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 12:52 -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. |
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: 2025-10-07 18:17:32 -0400 (Tue, 07 Oct 2025) |
EndedAt: 2025-10-07 18:24:09 -0400 (Tue, 07 Oct 2025) |
EllapsedTime: 397.0 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: aarch64-apple-darwin20 * R was compiled by Apple clang version 16.0.0 (clang-1600.0.26.6) GNU Fortran (GCC) 14.2.0 * running under: macOS Ventura 13.7.7 * 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 51.796 2.199 56.563 read_diann_proteingroups 34.216 0.948 35.997 awblinmod 12.591 0.079 13.221 read_rnaseq_counts 9.715 0.709 10.751 rm_diann_contaminants 7.175 0.202 7.312 LINMOD 7.150 0.094 7.615 default_formula 6.163 0.183 6.401 plot_exprs 5.963 0.028 6.290 plot_exprs_per_coef 5.602 0.031 5.809 * 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-arm64/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: aarch64-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 52.952 3.320 57.453
autonomics.Rcheck/autonomics-Ex.timings
name | user | system | elapsed | |
AUTONOMICS_DATASETS | 0.000 | 0.000 | 0.001 | |
COMPOUNDDISCOVERER_PATTERNS | 0 | 0 | 0 | |
LINMOD | 7.150 | 0.094 | 7.615 | |
LINMODENGINES | 0 | 0 | 0 | |
MAXQUANT_PATTERNS | 0 | 0 | 0 | |
TAXON_TO_ORGNAME | 0 | 0 | 0 | |
TESTS | 0 | 0 | 0 | |
X | 0.346 | 0.014 | 0.361 | |
abstract_fit | 0.291 | 0.015 | 0.306 | |
add_adjusted_pvalues | 0.158 | 0.003 | 0.163 | |
add_assay_means | 0.101 | 0.001 | 0.103 | |
add_facetvars | 0.388 | 0.016 | 0.406 | |
add_opentargets_by_uniprot | 0.120 | 0.002 | 0.124 | |
add_psp | 0.151 | 0.003 | 0.154 | |
add_smiles | 0.147 | 0.014 | 0.161 | |
all_non_numeric | 0.159 | 0.001 | 0.160 | |
analysis | 0.116 | 0.002 | 0.122 | |
analyze | 4.012 | 0.056 | 4.138 | |
annotate_maxquant | 0.323 | 0.024 | 0.372 | |
annotate_uniprot_rest | 0.032 | 0.006 | 2.199 | |
assert_is_valid_sumexp | 0.241 | 0.014 | 0.274 | |
awblinmod | 12.591 | 0.079 | 13.221 | |
biplot | 1.152 | 0.018 | 1.181 | |
biplot_corrections | 1.050 | 0.014 | 1.080 | |
biplot_covariates | 2.107 | 0.018 | 2.173 | |
block2limma | 0.001 | 0.000 | 0.001 | |
block2lm | 0.001 | 0.000 | 0.001 | |
block2lme | 0 | 0 | 0 | |
block2lmer | 0.000 | 0.001 | 0.002 | |
block_has_two_levels | 0.212 | 0.015 | 0.230 | |
center | 0.550 | 0.005 | 0.558 | |
code | 1.363 | 0.016 | 1.388 | |
collapsed_entrezg_to_symbol | 0.332 | 0.018 | 0.362 | |
contrast_subgroup_cols | 0.207 | 0.015 | 0.264 | |
contrastdt | 0.181 | 0.001 | 0.183 | |
count_in | 0.001 | 0.000 | 0.001 | |
counts | 0.092 | 0.000 | 0.095 | |
counts2cpm | 0.098 | 0.001 | 0.100 | |
counts2tpm | 0.080 | 0.001 | 0.081 | |
cpm | 0.098 | 0.001 | 0.098 | |
create_design | 0.204 | 0.013 | 0.217 | |
default_formula | 6.163 | 0.183 | 6.401 | |
default_geom | 0.146 | 0.014 | 0.245 | |
default_sfile | 0.001 | 0.000 | 0.001 | |
demultiplex | 0.004 | 0.000 | 0.004 | |
densities | 0.065 | 0.002 | 0.069 | |
dequantify | 0.000 | 0.000 | 0.001 | |
dequantify_compounddiscoverer | 0.000 | 0.000 | 0.001 | |
dot-coxph | 0.128 | 0.012 | 0.149 | |
dot-merge | 0.012 | 0.001 | 0.032 | |
dot-read_maxquant_proteingroups | 0.047 | 0.002 | 0.049 | |
download_data | 0 | 0 | 0 | |
download_gtf | 0 | 0 | 0 | |
download_mcclain21 | 0.000 | 0.001 | 0.000 | |
dt2mat | 0.001 | 0.000 | 0.002 | |
enrichment | 0.331 | 0.004 | 0.348 | |
entrezg_to_symbol | 0.051 | 0.002 | 0.055 | |
explore-transforms | 2.963 | 0.027 | 3.074 | |
extract_contrast_features | 1.361 | 0.036 | 1.447 | |
extract_rectangle | 0.043 | 0.014 | 0.061 | |
factor.vars | 0.049 | 0.000 | 0.049 | |
factorize | 0.246 | 0.004 | 0.258 | |
fcluster | 2.843 | 0.017 | 2.909 | |
fcor | 0.492 | 0.010 | 0.502 | |
fdata | 0.154 | 0.002 | 0.156 | |
fdr2p | 0.284 | 0.013 | 0.298 | |
filter_exprs_replicated_in_some_subgroup | 0.287 | 0.015 | 0.301 | |
filter_features | 0.147 | 0.013 | 0.160 | |
filter_medoid | 0.159 | 0.002 | 0.160 | |
filter_samples | 0.177 | 0.014 | 0.191 | |
fit_survival | 3.332 | 0.056 | 3.519 | |
fits | 0.089 | 0.000 | 0.090 | |
fix_xlgenes | 0.001 | 0.000 | 0.001 | |
flevels | 0.121 | 0.001 | 0.129 | |
fnames | 0.144 | 0.002 | 0.146 | |
formula2str | 0 | 0 | 0 | |
ftype | 2.562 | 0.105 | 2.884 | |
fvalues | 0.124 | 0.002 | 0.126 | |
fvars | 0.122 | 0.002 | 0.125 | |
genome_to_orgdb | 0 | 0 | 0 | |
group_by_level | 0.001 | 0.000 | 0.000 | |
guess_compounddiscoverer_quantity | 0 | 0 | 0 | |
guess_fitsep | 0.165 | 0.002 | 0.167 | |
guess_maxquant_quantity | 0.002 | 0.001 | 0.002 | |
guess_sep | 0.145 | 0.012 | 0.158 | |
has_multiple_levels | 0.016 | 0.001 | 0.016 | |
hdlproteins | 0.022 | 0.010 | 0.037 | |
impute | 1.067 | 0.009 | 1.104 | |
invert_subgroups | 0.184 | 0.002 | 0.186 | |
is_character_matrix | 0.04 | 0.00 | 0.04 | |
is_collapsed_subset | 0.000 | 0.000 | 0.001 | |
is_compounddiscoverer_output | 0.027 | 0.006 | 0.064 | |
is_correlation_matrix | 0 | 0 | 0 | |
is_diann_report | 0.048 | 0.005 | 0.046 | |
is_fastadt | 0.020 | 0.000 | 0.026 | |
is_file | 0 | 0 | 0 | |
is_fraction | 0.001 | 0.000 | 0.000 | |
is_fragpipe_tsv | 0.035 | 0.004 | 0.043 | |
is_imputed | 0.243 | 0.003 | 0.256 | |
is_maxquant_phosphosites | 0.028 | 0.002 | 0.029 | |
is_maxquant_proteingroups | 0.025 | 0.002 | 0.030 | |
is_positive_number | 0.001 | 0.000 | 0.000 | |
is_scalar_subset | 0.094 | 0.001 | 0.095 | |
is_sig | 0.414 | 0.002 | 0.427 | |
is_valid_formula | 0.013 | 0.001 | 0.014 | |
keep_estimable_features | 0.224 | 0.015 | 0.244 | |
label2index | 0.000 | 0.000 | 0.001 | |
list2mat | 0.001 | 0.000 | 0.000 | |
log2counts | 0.115 | 0.001 | 0.116 | |
log2cpm | 0.086 | 0.001 | 0.086 | |
log2diffs | 0.091 | 0.001 | 0.093 | |
log2proteins | 0.093 | 0.002 | 0.103 | |
log2sites | 0.117 | 0.001 | 0.120 | |
log2tpm | 0.088 | 0.001 | 0.097 | |
log2transform | 1.579 | 0.015 | 1.645 | |
logical2factor | 0.001 | 0.000 | 0.001 | |
make_alpha_palette | 0.162 | 0.015 | 0.210 | |
make_colors | 0.004 | 0.000 | 0.005 | |
make_volcano_dt | 0.324 | 0.006 | 0.332 | |
map_fvalues | 0.115 | 0.002 | 0.118 | |
matrix2sumexp | 0.320 | 0.015 | 0.352 | |
mclust_breaks | 0.209 | 0.020 | 0.238 | |
merge_sample_file | 0.158 | 0.004 | 0.169 | |
merge_sdata | 0.232 | 0.018 | 0.257 | |
message_df | 0.001 | 0.000 | 0.001 | |
model_coefs | 0.236 | 0.015 | 0.336 | |
modelvar | 1.100 | 0.020 | 1.234 | |
object1 | 0.176 | 0.002 | 0.195 | |
order_on_p | 0.446 | 0.015 | 0.512 | |
overall_parameters | 0.009 | 0.000 | 0.012 | |
pca | 1.070 | 0.019 | 1.187 | |
pg_to_canonical | 0.002 | 0.000 | 0.002 | |
plot_coef_densities | 0.434 | 0.015 | 0.509 | |
plot_contrast_venn | 0.689 | 0.019 | 0.779 | |
plot_contrastogram | 0.985 | 0.039 | 1.139 | |
plot_data | 0.545 | 0.018 | 0.614 | |
plot_densities | 3.791 | 0.089 | 4.389 | |
plot_design | 0.211 | 0.002 | 0.219 | |
plot_detections | 2.211 | 0.010 | 2.339 | |
plot_exprs | 5.963 | 0.028 | 6.290 | |
plot_exprs_per_coef | 5.602 | 0.031 | 5.809 | |
plot_fit_summary | 0.643 | 0.025 | 0.710 | |
plot_heatmap | 0.577 | 0.003 | 0.608 | |
plot_matrix | 0.149 | 0.015 | 0.169 | |
plot_subgroup_points | 1.751 | 0.020 | 1.827 | |
plot_summary | 3.830 | 0.022 | 4.054 | |
plot_venn | 0.012 | 0.001 | 0.013 | |
plot_venn_heatmap | 0.009 | 0.000 | 0.008 | |
plot_violins | 1.546 | 0.037 | 1.707 | |
plot_volcano | 4.078 | 0.030 | 4.429 | |
plot_xy_density | 1.989 | 0.009 | 2.045 | |
preprocess_rnaseq_counts | 0.105 | 0.001 | 0.106 | |
pull_columns | 0.001 | 0.001 | 0.001 | |
pvalues_estimable | 0.012 | 0.001 | 0.014 | |
read_affymetrix | 0.000 | 0.000 | 0.001 | |
read_diann_proteingroups | 34.216 | 0.948 | 35.997 | |
read_fragpipe | 1.892 | 0.048 | 2.010 | |
read_maxquant_phosphosites | 0.478 | 0.006 | 0.503 | |
read_maxquant_proteingroups | 0.373 | 0.007 | 0.391 | |
read_metabolon | 3.758 | 0.054 | 3.875 | |
read_msigdt | 0.000 | 0.000 | 0.001 | |
read_olink | 0.514 | 0.020 | 0.541 | |
read_rectangles | 0.064 | 0.007 | 0.071 | |
read_rnaseq_counts | 9.715 | 0.709 | 10.751 | |
read_salmon | 0.000 | 0.000 | 0.001 | |
read_somascan | 4.005 | 0.008 | 4.247 | |
read_uniprotdt | 0.100 | 0.006 | 0.107 | |
reset_fit | 1.427 | 0.053 | 1.558 | |
rm_diann_contaminants | 7.175 | 0.202 | 7.312 | |
rm_missing_in_some_samples | 0.143 | 0.019 | 0.166 | |
rm_unmatched_samples | 0.188 | 0.006 | 0.203 | |
sbind | 1.178 | 0.005 | 1.210 | |
scaledlibsizes | 0.145 | 0.015 | 0.160 | |
scoremat | 0.233 | 0.013 | 0.258 | |
slevels | 0.151 | 0.003 | 0.181 | |
snames | 0.126 | 0.002 | 0.173 | |
split_extract_fixed | 0.147 | 0.015 | 0.175 | |
split_samples | 0.362 | 0.014 | 0.376 | |
stepauc | 0.093 | 0.000 | 0.094 | |
stri_any_regex | 0 | 0 | 0 | |
stri_detect_fixed_in_collapsed | 0.125 | 0.001 | 0.131 | |
subgroup_matrix | 0.152 | 0.014 | 0.170 | |
subtract_baseline | 1.426 | 0.026 | 1.498 | |
sumexp_to_longdt | 0.564 | 0.027 | 0.649 | |
sumexp_to_tsv | 0.138 | 0.002 | 0.139 | |
sumexplist_to_longdt | 0.467 | 0.005 | 0.482 | |
summarize_fit | 0.475 | 0.017 | 0.525 | |
survobj | 0.063 | 0.000 | 0.063 | |
svalues | 0.125 | 0.001 | 0.136 | |
svars | 0.118 | 0.002 | 0.119 | |
systematic_nas | 0.172 | 0.002 | 0.176 | |
tag_features | 0.339 | 0.011 | 0.361 | |
tag_hdlproteins | 0.194 | 0.013 | 0.213 | |
taxon2org | 0.001 | 0.000 | 0.001 | |
tpm | 0.121 | 0.001 | 0.126 | |
uncollapse | 0.008 | 0.001 | 0.010 | |
values | 0.125 | 0.002 | 0.130 | |
varlevels_dont_clash | 0.009 | 0.000 | 0.013 | |
venn_detects | 0.155 | 0.003 | 0.183 | |
weights | 0.122 | 0.000 | 0.145 | |
write_xl | 51.796 | 2.199 | 56.563 | |
zero_to_na | 0.001 | 0.001 | 0.000 | |