Back to Multiple platform build/check report for BioC 3.22: simplified long |
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This page was generated on 2025-09-23 12:04 -0400 (Tue, 23 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" | 4816 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4605 |
kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4549 |
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 1.17.0 (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: 1.17.0 |
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_1.17.0.tar.gz |
StartedAt: 2025-09-22 19:23:14 -0400 (Mon, 22 Sep 2025) |
EndedAt: 2025-09-22 19:43:12 -0400 (Mon, 22 Sep 2025) |
EllapsedTime: 1198.2 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_1.17.0.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: 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 ‘1.17.0’ * 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 115.314 2.039 118.550 read_rnaseq_counts 43.189 3.493 47.440 fit_linmod 37.292 0.297 37.770 plot_exprs 28.740 0.246 29.133 plot_exprs_per_coef 28.253 0.172 28.561 rm_diann_contaminants 25.759 0.523 26.562 default_formula 19.665 0.332 20.154 read_somascan 19.585 0.159 19.945 read_metabolon 19.246 0.220 19.687 analyze 18.294 0.208 18.590 plot_summary 18.159 0.114 18.344 plot_volcano 16.065 0.127 16.263 plot_densities 12.193 0.206 12.469 fcluster 10.518 0.076 10.630 ftype 10.116 0.278 10.488 biplot_covariates 8.077 0.086 8.209 plot_sample_nas 8.083 0.071 8.198 extract_coef_features 7.467 0.082 7.597 read_fragpipe 7.314 0.117 7.504 plot_subgroup_points 7.045 0.103 7.190 fit_survival 6.446 0.064 6.543 reset_fit 6.343 0.101 6.519 subtract_baseline 6.187 0.127 6.447 code 5.970 0.075 6.076 log2transform 5.927 0.056 6.026 plot_violins 5.704 0.089 5.813 biplot 5.184 0.073 5.288 biplot_corrections 5.127 0.069 5.218 * 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-x86_64/Resources/library’ * installing *source* package ‘autonomics’ ... ** this is package ‘autonomics’ version ‘1.17.0’ ** 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 Patched (2025-09-10 r88807) -- "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 159.226 10.942 231.697
autonomics.Rcheck/autonomics-Ex.timings
name | user | system | elapsed | |
AUTONOMICS_DATASETS | 0.001 | 0.000 | 0.001 | |
COMPOUNDDISCOVERER_PATTERNS | 0.000 | 0.001 | 0.001 | |
FITSEP | 0.000 | 0.001 | 0.001 | |
LINMODENGINES | 0 | 0 | 0 | |
MAXQUANT_PATTERNS | 0 | 0 | 0 | |
SURVIVALENGINES | 0.001 | 0.000 | 0.001 | |
TAXON_TO_ORGNAME | 0 | 0 | 0 | |
TESTS | 0.000 | 0.000 | 0.001 | |
X | 1.765 | 0.146 | 1.925 | |
abstract_fit | 1.970 | 0.085 | 2.072 | |
add_adjusted_pvalues | 0.661 | 0.019 | 0.687 | |
add_assay_means | 0.437 | 0.010 | 0.451 | |
add_facetvars | 1.845 | 0.062 | 1.919 | |
add_opentargets_by_uniprot | 0.479 | 0.009 | 0.494 | |
add_psp | 0.608 | 0.016 | 0.628 | |
add_smiles | 0.534 | 0.045 | 0.583 | |
analysis | 0.414 | 0.007 | 0.424 | |
analyze | 18.294 | 0.208 | 18.590 | |
annotate_maxquant | 1.051 | 0.107 | 1.171 | |
annotate_uniprot_rest | 0.091 | 0.014 | 1.979 | |
assert_is_valid_sumexp | 0.628 | 0.043 | 0.675 | |
bin | 0.441 | 0.010 | 0.452 | |
biplot | 5.184 | 0.073 | 5.288 | |
biplot_corrections | 5.127 | 0.069 | 5.218 | |
biplot_covariates | 8.077 | 0.086 | 8.209 | |
block2lme | 0.004 | 0.001 | 0.005 | |
center | 2.033 | 0.021 | 2.066 | |
code | 5.970 | 0.075 | 6.076 | |
coefs | 0.883 | 0.039 | 0.925 | |
collapsed_entrezg_to_symbol | 0.001 | 0.000 | 0.001 | |
contrast_subgroup_cols | 0.642 | 0.049 | 0.695 | |
count_in | 0.001 | 0.001 | 0.003 | |
counts | 0.383 | 0.003 | 0.390 | |
counts2cpm | 0.442 | 0.003 | 0.446 | |
counts2tpm | 0.347 | 0.003 | 0.351 | |
cpm | 0.367 | 0.003 | 0.378 | |
create_design | 0.806 | 0.053 | 0.876 | |
default_formula | 19.665 | 0.332 | 20.154 | |
default_geom | 0.544 | 0.044 | 0.595 | |
default_sfile | 0.002 | 0.001 | 0.002 | |
demultiplex | 0.017 | 0.001 | 0.018 | |
dequantify | 0.003 | 0.001 | 0.003 | |
dequantify_compounddiscoverer | 0.001 | 0.001 | 0.002 | |
dot-coxph | 0.494 | 0.050 | 0.549 | |
dot-merge | 0.024 | 0.001 | 0.025 | |
dot-read_maxquant_proteingroups | 0.130 | 0.006 | 0.137 | |
download_data | 0.000 | 0.001 | 0.001 | |
download_gtf | 0 | 0 | 0 | |
download_mcclain21 | 0.001 | 0.000 | 0.001 | |
dt2mat | 0.003 | 0.001 | 0.004 | |
enrichment | 1.971 | 0.010 | 1.989 | |
entrezg_to_symbol | 0.000 | 0.000 | 0.001 | |
extract_coef_features | 7.467 | 0.082 | 7.597 | |
extract_rectangle | 0.152 | 0.046 | 0.206 | |
fcluster | 10.518 | 0.076 | 10.630 | |
fcor | 1.750 | 0.042 | 1.801 | |
fdata | 0.575 | 0.014 | 0.590 | |
fdr2p | 1.033 | 0.039 | 1.075 | |
filter_exprs_replicated_in_some_subgroup | 1.072 | 0.062 | 1.159 | |
filter_features | 0.621 | 0.039 | 0.663 | |
filter_medoid | 0.858 | 0.022 | 0.884 | |
filter_samples | 0.590 | 0.042 | 0.637 | |
fit_linmod | 37.292 | 0.297 | 37.770 | |
fit_survival | 6.446 | 0.064 | 6.543 | |
fitcoefs | 1.025 | 0.044 | 1.075 | |
fits | 0.876 | 0.044 | 0.926 | |
fix_xlgenes | 0.002 | 0.000 | 0.002 | |
flevels | 0.520 | 0.009 | 0.535 | |
fnames | 0.590 | 0.012 | 0.608 | |
formula2str | 0 | 0 | 0 | |
ftype | 10.116 | 0.278 | 10.488 | |
fvalues | 0.452 | 0.007 | 0.461 | |
fvars | 0.519 | 0.007 | 0.530 | |
genome_to_orgdb | 0.000 | 0.001 | 0.001 | |
group_by_level | 0.001 | 0.001 | 0.002 | |
guess_compounddiscoverer_quantity | 0.001 | 0.000 | 0.002 | |
guess_fitsep | 0.499 | 0.006 | 0.508 | |
guess_maxquant_quantity | 0.007 | 0.002 | 0.009 | |
guess_sep | 0.621 | 0.046 | 0.673 | |
has_multiple_levels | 0.069 | 0.004 | 0.077 | |
hdlproteins | 0.050 | 0.029 | 0.083 | |
impute | 4.374 | 0.044 | 4.454 | |
invert_subgroups | 0.888 | 0.009 | 0.904 | |
is_collapsed_subset | 0.000 | 0.001 | 0.001 | |
is_correlation_matrix | 0.001 | 0.000 | 0.001 | |
is_diann_report | 0.260 | 0.051 | 0.391 | |
is_fastadt | 0.064 | 0.001 | 0.066 | |
is_file | 0.000 | 0.000 | 0.001 | |
is_fraction | 0.002 | 0.000 | 0.002 | |
is_imputed | 0.862 | 0.007 | 0.874 | |
is_positive_number | 0.001 | 0.000 | 0.002 | |
is_scalar_subset | 0.481 | 0.005 | 0.492 | |
is_sig | 2.294 | 0.014 | 2.325 | |
is_valid_formula | 0.066 | 0.002 | 0.068 | |
keep_connected_blocks | 0.733 | 0.078 | 0.840 | |
keep_connected_features | 1.860 | 0.079 | 1.959 | |
keep_replicated_features | 0.944 | 0.055 | 1.013 | |
label2index | 0.001 | 0.000 | 0.001 | |
list2mat | 0.000 | 0.000 | 0.001 | |
log2counts | 0.413 | 0.008 | 0.427 | |
log2cpm | 0.404 | 0.005 | 0.412 | |
log2diffs | 0.422 | 0.007 | 0.433 | |
log2proteins | 0.421 | 0.007 | 0.430 | |
log2sites | 0.399 | 0.008 | 0.408 | |
log2tpm | 0.456 | 0.004 | 0.464 | |
log2transform | 5.927 | 0.056 | 6.026 | |
logical2factor | 0.001 | 0.000 | 0.001 | |
make_alpha_palette | 0.624 | 0.043 | 0.670 | |
make_colors | 0.011 | 0.002 | 0.012 | |
make_volcano_dt | 1.049 | 0.014 | 1.071 | |
map_fvalues | 0.491 | 0.010 | 0.506 | |
matrix2sumexp | 1.218 | 0.064 | 1.302 | |
merge_sample_file | 0.523 | 0.009 | 0.534 | |
merge_sdata | 0.587 | 0.053 | 0.644 | |
message_df | 0.002 | 0.000 | 0.003 | |
model_coefs | 0.845 | 0.054 | 0.918 | |
modelvar | 4.153 | 0.074 | 4.264 | |
order_on_p | 1.436 | 0.054 | 1.502 | |
pca | 4.283 | 0.072 | 4.389 | |
pg_to_canonical | 0.005 | 0.000 | 0.005 | |
plot_coef_densities | 1.675 | 0.045 | 1.730 | |
plot_contrast_venn | 2.876 | 0.063 | 2.961 | |
plot_contrastogram | 3.615 | 0.166 | 3.846 | |
plot_data | 2.223 | 0.065 | 2.313 | |
plot_densities | 12.193 | 0.206 | 12.469 | |
plot_design | 0.877 | 0.009 | 0.889 | |
plot_exprs | 28.740 | 0.246 | 29.133 | |
plot_exprs_per_coef | 28.253 | 0.172 | 28.561 | |
plot_fit_summary | 2.571 | 0.056 | 2.639 | |
plot_heatmap | 2.699 | 0.016 | 2.723 | |
plot_joint_density | 4.724 | 0.078 | 4.821 | |
plot_matrix | 0.580 | 0.043 | 0.627 | |
plot_sample_nas | 8.083 | 0.071 | 8.198 | |
plot_subgroup_points | 7.045 | 0.103 | 7.190 | |
plot_summary | 18.159 | 0.114 | 18.344 | |
plot_survival | 4.511 | 0.030 | 4.556 | |
plot_venn | 0.005 | 0.002 | 0.007 | |
plot_venn_heatmap | 0.024 | 0.002 | 0.026 | |
plot_violins | 5.704 | 0.089 | 5.813 | |
plot_volcano | 16.065 | 0.127 | 16.263 | |
preprocess_rnaseq_counts | 0.351 | 0.003 | 0.359 | |
pull_columns | 0.003 | 0.001 | 0.003 | |
read_affymetrix | 0.000 | 0.000 | 0.001 | |
read_diann_proteingroups | 115.314 | 2.039 | 118.550 | |
read_fragpipe | 7.314 | 0.117 | 7.504 | |
read_maxquant_phosphosites | 1.764 | 0.036 | 1.815 | |
read_maxquant_proteingroups | 1.437 | 0.023 | 1.468 | |
read_metabolon | 19.246 | 0.220 | 19.687 | |
read_msigdt | 0.001 | 0.001 | 0.001 | |
read_olink | 1.863 | 0.090 | 2.104 | |
read_rectangles | 0.237 | 0.031 | 0.280 | |
read_rnaseq_counts | 43.189 | 3.493 | 47.440 | |
read_salmon | 0.001 | 0.001 | 0.002 | |
read_somascan | 19.585 | 0.159 | 19.945 | |
read_uniprotdt | 0.446 | 0.040 | 0.491 | |
reset_fit | 6.343 | 0.101 | 6.519 | |
rm_diann_contaminants | 25.759 | 0.523 | 26.562 | |
rm_missing_in_some_samples | 0.564 | 0.050 | 0.623 | |
rm_unmatched_samples | 0.805 | 0.018 | 0.829 | |
scaledlibsizes | 0.370 | 0.006 | 0.379 | |
scoremat | 1.189 | 0.061 | 1.275 | |
slevels | 0.480 | 0.021 | 0.508 | |
snames | 0.495 | 0.011 | 0.513 | |
split_extract_fixed | 0.656 | 0.059 | 0.726 | |
split_samples | 1.448 | 0.064 | 1.529 | |
stri_any_regex | 0.000 | 0.002 | 0.003 | |
stri_detect_fixed_in_collapsed | 0.408 | 0.009 | 0.434 | |
subgroup_matrix | 0.637 | 0.054 | 0.705 | |
subtract_baseline | 6.187 | 0.127 | 6.447 | |
sumexp_to_longdt | 2.125 | 0.195 | 2.404 | |
sumexp_to_tsv | 0.648 | 0.015 | 0.686 | |
sumexplist_to_longdt | 1.788 | 0.032 | 1.905 | |
summarize_fit | 1.820 | 0.072 | 1.924 | |
svalues | 0.458 | 0.011 | 0.485 | |
svars | 0.503 | 0.010 | 0.558 | |
systematic_nas | 0.627 | 0.010 | 0.650 | |
tag_features | 1.292 | 0.045 | 1.380 | |
tag_hdlproteins | 0.623 | 0.038 | 0.671 | |
taxon2org | 0.001 | 0.001 | 0.001 | |
tpm | 0.381 | 0.006 | 0.391 | |
uncollapse | 0.038 | 0.003 | 0.040 | |
values | 1.604 | 0.064 | 1.686 | |
varlevels_dont_clash | 0.027 | 0.001 | 0.028 | |
venn_detects | 0.664 | 0.027 | 0.702 | |
weights | 0.406 | 0.005 | 0.415 | |
write_xl | 0.880 | 0.061 | 0.953 | |
zero_to_na | 0.001 | 0.001 | 0.003 | |