Back to Multiple platform build/check report for BioC 3.22: simplified long |
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This page was generated on 2025-08-20 12:03 -0400 (Wed, 20 Aug 2025).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4818 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4596 |
kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" | 4538 |
taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4536 |
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 116/2317 | 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: /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_1.17.0.tar.gz |
StartedAt: 2025-08-19 20:11:15 -0400 (Tue, 19 Aug 2025) |
EndedAt: 2025-08-19 20:26:43 -0400 (Tue, 19 Aug 2025) |
EllapsedTime: 928.0 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_1.17.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/autonomics.Rcheck’ * using R version 4.5.1 (2025-06-13) * 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 ‘1.17.0’ * 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 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 read_diann_proteingroups 89.721 0.773 85.950 read_rnaseq_counts 30.361 1.013 31.097 fit_linmod 29.167 0.192 28.844 plot_exprs_per_coef 22.009 0.131 22.015 plot_exprs 20.697 0.073 20.666 rm_diann_contaminants 18.405 0.195 17.396 default_formula 16.224 0.502 16.338 read_somascan 14.072 0.124 14.107 analyze 13.970 0.204 14.039 read_metabolon 13.622 0.054 13.589 plot_summary 13.553 0.045 13.425 plot_volcano 11.342 0.098 11.382 ftype 8.299 0.178 8.171 plot_densities 7.473 0.106 7.487 extract_coef_features 6.302 0.067 6.347 reset_fit 6.017 0.178 6.099 fcluster 5.790 0.069 5.774 plot_sample_nas 5.749 0.005 5.712 read_fragpipe 5.620 0.089 5.409 code 5.059 0.118 5.145 fit_survival 4.967 0.035 4.991 * 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 ‘1.17.0’ ** 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 (2025-06-13) -- "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 2 | SKIP 0 | PASS 158 ] [ FAIL 0 | WARN 2 | SKIP 0 | PASS 158 ] > > proc.time() user system elapsed 141.666 3.576 142.343
autonomics.Rcheck/autonomics-Ex.timings
name | user | system | elapsed | |
AUTONOMICS_DATASETS | 0.000 | 0.001 | 0.000 | |
COMPOUNDDISCOVERER_PATTERNS | 0 | 0 | 0 | |
FITSEP | 0 | 0 | 0 | |
LINMODENGINES | 0 | 0 | 0 | |
MAXQUANT_PATTERNS | 0.000 | 0.000 | 0.001 | |
SURVIVALENGINES | 0.000 | 0.001 | 0.000 | |
TAXON_TO_ORGNAME | 0.000 | 0.000 | 0.001 | |
TESTS | 0 | 0 | 0 | |
X | 2.116 | 0.016 | 2.109 | |
abstract_fit | 1.587 | 0.066 | 1.631 | |
add_adjusted_pvalues | 0.528 | 0.009 | 0.538 | |
add_assay_means | 0.325 | 0.004 | 0.329 | |
add_facetvars | 1.442 | 0.024 | 1.445 | |
add_opentargets_by_uniprot | 0.349 | 0.006 | 0.357 | |
add_psp | 0.472 | 0.008 | 0.482 | |
add_smiles | 0.408 | 0.008 | 0.395 | |
analysis | 0.341 | 0.002 | 0.343 | |
analyze | 13.970 | 0.204 | 14.039 | |
annotate_maxquant | 0.943 | 0.038 | 0.981 | |
annotate_uniprot_rest | 0.314 | 0.020 | 2.011 | |
assert_is_valid_sumexp | 0.548 | 0.022 | 0.543 | |
bin | 1.092 | 0.077 | 1.169 | |
biplot | 4.009 | 0.213 | 4.199 | |
biplot_corrections | 2.831 | 0.134 | 2.942 | |
biplot_covariates | 4.640 | 0.187 | 4.804 | |
block2lme | 0.003 | 0.000 | 0.003 | |
center | 1.304 | 0.041 | 1.346 | |
code | 5.059 | 0.118 | 5.145 | |
coefs | 0.758 | 0.016 | 0.752 | |
collapsed_entrezg_to_symbol | 0 | 0 | 0 | |
contrast_subgroup_cols | 0.559 | 0.025 | 0.562 | |
count_in | 0.001 | 0.000 | 0.001 | |
counts | 0.308 | 0.002 | 0.311 | |
counts2cpm | 0.291 | 0.001 | 0.292 | |
counts2tpm | 0.267 | 0.008 | 0.276 | |
cpm | 0.305 | 0.008 | 0.313 | |
create_design | 0.663 | 0.008 | 0.650 | |
default_formula | 16.224 | 0.502 | 16.338 | |
default_geom | 0.488 | 0.025 | 0.485 | |
default_sfile | 0.002 | 0.000 | 0.002 | |
demultiplex | 0.014 | 0.000 | 0.014 | |
dequantify | 0.002 | 0.000 | 0.002 | |
dequantify_compounddiscoverer | 0.000 | 0.000 | 0.001 | |
dot-coxph | 0.366 | 0.010 | 0.376 | |
dot-merge | 0.015 | 0.000 | 0.015 | |
dot-read_maxquant_proteingroups | 0.105 | 0.003 | 0.108 | |
download_data | 0 | 0 | 0 | |
download_gtf | 0 | 0 | 0 | |
download_mcclain21 | 0.001 | 0.000 | 0.000 | |
dt2mat | 0.003 | 0.000 | 0.003 | |
enrichment | 1.738 | 0.037 | 1.776 | |
entrezg_to_symbol | 0.000 | 0.000 | 0.001 | |
extract_coef_features | 6.302 | 0.067 | 6.347 | |
extract_rectangle | 0.098 | 0.008 | 0.105 | |
fcluster | 5.790 | 0.069 | 5.774 | |
fcor | 0.982 | 0.004 | 0.986 | |
fdata | 0.466 | 0.004 | 0.470 | |
fdr2p | 0.923 | 0.057 | 0.959 | |
filter_exprs_replicated_in_some_subgroup | 0.938 | 0.014 | 0.892 | |
filter_features | 0.494 | 0.007 | 0.479 | |
filter_medoid | 0.640 | 0.005 | 0.644 | |
filter_samples | 0.485 | 0.008 | 0.471 | |
fit_linmod | 29.167 | 0.192 | 28.844 | |
fit_survival | 4.967 | 0.035 | 4.991 | |
fitcoefs | 0.821 | 0.013 | 0.812 | |
fits | 0.768 | 0.007 | 0.738 | |
fix_xlgenes | 0.002 | 0.000 | 0.001 | |
flevels | 0.373 | 0.001 | 0.374 | |
fnames | 0.454 | 0.003 | 0.458 | |
formula2str | 0 | 0 | 0 | |
ftype | 8.299 | 0.178 | 8.171 | |
fvalues | 0.389 | 0.014 | 0.403 | |
fvars | 0.337 | 0.000 | 0.338 | |
genome_to_orgdb | 0 | 0 | 0 | |
group_by_level | 0.000 | 0.000 | 0.001 | |
guess_compounddiscoverer_quantity | 0.001 | 0.000 | 0.000 | |
guess_fitsep | 0.400 | 0.008 | 0.408 | |
guess_maxquant_quantity | 0.003 | 0.002 | 0.005 | |
guess_sep | 0.441 | 0.007 | 0.427 | |
has_multiple_levels | 0.051 | 0.000 | 0.050 | |
hdlproteins | 0.039 | 0.016 | 0.058 | |
impute | 2.690 | 0.015 | 2.707 | |
invert_subgroups | 0.571 | 0.006 | 0.578 | |
is_collapsed_subset | 0.000 | 0.000 | 0.001 | |
is_correlation_matrix | 0.001 | 0.000 | 0.001 | |
is_diann_report | 0.368 | 0.036 | 0.400 | |
is_fastadt | 0.056 | 0.000 | 0.056 | |
is_file | 0.001 | 0.000 | 0.001 | |
is_fraction | 0.001 | 0.000 | 0.001 | |
is_imputed | 0.616 | 0.004 | 0.620 | |
is_positive_number | 0.001 | 0.000 | 0.001 | |
is_scalar_subset | 0.291 | 0.002 | 0.294 | |
is_sig | 1.555 | 0.002 | 1.557 | |
is_valid_formula | 0.041 | 0.000 | 0.041 | |
keep_connected_blocks | 0.484 | 0.005 | 0.445 | |
keep_connected_features | 0.697 | 0.002 | 0.607 | |
keep_replicated_features | 0.775 | 0.004 | 0.676 | |
label2index | 0 | 0 | 0 | |
list2mat | 0.001 | 0.000 | 0.000 | |
log2counts | 0.277 | 0.000 | 0.276 | |
log2cpm | 0.291 | 0.000 | 0.292 | |
log2diffs | 0.283 | 0.003 | 0.286 | |
log2proteins | 0.299 | 0.007 | 0.306 | |
log2sites | 0.289 | 0.004 | 0.295 | |
log2tpm | 0.272 | 0.000 | 0.273 | |
log2transform | 3.322 | 0.028 | 3.351 | |
logical2factor | 0.001 | 0.000 | 0.001 | |
make_alpha_palette | 0.466 | 0.002 | 0.446 | |
make_colors | 0.009 | 0.000 | 0.009 | |
make_volcano_dt | 0.783 | 0.006 | 0.790 | |
map_fvalues | 0.340 | 0.000 | 0.341 | |
matrix2sumexp | 0.817 | 0.016 | 0.812 | |
merge_sample_file | 0.384 | 0.008 | 0.393 | |
merge_sdata | 0.494 | 0.010 | 0.469 | |
message_df | 0.002 | 0.000 | 0.002 | |
model_coefs | 0.691 | 0.006 | 0.658 | |
modelvar | 3.484 | 0.013 | 3.407 | |
order_on_p | 1.146 | 0.018 | 1.136 | |
pca | 2.655 | 0.023 | 2.657 | |
pg_to_canonical | 0.005 | 0.000 | 0.005 | |
plot_coef_densities | 1.090 | 0.008 | 1.076 | |
plot_contrast_venn | 2.410 | 0.018 | 2.345 | |
plot_contrastogram | 2.631 | 0.061 | 2.622 | |
plot_data | 1.129 | 0.015 | 1.113 | |
plot_densities | 7.473 | 0.106 | 7.487 | |
plot_design | 0.590 | 0.001 | 0.592 | |
plot_exprs | 20.697 | 0.073 | 20.666 | |
plot_exprs_per_coef | 22.009 | 0.131 | 22.015 | |
plot_fit_summary | 2.041 | 0.020 | 1.936 | |
plot_heatmap | 2.136 | 0.014 | 2.150 | |
plot_joint_density | 2.681 | 0.014 | 2.672 | |
plot_matrix | 0.472 | 0.009 | 0.458 | |
plot_sample_nas | 5.749 | 0.005 | 5.712 | |
plot_subgroup_points | 4.298 | 0.010 | 4.236 | |
plot_summary | 13.553 | 0.045 | 13.425 | |
plot_survival | 3.298 | 0.006 | 3.285 | |
plot_venn | 0.005 | 0.000 | 0.005 | |
plot_venn_heatmap | 0.021 | 0.000 | 0.022 | |
plot_violins | 3.569 | 0.039 | 3.588 | |
plot_volcano | 11.342 | 0.098 | 11.382 | |
preprocess_rnaseq_counts | 0.413 | 0.015 | 0.428 | |
pull_columns | 0.002 | 0.000 | 0.002 | |
read_affymetrix | 0.000 | 0.000 | 0.001 | |
read_diann_proteingroups | 89.721 | 0.773 | 85.950 | |
read_fragpipe | 5.620 | 0.089 | 5.409 | |
read_maxquant_phosphosites | 1.370 | 0.009 | 1.379 | |
read_maxquant_proteingroups | 1.095 | 0.006 | 1.101 | |
read_metabolon | 13.622 | 0.054 | 13.589 | |
read_msigdt | 0 | 0 | 0 | |
read_olink | 1.257 | 0.016 | 1.204 | |
read_rectangles | 0.162 | 0.007 | 0.170 | |
read_rnaseq_counts | 30.361 | 1.013 | 31.097 | |
read_salmon | 0 | 0 | 0 | |
read_somascan | 14.072 | 0.124 | 14.107 | |
read_uniprotdt | 0.294 | 0.005 | 0.299 | |
reset_fit | 6.017 | 0.178 | 6.099 | |
rm_diann_contaminants | 18.405 | 0.195 | 17.396 | |
rm_missing_in_some_samples | 0.440 | 0.007 | 0.420 | |
rm_unmatched_samples | 0.587 | 0.000 | 0.587 | |
scaledlibsizes | 0.265 | 0.001 | 0.266 | |
scoremat | 0.915 | 0.009 | 0.903 | |
slevels | 0.345 | 0.001 | 0.346 | |
snames | 0.361 | 0.000 | 0.361 | |
split_extract_fixed | 0.623 | 0.009 | 0.593 | |
split_samples | 1.082 | 0.005 | 1.065 | |
stri_any_regex | 0.001 | 0.000 | 0.000 | |
stri_detect_fixed_in_collapsed | 0.298 | 0.000 | 0.299 | |
subgroup_matrix | 0.487 | 0.005 | 0.455 | |
subtract_baseline | 4.093 | 0.025 | 4.048 | |
sumexp_to_longdt | 1.683 | 0.014 | 1.644 | |
sumexp_to_tsv | 0.488 | 0.004 | 0.492 | |
sumexplist_to_longdt | 1.322 | 0.007 | 1.328 | |
summarize_fit | 1.551 | 0.007 | 1.488 | |
svalues | 0.361 | 0.002 | 0.361 | |
svars | 0.396 | 0.000 | 0.396 | |
systematic_nas | 0.48 | 0.00 | 0.48 | |
tag_features | 0.874 | 0.009 | 0.883 | |
tag_hdlproteins | 0.524 | 0.014 | 0.540 | |
taxon2org | 0.001 | 0.000 | 0.001 | |
tpm | 0.272 | 0.001 | 0.272 | |
uncollapse | 0.029 | 0.000 | 0.030 | |
values | 0.362 | 0.006 | 0.368 | |
varlevels_dont_clash | 0.016 | 0.001 | 0.018 | |
venn_detects | 0.529 | 0.001 | 0.530 | |
weights | 0.286 | 0.001 | 0.287 | |
write_xl | 0.667 | 0.005 | 0.650 | |
zero_to_na | 0.002 | 0.000 | 0.001 | |