Back to Multiple platform build/check report for BioC 3.22: simplified long |
|
This page was generated on 2025-10-10 12:07 -0400 (Fri, 10 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" | 4642 |
kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4587 |
taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4586 |
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: 2025-10-10 05:34:41 -0000 (Fri, 10 Oct 2025) |
EndedAt: 2025-10-10 05:57:47 -0000 (Fri, 10 Oct 2025) |
EllapsedTime: 1386.6 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 231.319 1.663 233.742 awblinmod 58.109 1.926 60.139 read_rnaseq_counts 39.717 1.415 41.331 read_diann_proteingroups 37.077 0.299 37.101 LINMOD 34.006 0.530 34.620 plot_exprs 29.797 0.882 30.759 plot_exprs_per_coef 28.860 0.164 29.101 default_formula 25.174 0.674 25.754 read_somascan 19.387 0.044 19.493 analyze 19.185 0.168 19.406 read_metabolon 19.026 0.064 19.137 plot_volcano 18.931 0.080 19.045 plot_summary 18.786 0.160 18.993 fit_survival 15.430 0.084 15.568 explore-transforms 14.302 0.040 14.382 plot_densities 14.192 0.103 14.329 fcluster 13.561 0.072 13.662 ftype 11.809 0.116 11.913 plot_detections 10.277 0.024 10.327 biplot_covariates 9.841 0.100 9.966 plot_xy_density 8.833 0.008 8.859 read_fragpipe 8.695 0.020 8.576 rm_diann_contaminants 8.203 0.184 8.290 plot_subgroup_points 8.232 0.075 8.324 log2transform 7.354 0.016 7.393 subtract_baseline 6.973 0.023 7.012 code 6.966 0.028 7.011 plot_violins 6.862 0.032 6.908 reset_fit 6.571 0.103 6.689 extract_contrast_features 6.243 0.032 6.285 sbind 5.963 0.008 5.989 modelvar 5.603 0.128 5.740 biplot 5.403 0.076 5.490 biplot_corrections 4.971 0.024 5.005 annotate_uniprot_rest 0.936 0.060 6.417 * 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 182.218 2.118 183.724
autonomics.Rcheck/autonomics-Ex.timings
name | user | system | elapsed | |
AUTONOMICS_DATASETS | 0.000 | 0.000 | 0.001 | |
COMPOUNDDISCOVERER_PATTERNS | 0 | 0 | 0 | |
LINMOD | 34.006 | 0.530 | 34.620 | |
LINMODENGINES | 0 | 0 | 0 | |
MAXQUANT_PATTERNS | 0.000 | 0.000 | 0.001 | |
TAXON_TO_ORGNAME | 0 | 0 | 0 | |
TESTS | 0 | 0 | 0 | |
X | 1.681 | 0.020 | 1.704 | |
abstract_fit | 1.413 | 0.051 | 1.466 | |
add_adjusted_pvalues | 0.699 | 0.016 | 0.720 | |
add_assay_means | 0.456 | 0.000 | 0.457 | |
add_facetvars | 1.928 | 0.032 | 1.963 | |
add_opentargets_by_uniprot | 0.504 | 0.012 | 0.521 | |
add_psp | 0.649 | 0.008 | 0.661 | |
add_smiles | 0.588 | 0.016 | 0.603 | |
all_non_numeric | 0.810 | 0.000 | 0.812 | |
analysis | 0.586 | 0.012 | 0.599 | |
analyze | 19.185 | 0.168 | 19.406 | |
annotate_maxquant | 1.201 | 0.028 | 1.236 | |
annotate_uniprot_rest | 0.936 | 0.060 | 6.417 | |
assert_is_valid_sumexp | 0.686 | 0.012 | 0.698 | |
awblinmod | 58.109 | 1.926 | 60.139 | |
biplot | 5.403 | 0.076 | 5.490 | |
biplot_corrections | 4.971 | 0.024 | 5.005 | |
biplot_covariates | 9.841 | 0.100 | 9.966 | |
block2limma | 0.002 | 0.000 | 0.002 | |
block2lm | 0.004 | 0.000 | 0.004 | |
block2lme | 0.003 | 0.000 | 0.002 | |
block2lmer | 0.004 | 0.000 | 0.005 | |
block_has_two_levels | 0.880 | 0.003 | 0.882 | |
center | 2.636 | 0.020 | 2.665 | |
code | 6.966 | 0.028 | 7.011 | |
collapsed_entrezg_to_symbol | 1.217 | 0.052 | 1.272 | |
contrast_subgroup_cols | 0.765 | 0.008 | 0.772 | |
contrastdt | 0.799 | 0.000 | 0.801 | |
count_in | 0.001 | 0.000 | 0.002 | |
counts | 0.473 | 0.008 | 0.483 | |
counts2cpm | 0.404 | 0.000 | 0.404 | |
counts2tpm | 0.392 | 0.000 | 0.393 | |
cpm | 0.457 | 0.000 | 0.459 | |
create_design | 0.930 | 0.012 | 0.941 | |
default_formula | 25.174 | 0.674 | 25.754 | |
default_geom | 0.640 | 0.008 | 0.646 | |
default_sfile | 0.002 | 0.000 | 0.002 | |
demultiplex | 0.02 | 0.00 | 0.02 | |
densities | 0.302 | 0.000 | 0.303 | |
dequantify | 0.003 | 0.000 | 0.003 | |
dequantify_compounddiscoverer | 0.001 | 0.000 | 0.001 | |
dot-coxph | 0.499 | 0.004 | 0.506 | |
dot-merge | 0.027 | 0.000 | 0.027 | |
dot-read_maxquant_proteingroups | 0.126 | 0.000 | 0.127 | |
download_data | 0 | 0 | 0 | |
download_gtf | 0 | 0 | 0 | |
download_mcclain21 | 0.001 | 0.000 | 0.001 | |
dt2mat | 0.004 | 0.000 | 0.004 | |
enrichment | 1.605 | 0.000 | 1.611 | |
entrezg_to_symbol | 0.170 | 0.004 | 0.174 | |
explore-transforms | 14.302 | 0.040 | 14.382 | |
extract_contrast_features | 6.243 | 0.032 | 6.285 | |
extract_rectangle | 0.147 | 0.000 | 0.148 | |
factor.vars | 0.254 | 0.000 | 0.254 | |
factorize | 1.165 | 0.004 | 1.172 | |
fcluster | 13.561 | 0.072 | 13.662 | |
fcor | 2.068 | 0.080 | 2.154 | |
fdata | 0.726 | 0.012 | 0.740 | |
fdr2p | 1.313 | 0.004 | 1.318 | |
filter_exprs_replicated_in_some_subgroup | 1.371 | 0.023 | 1.392 | |
filter_features | 0.721 | 0.012 | 0.732 | |
filter_medoid | 0.802 | 0.012 | 0.818 | |
filter_samples | 0.742 | 0.004 | 0.744 | |
fit_survival | 15.430 | 0.084 | 15.568 | |
fits | 0.415 | 0.000 | 0.416 | |
fix_xlgenes | 0.001 | 0.000 | 0.002 | |
flevels | 0.524 | 0.004 | 0.530 | |
fnames | 0.651 | 0.000 | 0.653 | |
formula2str | 0 | 0 | 0 | |
ftype | 11.809 | 0.116 | 11.913 | |
fvalues | 0.516 | 0.000 | 0.518 | |
fvars | 0.499 | 0.000 | 0.501 | |
genome_to_orgdb | 0.001 | 0.000 | 0.001 | |
group_by_level | 0.001 | 0.000 | 0.001 | |
guess_compounddiscoverer_quantity | 0.001 | 0.000 | 0.002 | |
guess_fitsep | 0.666 | 0.000 | 0.667 | |
guess_maxquant_quantity | 0.006 | 0.000 | 0.007 | |
guess_sep | 0.613 | 0.012 | 0.624 | |
has_multiple_levels | 0.075 | 0.000 | 0.075 | |
hdlproteins | 0.050 | 0.004 | 0.065 | |
impute | 4.686 | 0.008 | 4.706 | |
invert_subgroups | 0.833 | 0.000 | 0.836 | |
is_character_matrix | 0.196 | 0.000 | 0.197 | |
is_collapsed_subset | 0.001 | 0.000 | 0.000 | |
is_compounddiscoverer_output | 0.057 | 0.004 | 0.103 | |
is_correlation_matrix | 0.001 | 0.000 | 0.001 | |
is_diann_report | 0.086 | 0.000 | 0.064 | |
is_fastadt | 0.086 | 0.000 | 0.086 | |
is_file | 0 | 0 | 0 | |
is_fraction | 0.002 | 0.000 | 0.002 | |
is_fragpipe_tsv | 0.092 | 0.004 | 0.070 | |
is_imputed | 1.006 | 0.000 | 1.008 | |
is_maxquant_phosphosites | 0.065 | 0.000 | 0.053 | |
is_maxquant_proteingroups | 0.061 | 0.000 | 0.049 | |
is_positive_number | 0.002 | 0.000 | 0.002 | |
is_scalar_subset | 0.406 | 0.000 | 0.407 | |
is_sig | 1.925 | 0.000 | 1.929 | |
is_valid_formula | 0.064 | 0.000 | 0.063 | |
keep_estimable_features | 1.084 | 0.008 | 1.091 | |
label2index | 0.001 | 0.000 | 0.001 | |
list2mat | 0.001 | 0.000 | 0.001 | |
log2counts | 0.537 | 0.000 | 0.539 | |
log2cpm | 0.456 | 0.004 | 0.462 | |
log2diffs | 0.455 | 0.008 | 0.464 | |
log2proteins | 0.449 | 0.000 | 0.450 | |
log2sites | 0.541 | 0.008 | 0.550 | |
log2tpm | 0.45 | 0.00 | 0.45 | |
log2transform | 7.354 | 0.016 | 7.393 | |
logical2factor | 0.002 | 0.000 | 0.002 | |
make_alpha_palette | 0.674 | 0.032 | 0.704 | |
make_colors | 0.011 | 0.000 | 0.012 | |
make_volcano_dt | 1.211 | 0.012 | 1.227 | |
map_fvalues | 0.496 | 0.000 | 0.498 | |
matrix2sumexp | 1.387 | 0.008 | 1.396 | |
mclust_breaks | 0.701 | 0.024 | 0.726 | |
merge_sample_file | 0.640 | 0.004 | 0.646 | |
merge_sdata | 0.800 | 0.015 | 0.815 | |
message_df | 0.003 | 0.001 | 0.003 | |
model_coefs | 0.980 | 0.011 | 0.991 | |
modelvar | 5.603 | 0.128 | 5.740 | |
object1 | 0.676 | 0.000 | 0.677 | |
order_on_p | 1.836 | 0.008 | 1.846 | |
overall_parameters | 0.038 | 0.000 | 0.038 | |
pca | 4.484 | 0.004 | 4.499 | |
pg_to_canonical | 0.008 | 0.000 | 0.009 | |
plot_coef_densities | 1.906 | 0.040 | 1.949 | |
plot_contrast_venn | 3.138 | 0.028 | 3.166 | |
plot_contrastogram | 3.742 | 0.028 | 3.790 | |
plot_data | 2.224 | 0.012 | 2.240 | |
plot_densities | 14.192 | 0.103 | 14.329 | |
plot_design | 1.182 | 0.004 | 1.189 | |
plot_detections | 10.277 | 0.024 | 10.327 | |
plot_exprs | 29.797 | 0.882 | 30.759 | |
plot_exprs_per_coef | 28.860 | 0.164 | 29.101 | |
plot_fit_summary | 2.996 | 0.008 | 3.006 | |
plot_heatmap | 2.666 | 0.016 | 2.687 | |
plot_matrix | 0.658 | 0.012 | 0.669 | |
plot_subgroup_points | 8.232 | 0.075 | 8.324 | |
plot_summary | 18.786 | 0.160 | 18.993 | |
plot_venn | 0.019 | 0.000 | 0.018 | |
plot_venn_heatmap | 0.030 | 0.000 | 0.029 | |
plot_violins | 6.862 | 0.032 | 6.908 | |
plot_volcano | 18.931 | 0.080 | 19.045 | |
plot_xy_density | 8.833 | 0.008 | 8.859 | |
preprocess_rnaseq_counts | 0.426 | 0.016 | 0.443 | |
pull_columns | 0.003 | 0.000 | 0.003 | |
pvalues_estimable | 0.048 | 0.004 | 0.052 | |
read_affymetrix | 0 | 0 | 0 | |
read_diann_proteingroups | 37.077 | 0.299 | 37.101 | |
read_fragpipe | 8.695 | 0.020 | 8.576 | |
read_maxquant_phosphosites | 2.098 | 0.016 | 2.120 | |
read_maxquant_proteingroups | 1.699 | 0.000 | 1.704 | |
read_metabolon | 19.026 | 0.064 | 19.137 | |
read_msigdt | 0.001 | 0.000 | 0.002 | |
read_olink | 1.763 | 0.008 | 1.757 | |
read_rectangles | 0.226 | 0.012 | 0.238 | |
read_rnaseq_counts | 39.717 | 1.415 | 41.331 | |
read_salmon | 0.001 | 0.000 | 0.000 | |
read_somascan | 19.387 | 0.044 | 19.493 | |
read_uniprotdt | 0.444 | 0.016 | 0.462 | |
reset_fit | 6.571 | 0.103 | 6.689 | |
rm_diann_contaminants | 8.203 | 0.184 | 8.290 | |
rm_missing_in_some_samples | 0.636 | 0.020 | 0.655 | |
rm_unmatched_samples | 0.926 | 0.000 | 0.929 | |
sbind | 5.963 | 0.008 | 5.989 | |
scaledlibsizes | 0.511 | 0.000 | 0.513 | |
scoremat | 1.148 | 0.016 | 1.166 | |
slevels | 0.618 | 0.008 | 0.629 | |
snames | 0.539 | 0.004 | 0.545 | |
split_extract_fixed | 0.667 | 0.020 | 0.687 | |
split_samples | 1.693 | 0.012 | 1.707 | |
stepauc | 0.529 | 0.000 | 0.531 | |
stri_any_regex | 0.001 | 0.000 | 0.001 | |
stri_detect_fixed_in_collapsed | 0.444 | 0.007 | 0.453 | |
subgroup_matrix | 0.695 | 0.009 | 0.702 | |
subtract_baseline | 6.973 | 0.023 | 7.012 | |
sumexp_to_longdt | 2.626 | 0.025 | 2.651 | |
sumexp_to_tsv | 0.646 | 0.003 | 0.652 | |
sumexplist_to_longdt | 2.127 | 0.012 | 2.146 | |
summarize_fit | 2.362 | 0.004 | 2.368 | |
survobj | 0.202 | 0.000 | 0.202 | |
svalues | 0.540 | 0.004 | 0.551 | |
svars | 0.543 | 0.000 | 0.545 | |
systematic_nas | 0.831 | 0.000 | 0.833 | |
tag_features | 1.253 | 0.016 | 1.273 | |
tag_hdlproteins | 0.804 | 0.020 | 0.826 | |
taxon2org | 0.001 | 0.000 | 0.001 | |
tpm | 0.455 | 0.000 | 0.457 | |
uncollapse | 0.036 | 0.008 | 0.044 | |
values | 0.578 | 0.004 | 0.583 | |
varlevels_dont_clash | 0.031 | 0.000 | 0.031 | |
venn_detects | 0.814 | 0.000 | 0.817 | |
weights | 0.469 | 0.000 | 0.471 | |
write_xl | 231.319 | 1.663 | 233.742 | |
zero_to_na | 0.002 | 0.000 | 0.002 | |