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 12:03 -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: /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_1.17.16.tar.gz |
StartedAt: 2025-10-17 21:07:03 -0400 (Fri, 17 Oct 2025) |
EndedAt: 2025-10-17 21:26:15 -0400 (Fri, 17 Oct 2025) |
EllapsedTime: 1152.0 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_1.17.16.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 ‘1.17.16’ * 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 159.232 1.856 161.071 read_diann_proteingroups 95.104 0.943 91.542 awblinmod 40.011 0.236 38.529 read_rnaseq_counts 29.013 2.633 31.463 LINMOD 23.477 0.398 23.125 rm_diann_contaminants 21.955 0.899 21.372 plot_exprs 19.137 0.068 19.088 plot_exprs_per_coef 18.481 0.037 18.389 default_formula 17.473 0.356 17.409 read_somascan 13.124 0.403 13.433 plot_volcano 13.161 0.052 13.161 analyze 12.850 0.090 12.826 plot_summary 12.300 0.067 12.285 read_metabolon 11.912 0.004 11.812 fit_survival 10.037 0.075 10.115 explore-transforms 9.288 0.024 9.313 plot_densities 9.110 0.057 9.093 fcluster 8.770 0.074 8.754 ftype 7.900 0.081 7.538 plot_detections 6.887 0.061 6.901 biplot_covariates 6.458 0.029 6.449 plot_xy_density 6.052 0.007 6.059 read_fragpipe 5.763 0.012 5.474 plot_subgroup_points 5.488 0.061 5.470 subtract_baseline 5.108 0.025 5.043 * 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 ‘1.17.16’ ** 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 (2025-08-23 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 137.495 4.162 139.405
autonomics.Rcheck/autonomics-Ex.timings
name | user | system | elapsed | |
AUTONOMICS_DATASETS | 0.000 | 0.000 | 0.001 | |
COMPOUNDDISCOVERER_PATTERNS | 0 | 0 | 0 | |
LINMOD | 23.477 | 0.398 | 23.125 | |
LINMODENGINES | 0 | 0 | 0 | |
MAXQUANT_PATTERNS | 0.001 | 0.000 | 0.000 | |
TAXON_TO_ORGNAME | 0.000 | 0.001 | 0.000 | |
TESTS | 0 | 0 | 0 | |
X | 1.190 | 0.013 | 1.182 | |
abstract_fit | 1.027 | 0.010 | 1.002 | |
add_adjusted_pvalues | 0.508 | 0.006 | 0.516 | |
add_assay_means | 0.324 | 0.015 | 0.339 | |
add_facetvars | 1.342 | 0.055 | 1.375 | |
add_opentargets_by_uniprot | 0.349 | 0.008 | 0.358 | |
add_psp | 0.460 | 0.010 | 0.471 | |
add_smiles | 0.429 | 0.009 | 0.417 | |
all_non_numeric | 0.543 | 0.001 | 0.544 | |
analysis | 0.438 | 0.009 | 0.447 | |
analyze | 12.850 | 0.090 | 12.826 | |
annotate_maxquant | 0.854 | 0.022 | 0.876 | |
annotate_uniprot_rest | 1.223 | 0.101 | 3.723 | |
assert_is_valid_sumexp | 0.537 | 0.010 | 0.510 | |
awblinmod | 40.011 | 0.236 | 38.529 | |
biplot | 3.581 | 0.015 | 3.557 | |
biplot_corrections | 3.382 | 0.024 | 3.377 | |
biplot_covariates | 6.458 | 0.029 | 6.449 | |
block2limma | 0.001 | 0.000 | 0.001 | |
block2lm | 0.002 | 0.000 | 0.002 | |
block2lme | 0.002 | 0.000 | 0.001 | |
block2lmer | 0.003 | 0.000 | 0.003 | |
block_has_two_levels | 0.621 | 0.008 | 0.592 | |
center | 1.777 | 0.004 | 1.777 | |
code | 4.525 | 0.072 | 4.575 | |
collapsed_entrezg_to_symbol | 0.863 | 0.045 | 0.909 | |
contrast_subgroup_cols | 0.575 | 0.006 | 0.545 | |
contrastdt | 0.548 | 0.001 | 0.549 | |
count_in | 0.001 | 0.000 | 0.001 | |
counts | 0.337 | 0.001 | 0.338 | |
counts2cpm | 0.294 | 0.000 | 0.293 | |
counts2tpm | 0.282 | 0.001 | 0.282 | |
cpm | 0.310 | 0.000 | 0.309 | |
create_design | 0.677 | 0.006 | 0.645 | |
default_formula | 17.473 | 0.356 | 17.409 | |
default_geom | 0.470 | 0.006 | 0.445 | |
default_sfile | 0.001 | 0.000 | 0.001 | |
demultiplex | 0.013 | 0.000 | 0.013 | |
densities | 0.201 | 0.001 | 0.203 | |
dequantify | 0.002 | 0.000 | 0.002 | |
dequantify_compounddiscoverer | 0.001 | 0.000 | 0.001 | |
dot-coxph | 0.346 | 0.009 | 0.355 | |
dot-merge | 0.018 | 0.001 | 0.019 | |
dot-read_maxquant_proteingroups | 0.109 | 0.002 | 0.111 | |
download_data | 0.000 | 0.000 | 0.001 | |
download_gtf | 0 | 0 | 0 | |
download_mcclain21 | 0.001 | 0.000 | 0.001 | |
dt2mat | 0.003 | 0.000 | 0.003 | |
enrichment | 1.101 | 0.001 | 1.102 | |
entrezg_to_symbol | 0.119 | 0.003 | 0.121 | |
explore-transforms | 9.288 | 0.024 | 9.313 | |
extract_contrast_features | 4.279 | 0.068 | 4.310 | |
extract_rectangle | 0.104 | 0.005 | 0.109 | |
factor.vars | 0.164 | 0.001 | 0.165 | |
factorize | 0.775 | 0.002 | 0.777 | |
fcluster | 8.770 | 0.074 | 8.754 | |
fcor | 1.364 | 0.010 | 1.375 | |
fdata | 0.472 | 0.000 | 0.471 | |
fdr2p | 0.881 | 0.007 | 0.866 | |
filter_exprs_replicated_in_some_subgroup | 0.949 | 0.003 | 0.897 | |
filter_features | 0.488 | 0.007 | 0.474 | |
filter_medoid | 0.522 | 0.001 | 0.523 | |
filter_samples | 0.521 | 0.004 | 0.505 | |
fit_survival | 10.037 | 0.075 | 10.115 | |
fits | 0.276 | 0.001 | 0.278 | |
fix_xlgenes | 0.001 | 0.000 | 0.002 | |
flevels | 0.363 | 0.003 | 0.366 | |
fnames | 0.433 | 0.005 | 0.438 | |
formula2str | 0 | 0 | 0 | |
ftype | 7.900 | 0.081 | 7.538 | |
fvalues | 0.359 | 0.004 | 0.364 | |
fvars | 0.355 | 0.002 | 0.357 | |
genome_to_orgdb | 0 | 0 | 0 | |
group_by_level | 0 | 0 | 0 | |
guess_compounddiscoverer_quantity | 0.001 | 0.000 | 0.001 | |
guess_fitsep | 0.451 | 0.002 | 0.453 | |
guess_maxquant_quantity | 0.005 | 0.000 | 0.005 | |
guess_sep | 0.437 | 0.011 | 0.428 | |
has_multiple_levels | 0.050 | 0.000 | 0.051 | |
hdlproteins | 0.037 | 0.004 | 0.043 | |
impute | 3.160 | 0.006 | 3.166 | |
invert_subgroups | 0.615 | 0.002 | 0.617 | |
is_character_matrix | 0.134 | 0.000 | 0.134 | |
is_collapsed_subset | 0.001 | 0.000 | 0.001 | |
is_compounddiscoverer_output | 0.083 | 0.028 | 0.181 | |
is_correlation_matrix | 0.003 | 0.000 | 0.001 | |
is_diann_report | 0.167 | 0.007 | 0.110 | |
is_fastadt | 0.062 | 0.001 | 0.059 | |
is_file | 0.000 | 0.000 | 0.001 | |
is_fraction | 0.002 | 0.000 | 0.001 | |
is_fragpipe_tsv | 0.088 | 0.005 | 0.065 | |
is_imputed | 0.686 | 0.000 | 0.682 | |
is_maxquant_phosphosites | 0.081 | 0.003 | 0.062 | |
is_maxquant_proteingroups | 0.084 | 0.000 | 0.059 | |
is_positive_number | 0.002 | 0.000 | 0.002 | |
is_scalar_subset | 0.281 | 0.003 | 0.284 | |
is_sig | 1.314 | 0.002 | 1.316 | |
is_valid_formula | 0.04 | 0.00 | 0.04 | |
keep_estimable_features | 0.729 | 0.009 | 0.691 | |
label2index | 0.001 | 0.000 | 0.001 | |
list2mat | 0.001 | 0.000 | 0.001 | |
log2counts | 0.332 | 0.000 | 0.332 | |
log2cpm | 0.281 | 0.001 | 0.282 | |
log2diffs | 0.293 | 0.001 | 0.294 | |
log2proteins | 0.289 | 0.001 | 0.290 | |
log2sites | 0.339 | 0.001 | 0.340 | |
log2tpm | 0.293 | 0.002 | 0.295 | |
log2transform | 4.770 | 0.006 | 4.777 | |
logical2factor | 0.002 | 0.000 | 0.002 | |
make_alpha_palette | 0.482 | 0.009 | 0.469 | |
make_colors | 0.009 | 0.001 | 0.009 | |
make_volcano_dt | 0.825 | 0.018 | 0.843 | |
map_fvalues | 0.352 | 0.000 | 0.352 | |
matrix2sumexp | 0.972 | 0.009 | 0.959 | |
mclust_breaks | 0.487 | 0.010 | 0.497 | |
merge_sample_file | 0.441 | 0.002 | 0.443 | |
merge_sdata | 0.600 | 0.007 | 0.570 | |
message_df | 0.003 | 0.000 | 0.002 | |
model_coefs | 0.694 | 0.004 | 0.660 | |
modelvar | 4.044 | 0.092 | 4.082 | |
object1 | 0.441 | 0.000 | 0.441 | |
order_on_p | 1.193 | 0.007 | 1.178 | |
overall_parameters | 0.025 | 0.000 | 0.025 | |
pca | 2.885 | 0.029 | 2.893 | |
pg_to_canonical | 0.005 | 0.000 | 0.005 | |
plot_coef_densities | 1.199 | 0.005 | 1.182 | |
plot_contrast_venn | 2.106 | 0.014 | 2.044 | |
plot_contrastogram | 2.633 | 0.010 | 2.575 | |
plot_data | 1.539 | 0.007 | 1.525 | |
plot_densities | 9.110 | 0.057 | 9.093 | |
plot_design | 0.646 | 0.001 | 0.647 | |
plot_detections | 6.887 | 0.061 | 6.901 | |
plot_exprs | 19.137 | 0.068 | 19.088 | |
plot_exprs_per_coef | 18.481 | 0.037 | 18.389 | |
plot_fit_summary | 2.092 | 0.008 | 1.989 | |
plot_heatmap | 1.773 | 0.004 | 1.777 | |
plot_matrix | 0.477 | 0.005 | 0.445 | |
plot_subgroup_points | 5.488 | 0.061 | 5.470 | |
plot_summary | 12.300 | 0.067 | 12.285 | |
plot_venn | 0.016 | 0.000 | 0.016 | |
plot_venn_heatmap | 0.019 | 0.002 | 0.021 | |
plot_violins | 4.573 | 0.026 | 4.578 | |
plot_volcano | 13.161 | 0.052 | 13.161 | |
plot_xy_density | 6.052 | 0.007 | 6.059 | |
preprocess_rnaseq_counts | 0.318 | 0.001 | 0.319 | |
pull_columns | 0.002 | 0.000 | 0.002 | |
pvalues_estimable | 0.031 | 0.003 | 0.034 | |
read_affymetrix | 0 | 0 | 0 | |
read_diann_proteingroups | 95.104 | 0.943 | 91.542 | |
read_fragpipe | 5.763 | 0.012 | 5.474 | |
read_maxquant_phosphosites | 2.433 | 0.003 | 2.436 | |
read_maxquant_proteingroups | 1.124 | 0.005 | 1.129 | |
read_metabolon | 11.912 | 0.004 | 11.812 | |
read_msigdt | 0.000 | 0.001 | 0.000 | |
read_olink | 1.342 | 0.008 | 1.257 | |
read_rectangles | 0.168 | 0.001 | 0.169 | |
read_rnaseq_counts | 29.013 | 2.633 | 31.463 | |
read_salmon | 0 | 0 | 0 | |
read_somascan | 13.124 | 0.403 | 13.433 | |
read_uniprotdt | 0.277 | 0.008 | 0.285 | |
reset_fit | 4.726 | 0.132 | 4.739 | |
rm_diann_contaminants | 21.955 | 0.899 | 21.372 | |
rm_missing_in_some_samples | 0.511 | 0.008 | 0.491 | |
rm_unmatched_samples | 0.674 | 0.009 | 0.683 | |
sbind | 4.244 | 0.027 | 4.272 | |
scaledlibsizes | 0.32 | 0.00 | 0.32 | |
scoremat | 0.887 | 0.005 | 0.859 | |
slevels | 0.395 | 0.002 | 0.397 | |
snames | 0.380 | 0.005 | 0.385 | |
split_extract_fixed | 0.581 | 0.006 | 0.549 | |
split_samples | 1.260 | 0.005 | 1.225 | |
stepauc | 0.324 | 0.000 | 0.324 | |
stri_any_regex | 0 | 0 | 0 | |
stri_detect_fixed_in_collapsed | 0.341 | 0.001 | 0.342 | |
subgroup_matrix | 0.601 | 0.013 | 0.572 | |
subtract_baseline | 5.108 | 0.025 | 5.043 | |
sumexp_to_longdt | 1.968 | 0.029 | 1.900 | |
sumexp_to_tsv | 0.466 | 0.001 | 0.468 | |
sumexplist_to_longdt | 1.510 | 0.054 | 1.564 | |
summarize_fit | 1.850 | 0.018 | 1.742 | |
survobj | 0.136 | 0.000 | 0.137 | |
svalues | 0.381 | 0.001 | 0.382 | |
svars | 0.470 | 0.044 | 0.514 | |
systematic_nas | 0.553 | 0.013 | 0.566 | |
tag_features | 1.229 | 0.019 | 1.249 | |
tag_hdlproteins | 0.536 | 0.006 | 0.541 | |
taxon2org | 0.001 | 0.000 | 0.001 | |
tpm | 0.311 | 0.001 | 0.312 | |
uncollapse | 0.029 | 0.000 | 0.029 | |
values | 0.520 | 0.035 | 0.555 | |
varlevels_dont_clash | 0.025 | 0.001 | 0.026 | |
venn_detects | 0.538 | 0.006 | 0.544 | |
weights | 0.318 | 0.004 | 0.321 | |
write_xl | 159.232 | 1.856 | 161.071 | |
zero_to_na | 0.000 | 0.001 | 0.002 | |