Back to Multiple platform build/check report for BioC 3.22: simplified long |
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This page was generated on 2025-10-08 12:53 -0400 (Wed, 08 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" | 4854 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4641 |
kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4586 |
taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4584 |
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 117/2341 | 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 12.7.1 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. - See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host. |
Package: autonomics |
Version: 1.17.16 |
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_1.17.16.tar.gz |
StartedAt: 2025-10-07 04:26:01 -0000 (Tue, 07 Oct 2025) |
EndedAt: 2025-10-07 04:49:18 -0000 (Tue, 07 Oct 2025) |
EllapsedTime: 1396.7 seconds |
RetCode: 0 |
Status: OK |
CheckDir: autonomics.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### 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_1.17.16.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 ‘1.17.16’ * 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 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 233.854 1.408 235.914 awblinmod 56.465 0.354 56.962 read_rnaseq_counts 40.636 0.824 41.652 read_diann_proteingroups 35.950 0.463 36.161 LINMOD 33.840 0.546 34.477 plot_exprs 28.609 0.167 28.860 plot_exprs_per_coef 27.409 0.088 27.565 default_formula 24.872 0.434 25.230 analyze 19.128 0.842 20.538 read_somascan 19.197 0.024 19.271 plot_volcano 18.628 0.052 18.729 plot_summary 17.860 0.163 18.073 read_metabolon 17.872 0.071 17.985 fit_survival 14.626 0.040 14.731 explore-transforms 14.142 0.048 14.240 plot_densities 13.948 0.056 14.036 fcluster 12.787 0.048 12.872 ftype 11.311 0.144 11.453 plot_detections 10.194 0.008 10.231 biplot_covariates 9.598 0.028 9.657 plot_xy_density 8.692 0.016 8.737 read_fragpipe 8.513 0.096 8.476 plot_subgroup_points 8.220 0.016 8.258 rm_diann_contaminants 8.007 0.076 7.996 subtract_baseline 6.904 0.036 6.950 log2transform 6.861 0.016 6.900 plot_violins 6.762 0.080 6.858 reset_fit 6.623 0.028 6.660 code 6.627 0.000 6.645 extract_contrast_features 6.237 0.020 6.276 sbind 5.953 0.004 5.972 modelvar 5.540 0.108 5.659 biplot 5.275 0.024 5.313 annotate_uniprot_rest 1.018 0.044 9.593 * 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 ‘/home/biocbuild/bbs-3.22-bioc/meat/autonomics.Rcheck/00check.log’ for details.
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 ‘1.17.16’ ** 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 4.5.0 (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") [ FAIL 0 | WARN 3 | SKIP 0 | PASS 158 ] [ FAIL 0 | WARN 3 | SKIP 0 | PASS 158 ] > > proc.time() user system elapsed 182.025 3.497 184.933
autonomics.Rcheck/autonomics-Ex.timings
name | user | system | elapsed | |
AUTONOMICS_DATASETS | 0.000 | 0.000 | 0.001 | |
COMPOUNDDISCOVERER_PATTERNS | 0.001 | 0.000 | 0.000 | |
LINMOD | 33.840 | 0.546 | 34.477 | |
LINMODENGINES | 0 | 0 | 0 | |
MAXQUANT_PATTERNS | 0 | 0 | 0 | |
TAXON_TO_ORGNAME | 0.000 | 0.000 | 0.001 | |
TESTS | 0 | 0 | 0 | |
X | 1.712 | 0.036 | 1.751 | |
abstract_fit | 1.427 | 0.019 | 1.449 | |
add_adjusted_pvalues | 0.715 | 0.032 | 0.753 | |
add_assay_means | 0.477 | 0.012 | 0.491 | |
add_facetvars | 1.957 | 0.044 | 2.004 | |
add_opentargets_by_uniprot | 0.516 | 0.008 | 0.532 | |
add_psp | 0.686 | 0.007 | 0.699 | |
add_smiles | 0.641 | 0.004 | 0.643 | |
all_non_numeric | 0.816 | 0.004 | 0.823 | |
analysis | 0.627 | 0.008 | 0.638 | |
analyze | 19.128 | 0.842 | 20.538 | |
annotate_maxquant | 1.226 | 0.073 | 1.344 | |
annotate_uniprot_rest | 1.018 | 0.044 | 9.593 | |
assert_is_valid_sumexp | 0.679 | 0.016 | 0.694 | |
awblinmod | 56.465 | 0.354 | 56.962 | |
biplot | 5.275 | 0.024 | 5.313 | |
biplot_corrections | 4.796 | 0.063 | 4.873 | |
biplot_covariates | 9.598 | 0.028 | 9.657 | |
block2limma | 0.003 | 0.000 | 0.002 | |
block2lm | 0.004 | 0.000 | 0.004 | |
block2lme | 0.003 | 0.000 | 0.002 | |
block2lmer | 0.005 | 0.000 | 0.005 | |
block_has_two_levels | 0.866 | 0.016 | 0.880 | |
center | 2.516 | 0.020 | 2.543 | |
code | 6.627 | 0.000 | 6.645 | |
collapsed_entrezg_to_symbol | 1.223 | 0.032 | 1.259 | |
contrast_subgroup_cols | 0.817 | 0.024 | 0.841 | |
contrastdt | 0.846 | 0.004 | 0.853 | |
count_in | 0.002 | 0.000 | 0.001 | |
counts | 0.495 | 0.000 | 0.497 | |
counts2cpm | 0.450 | 0.000 | 0.451 | |
counts2tpm | 0.406 | 0.004 | 0.412 | |
cpm | 0.454 | 0.000 | 0.456 | |
create_design | 0.952 | 0.012 | 0.964 | |
default_formula | 24.872 | 0.434 | 25.230 | |
default_geom | 0.636 | 0.016 | 0.651 | |
default_sfile | 0.002 | 0.000 | 0.001 | |
demultiplex | 0.019 | 0.000 | 0.020 | |
densities | 0.299 | 0.000 | 0.301 | |
dequantify | 0.003 | 0.000 | 0.003 | |
dequantify_compounddiscoverer | 0.002 | 0.000 | 0.001 | |
dot-coxph | 0.493 | 0.012 | 0.507 | |
dot-merge | 0.027 | 0.000 | 0.027 | |
dot-read_maxquant_proteingroups | 0.125 | 0.004 | 0.129 | |
download_data | 0.001 | 0.000 | 0.000 | |
download_gtf | 0 | 0 | 0 | |
download_mcclain21 | 0 | 0 | 0 | |
dt2mat | 0.004 | 0.000 | 0.004 | |
enrichment | 1.616 | 0.000 | 1.624 | |
entrezg_to_symbol | 0.174 | 0.004 | 0.178 | |
explore-transforms | 14.142 | 0.048 | 14.240 | |
extract_contrast_features | 6.237 | 0.020 | 6.276 | |
extract_rectangle | 0.143 | 0.004 | 0.147 | |
factor.vars | 0.244 | 0.000 | 0.246 | |
factorize | 1.114 | 0.000 | 1.118 | |
fcluster | 12.787 | 0.048 | 12.872 | |
fcor | 2.023 | 0.004 | 2.034 | |
fdata | 0.694 | 0.000 | 0.696 | |
fdr2p | 1.279 | 0.016 | 1.297 | |
filter_exprs_replicated_in_some_subgroup | 1.308 | 0.012 | 1.319 | |
filter_features | 0.660 | 0.008 | 0.668 | |
filter_medoid | 0.779 | 0.000 | 0.784 | |
filter_samples | 0.707 | 0.016 | 0.723 | |
fit_survival | 14.626 | 0.040 | 14.731 | |
fits | 0.421 | 0.004 | 0.426 | |
fix_xlgenes | 0.002 | 0.000 | 0.002 | |
flevels | 0.512 | 0.011 | 0.526 | |
fnames | 0.642 | 0.004 | 0.648 | |
formula2str | 0 | 0 | 0 | |
ftype | 11.311 | 0.144 | 11.453 | |
fvalues | 0.510 | 0.004 | 0.517 | |
fvars | 0.495 | 0.008 | 0.505 | |
genome_to_orgdb | 0.000 | 0.000 | 0.001 | |
group_by_level | 0.001 | 0.000 | 0.001 | |
guess_compounddiscoverer_quantity | 0.001 | 0.000 | 0.001 | |
guess_fitsep | 0.661 | 0.004 | 0.668 | |
guess_maxquant_quantity | 0.007 | 0.000 | 0.007 | |
guess_sep | 0.619 | 0.000 | 0.619 | |
has_multiple_levels | 0.072 | 0.000 | 0.072 | |
hdlproteins | 0.046 | 0.004 | 0.062 | |
impute | 4.623 | 0.008 | 4.647 | |
invert_subgroups | 0.898 | 0.004 | 0.905 | |
is_character_matrix | 0.192 | 0.000 | 0.193 | |
is_collapsed_subset | 0 | 0 | 0 | |
is_compounddiscoverer_output | 0.049 | 0.012 | 0.104 | |
is_correlation_matrix | 0.002 | 0.000 | 0.001 | |
is_diann_report | 0.083 | 0.004 | 0.065 | |
is_fastadt | 0.085 | 0.000 | 0.086 | |
is_file | 0 | 0 | 0 | |
is_fraction | 0.002 | 0.000 | 0.002 | |
is_fragpipe_tsv | 0.096 | 0.000 | 0.069 | |
is_imputed | 1.008 | 0.016 | 1.027 | |
is_maxquant_phosphosites | 0.062 | 0.004 | 0.054 | |
is_maxquant_proteingroups | 0.061 | 0.000 | 0.049 | |
is_positive_number | 0.002 | 0.000 | 0.002 | |
is_scalar_subset | 0.415 | 0.000 | 0.417 | |
is_sig | 1.896 | 0.004 | 1.906 | |
is_valid_formula | 0.059 | 0.000 | 0.060 | |
keep_estimable_features | 0.985 | 0.012 | 0.996 | |
label2index | 0.001 | 0.000 | 0.000 | |
list2mat | 0.001 | 0.000 | 0.001 | |
log2counts | 0.494 | 0.000 | 0.497 | |
log2cpm | 0.419 | 0.000 | 0.421 | |
log2diffs | 0.405 | 0.004 | 0.411 | |
log2proteins | 0.402 | 0.000 | 0.403 | |
log2sites | 0.487 | 0.000 | 0.489 | |
log2tpm | 0.419 | 0.000 | 0.420 | |
log2transform | 6.861 | 0.016 | 6.900 | |
logical2factor | 0.002 | 0.000 | 0.002 | |
make_alpha_palette | 0.677 | 0.012 | 0.688 | |
make_colors | 0.006 | 0.005 | 0.011 | |
make_volcano_dt | 1.188 | 0.002 | 1.194 | |
map_fvalues | 0.525 | 0.008 | 0.534 | |
matrix2sumexp | 1.389 | 0.004 | 1.395 | |
mclust_breaks | 0.686 | 0.023 | 0.712 | |
merge_sample_file | 0.652 | 0.004 | 0.658 | |
merge_sdata | 0.803 | 0.020 | 0.823 | |
message_df | 0.002 | 0.000 | 0.002 | |
model_coefs | 1.056 | 0.016 | 1.073 | |
modelvar | 5.540 | 0.108 | 5.659 | |
object1 | 0.629 | 0.000 | 0.630 | |
order_on_p | 1.710 | 0.016 | 1.729 | |
overall_parameters | 0.036 | 0.000 | 0.036 | |
pca | 4.293 | 0.060 | 4.363 | |
pg_to_canonical | 0.008 | 0.000 | 0.008 | |
plot_coef_densities | 1.864 | 0.016 | 1.883 | |
plot_contrast_venn | 3.007 | 0.000 | 3.006 | |
plot_contrastogram | 3.997 | 0.056 | 4.073 | |
plot_data | 2.438 | 0.012 | 2.454 | |
plot_densities | 13.948 | 0.056 | 14.036 | |
plot_design | 0.936 | 0.000 | 0.939 | |
plot_detections | 10.194 | 0.008 | 10.231 | |
plot_exprs | 28.609 | 0.167 | 28.860 | |
plot_exprs_per_coef | 27.409 | 0.088 | 27.565 | |
plot_fit_summary | 2.970 | 0.024 | 2.997 | |
plot_heatmap | 2.663 | 0.008 | 2.678 | |
plot_matrix | 0.681 | 0.008 | 0.689 | |
plot_subgroup_points | 8.220 | 0.016 | 8.258 | |
plot_summary | 17.860 | 0.163 | 18.073 | |
plot_venn | 0.014 | 0.004 | 0.018 | |
plot_venn_heatmap | 0.027 | 0.000 | 0.028 | |
plot_violins | 6.762 | 0.080 | 6.858 | |
plot_volcano | 18.628 | 0.052 | 18.729 | |
plot_xy_density | 8.692 | 0.016 | 8.737 | |
preprocess_rnaseq_counts | 0.426 | 0.000 | 0.427 | |
pull_columns | 0.003 | 0.000 | 0.003 | |
pvalues_estimable | 0.05 | 0.00 | 0.05 | |
read_affymetrix | 0 | 0 | 0 | |
read_diann_proteingroups | 35.950 | 0.463 | 36.161 | |
read_fragpipe | 8.513 | 0.096 | 8.476 | |
read_maxquant_phosphosites | 1.950 | 0.008 | 1.963 | |
read_maxquant_proteingroups | 1.596 | 0.028 | 1.628 | |
read_metabolon | 17.872 | 0.071 | 17.985 | |
read_msigdt | 0.001 | 0.000 | 0.001 | |
read_olink | 1.840 | 0.016 | 1.844 | |
read_rectangles | 0.232 | 0.004 | 0.237 | |
read_rnaseq_counts | 40.636 | 0.824 | 41.652 | |
read_salmon | 0 | 0 | 0 | |
read_somascan | 19.197 | 0.024 | 19.271 | |
read_uniprotdt | 0.387 | 0.008 | 0.396 | |
reset_fit | 6.623 | 0.028 | 6.660 | |
rm_diann_contaminants | 8.007 | 0.076 | 7.996 | |
rm_missing_in_some_samples | 0.690 | 0.020 | 0.709 | |
rm_unmatched_samples | 0.958 | 0.036 | 0.998 | |
sbind | 5.953 | 0.004 | 5.972 | |
scaledlibsizes | 0.482 | 0.004 | 0.486 | |
scoremat | 1.126 | 0.012 | 1.137 | |
slevels | 0.604 | 0.000 | 0.606 | |
snames | 0.550 | 0.000 | 0.551 | |
split_extract_fixed | 0.704 | 0.028 | 0.731 | |
split_samples | 1.693 | 0.059 | 1.754 | |
stepauc | 0.481 | 0.000 | 0.482 | |
stri_any_regex | 0.000 | 0.000 | 0.001 | |
stri_detect_fixed_in_collapsed | 0.548 | 0.004 | 0.554 | |
subgroup_matrix | 0.718 | 0.016 | 0.733 | |
subtract_baseline | 6.904 | 0.036 | 6.950 | |
sumexp_to_longdt | 2.629 | 0.020 | 2.649 | |
sumexp_to_tsv | 0.675 | 0.008 | 0.684 | |
sumexplist_to_longdt | 2.072 | 0.004 | 2.082 | |
summarize_fit | 2.386 | 0.028 | 2.414 | |
survobj | 0.199 | 0.000 | 0.199 | |
svalues | 0.564 | 0.000 | 0.565 | |
svars | 0.603 | 0.000 | 0.605 | |
systematic_nas | 0.765 | 0.016 | 0.783 | |
tag_features | 1.270 | 0.036 | 1.310 | |
tag_hdlproteins | 0.771 | 0.004 | 0.777 | |
taxon2org | 0.002 | 0.000 | 0.001 | |
tpm | 0.455 | 0.004 | 0.460 | |
uncollapse | 0.042 | 0.000 | 0.043 | |
values | 0.556 | 0.008 | 0.566 | |
varlevels_dont_clash | 0.028 | 0.000 | 0.029 | |
venn_detects | 0.819 | 0.004 | 0.825 | |
weights | 0.453 | 0.000 | 0.454 | |
write_xl | 233.854 | 1.408 | 235.914 | |
zero_to_na | 0.002 | 0.000 | 0.002 | |