplist_to_longdt | 2.000 | 0.035 | 2.076 | |
summarize_fit | 2.220 | 0.078 | 2.331 | |
survobj | 0.195 | 0.002 | 0.202 | |
svalues | 0.523 | 0.013 | 0.551 | |
svars | 0.519 | 0.011 | 0.544 | |
systematic_nas | 0.792 | 0.013 | 0.821 | |
tag_features | 1.449 | 0.069 | 1.576 | |
tag_hdlproteins | 0.776 | 0.045 | 0.836 | |
taxon2org | 0.001 | 0.001 | 0.002 | |
tpm | 0.427 | 0.008 | 0.441 | |
uncollapse | 0.039 | 0.004 | 0.049 | |
values | 0.556 | 0.016 | 0.586 | |
varlevels_dont_clash | 0.028 | 0.002 | 0.032 | |
venn_detects | 0.829 | 0.020 | 0.866 | |
weights | 0.434 | 0.007 | 0.445 | |
write_xl | 173.515 | 11.247 | 254.738 | |
zero_to_na | 0.002 | 0.006 | 0.065 | |