Back to Multiple platform build/check report for BioC 3.22: simplified long |
|
This page was generated on 2025-08-30 12:05 -0400 (Sat, 30 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" | 4824 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4615 |
kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" | 4562 |
taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4541 |
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 116/2320 | 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: 2025-08-29 19:12:08 -0400 (Fri, 29 Aug 2025) |
EndedAt: 2025-08-29 19:30:01 -0400 (Fri, 29 Aug 2025) |
EllapsedTime: 1073.3 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 (2025-06-13) * 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 108.436 1.954 111.395 read_rnaseq_counts 38.708 2.932 42.299 fit_linmod 33.962 0.310 34.483 plot_exprs_per_coef 26.399 0.200 26.728 plot_exprs 26.250 0.172 26.611 rm_diann_contaminants 23.965 0.452 24.666 read_somascan 18.662 0.150 19.038 default_formula 18.224 0.383 18.785 read_metabolon 16.438 0.174 16.751 plot_summary 16.344 0.145 16.583 analyze 16.233 0.187 16.524 plot_volcano 13.744 0.119 13.921 ftype 9.651 0.270 9.984 plot_densities 9.380 0.162 9.592 reset_fit 7.505 0.168 7.733 extract_coef_features 7.322 0.072 7.423 plot_sample_nas 7.291 0.057 7.383 fcluster 7.101 0.079 7.209 read_fragpipe 6.888 0.153 7.112 fit_survival 6.028 0.074 6.140 subtract_baseline 5.607 0.180 5.881 code 5.625 0.079 5.728 biplot_covariates 5.541 0.068 5.636 plot_subgroup_points 5.288 0.107 5.435 * 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 (2025-06-13) -- "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 2 | SKIP 0 | PASS 158 ] [ FAIL 0 | WARN 2 | SKIP 0 | PASS 158 ] > > proc.time() user system elapsed 164.049 9.002 192.064
autonomics.Rcheck/autonomics-Ex.timings
name | user | system | elapsed | |
AUTONOMICS_DATASETS | 0.001 | 0.000 | 0.001 | |
COMPOUNDDISCOVERER_PATTERNS | 0.000 | 0.000 | 0.001 | |
FITSEP | 0.000 | 0.001 | 0.000 | |
LINMODENGINES | 0 | 0 | 0 | |
MAXQUANT_PATTERNS | 0.000 | 0.001 | 0.000 | |
SURVIVALENGINES | 0 | 0 | 0 | |
TAXON_TO_ORGNAME | 0.000 | 0.001 | 0.000 | |
TESTS | 0.001 | 0.000 | 0.000 | |
X | 2.565 | 0.080 | 2.665 | |
abstract_fit | 1.916 | 0.097 | 2.033 | |
add_adjusted_pvalues | 0.662 | 0.020 | 0.686 | |
add_assay_means | 0.381 | 0.009 | 0.392 | |
add_facetvars | 1.689 | 0.060 | 1.761 | |
add_opentargets_by_uniprot | 0.456 | 0.009 | 0.471 | |
add_psp | 0.579 | 0.016 | 0.599 | |
add_smiles | 0.510 | 0.042 | 0.557 | |
analysis | 0.443 | 0.009 | 0.454 | |
analyze | 16.233 | 0.187 | 16.524 | |
annotate_maxquant | 1.124 | 0.103 | 1.237 | |
annotate_uniprot_rest | 0.087 | 0.013 | 2.041 | |
assert_is_valid_sumexp | 0.577 | 0.034 | 0.613 | |
bin | 1.188 | 0.016 | 1.209 | |
biplot | 4.532 | 0.075 | 4.632 | |
biplot_corrections | 3.352 | 0.057 | 3.428 | |
biplot_covariates | 5.541 | 0.068 | 5.636 | |
block2lme | 0.004 | 0.001 | 0.005 | |
center | 1.494 | 0.019 | 1.521 | |
code | 5.625 | 0.079 | 5.728 | |
coefs | 0.865 | 0.048 | 0.923 | |
collapsed_entrezg_to_symbol | 0.001 | 0.001 | 0.001 | |
contrast_subgroup_cols | 0.627 | 0.040 | 0.670 | |
count_in | 0.001 | 0.001 | 0.001 | |
counts | 0.349 | 0.004 | 0.355 | |
counts2cpm | 0.353 | 0.003 | 0.357 | |
counts2tpm | 0.296 | 0.003 | 0.300 | |
cpm | 0.340 | 0.004 | 0.344 | |
create_design | 0.747 | 0.045 | 0.795 | |
default_formula | 18.224 | 0.383 | 18.785 | |
default_geom | 0.580 | 0.048 | 0.633 | |
default_sfile | 0.002 | 0.000 | 0.002 | |
demultiplex | 0.015 | 0.001 | 0.015 | |
dequantify | 0.001 | 0.000 | 0.002 | |
dequantify_compounddiscoverer | 0.001 | 0.000 | 0.002 | |
dot-coxph | 0.466 | 0.049 | 0.518 | |
dot-merge | 0.025 | 0.001 | 0.026 | |
dot-read_maxquant_proteingroups | 0.117 | 0.006 | 0.122 | |
download_data | 0.000 | 0.000 | 0.001 | |
download_gtf | 0 | 0 | 0 | |
download_mcclain21 | 0 | 0 | 0 | |
dt2mat | 0.002 | 0.000 | 0.003 | |
enrichment | 2.044 | 0.014 | 2.070 | |
entrezg_to_symbol | 0.001 | 0.000 | 0.001 | |
extract_coef_features | 7.322 | 0.072 | 7.423 | |
extract_rectangle | 0.144 | 0.039 | 0.184 | |
fcluster | 7.101 | 0.079 | 7.209 | |
fcor | 1.130 | 0.032 | 1.173 | |
fdata | 0.552 | 0.015 | 0.568 | |
fdr2p | 1.102 | 0.045 | 1.155 | |
filter_exprs_replicated_in_some_subgroup | 1.020 | 0.043 | 1.067 | |
filter_features | 0.605 | 0.047 | 0.655 | |
filter_medoid | 0.765 | 0.020 | 0.789 | |
filter_samples | 0.570 | 0.043 | 0.618 | |
fit_linmod | 33.962 | 0.310 | 34.483 | |
fit_survival | 6.028 | 0.074 | 6.140 | |
fitcoefs | 0.945 | 0.043 | 0.998 | |
fits | 0.937 | 0.051 | 0.995 | |
fix_xlgenes | 0.002 | 0.001 | 0.003 | |
flevels | 0.438 | 0.006 | 0.444 | |
fnames | 0.535 | 0.007 | 0.544 | |
formula2str | 0.000 | 0.000 | 0.001 | |
ftype | 9.651 | 0.270 | 9.984 | |
fvalues | 0.479 | 0.011 | 0.492 | |
fvars | 0.410 | 0.007 | 0.420 | |
genome_to_orgdb | 0.001 | 0.000 | 0.001 | |
group_by_level | 0.001 | 0.000 | 0.001 | |
guess_compounddiscoverer_quantity | 0.002 | 0.000 | 0.002 | |
guess_fitsep | 0.497 | 0.006 | 0.506 | |
guess_maxquant_quantity | 0.006 | 0.001 | 0.008 | |
guess_sep | 0.573 | 0.055 | 0.653 | |
has_multiple_levels | 0.067 | 0.003 | 0.070 | |
hdlproteins | 0.052 | 0.032 | 0.086 | |
impute | 3.402 | 0.042 | 3.476 | |
invert_subgroups | 0.818 | 0.015 | 0.840 | |
is_collapsed_subset | 0.001 | 0.000 | 0.001 | |
is_correlation_matrix | 0.002 | 0.000 | 0.001 | |
is_diann_report | 0.269 | 0.055 | 0.402 | |
is_fastadt | 0.074 | 0.002 | 0.078 | |
is_file | 0.000 | 0.001 | 0.001 | |
is_fraction | 0.002 | 0.000 | 0.003 | |
is_imputed | 0.897 | 0.012 | 0.917 | |
is_positive_number | 0.002 | 0.000 | 0.002 | |
is_scalar_subset | 0.413 | 0.007 | 0.423 | |
is_sig | 2.113 | 0.022 | 2.152 | |
is_valid_formula | 0.060 | 0.002 | 0.062 | |
keep_connected_blocks | 0.631 | 0.059 | 0.702 | |
keep_connected_features | 0.907 | 0.058 | 0.981 | |
keep_replicated_features | 0.992 | 0.063 | 1.069 | |
label2index | 0.001 | 0.001 | 0.001 | |
list2mat | 0.001 | 0.000 | 0.001 | |
log2counts | 0.420 | 0.005 | 0.432 | |
log2cpm | 0.444 | 0.005 | 0.450 | |
log2diffs | 0.375 | 0.007 | 0.384 | |
log2proteins | 0.383 | 0.006 | 0.390 | |
log2sites | 0.395 | 0.007 | 0.403 | |
log2tpm | 0.387 | 0.002 | 0.392 | |
log2transform | 4.386 | 0.055 | 4.472 | |
logical2factor | 0.002 | 0.001 | 0.002 | |
make_alpha_palette | 0.588 | 0.046 | 0.642 | |
make_colors | 0.010 | 0.001 | 0.012 | |
make_volcano_dt | 0.991 | 0.011 | 1.007 | |
map_fvalues | 0.467 | 0.007 | 0.478 | |
matrix2sumexp | 1.168 | 0.053 | 1.232 | |
merge_sample_file | 0.522 | 0.008 | 0.532 | |
merge_sdata | 0.637 | 0.060 | 0.704 | |
message_df | 0.003 | 0.000 | 0.003 | |
model_coefs | 0.926 | 0.050 | 0.988 | |
modelvar | 4.503 | 0.070 | 4.599 | |
order_on_p | 1.412 | 0.056 | 1.477 | |
pca | 3.701 | 0.087 | 3.822 | |
pg_to_canonical | 0.005 | 0.001 | 0.006 | |
plot_coef_densities | 1.482 | 0.045 | 1.539 | |
plot_contrast_venn | 3.094 | 0.184 | 3.325 | |
plot_contrastogram | 3.254 | 0.111 | 3.387 | |
plot_data | 1.437 | 0.051 | 1.496 | |
plot_densities | 9.380 | 0.162 | 9.592 | |
plot_design | 0.720 | 0.010 | 0.735 | |
plot_exprs | 26.250 | 0.172 | 26.611 | |
plot_exprs_per_coef | 26.399 | 0.200 | 26.728 | |
plot_fit_summary | 2.267 | 0.057 | 2.337 | |
plot_heatmap | 2.592 | 0.019 | 2.630 | |
plot_joint_density | 3.412 | 0.070 | 3.502 | |
plot_matrix | 0.577 | 0.047 | 0.628 | |
plot_sample_nas | 7.291 | 0.057 | 7.383 | |
plot_subgroup_points | 5.288 | 0.107 | 5.435 | |
plot_summary | 16.344 | 0.145 | 16.583 | |
plot_survival | 3.937 | 0.032 | 3.988 | |
plot_venn | 0.004 | 0.001 | 0.006 | |
plot_venn_heatmap | 0.024 | 0.001 | 0.026 | |
plot_violins | 4.229 | 0.081 | 4.335 | |
plot_volcano | 13.744 | 0.119 | 13.921 | |
preprocess_rnaseq_counts | 0.489 | 0.024 | 0.515 | |
pull_columns | 0.002 | 0.000 | 0.003 | |
read_affymetrix | 0.000 | 0.000 | 0.001 | |
read_diann_proteingroups | 108.436 | 1.954 | 111.395 | |
read_fragpipe | 6.888 | 0.153 | 7.112 | |
read_maxquant_phosphosites | 1.762 | 0.038 | 1.812 | |
read_maxquant_proteingroups | 1.350 | 0.024 | 1.386 | |
read_metabolon | 16.438 | 0.174 | 16.751 | |
read_msigdt | 0.000 | 0.000 | 0.001 | |
read_olink | 1.536 | 0.081 | 1.639 | |
read_rectangles | 0.206 | 0.026 | 0.234 | |
read_rnaseq_counts | 38.708 | 2.932 | 42.299 | |
read_salmon | 0.000 | 0.000 | 0.001 | |
read_somascan | 18.662 | 0.150 | 19.038 | |
read_uniprotdt | 0.432 | 0.043 | 0.489 | |
reset_fit | 7.505 | 0.168 | 7.733 | |
rm_diann_contaminants | 23.965 | 0.452 | 24.666 | |
rm_missing_in_some_samples | 0.568 | 0.049 | 0.635 | |
rm_unmatched_samples | 0.754 | 0.022 | 0.793 | |
scaledlibsizes | 0.343 | 0.006 | 0.353 | |
scoremat | 1.139 | 0.055 | 1.211 | |
slevels | 0.457 | 0.010 | 0.472 | |
snames | 0.433 | 0.011 | 0.447 | |
split_extract_fixed | 0.837 | 0.167 | 1.017 | |
split_samples | 1.375 | 0.065 | 1.456 | |
stri_any_regex | 0.001 | 0.001 | 0.002 | |
stri_detect_fixed_in_collapsed | 0.413 | 0.009 | 0.429 | |
subgroup_matrix | 0.656 | 0.054 | 0.723 | |
subtract_baseline | 5.607 | 0.180 | 5.881 | |
sumexp_to_longdt | 2.115 | 0.174 | 2.338 | |
sumexp_to_tsv | 0.646 | 0.011 | 0.662 | |
sumexplist_to_longdt | 1.721 | 0.030 | 1.767 | |
summarize_fit | 2.043 | 0.074 | 2.145 | |
svalues | 0.450 | 0.007 | 0.460 | |
svars | 0.484 | 0.007 | 0.497 | |
systematic_nas | 0.624 | 0.007 | 0.636 | |
tag_features | 1.191 | 0.032 | 1.237 | |
tag_hdlproteins | 0.731 | 0.077 | 0.815 | |
taxon2org | 0.001 | 0.000 | 0.002 | |
tpm | 0.419 | 0.003 | 0.425 | |
uncollapse | 0.035 | 0.001 | 0.036 | |
values | 0.497 | 0.012 | 0.517 | |
varlevels_dont_clash | 0.024 | 0.001 | 0.026 | |
venn_detects | 0.787 | 0.025 | 0.822 | |
weights | 0.420 | 0.003 | 0.429 | |
write_xl | 0.902 | 0.060 | 0.969 | |
zero_to_na | 0.002 | 0.001 | 0.003 | |