Back to Multiple platform build/check report for BioC 3.22: simplified long |
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This page was generated on 2025-08-08 12:05 -0400 (Fri, 08 Aug 2025).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 24.04.2 LTS) | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4815 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.5.1 (2025-06-13 ucrt) -- "Great Square Root" | 4550 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4592 |
kjohnson3 | macOS 13.7.1 Ventura | arm64 | 4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" | 4534 |
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 116/2315 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
autonomics 1.17.0 (landing page) Aditya Bhagwat
| nebbiolo2 | Linux (Ubuntu 24.04.2 LTS) / x86_64 | OK | OK | OK | ![]() | ||||||||
palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | ![]() | ||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | ![]() | ||||||||
kjohnson3 | macOS 13.7.1 Ventura / arm64 | OK | 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: 2025-08-07 20:10:08 -0400 (Thu, 07 Aug 2025) |
EndedAt: 2025-08-07 20:26:01 -0400 (Thu, 07 Aug 2025) |
EllapsedTime: 953.0 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 24.04.2 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 93.007 0.725 89.020 read_rnaseq_counts 31.790 2.232 33.805 fit_linmod 30.713 0.071 30.108 plot_exprs_per_coef 22.175 0.105 22.117 plot_exprs 21.444 0.076 21.417 rm_diann_contaminants 19.454 0.463 18.547 default_formula 16.730 0.394 16.673 read_somascan 14.701 0.358 15.003 analyze 14.343 0.181 14.376 read_metabolon 14.104 0.015 13.986 plot_summary 13.757 0.011 13.633 plot_volcano 11.567 0.011 11.489 ftype 8.568 0.123 8.387 plot_densities 7.834 0.047 7.754 reset_fit 6.549 0.243 6.667 extract_coef_features 6.610 0.034 6.617 fcluster 6.492 0.074 6.470 plot_sample_nas 5.836 0.007 5.798 read_fragpipe 5.791 0.014 5.505 code 5.089 0.031 5.098 fit_survival 5.071 0.014 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 ‘1.17.0’ ** 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 146.796 3.467 147.550
autonomics.Rcheck/autonomics-Ex.timings
name | user | system | elapsed | |
AUTONOMICS_DATASETS | 0 | 0 | 0 | |
COMPOUNDDISCOVERER_PATTERNS | 0 | 0 | 0 | |
FITSEP | 0.001 | 0.001 | 0.001 | |
LINMODENGINES | 0 | 0 | 0 | |
MAXQUANT_PATTERNS | 0.000 | 0.000 | 0.001 | |
SURVIVALENGINES | 0 | 0 | 0 | |
TAXON_TO_ORGNAME | 0 | 0 | 0 | |
TESTS | 0 | 0 | 0 | |
X | 2.240 | 0.072 | 2.289 | |
abstract_fit | 1.611 | 0.041 | 1.629 | |
add_adjusted_pvalues | 0.569 | 0.007 | 0.577 | |
add_assay_means | 0.335 | 0.018 | 0.353 | |
add_facetvars | 1.479 | 0.020 | 1.472 | |
add_opentargets_by_uniprot | 0.372 | 0.003 | 0.376 | |
add_psp | 0.475 | 0.010 | 0.486 | |
add_smiles | 0.434 | 0.020 | 0.420 | |
analysis | 0.357 | 0.020 | 0.377 | |
analyze | 14.343 | 0.181 | 14.376 | |
annotate_maxquant | 0.973 | 0.032 | 1.005 | |
annotate_uniprot_rest | 0.298 | 0.010 | 1.873 | |
assert_is_valid_sumexp | 0.515 | 0.023 | 0.516 | |
bin | 1.122 | 0.059 | 1.181 | |
biplot | 4.193 | 0.015 | 4.187 | |
biplot_corrections | 2.943 | 0.009 | 2.929 | |
biplot_covariates | 4.806 | 0.011 | 4.795 | |
block2lme | 0.003 | 0.000 | 0.003 | |
center | 1.352 | 0.005 | 1.358 | |
code | 5.089 | 0.031 | 5.098 | |
coefs | 0.774 | 0.003 | 0.754 | |
collapsed_entrezg_to_symbol | 0 | 0 | 0 | |
contrast_subgroup_cols | 0.583 | 0.004 | 0.563 | |
count_in | 0.001 | 0.000 | 0.001 | |
counts | 0.319 | 0.000 | 0.320 | |
counts2cpm | 0.309 | 0.017 | 0.325 | |
counts2tpm | 0.270 | 0.001 | 0.272 | |
cpm | 0.312 | 0.005 | 0.317 | |
create_design | 0.655 | 0.008 | 0.642 | |
default_formula | 16.730 | 0.394 | 16.673 | |
default_geom | 0.520 | 0.030 | 0.529 | |
default_sfile | 0.002 | 0.000 | 0.002 | |
demultiplex | 0.014 | 0.000 | 0.014 | |
dequantify | 0.002 | 0.000 | 0.003 | |
dequantify_compounddiscoverer | 0.001 | 0.001 | 0.001 | |
dot-coxph | 0.390 | 0.010 | 0.401 | |
dot-merge | 0.018 | 0.000 | 0.018 | |
dot-read_maxquant_proteingroups | 0.111 | 0.002 | 0.113 | |
download_data | 0 | 0 | 0 | |
download_gtf | 0 | 0 | 0 | |
download_mcclain21 | 0 | 0 | 0 | |
dt2mat | 0.003 | 0.000 | 0.003 | |
enrichment | 1.849 | 0.004 | 1.853 | |
entrezg_to_symbol | 0.001 | 0.000 | 0.000 | |
extract_coef_features | 6.610 | 0.034 | 6.617 | |
extract_rectangle | 0.107 | 0.004 | 0.111 | |
fcluster | 6.492 | 0.074 | 6.470 | |
fcor | 1.081 | 0.001 | 1.083 | |
fdata | 0.532 | 0.007 | 0.539 | |
fdr2p | 1.012 | 0.038 | 1.028 | |
filter_exprs_replicated_in_some_subgroup | 1.057 | 0.006 | 0.938 | |
filter_features | 0.523 | 0.006 | 0.498 | |
filter_medoid | 0.679 | 0.006 | 0.685 | |
filter_samples | 0.520 | 0.007 | 0.488 | |
fit_linmod | 30.713 | 0.071 | 30.108 | |
fit_survival | 5.071 | 0.014 | 5.057 | |
fitcoefs | 0.846 | 0.004 | 0.811 | |
fits | 0.778 | 0.004 | 0.745 | |
fix_xlgenes | 0.002 | 0.000 | 0.002 | |
flevels | 0.381 | 0.010 | 0.392 | |
fnames | 0.487 | 0.015 | 0.502 | |
formula2str | 0 | 0 | 0 | |
ftype | 8.568 | 0.123 | 8.387 | |
fvalues | 0.401 | 0.020 | 0.421 | |
fvars | 0.349 | 0.013 | 0.362 | |
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 | 0.419 | 0.006 | 0.425 | |
guess_maxquant_quantity | 0.004 | 0.001 | 0.005 | |
guess_sep | 0.461 | 0.007 | 0.446 | |
has_multiple_levels | 0.049 | 0.000 | 0.049 | |
hdlproteins | 0.037 | 0.016 | 0.056 | |
impute | 2.794 | 0.009 | 2.803 | |
invert_subgroups | 0.595 | 0.011 | 0.606 | |
is_collapsed_subset | 0.000 | 0.000 | 0.001 | |
is_correlation_matrix | 0.000 | 0.001 | 0.001 | |
is_diann_report | 0.413 | 0.037 | 0.427 | |
is_fastadt | 0.057 | 0.000 | 0.057 | |
is_file | 0.001 | 0.000 | 0.000 | |
is_fraction | 0.001 | 0.000 | 0.002 | |
is_imputed | 0.659 | 0.001 | 0.661 | |
is_positive_number | 0.001 | 0.000 | 0.002 | |
is_scalar_subset | 0.334 | 0.002 | 0.336 | |
is_sig | 1.634 | 0.010 | 1.643 | |
is_valid_formula | 0.041 | 0.000 | 0.041 | |
keep_connected_blocks | 0.460 | 0.008 | 0.439 | |
keep_connected_features | 0.708 | 0.003 | 0.652 | |
keep_replicated_features | 0.818 | 0.009 | 0.718 | |
label2index | 0 | 0 | 0 | |
list2mat | 0 | 0 | 0 | |
log2counts | 0.306 | 0.006 | 0.312 | |
log2cpm | 0.301 | 0.000 | 0.301 | |
log2diffs | 0.286 | 0.002 | 0.288 | |
log2proteins | 0.303 | 0.004 | 0.307 | |
log2sites | 0.301 | 0.003 | 0.303 | |
log2tpm | 0.301 | 0.000 | 0.301 | |
log2transform | 3.535 | 0.017 | 3.552 | |
logical2factor | 0.002 | 0.000 | 0.001 | |
make_alpha_palette | 0.477 | 0.006 | 0.462 | |
make_colors | 0.01 | 0.00 | 0.01 | |
make_volcano_dt | 0.825 | 0.000 | 0.825 | |
map_fvalues | 0.374 | 0.002 | 0.376 | |
matrix2sumexp | 0.899 | 0.008 | 0.871 | |
merge_sample_file | 0.407 | 0.004 | 0.411 | |
merge_sdata | 0.518 | 0.010 | 0.500 | |
message_df | 0.002 | 0.000 | 0.002 | |
model_coefs | 0.717 | 0.007 | 0.701 | |
modelvar | 3.621 | 0.004 | 3.567 | |
order_on_p | 1.191 | 0.005 | 1.173 | |
pca | 2.743 | 0.006 | 2.729 | |
pg_to_canonical | 0.006 | 0.000 | 0.006 | |
plot_coef_densities | 1.153 | 0.013 | 1.128 | |
plot_contrast_venn | 2.587 | 0.032 | 2.504 | |
plot_contrastogram | 2.806 | 0.015 | 2.735 | |
plot_data | 1.199 | 0.006 | 1.172 | |
plot_densities | 7.834 | 0.047 | 7.754 | |
plot_design | 0.640 | 0.008 | 0.648 | |
plot_exprs | 21.444 | 0.076 | 21.417 | |
plot_exprs_per_coef | 22.175 | 0.105 | 22.117 | |
plot_fit_summary | 1.924 | 0.010 | 1.842 | |
plot_heatmap | 2.096 | 0.004 | 2.100 | |
plot_joint_density | 2.682 | 0.013 | 2.673 | |
plot_matrix | 0.452 | 0.009 | 0.439 | |
plot_sample_nas | 5.836 | 0.007 | 5.798 | |
plot_subgroup_points | 4.425 | 0.008 | 4.352 | |
plot_summary | 13.757 | 0.011 | 13.633 | |
plot_survival | 3.392 | 0.004 | 3.376 | |
plot_venn | 0.004 | 0.000 | 0.004 | |
plot_venn_heatmap | 0.021 | 0.000 | 0.022 | |
plot_violins | 3.735 | 0.017 | 3.713 | |
plot_volcano | 11.567 | 0.011 | 11.489 | |
preprocess_rnaseq_counts | 0.404 | 0.019 | 0.422 | |
pull_columns | 0.002 | 0.000 | 0.002 | |
read_affymetrix | 0 | 0 | 0 | |
read_diann_proteingroups | 93.007 | 0.725 | 89.020 | |
read_fragpipe | 5.791 | 0.014 | 5.505 | |
read_maxquant_phosphosites | 1.443 | 0.025 | 1.469 | |
read_maxquant_proteingroups | 1.172 | 0.004 | 1.176 | |
read_metabolon | 14.104 | 0.015 | 13.986 | |
read_msigdt | 0.000 | 0.000 | 0.001 | |
read_olink | 1.272 | 0.014 | 1.215 | |
read_rectangles | 0.175 | 0.014 | 0.188 | |
read_rnaseq_counts | 31.790 | 2.232 | 33.805 | |
read_salmon | 0 | 0 | 0 | |
read_somascan | 14.701 | 0.358 | 15.003 | |
read_uniprotdt | 0.310 | 0.009 | 0.319 | |
reset_fit | 6.549 | 0.243 | 6.667 | |
rm_diann_contaminants | 19.454 | 0.463 | 18.547 | |
rm_missing_in_some_samples | 0.471 | 0.028 | 0.471 | |
rm_unmatched_samples | 0.658 | 0.027 | 0.686 | |
scaledlibsizes | 0.279 | 0.012 | 0.290 | |
scoremat | 1.010 | 0.016 | 1.003 | |
slevels | 0.360 | 0.003 | 0.363 | |
snames | 0.372 | 0.010 | 0.382 | |
split_extract_fixed | 0.670 | 0.041 | 0.673 | |
split_samples | 1.162 | 0.009 | 1.150 | |
stri_any_regex | 0 | 0 | 0 | |
stri_detect_fixed_in_collapsed | 0.334 | 0.011 | 0.345 | |
subgroup_matrix | 0.508 | 0.006 | 0.489 | |
subtract_baseline | 4.518 | 0.011 | 4.443 | |
sumexp_to_longdt | 1.845 | 0.030 | 1.796 | |
sumexp_to_tsv | 0.523 | 0.009 | 0.532 | |
sumexplist_to_longdt | 1.455 | 0.007 | 1.463 | |
summarize_fit | 1.797 | 0.023 | 1.703 | |
svalues | 0.409 | 0.004 | 0.403 | |
svars | 0.465 | 0.001 | 0.465 | |
systematic_nas | 0.521 | 0.016 | 0.538 | |
tag_features | 0.998 | 0.052 | 1.050 | |
tag_hdlproteins | 0.598 | 0.016 | 0.614 | |
taxon2org | 0.001 | 0.000 | 0.001 | |
tpm | 0.296 | 0.001 | 0.297 | |
uncollapse | 0.030 | 0.002 | 0.032 | |
values | 0.395 | 0.001 | 0.396 | |
varlevels_dont_clash | 0.019 | 0.000 | 0.019 | |
venn_detects | 0.584 | 0.024 | 0.608 | |
weights | 0.337 | 0.004 | 0.341 | |
write_xl | 0.756 | 0.029 | 0.758 | |
zero_to_na | 0.001 | 0.000 | 0.001 | |