Back to Multiple platform build/check report for BioC 3.21: simplified long |
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This page was generated on 2025-08-04 11:45 -0400 (Mon, 04 Aug 2025).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo1 | Linux (Ubuntu 24.04.2 LTS) | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4823 |
palomino7 | Windows Server 2022 Datacenter | x64 | 4.5.1 (2025-06-13 ucrt) -- "Great Square Root" | 4565 |
merida1 | macOS 12.7.5 Monterey | x86_64 | 4.5.1 RC (2025-06-05 r88288) -- "Great Square Root" | 4603 |
kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" | 4544 |
kunpeng2 | Linux (openEuler 24.03 LTS) | aarch64 | R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" | 4579 |
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 117/2341 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
autonomics 1.16.0 (landing page) Aditya Bhagwat
| nebbiolo1 | Linux (Ubuntu 24.04.2 LTS) / x86_64 | OK | OK | OK | ![]() | ||||||||
palomino7 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | ![]() | ||||||||
merida1 | macOS 12.7.5 Monterey / x86_64 | OK | OK | OK | OK | ![]() | ||||||||
kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | OK | OK | ![]() | ||||||||
kunpeng2 | 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: 1.16.0 |
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_1.16.0.tar.gz |
StartedAt: 2025-08-01 12:22:23 -0400 (Fri, 01 Aug 2025) |
EndedAt: 2025-08-01 12:38:04 -0400 (Fri, 01 Aug 2025) |
EllapsedTime: 941.3 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_1.16.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/autonomics.Rcheck’ * using R version 4.5.1 Patched (2025-06-14 r88325) * using platform: aarch64-apple-darwin20 * R was compiled by Apple clang version 16.0.0 (clang-1600.0.26.6) GNU Fortran (GCC) 14.2.0 * running under: macOS Ventura 13.7.5 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘autonomics/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘autonomics’ version ‘1.16.0’ * 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 97.389 2.211 96.532 read_rnaseq_counts 31.976 1.222 33.848 fit_linmod 30.167 0.272 30.572 plot_exprs_per_coef 22.729 0.166 23.209 rm_diann_contaminants 21.043 0.487 20.296 plot_exprs 21.305 0.163 21.781 default_formula 16.720 0.532 16.851 plot_summary 14.390 0.111 14.666 read_metabolon 13.865 0.112 14.437 read_somascan 13.518 0.069 13.886 analyze 13.167 0.141 13.445 plot_volcano 11.739 0.115 11.898 ftype 8.893 0.478 9.383 plot_densities 8.461 0.203 8.775 read_fragpipe 7.831 0.184 8.164 fcluster 6.454 0.064 6.540 extract_coef_features 6.362 0.092 6.461 plot_sample_nas 5.767 0.048 6.068 fit_survival 5.253 0.053 5.315 code 5.136 0.083 5.229 biplot_covariates 5.082 0.063 5.150 * 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-3.21-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-arm64/Resources/library’ * installing *source* package ‘autonomics’ ... ** this is package ‘autonomics’ version ‘1.16.0’ ** 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 (2025-06-14 r88325) -- "Great Square Root" Copyright (C) 2025 The R Foundation for Statistical Computing Platform: aarch64-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 160.991 9.137 168.533
autonomics.Rcheck/autonomics-Ex.timings
name | user | system | elapsed | |
AUTONOMICS_DATASETS | 0.000 | 0.001 | 0.001 | |
COMPOUNDDISCOVERER_PATTERNS | 0.000 | 0.000 | 0.001 | |
FITSEP | 0.001 | 0.000 | 0.000 | |
LINMODENGINES | 0.000 | 0.000 | 0.001 | |
MAXQUANT_PATTERNS | 0.001 | 0.000 | 0.001 | |
SURVIVALENGINES | 0.000 | 0.000 | 0.001 | |
TAXON_TO_ORGNAME | 0.001 | 0.001 | 0.001 | |
TESTS | 0 | 0 | 0 | |
X | 2.428 | 0.108 | 2.544 | |
abstract_fit | 1.580 | 0.095 | 1.676 | |
add_adjusted_pvalues | 0.553 | 0.016 | 0.572 | |
add_assay_means | 0.345 | 0.009 | 0.355 | |
add_facetvars | 1.400 | 0.056 | 1.458 | |
add_opentargets_by_uniprot | 0.376 | 0.009 | 0.387 | |
add_psp | 0.524 | 0.017 | 0.542 | |
add_smiles | 0.452 | 0.046 | 0.501 | |
analysis | 0.451 | 0.041 | 0.509 | |
analyze | 13.167 | 0.141 | 13.445 | |
annotate_maxquant | 1.145 | 0.071 | 1.263 | |
annotate_uniprot_rest | 0.099 | 0.019 | 0.795 | |
assert_is_valid_sumexp | 1.620 | 0.050 | 1.671 | |
bin | 0.361 | 0.008 | 0.369 | |
biplot | 4.253 | 0.081 | 4.338 | |
biplot_corrections | 3.059 | 0.059 | 3.155 | |
biplot_covariates | 5.082 | 0.063 | 5.150 | |
block2lme | 0.004 | 0.001 | 0.004 | |
center | 1.418 | 0.022 | 1.443 | |
code | 5.136 | 0.083 | 5.229 | |
coefs | 0.795 | 0.045 | 0.840 | |
collapsed_entrezg_to_symbol | 0.000 | 0.001 | 0.001 | |
contrast_subgroup_cols | 0.535 | 0.050 | 0.618 | |
count_in | 0.001 | 0.001 | 0.002 | |
counts | 0.377 | 0.003 | 0.381 | |
counts2cpm | 0.306 | 0.003 | 0.308 | |
counts2tpm | 0.316 | 0.004 | 0.320 | |
cpm | 0.296 | 0.002 | 0.298 | |
create_design | 0.672 | 0.045 | 0.719 | |
default_formula | 16.720 | 0.532 | 16.851 | |
default_geom | 0.498 | 0.044 | 0.543 | |
default_sfile | 0.002 | 0.001 | 0.003 | |
demultiplex | 0.011 | 0.001 | 0.012 | |
dequantify | 0.002 | 0.001 | 0.003 | |
dequantify_compounddiscoverer | 0.001 | 0.000 | 0.001 | |
dot-coxph | 0.469 | 0.029 | 0.500 | |
dot-merge | 0.022 | 0.001 | 0.023 | |
dot-read_maxquant_proteingroups | 0.143 | 0.004 | 0.147 | |
download_data | 0.000 | 0.001 | 0.001 | |
download_gtf | 0 | 0 | 0 | |
download_mcclain21 | 0.001 | 0.000 | 0.002 | |
dt2mat | 0.004 | 0.000 | 0.004 | |
enrichment | 1.756 | 0.014 | 1.786 | |
entrezg_to_symbol | 0.001 | 0.000 | 0.001 | |
extract_coef_features | 6.362 | 0.092 | 6.461 | |
extract_rectangle | 0.153 | 0.041 | 0.194 | |
fcluster | 6.454 | 0.064 | 6.540 | |
fcor | 1.134 | 0.032 | 1.171 | |
fdata | 0.487 | 0.012 | 0.500 | |
fdr2p | 0.973 | 0.043 | 1.018 | |
filter_exprs_replicated_in_some_subgroup | 0.975 | 0.046 | 1.023 | |
filter_features | 0.541 | 0.042 | 0.584 | |
filter_medoid | 0.705 | 0.015 | 0.720 | |
filter_samples | 0.536 | 0.042 | 0.580 | |
fit_linmod | 30.167 | 0.272 | 30.572 | |
fit_survival | 5.253 | 0.053 | 5.315 | |
fitcoefs | 0.903 | 0.050 | 0.985 | |
fits | 0.800 | 0.043 | 0.844 | |
fix_xlgenes | 0.002 | 0.000 | 0.002 | |
flevels | 0.395 | 0.006 | 0.402 | |
fnames | 0.546 | 0.006 | 0.553 | |
formula2str | 0 | 0 | 0 | |
ftype | 8.893 | 0.478 | 9.383 | |
fvalues | 0.384 | 0.012 | 0.396 | |
fvars | 0.410 | 0.008 | 0.418 | |
genome_to_orgdb | 0.000 | 0.001 | 0.001 | |
group_by_level | 0.002 | 0.001 | 0.001 | |
guess_compounddiscoverer_quantity | 0.001 | 0.000 | 0.002 | |
guess_fitsep | 0.456 | 0.006 | 0.463 | |
guess_maxquant_quantity | 0.005 | 0.001 | 0.007 | |
guess_sep | 0.472 | 0.041 | 0.513 | |
has_multiple_levels | 0.058 | 0.002 | 0.060 | |
hdlproteins | 0.062 | 0.035 | 0.099 | |
impute | 2.950 | 0.042 | 2.995 | |
invert_subgroups | 0.637 | 0.018 | 0.657 | |
is_collapsed_subset | 0.001 | 0.000 | 0.001 | |
is_correlation_matrix | 0.002 | 0.000 | 0.002 | |
is_diann_report | 0.421 | 0.051 | 0.444 | |
is_fastadt | 0.056 | 0.001 | 0.056 | |
is_file | 0.001 | 0.000 | 0.001 | |
is_fraction | 0.002 | 0.001 | 0.001 | |
is_imputed | 0.730 | 0.009 | 0.739 | |
is_positive_number | 0.001 | 0.001 | 0.002 | |
is_scalar_subset | 0.315 | 0.005 | 0.320 | |
is_sig | 1.701 | 0.014 | 1.722 | |
is_valid_formula | 0.052 | 0.001 | 0.053 | |
keep_connected_blocks | 0.540 | 0.045 | 0.592 | |
keep_connected_features | 0.676 | 0.045 | 0.731 | |
keep_replicated_features | 0.817 | 0.049 | 0.873 | |
label2index | 0 | 0 | 0 | |
list2mat | 0.000 | 0.001 | 0.001 | |
log2counts | 0.327 | 0.003 | 0.331 | |
log2cpm | 0.326 | 0.003 | 0.333 | |
log2diffs | 0.382 | 0.008 | 0.392 | |
log2proteins | 0.335 | 0.006 | 0.344 | |
log2sites | 0.321 | 0.006 | 0.330 | |
log2tpm | 0.308 | 0.003 | 0.314 | |
log2transform | 3.865 | 0.057 | 3.962 | |
logical2factor | 0.001 | 0.001 | 0.003 | |
make_alpha_palette | 0.520 | 0.044 | 0.568 | |
make_colors | 0.014 | 0.001 | 0.015 | |
make_volcano_dt | 0.908 | 0.011 | 0.925 | |
map_fvalues | 0.403 | 0.007 | 0.413 | |
matrix2sumexp | 0.967 | 0.046 | 1.021 | |
merge_sample_file | 0.454 | 0.010 | 0.465 | |
merge_sdata | 0.572 | 0.051 | 0.630 | |
message_df | 0.002 | 0.000 | 0.003 | |
model_coefs | 0.767 | 0.045 | 0.840 | |
modelvar | 3.561 | 0.065 | 3.658 | |
order_on_p | 1.262 | 0.048 | 1.326 | |
pca | 2.867 | 0.064 | 2.957 | |
pg_to_canonical | 0.005 | 0.000 | 0.007 | |
plot_coef_densities | 1.375 | 0.075 | 1.457 | |
plot_contrast_venn | 2.484 | 0.076 | 2.588 | |
plot_contrastogram | 2.925 | 0.126 | 3.100 | |
plot_data | 1.254 | 0.053 | 1.317 | |
plot_densities | 8.461 | 0.203 | 8.775 | |
plot_design | 0.601 | 0.008 | 0.621 | |
plot_exprs | 21.305 | 0.163 | 21.781 | |
plot_exprs_per_coef | 22.729 | 0.166 | 23.209 | |
plot_fit_summary | 2.043 | 0.057 | 2.146 | |
plot_heatmap | 2.145 | 0.013 | 2.177 | |
plot_joint_density | 2.987 | 0.078 | 3.099 | |
plot_matrix | 0.554 | 0.048 | 0.608 | |
plot_sample_nas | 5.767 | 0.048 | 6.068 | |
plot_subgroup_points | 4.685 | 0.073 | 4.815 | |
plot_summary | 14.390 | 0.111 | 14.666 | |
plot_survival | 3.666 | 0.033 | 3.727 | |
plot_venn | 0.005 | 0.001 | 0.006 | |
plot_venn_heatmap | 0.026 | 0.001 | 0.028 | |
plot_violins | 3.996 | 0.083 | 4.111 | |
plot_volcano | 11.739 | 0.115 | 11.898 | |
preprocess_rnaseq_counts | 0.501 | 0.012 | 0.516 | |
pull_columns | 0.004 | 0.001 | 0.004 | |
read_affymetrix | 0 | 0 | 0 | |
read_diann_proteingroups | 97.389 | 2.211 | 96.532 | |
read_fragpipe | 7.831 | 0.184 | 8.164 | |
read_maxquant_phosphosites | 1.554 | 0.039 | 1.680 | |
read_maxquant_proteingroups | 1.182 | 0.029 | 1.251 | |
read_metabolon | 13.865 | 0.112 | 14.437 | |
read_msigdt | 0.000 | 0.000 | 0.001 | |
read_olink | 1.443 | 0.063 | 1.511 | |
read_rectangles | 0.211 | 0.024 | 0.237 | |
read_rnaseq_counts | 31.976 | 1.222 | 33.848 | |
read_salmon | 0.000 | 0.000 | 0.001 | |
read_somascan | 13.518 | 0.069 | 13.886 | |
read_uniprotdt | 0.329 | 0.023 | 0.362 | |
reset_fit | 4.862 | 0.074 | 4.997 | |
rm_diann_contaminants | 21.043 | 0.487 | 20.296 | |
rm_missing_in_some_samples | 0.464 | 0.047 | 0.525 | |
rm_unmatched_samples | 0.587 | 0.007 | 0.594 | |
scaledlibsizes | 0.302 | 0.003 | 0.305 | |
scoremat | 0.938 | 0.044 | 0.985 | |
slevels | 0.384 | 0.007 | 0.391 | |
snames | 0.384 | 0.005 | 0.389 | |
split_extract_fixed | 0.516 | 0.041 | 0.565 | |
split_samples | 1.047 | 0.044 | 1.105 | |
stri_any_regex | 0.001 | 0.000 | 0.001 | |
stri_detect_fixed_in_collapsed | 0.376 | 0.005 | 0.381 | |
subgroup_matrix | 0.491 | 0.040 | 0.534 | |
subtract_baseline | 4.169 | 0.063 | 4.266 | |
sumexp_to_longdt | 1.875 | 0.136 | 2.035 | |
sumexp_to_tsv | 0.488 | 0.013 | 0.508 | |
sumexplist_to_longdt | 1.558 | 0.021 | 1.589 | |
summarize_fit | 1.340 | 0.049 | 1.481 | |
svalues | 0.266 | 0.005 | 0.275 | |
svars | 0.360 | 0.006 | 0.366 | |
systematic_nas | 0.566 | 0.007 | 0.574 | |
tag_features | 1.048 | 0.027 | 1.082 | |
tag_hdlproteins | 0.611 | 0.029 | 0.669 | |
taxon2org | 0.001 | 0.001 | 0.001 | |
tpm | 0.302 | 0.003 | 0.305 | |
uncollapse | 0.030 | 0.002 | 0.032 | |
values | 0.407 | 0.006 | 0.414 | |
varlevels_dont_clash | 0.022 | 0.001 | 0.023 | |
venn_detects | 0.587 | 0.008 | 0.596 | |
weights | 0.299 | 0.002 | 0.301 | |
write_xl | 0.636 | 0.044 | 0.683 | |
zero_to_na | 0.001 | 0.000 | 0.002 | |