Back to Multiple platform build/check report for BioC 3.21: simplified long |
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This page was generated on 2025-10-13 11:38 -0400 (Mon, 13 Oct 2025).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4833 |
merida1 | macOS 12.7.5 Monterey | x86_64 | 4.5.1 RC (2025-06-05 r88288) -- "Great Square Root" | 4614 |
kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" | 4555 |
kunpeng2 | Linux (openEuler 24.03 LTS) | aarch64 | R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" | 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 1.16.0 (landing page) Aditya Bhagwat
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | OK | ![]() | ||||||||
merida1 | macOS 12.7.5 Monterey / x86_64 | OK | OK | OK | OK | ![]() | ||||||||
kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | OK | OK | ![]() | ||||||||
kunpeng2 | Linux (openEuler 24.03 LTS) / aarch64 | OK | OK | ERROR | ||||||||||
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: 1.16.0 |
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_1.16.0.tar.gz |
StartedAt: 2025-10-10 00:13:15 -0400 (Fri, 10 Oct 2025) |
EndedAt: 2025-10-10 00:51:38 -0400 (Fri, 10 Oct 2025) |
EllapsedTime: 2302.4 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_1.16.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/autonomics.Rcheck’ * using R version 4.5.1 RC (2025-06-05 r88288) * using platform: x86_64-apple-darwin20 * R was compiled by Apple clang version 14.0.0 (clang-1400.0.29.202) GNU Fortran (GCC) 14.2.0 * running under: macOS Monterey 12.7.6 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘autonomics/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘autonomics’ version ‘1.16.0’ * package encoding: UTF-8 * checking package namespace information ... OK * checking package dependencies ... INFO Imports includes 30 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 read_diann_proteingroups 232.506 4.506 270.063 read_rnaseq_counts 77.163 3.302 85.857 fit_linmod 77.583 0.441 81.795 plot_exprs_per_coef 63.760 0.302 67.599 plot_exprs 61.884 0.274 64.967 rm_diann_contaminants 44.909 0.461 46.034 analyze 40.393 0.325 41.769 default_formula 40.095 0.484 42.980 read_metabolon 38.896 0.548 44.424 plot_summary 38.197 0.394 42.751 read_somascan 35.719 0.200 37.400 plot_volcano 34.222 0.637 41.752 plot_densities 23.399 0.252 26.287 fcluster 21.824 0.134 23.362 ftype 19.840 0.423 21.388 plot_sample_nas 16.542 0.113 18.139 biplot_covariates 16.369 0.100 16.563 extract_coef_features 16.325 0.122 17.290 read_fragpipe 14.682 0.194 18.082 plot_subgroup_points 14.247 0.144 15.475 code 13.072 0.122 13.418 fit_survival 12.541 0.092 13.214 log2transform 12.368 0.097 13.174 subtract_baseline 12.096 0.159 22.938 plot_violins 11.781 0.384 15.327 reset_fit 11.793 0.110 11.999 biplot 10.977 0.119 11.360 plot_joint_density 10.604 0.153 11.373 biplot_corrections 9.916 0.103 10.055 plot_survival 9.780 0.226 12.550 modelvar 8.871 0.097 9.697 pca 8.286 0.113 8.853 impute 8.219 0.055 8.632 plot_contrastogram 6.885 0.180 7.651 plot_heatmap 6.030 0.027 6.403 plot_contrast_venn 5.896 0.079 6.194 plot_fit_summary 5.459 0.093 5.900 sumexp_to_longdt 4.345 0.198 8.524 summarize_fit 4.225 0.105 8.003 sumexplist_to_longdt 3.414 0.041 6.731 * 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-3.21-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-x86_64/Resources/library’ * installing *source* package ‘autonomics’ ... ** this is package ‘autonomics’ version ‘1.16.0’ ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** 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 RC (2025-06-05 r88288) -- "Great Square Root" Copyright (C) 2025 The R Foundation for Statistical Computing Platform: x86_64-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 284.425 19.372 377.615
autonomics.Rcheck/autonomics-Ex.timings
name | user | system | elapsed | |
AUTONOMICS_DATASETS | 0.000 | 0.001 | 0.002 | |
COMPOUNDDISCOVERER_PATTERNS | 0.000 | 0.000 | 0.001 | |
FITSEP | 0.000 | 0.000 | 0.001 | |
LINMODENGINES | 0.000 | 0.000 | 0.001 | |
MAXQUANT_PATTERNS | 0.001 | 0.001 | 0.001 | |
SURVIVALENGINES | 0 | 0 | 0 | |
TAXON_TO_ORGNAME | 0.001 | 0.000 | 0.002 | |
TESTS | 0.000 | 0.001 | 0.001 | |
X | 3.597 | 0.272 | 4.044 | |
abstract_fit | 4.337 | 0.172 | 4.748 | |
add_adjusted_pvalues | 1.287 | 0.035 | 1.370 | |
add_assay_means | 0.835 | 0.016 | 0.884 | |
add_facetvars | 3.747 | 0.104 | 4.019 | |
add_opentargets_by_uniprot | 0.880 | 0.010 | 0.986 | |
add_psp | 1.139 | 0.024 | 1.254 | |
add_smiles | 1.069 | 0.066 | 1.188 | |
analysis | 0.842 | 0.010 | 0.896 | |
analyze | 40.393 | 0.325 | 41.769 | |
annotate_maxquant | 1.922 | 0.123 | 2.052 | |
annotate_uniprot_rest | 0.147 | 0.020 | 1.992 | |
assert_is_valid_sumexp | 1.209 | 0.067 | 1.296 | |
bin | 0.889 | 0.019 | 0.911 | |
biplot | 10.977 | 0.119 | 11.360 | |
biplot_corrections | 9.916 | 0.103 | 10.055 | |
biplot_covariates | 16.369 | 0.100 | 16.563 | |
block2lme | 0.006 | 0.002 | 0.007 | |
center | 4.034 | 0.030 | 4.071 | |
code | 13.072 | 0.122 | 13.418 | |
coefs | 1.925 | 0.071 | 2.009 | |
collapsed_entrezg_to_symbol | 0.001 | 0.001 | 0.001 | |
contrast_subgroup_cols | 1.365 | 0.069 | 1.458 | |
count_in | 0.002 | 0.002 | 0.005 | |
counts | 0.739 | 0.004 | 0.745 | |
counts2cpm | 0.733 | 0.004 | 0.747 | |
counts2tpm | 0.669 | 0.004 | 0.697 | |
cpm | 0.726 | 0.005 | 0.762 | |
create_design | 1.752 | 0.088 | 1.945 | |
default_formula | 40.095 | 0.484 | 42.980 | |
default_geom | 1.192 | 0.069 | 1.339 | |
default_sfile | 0.003 | 0.001 | 0.003 | |
demultiplex | 0.035 | 0.002 | 0.039 | |
dequantify | 0.004 | 0.000 | 0.006 | |
dequantify_compounddiscoverer | 0.003 | 0.001 | 0.005 | |
dot-coxph | 0.945 | 0.058 | 1.077 | |
dot-merge | 0.034 | 0.002 | 0.039 | |
dot-read_maxquant_proteingroups | 0.204 | 0.008 | 0.223 | |
download_data | 0.000 | 0.001 | 0.001 | |
download_gtf | 0.000 | 0.000 | 0.001 | |
download_mcclain21 | 0.001 | 0.000 | 0.001 | |
dt2mat | 0.007 | 0.001 | 0.008 | |
enrichment | 4.501 | 0.017 | 4.738 | |
entrezg_to_symbol | 0.001 | 0.001 | 0.001 | |
extract_coef_features | 16.325 | 0.122 | 17.290 | |
extract_rectangle | 0.268 | 0.065 | 0.345 | |
fcluster | 21.824 | 0.134 | 23.362 | |
fcor | 3.344 | 0.054 | 3.544 | |
fdata | 1.270 | 0.035 | 1.338 | |
fdr2p | 2.257 | 0.075 | 2.397 | |
filter_exprs_replicated_in_some_subgroup | 2.243 | 0.072 | 2.416 | |
filter_features | 1.156 | 0.069 | 1.280 | |
filter_medoid | 1.607 | 0.028 | 1.760 | |
filter_samples | 1.208 | 0.067 | 1.375 | |
fit_linmod | 77.583 | 0.441 | 81.795 | |
fit_survival | 12.541 | 0.092 | 13.214 | |
fitcoefs | 2.027 | 0.069 | 2.199 | |
fits | 1.805 | 0.069 | 1.969 | |
fix_xlgenes | 0.003 | 0.001 | 0.004 | |
flevels | 0.940 | 0.011 | 0.996 | |
fnames | 1.023 | 0.010 | 1.124 | |
formula2str | 0.000 | 0.000 | 0.001 | |
ftype | 19.840 | 0.423 | 21.388 | |
fvalues | 0.978 | 0.010 | 1.032 | |
fvars | 0.886 | 0.009 | 0.941 | |
genome_to_orgdb | 0.001 | 0.001 | 0.001 | |
group_by_level | 0.003 | 0.002 | 0.004 | |
guess_compounddiscoverer_quantity | 0.002 | 0.001 | 0.004 | |
guess_fitsep | 1.094 | 0.011 | 1.188 | |
guess_maxquant_quantity | 0.011 | 0.002 | 0.014 | |
guess_sep | 1.155 | 0.070 | 1.566 | |
has_multiple_levels | 0.129 | 0.006 | 0.149 | |
hdlproteins | 0.082 | 0.067 | 0.174 | |
impute | 8.219 | 0.055 | 8.632 | |
invert_subgroups | 1.509 | 0.012 | 1.590 | |
is_collapsed_subset | 0.001 | 0.000 | 0.002 | |
is_correlation_matrix | 0.002 | 0.001 | 0.003 | |
is_diann_report | 0.390 | 0.087 | 0.554 | |
is_fastadt | 0.140 | 0.002 | 0.154 | |
is_file | 0.000 | 0.001 | 0.002 | |
is_fraction | 0.004 | 0.002 | 0.005 | |
is_imputed | 1.723 | 0.012 | 1.819 | |
is_positive_number | 0.004 | 0.001 | 0.006 | |
is_scalar_subset | 0.721 | 0.009 | 0.769 | |
is_sig | 4.270 | 0.021 | 4.486 | |
is_valid_formula | 0.099 | 0.003 | 0.107 | |
keep_connected_blocks | 1.126 | 0.067 | 1.265 | |
keep_connected_features | 1.663 | 0.068 | 1.834 | |
keep_replicated_features | 1.857 | 0.071 | 2.005 | |
label2index | 0.002 | 0.001 | 0.003 | |
list2mat | 0.001 | 0.001 | 0.002 | |
log2counts | 0.791 | 0.005 | 0.874 | |
log2cpm | 0.713 | 0.005 | 0.801 | |
log2diffs | 0.757 | 0.010 | 0.827 | |
log2proteins | 0.699 | 0.011 | 0.738 | |
log2sites | 0.703 | 0.007 | 0.751 | |
log2tpm | 0.772 | 0.005 | 0.817 | |
log2transform | 12.368 | 0.097 | 13.174 | |
logical2factor | 0.002 | 0.001 | 0.004 | |
make_alpha_palette | 1.210 | 0.069 | 1.352 | |
make_colors | 0.017 | 0.003 | 0.019 | |
make_volcano_dt | 2.048 | 0.018 | 2.156 | |
map_fvalues | 0.878 | 0.015 | 0.937 | |
matrix2sumexp | 2.377 | 0.074 | 2.568 | |
merge_sample_file | 0.954 | 0.014 | 1.014 | |
merge_sdata | 1.271 | 0.096 | 1.435 | |
message_df | 0.006 | 0.000 | 0.006 | |
model_coefs | 1.713 | 0.072 | 1.890 | |
modelvar | 8.871 | 0.097 | 9.697 | |
order_on_p | 2.818 | 0.074 | 3.048 | |
pca | 8.286 | 0.113 | 8.853 | |
pg_to_canonical | 0.014 | 0.001 | 0.015 | |
plot_coef_densities | 3.213 | 0.074 | 3.425 | |
plot_contrast_venn | 5.896 | 0.079 | 6.194 | |
plot_contrastogram | 6.885 | 0.180 | 7.651 | |
plot_data | 3.820 | 0.084 | 4.367 | |
plot_densities | 23.399 | 0.252 | 26.287 | |
plot_design | 1.657 | 0.014 | 1.795 | |
plot_exprs | 61.884 | 0.274 | 64.967 | |
plot_exprs_per_coef | 63.760 | 0.302 | 67.599 | |
plot_fit_summary | 5.459 | 0.093 | 5.900 | |
plot_heatmap | 6.030 | 0.027 | 6.403 | |
plot_joint_density | 10.604 | 0.153 | 11.373 | |
plot_matrix | 1.181 | 0.076 | 1.331 | |
plot_sample_nas | 16.542 | 0.113 | 18.139 | |
plot_subgroup_points | 14.247 | 0.144 | 15.475 | |
plot_summary | 38.197 | 0.394 | 42.751 | |
plot_survival | 9.780 | 0.226 | 12.550 | |
plot_venn | 0.007 | 0.002 | 0.011 | |
plot_venn_heatmap | 0.049 | 0.005 | 0.064 | |
plot_violins | 11.781 | 0.384 | 15.327 | |
plot_volcano | 34.222 | 0.637 | 41.752 | |
preprocess_rnaseq_counts | 0.683 | 0.007 | 0.783 | |
pull_columns | 0.005 | 0.001 | 0.006 | |
read_affymetrix | 0.000 | 0.001 | 0.001 | |
read_diann_proteingroups | 232.506 | 4.506 | 270.063 | |
read_fragpipe | 14.682 | 0.194 | 18.082 | |
read_maxquant_phosphosites | 3.283 | 0.077 | 4.207 | |
read_maxquant_proteingroups | 2.744 | 0.064 | 3.411 | |
read_metabolon | 38.896 | 0.548 | 44.424 | |
read_msigdt | 0.002 | 0.001 | 0.003 | |
read_olink | 3.155 | 0.137 | 3.729 | |
read_rectangles | 0.389 | 0.038 | 0.515 | |
read_rnaseq_counts | 77.163 | 3.302 | 85.857 | |
read_salmon | 0.001 | 0.001 | 0.003 | |
read_somascan | 35.719 | 0.200 | 37.400 | |
read_uniprotdt | 0.613 | 0.052 | 0.668 | |
reset_fit | 11.793 | 0.110 | 11.999 | |
rm_diann_contaminants | 44.909 | 0.461 | 46.034 | |
rm_missing_in_some_samples | 1.021 | 0.061 | 1.088 | |
rm_unmatched_samples | 1.294 | 0.015 | 1.310 | |
scaledlibsizes | 0.646 | 0.004 | 0.651 | |
scoremat | 2.129 | 0.075 | 2.230 | |
slevels | 0.827 | 0.013 | 0.845 | |
snames | 1.129 | 0.180 | 1.316 | |
split_extract_fixed | 1.121 | 0.086 | 1.231 | |
split_samples | 2.720 | 0.096 | 4.052 | |
stri_any_regex | 0.000 | 0.001 | 0.002 | |
stri_detect_fixed_in_collapsed | 0.786 | 0.022 | 1.526 | |
subgroup_matrix | 1.303 | 0.074 | 2.573 | |
subtract_baseline | 12.096 | 0.159 | 22.938 | |
sumexp_to_longdt | 4.345 | 0.198 | 8.524 | |
sumexp_to_tsv | 1.158 | 0.012 | 2.107 | |
sumexplist_to_longdt | 3.414 | 0.041 | 6.731 | |
summarize_fit | 4.225 | 0.105 | 8.003 | |
svalues | 0.876 | 0.016 | 1.650 | |
svars | 1.017 | 0.016 | 1.891 | |
systematic_nas | 1.293 | 0.017 | 2.339 | |
tag_features | 2.287 | 0.074 | 4.265 | |
tag_hdlproteins | 1.147 | 0.108 | 2.384 | |
taxon2org | 0.001 | 0.001 | 0.003 | |
tpm | 0.847 | 0.052 | 1.569 | |
uncollapse | 0.061 | 0.005 | 0.131 | |
values | 0.905 | 0.023 | 1.806 | |
varlevels_dont_clash | 0.033 | 0.002 | 0.054 | |
venn_detects | 1.089 | 0.018 | 1.898 | |
weights | 0.443 | 0.006 | 0.548 | |
write_xl | 0.997 | 0.319 | 2.098 | |
zero_to_na | 0.003 | 0.003 | 0.005 | |