Back to Multiple platform build/check report for BioC 3.22: simplified long |
|
This page was generated on 2025-09-26 12:03 -0400 (Fri, 26 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" | 4831 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4619 |
kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4563 |
taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4563 |
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 1.17.2 (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: 1.17.2 |
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_1.17.2.tar.gz |
StartedAt: 2025-09-25 21:06:04 -0400 (Thu, 25 Sep 2025) |
EndedAt: 2025-09-25 21:26:28 -0400 (Thu, 25 Sep 2025) |
EllapsedTime: 1224.4 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_1.17.2.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/autonomics.Rcheck’ * using R version 4.5.1 Patched (2025-08-23 r88802) * 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 ‘1.17.2’ * 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 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 258.531 5.590 106.216 rm_diann_contaminants 108.279 1.455 23.416 awblinmod 42.513 0.168 41.293 read_rnaseq_counts 38.802 2.058 35.102 ftype 38.430 0.248 10.470 default_formula 28.788 0.492 19.362 plot_exprs 26.409 0.457 22.830 LINMOD 26.191 0.446 24.656 plot_exprs_per_coef 22.316 0.336 22.594 plot_contrastogram 18.123 0.242 3.888 plot_volcano 16.497 0.459 16.874 plot_summary 16.204 0.423 16.502 read_somascan 15.214 0.202 15.068 read_metabolon 14.496 0.168 14.582 analyze 13.933 0.125 13.926 plot_densities 13.013 0.254 11.216 explore-transforms 11.727 0.027 11.756 fit_survival 11.088 0.034 11.125 fcluster 9.747 0.035 9.592 plot_subgroup_points 8.860 0.292 7.355 plot_detections 8.236 0.149 8.344 read_fragpipe 7.638 0.079 5.802 plot_xy_density 7.455 0.212 7.709 biplot_covariates 7.202 0.027 7.207 is_diann_report 6.759 0.130 0.685 plot_violins 6.238 0.063 6.278 subtract_baseline 6.000 0.180 5.387 log2transform 5.042 0.378 5.441 code 5.068 0.019 5.057 * 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 ‘1.17.2’ ** 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 (2025-08-23 r88802) -- "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 3 | SKIP 0 | PASS 158 ] [ FAIL 0 | WARN 3 | SKIP 0 | PASS 158 ] > > proc.time() user system elapsed 259.061 9.626 221.836
autonomics.Rcheck/autonomics-Ex.timings
name | user | system | elapsed | |
AUTONOMICS_DATASETS | 0.000 | 0.001 | 0.000 | |
COMPOUNDDISCOVERER_PATTERNS | 0 | 0 | 0 | |
LINMOD | 26.191 | 0.446 | 24.656 | |
LINMODENGINES | 0 | 0 | 0 | |
MAXQUANT_PATTERNS | 0 | 0 | 0 | |
TAXON_TO_ORGNAME | 0 | 0 | 0 | |
TESTS | 0 | 0 | 0 | |
X | 1.215 | 0.018 | 1.209 | |
abstract_fit | 1.066 | 0.005 | 1.037 | |
add_adjusted_pvalues | 0.519 | 0.004 | 0.523 | |
add_assay_means | 0.355 | 0.009 | 0.364 | |
add_facetvars | 1.425 | 0.037 | 1.423 | |
add_opentargets_by_uniprot | 0.374 | 0.007 | 0.382 | |
add_psp | 0.498 | 0.009 | 0.508 | |
add_smiles | 0.478 | 0.004 | 0.445 | |
all_non_numeric | 0.587 | 0.000 | 0.587 | |
analysis | 0.474 | 0.006 | 0.480 | |
analyze | 13.933 | 0.125 | 13.926 | |
annotate_maxquant | 0.887 | 0.019 | 0.906 | |
annotate_uniprot_rest | 1.324 | 0.095 | 3.312 | |
assert_is_valid_sumexp | 0.585 | 0.029 | 0.575 | |
awblinmod | 42.513 | 0.168 | 41.293 | |
biplot | 4.127 | 0.060 | 4.165 | |
biplot_corrections | 3.660 | 0.012 | 3.635 | |
biplot_covariates | 7.202 | 0.027 | 7.207 | |
block2limma | 0.002 | 0.000 | 0.003 | |
block2lm | 0.002 | 0.001 | 0.003 | |
block2lme | 0.001 | 0.001 | 0.003 | |
block2lmer | 0.004 | 0.000 | 0.005 | |
block_has_two_levels | 0.709 | 0.018 | 0.689 | |
center | 2.045 | 0.007 | 2.050 | |
code | 5.068 | 0.019 | 5.057 | |
collapsed_entrezg_to_symbol | 1.025 | 0.039 | 1.064 | |
contrast_subgroup_cols | 0.656 | 0.005 | 0.639 | |
contrastdt | 0.368 | 0.000 | 0.368 | |
count_in | 0.001 | 0.000 | 0.001 | |
counts | 0.331 | 0.000 | 0.331 | |
counts2cpm | 0.361 | 0.001 | 0.361 | |
counts2tpm | 0.305 | 0.001 | 0.306 | |
cpm | 0.366 | 0.001 | 0.367 | |
create_design | 0.732 | 0.010 | 0.704 | |
default_formula | 28.788 | 0.492 | 19.362 | |
default_geom | 0.581 | 0.019 | 0.574 | |
default_sfile | 0.002 | 0.000 | 0.001 | |
demultiplex | 0.015 | 0.000 | 0.014 | |
densities | 0.215 | 0.001 | 0.215 | |
dequantify | 0.003 | 0.000 | 0.003 | |
dequantify_compounddiscoverer | 0.001 | 0.000 | 0.001 | |
dot-coxph | 0.394 | 0.007 | 0.401 | |
dot-merge | 0.022 | 0.000 | 0.022 | |
dot-read_maxquant_proteingroups | 0.117 | 0.000 | 0.116 | |
download_data | 0 | 0 | 0 | |
download_gtf | 0 | 0 | 0 | |
download_mcclain21 | 0 | 0 | 0 | |
dt2mat | 0.003 | 0.000 | 0.003 | |
enrichment | 1.224 | 0.002 | 1.226 | |
entrezg_to_symbol | 0.155 | 0.002 | 0.157 | |
explore-transforms | 11.727 | 0.027 | 11.756 | |
extract_contrast_features | 4.758 | 0.005 | 4.740 | |
extract_rectangle | 0.108 | 0.009 | 0.117 | |
factor.vars | 0.175 | 0.001 | 0.176 | |
factorize | 0.800 | 0.006 | 0.806 | |
fcluster | 9.747 | 0.035 | 9.592 | |
fcor | 1.516 | 0.014 | 1.530 | |
fdata | 0.584 | 0.005 | 0.589 | |
fdr2p | 1.001 | 0.007 | 0.984 | |
filter_exprs_replicated_in_some_subgroup | 1.095 | 0.006 | 1.025 | |
filter_features | 0.574 | 0.005 | 0.554 | |
filter_medoid | 0.639 | 0.001 | 0.639 | |
filter_samples | 0.550 | 0.004 | 0.514 | |
fit_survival | 11.088 | 0.034 | 11.125 | |
fits | 0.303 | 0.000 | 0.304 | |
fix_xlgenes | 0.001 | 0.000 | 0.002 | |
flevels | 0.401 | 0.002 | 0.404 | |
fnames | 0.433 | 0.001 | 0.434 | |
formula2str | 0 | 0 | 0 | |
ftype | 38.430 | 0.248 | 10.470 | |
fvalues | 0.414 | 0.000 | 0.414 | |
fvars | 0.386 | 0.001 | 0.386 | |
genome_to_orgdb | 0.001 | 0.000 | 0.001 | |
group_by_level | 0.001 | 0.000 | 0.001 | |
guess_compounddiscoverer_quantity | 0.001 | 0.000 | 0.001 | |
guess_fitsep | 0.442 | 0.031 | 0.473 | |
guess_maxquant_quantity | 0.005 | 0.001 | 0.006 | |
guess_sep | 0.503 | 0.020 | 0.499 | |
has_multiple_levels | 0.053 | 0.000 | 0.054 | |
hdlproteins | 0.038 | 0.012 | 0.053 | |
impute | 3.400 | 0.013 | 3.413 | |
invert_subgroups | 0.604 | 0.003 | 0.607 | |
is_character_matrix | 0.142 | 0.000 | 0.143 | |
is_collapsed_subset | 0 | 0 | 0 | |
is_correlation_matrix | 0.001 | 0.000 | 0.001 | |
is_diann_report | 6.759 | 0.130 | 0.685 | |
is_fastadt | 0.063 | 0.001 | 0.063 | |
is_file | 0.001 | 0.001 | 0.001 | |
is_fraction | 0.001 | 0.000 | 0.002 | |
is_imputed | 0.690 | 0.002 | 0.692 | |
is_positive_number | 0.001 | 0.000 | 0.001 | |
is_scalar_subset | 0.292 | 0.003 | 0.296 | |
is_sig | 1.298 | 0.002 | 1.301 | |
is_valid_formula | 0.041 | 0.000 | 0.041 | |
keep_estimable_features | 0.875 | 0.016 | 0.909 | |
label2index | 0.001 | 0.000 | 0.001 | |
list2mat | 0.001 | 0.000 | 0.001 | |
log2counts | 0.316 | 0.002 | 0.326 | |
log2cpm | 0.313 | 0.011 | 0.324 | |
log2diffs | 0.299 | 0.005 | 0.304 | |
log2proteins | 0.356 | 0.033 | 0.396 | |
log2sites | 0.294 | 0.024 | 0.318 | |
log2tpm | 0.291 | 0.016 | 0.307 | |
log2transform | 5.042 | 0.378 | 5.441 | |
logical2factor | 0.002 | 0.000 | 0.002 | |
make_alpha_palette | 0.511 | 0.015 | 0.493 | |
make_colors | 0.009 | 0.000 | 0.010 | |
make_volcano_dt | 0.860 | 0.033 | 0.893 | |
map_fvalues | 0.375 | 0.019 | 0.393 | |
matrix2sumexp | 1.023 | 0.115 | 1.097 | |
mclust_breaks | 0.502 | 0.068 | 0.571 | |
merge_sample_file | 0.480 | 0.018 | 0.498 | |
merge_sdata | 0.681 | 0.027 | 0.680 | |
message_df | 0.002 | 0.000 | 0.002 | |
model_coefs | 0.705 | 0.014 | 0.697 | |
modelvar | 3.528 | 0.202 | 3.732 | |
object1 | 0.549 | 0.028 | 0.577 | |
order_on_p | 1.483 | 0.064 | 1.521 | |
overall_parameters | 0.037 | 0.000 | 0.037 | |
pca | 3.615 | 0.164 | 3.752 | |
pg_to_canonical | 0.005 | 0.001 | 0.005 | |
plot_coef_densities | 1.510 | 0.025 | 1.498 | |
plot_contrast_venn | 2.496 | 0.013 | 2.376 | |
plot_contrastogram | 18.123 | 0.242 | 3.888 | |
plot_data | 1.757 | 0.046 | 1.781 | |
plot_densities | 13.013 | 0.254 | 11.216 | |
plot_design | 0.765 | 0.013 | 0.778 | |
plot_detections | 8.236 | 0.149 | 8.344 | |
plot_exprs | 26.409 | 0.457 | 22.830 | |
plot_exprs_per_coef | 22.316 | 0.336 | 22.594 | |
plot_fit_summary | 2.487 | 0.016 | 2.451 | |
plot_heatmap | 2.153 | 0.005 | 2.158 | |
plot_matrix | 0.691 | 0.008 | 0.673 | |
plot_subgroup_points | 8.860 | 0.292 | 7.355 | |
plot_summary | 16.204 | 0.423 | 16.502 | |
plot_venn | 0.017 | 0.001 | 0.018 | |
plot_venn_heatmap | 0.027 | 0.001 | 0.029 | |
plot_violins | 6.238 | 0.063 | 6.278 | |
plot_volcano | 16.497 | 0.459 | 16.874 | |
plot_xy_density | 7.455 | 0.212 | 7.709 | |
preprocess_rnaseq_counts | 0.482 | 0.009 | 0.492 | |
pull_columns | 0.003 | 0.000 | 0.003 | |
pvalues_estimable | 0.043 | 0.002 | 0.045 | |
read_affymetrix | 0 | 0 | 0 | |
read_diann_proteingroups | 258.531 | 5.590 | 106.216 | |
read_fragpipe | 7.638 | 0.079 | 5.802 | |
read_maxquant_phosphosites | 1.628 | 0.023 | 1.652 | |
read_maxquant_proteingroups | 1.384 | 0.052 | 1.436 | |
read_metabolon | 14.496 | 0.168 | 14.582 | |
read_msigdt | 0.001 | 0.000 | 0.001 | |
read_olink | 3.829 | 0.039 | 1.567 | |
read_rectangles | 0.179 | 0.011 | 0.190 | |
read_rnaseq_counts | 38.802 | 2.058 | 35.102 | |
read_salmon | 0 | 0 | 0 | |
read_somascan | 15.214 | 0.202 | 15.068 | |
read_uniprotdt | 0.305 | 0.012 | 0.317 | |
reset_fit | 4.657 | 0.030 | 4.557 | |
rm_diann_contaminants | 108.279 | 1.455 | 23.416 | |
rm_missing_in_some_samples | 0.494 | 0.040 | 0.509 | |
rm_unmatched_samples | 0.680 | 0.074 | 0.754 | |
sbind | 4.220 | 0.201 | 4.432 | |
scaledlibsizes | 0.325 | 0.025 | 0.363 | |
scoremat | 0.920 | 0.031 | 0.937 | |
slevels | 0.400 | 0.014 | 0.413 | |
snames | 0.389 | 0.005 | 0.393 | |
split_extract_fixed | 0.544 | 0.016 | 0.532 | |
split_samples | 1.167 | 0.022 | 1.164 | |
stepauc | 0.311 | 0.006 | 0.317 | |
stri_any_regex | 0.001 | 0.000 | 0.000 | |
stri_detect_fixed_in_collapsed | 0.344 | 0.004 | 0.347 | |
subgroup_matrix | 0.686 | 0.015 | 0.689 | |
subtract_baseline | 6.000 | 0.180 | 5.387 | |
sumexp_to_longdt | 1.927 | 0.026 | 1.941 | |
sumexp_to_tsv | 0.622 | 0.000 | 0.622 | |
sumexplist_to_longdt | 1.606 | 0.012 | 1.625 | |
summarize_fit | 1.684 | 0.021 | 1.643 | |
survobj | 0.150 | 0.001 | 0.151 | |
svalues | 0.380 | 0.003 | 0.382 | |
svars | 0.399 | 0.003 | 0.420 | |
systematic_nas | 0.644 | 0.002 | 0.650 | |
tag_features | 0.959 | 0.020 | 0.981 | |
tag_hdlproteins | 0.599 | 0.021 | 0.621 | |
taxon2org | 0.000 | 0.001 | 0.001 | |
tpm | 0.318 | 0.001 | 0.319 | |
uncollapse | 0.029 | 0.000 | 0.029 | |
values | 0.420 | 0.007 | 0.427 | |
varlevels_dont_clash | 0.023 | 0.000 | 0.023 | |
venn_detects | 0.596 | 0.001 | 0.598 | |
weights | 0.315 | 0.000 | 0.314 | |
write_xl | 0.812 | 0.060 | 0.846 | |
zero_to_na | 0.001 | 0.000 | 0.001 | |