Back to Multiple platform build/check report for BioC 3.22: simplified long |
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This page was generated on 2025-09-25 12:03 -0400 (Thu, 25 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" | 4831 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4618 |
kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4562 |
taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4560 |
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 1.17.1 (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: 1.17.1 |
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_1.17.1.tar.gz |
StartedAt: 2025-09-24 21:08:04 -0400 (Wed, 24 Sep 2025) |
EndedAt: 2025-09-24 21:28:04 -0400 (Wed, 24 Sep 2025) |
EllapsedTime: 1199.5 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_1.17.1.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/autonomics.Rcheck’ * using R version 4.5.1 Patched (2025-08-23 r88802) * 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 ‘1.17.1’ * 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 read_diann_proteingroups 250.815 4.284 99.877 rm_diann_contaminants 86.427 1.492 23.928 awblinmod 42.747 0.595 41.850 read_rnaseq_counts 37.016 1.727 32.685 plot_exprs 26.015 1.032 23.117 LINMOD 25.376 0.812 24.264 default_formula 24.549 0.562 18.696 plot_exprs_per_coef 20.146 0.444 20.484 ftype 16.905 0.397 9.251 read_somascan 15.704 0.410 15.665 plot_volcano 15.814 0.144 15.912 analyze 13.624 0.371 13.911 plot_summary 13.709 0.130 13.749 read_metabolon 13.182 0.261 13.409 plot_densities 12.379 0.162 10.353 read_olink 12.037 0.039 1.795 explore-transforms 10.954 0.066 11.021 fit_survival 10.663 0.093 10.760 plot_contrastogram 10.128 0.115 3.049 fcluster 9.403 0.152 9.390 plot_detections 7.611 0.554 8.099 plot_subgroup_points 7.844 0.104 6.246 read_fragpipe 7.288 0.278 5.665 plot_xy_density 7.119 0.081 7.218 biplot_covariates 6.904 0.148 7.029 plot_violins 5.807 0.030 5.818 reset_fit 5.528 0.017 5.526 subtract_baseline 5.294 0.107 4.784 * 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 ‘1.17.1’ ** 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 (2025-08-23 r88802) -- "Great Square Root" 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 259.677 4.934 223.361
autonomics.Rcheck/autonomics-Ex.timings
name | user | system | elapsed | |
AUTONOMICS_DATASETS | 0.001 | 0.000 | 0.000 | |
COMPOUNDDISCOVERER_PATTERNS | 0 | 0 | 0 | |
LINMOD | 25.376 | 0.812 | 24.264 | |
LINMODENGINES | 0 | 0 | 0 | |
MAXQUANT_PATTERNS | 0 | 0 | 0 | |
TAXON_TO_ORGNAME | 0 | 0 | 0 | |
TESTS | 0 | 0 | 0 | |
X | 1.285 | 0.375 | 1.619 | |
abstract_fit | 1.035 | 0.061 | 1.057 | |
add_adjusted_pvalues | 0.523 | 0.053 | 0.577 | |
add_assay_means | 0.347 | 0.024 | 0.371 | |
add_facetvars | 1.445 | 0.061 | 1.466 | |
add_opentargets_by_uniprot | 0.378 | 0.013 | 0.393 | |
add_psp | 0.495 | 0.030 | 0.527 | |
add_smiles | 0.486 | 0.034 | 0.495 | |
all_non_numeric | 0.597 | 0.050 | 0.648 | |
analysis | 0.499 | 0.027 | 0.526 | |
analyze | 13.624 | 0.371 | 13.911 | |
annotate_maxquant | 0.890 | 0.054 | 0.945 | |
annotate_uniprot_rest | 1.406 | 0.090 | 3.045 | |
assert_is_valid_sumexp | 0.545 | 0.021 | 0.536 | |
awblinmod | 42.747 | 0.595 | 41.850 | |
biplot | 3.795 | 0.055 | 3.809 | |
biplot_corrections | 3.516 | 0.086 | 3.567 | |
biplot_covariates | 6.904 | 0.148 | 7.029 | |
block2limma | 0.002 | 0.000 | 0.002 | |
block2lm | 0.003 | 0.000 | 0.003 | |
block2lme | 0.001 | 0.000 | 0.002 | |
block2lmer | 0.003 | 0.000 | 0.003 | |
block_has_two_levels | 0.670 | 0.045 | 0.677 | |
center | 1.924 | 0.010 | 1.931 | |
code | 4.892 | 0.007 | 4.876 | |
collapsed_entrezg_to_symbol | 0.980 | 0.045 | 1.026 | |
contrast_subgroup_cols | 0.579 | 0.005 | 0.563 | |
contrastdt | 0.367 | 0.000 | 0.368 | |
count_in | 0.001 | 0.000 | 0.001 | |
counts | 0.327 | 0.000 | 0.327 | |
counts2cpm | 0.353 | 0.000 | 0.352 | |
counts2tpm | 0.275 | 0.001 | 0.276 | |
cpm | 0.323 | 0.002 | 0.326 | |
create_design | 0.721 | 0.009 | 0.709 | |
default_formula | 24.549 | 0.562 | 18.696 | |
default_geom | 0.558 | 0.009 | 0.533 | |
default_sfile | 0.002 | 0.000 | 0.001 | |
demultiplex | 0.015 | 0.000 | 0.014 | |
densities | 0.207 | 0.002 | 0.209 | |
dequantify | 0.002 | 0.000 | 0.003 | |
dequantify_compounddiscoverer | 0.001 | 0.000 | 0.001 | |
dot-coxph | 0.373 | 0.009 | 0.382 | |
dot-merge | 0.019 | 0.001 | 0.019 | |
dot-read_maxquant_proteingroups | 0.113 | 0.002 | 0.116 | |
download_data | 0.000 | 0.000 | 0.001 | |
download_gtf | 0.001 | 0.000 | 0.000 | |
download_mcclain21 | 0.000 | 0.000 | 0.001 | |
dt2mat | 0.004 | 0.000 | 0.003 | |
enrichment | 1.162 | 0.001 | 1.163 | |
entrezg_to_symbol | 0.137 | 0.001 | 0.138 | |
explore-transforms | 10.954 | 0.066 | 11.021 | |
extract_contrast_features | 4.369 | 0.042 | 4.389 | |
extract_rectangle | 0.114 | 0.004 | 0.118 | |
factor.vars | 0.189 | 0.001 | 0.190 | |
factorize | 0.772 | 0.036 | 0.809 | |
fcluster | 9.403 | 0.152 | 9.390 | |
fcor | 1.535 | 0.024 | 1.560 | |
fdata | 0.583 | 0.005 | 0.588 | |
fdr2p | 0.942 | 0.015 | 0.933 | |
filter_exprs_replicated_in_some_subgroup | 1.085 | 0.031 | 1.030 | |
filter_features | 0.548 | 0.036 | 0.544 | |
filter_medoid | 0.648 | 0.058 | 0.706 | |
filter_samples | 0.525 | 0.016 | 0.501 | |
fit_survival | 10.663 | 0.093 | 10.760 | |
fits | 0.325 | 0.005 | 0.329 | |
fix_xlgenes | 0.001 | 0.001 | 0.002 | |
flevels | 0.415 | 0.004 | 0.419 | |
fnames | 0.419 | 0.002 | 0.421 | |
formula2str | 0 | 0 | 0 | |
ftype | 16.905 | 0.397 | 9.251 | |
fvalues | 0.436 | 0.000 | 0.436 | |
fvars | 0.391 | 0.003 | 0.394 | |
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 | 0.473 | 0.005 | 0.478 | |
guess_maxquant_quantity | 0.006 | 0.000 | 0.005 | |
guess_sep | 0.529 | 0.006 | 0.511 | |
has_multiple_levels | 0.053 | 0.003 | 0.056 | |
hdlproteins | 0.038 | 0.011 | 0.052 | |
impute | 3.449 | 0.008 | 3.458 | |
invert_subgroups | 0.599 | 0.014 | 0.613 | |
is_character_matrix | 0.143 | 0.000 | 0.143 | |
is_collapsed_subset | 0.001 | 0.000 | 0.001 | |
is_correlation_matrix | 0.002 | 0.000 | 0.001 | |
is_diann_report | 4.608 | 0.127 | 0.630 | |
is_fastadt | 0.057 | 0.001 | 0.057 | |
is_file | 0.001 | 0.000 | 0.000 | |
is_fraction | 0.001 | 0.000 | 0.001 | |
is_imputed | 0.641 | 0.001 | 0.643 | |
is_positive_number | 0.001 | 0.000 | 0.002 | |
is_scalar_subset | 0.290 | 0.002 | 0.292 | |
is_sig | 1.312 | 0.000 | 1.312 | |
is_valid_formula | 0.041 | 0.000 | 0.041 | |
keep_estimable_features | 0.825 | 0.023 | 0.768 | |
label2index | 0.001 | 0.000 | 0.000 | |
list2mat | 0.001 | 0.000 | 0.000 | |
log2counts | 0.280 | 0.001 | 0.281 | |
log2cpm | 0.276 | 0.000 | 0.276 | |
log2diffs | 0.280 | 0.004 | 0.284 | |
log2proteins | 0.353 | 0.001 | 0.354 | |
log2sites | 0.312 | 0.000 | 0.311 | |
log2tpm | 0.308 | 0.000 | 0.309 | |
log2transform | 4.857 | 0.121 | 4.981 | |
logical2factor | 0.002 | 0.000 | 0.002 | |
make_alpha_palette | 0.494 | 0.026 | 0.497 | |
make_colors | 0.01 | 0.00 | 0.01 | |
make_volcano_dt | 0.861 | 0.010 | 0.876 | |
map_fvalues | 0.353 | 0.000 | 0.353 | |
matrix2sumexp | 0.955 | 0.010 | 0.943 | |
mclust_breaks | 0.477 | 0.054 | 0.531 | |
merge_sample_file | 0.445 | 0.009 | 0.454 | |
merge_sdata | 0.573 | 0.019 | 0.567 | |
message_df | 0.002 | 0.000 | 0.002 | |
model_coefs | 0.693 | 0.008 | 0.679 | |
modelvar | 3.191 | 0.015 | 3.131 | |
object1 | 0.481 | 0.001 | 0.482 | |
order_on_p | 1.290 | 0.003 | 1.263 | |
overall_parameters | 0.027 | 0.001 | 0.027 | |
pca | 3.295 | 0.020 | 3.285 | |
pg_to_canonical | 0.005 | 0.000 | 0.005 | |
plot_coef_densities | 1.336 | 0.010 | 1.320 | |
plot_contrast_venn | 2.258 | 0.022 | 2.209 | |
plot_contrastogram | 10.128 | 0.115 | 3.049 | |
plot_data | 1.547 | 0.028 | 1.553 | |
plot_densities | 12.379 | 0.162 | 10.353 | |
plot_design | 0.842 | 0.037 | 0.888 | |
plot_detections | 7.611 | 0.554 | 8.099 | |
plot_exprs | 26.015 | 1.032 | 23.117 | |
plot_exprs_per_coef | 20.146 | 0.444 | 20.484 | |
plot_fit_summary | 2.300 | 0.014 | 2.259 | |
plot_heatmap | 1.979 | 0.018 | 1.997 | |
plot_matrix | 0.610 | 0.004 | 0.597 | |
plot_subgroup_points | 7.844 | 0.104 | 6.246 | |
plot_summary | 13.709 | 0.130 | 13.749 | |
plot_venn | 0.018 | 0.000 | 0.017 | |
plot_venn_heatmap | 0.025 | 0.001 | 0.027 | |
plot_violins | 5.807 | 0.030 | 5.818 | |
plot_volcano | 15.814 | 0.144 | 15.912 | |
plot_xy_density | 7.119 | 0.081 | 7.218 | |
preprocess_rnaseq_counts | 0.455 | 0.021 | 0.482 | |
pull_columns | 0.003 | 0.000 | 0.002 | |
pvalues_estimable | 0.039 | 0.000 | 0.039 | |
read_affymetrix | 0 | 0 | 0 | |
read_diann_proteingroups | 250.815 | 4.284 | 99.877 | |
read_fragpipe | 7.288 | 0.278 | 5.665 | |
read_maxquant_phosphosites | 1.502 | 0.098 | 1.600 | |
read_maxquant_proteingroups | 1.217 | 0.071 | 1.289 | |
read_metabolon | 13.182 | 0.261 | 13.409 | |
read_msigdt | 0.000 | 0.000 | 0.001 | |
read_olink | 12.037 | 0.039 | 1.795 | |
read_rectangles | 0.168 | 0.011 | 0.179 | |
read_rnaseq_counts | 37.016 | 1.727 | 32.685 | |
read_salmon | 0 | 0 | 0 | |
read_somascan | 15.704 | 0.410 | 15.665 | |
read_uniprotdt | 0.346 | 0.006 | 0.352 | |
reset_fit | 5.528 | 0.017 | 5.526 | |
rm_diann_contaminants | 86.427 | 1.492 | 23.928 | |
rm_missing_in_some_samples | 0.511 | 0.004 | 0.491 | |
rm_unmatched_samples | 0.654 | 0.002 | 0.656 | |
sbind | 4.311 | 0.023 | 4.334 | |
scaledlibsizes | 0.29 | 0.00 | 0.29 | |
scoremat | 0.860 | 0.007 | 0.845 | |
slevels | 0.378 | 0.001 | 0.378 | |
snames | 0.370 | 0.005 | 0.375 | |
split_extract_fixed | 0.537 | 0.001 | 0.514 | |
split_samples | 1.149 | 0.044 | 1.172 | |
stepauc | 0.298 | 0.005 | 0.303 | |
stri_any_regex | 0 | 0 | 0 | |
stri_detect_fixed_in_collapsed | 0.320 | 0.009 | 0.329 | |
subgroup_matrix | 0.541 | 0.013 | 0.530 | |
subtract_baseline | 5.294 | 0.107 | 4.784 | |
sumexp_to_longdt | 1.937 | 0.044 | 1.884 | |
sumexp_to_tsv | 0.484 | 0.006 | 0.490 | |
sumexplist_to_longdt | 1.540 | 0.006 | 1.552 | |
summarize_fit | 1.707 | 0.016 | 1.663 | |
survobj | 0.145 | 0.000 | 0.144 | |
svalues | 0.383 | 0.005 | 0.388 | |
svars | 0.398 | 0.002 | 0.400 | |
systematic_nas | 0.577 | 0.003 | 0.580 | |
tag_features | 0.920 | 0.022 | 0.942 | |
tag_hdlproteins | 0.571 | 0.011 | 0.582 | |
taxon2org | 0.001 | 0.000 | 0.001 | |
tpm | 0.312 | 0.000 | 0.312 | |
uncollapse | 0.027 | 0.000 | 0.027 | |
values | 0.406 | 0.000 | 0.405 | |
varlevels_dont_clash | 0.019 | 0.000 | 0.020 | |
venn_detects | 0.583 | 0.002 | 0.585 | |
weights | 0.322 | 0.000 | 0.321 | |
write_xl | 0.795 | 0.027 | 0.779 | |
zero_to_na | 0.002 | 0.000 | 0.001 | |