Back to Multiple platform build/check report for BioC 3.22: simplified long |
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This page was generated on 2025-09-05 12:08 -0400 (Fri, 05 Sep 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" | 4823 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4618 |
kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" | 4565 |
taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4544 |
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 116/2322 | 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. - See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host. |
Package: autonomics |
Version: 1.17.0 |
Command: /home/biocbuild/R/R/bin/R CMD check --install=check:autonomics.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings autonomics_1.17.0.tar.gz |
StartedAt: 2025-09-05 04:16:41 -0000 (Fri, 05 Sep 2025) |
EndedAt: 2025-09-05 04:34:23 -0000 (Fri, 05 Sep 2025) |
EllapsedTime: 1062.5 seconds |
RetCode: 0 |
Status: OK |
CheckDir: autonomics.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD check --install=check:autonomics.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings autonomics_1.17.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/autonomics.Rcheck’ * using R version 4.5.0 (2025-04-11) * using platform: aarch64-unknown-linux-gnu * R was compiled by aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0 GNU Fortran (GCC) 14.2.0 * running under: openEuler 24.03 (LTS) * 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 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 fit_linmod 43.920 0.167 44.183 read_rnaseq_counts 41.754 1.426 43.343 plot_exprs_per_coef 34.688 0.060 34.837 read_diann_proteingroups 33.451 0.506 33.692 plot_exprs 33.031 0.215 33.336 default_formula 24.091 0.323 24.340 read_metabolon 20.996 0.112 21.166 analyze 20.992 0.044 21.085 plot_summary 20.927 0.036 21.011 read_somascan 20.364 0.223 20.646 plot_volcano 17.341 0.116 17.499 ftype 12.002 0.191 12.184 plot_densities 11.862 0.128 12.014 extract_coef_features 9.903 0.088 10.015 fcluster 8.822 0.032 8.873 plot_sample_nas 8.632 0.075 8.727 read_fragpipe 8.518 0.104 8.482 rm_diann_contaminants 7.568 0.084 7.565 code 7.522 0.008 7.547 reset_fit 7.454 0.016 7.504 biplot_covariates 7.360 0.024 7.398 fit_survival 7.028 0.032 7.077 plot_subgroup_points 6.600 0.040 6.656 subtract_baseline 6.517 0.028 6.557 biplot 5.842 0.068 5.924 plot_violins 5.652 0.032 5.698 modelvar 5.271 0.008 5.288 plot_survival 5.201 0.028 5.244 log2transform 5.003 0.028 5.046 annotate_uniprot_rest 0.125 0.004 5.749 * 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 ‘/home/biocbuild/bbs-3.22-bioc/meat/autonomics.Rcheck/00check.log’ for details.
autonomics.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD INSTALL autonomics ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-4.5.0/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 4.5.0 (2025-04-11) -- "How About a Twenty-Six" Copyright (C) 2025 The R Foundation for Statistical Computing Platform: aarch64-unknown-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 189.286 2.745 191.610
autonomics.Rcheck/autonomics-Ex.timings
name | user | system | elapsed | |
AUTONOMICS_DATASETS | 0.000 | 0.000 | 0.001 | |
COMPOUNDDISCOVERER_PATTERNS | 0 | 0 | 0 | |
FITSEP | 0 | 0 | 0 | |
LINMODENGINES | 0 | 0 | 0 | |
MAXQUANT_PATTERNS | 0 | 0 | 0 | |
SURVIVALENGINES | 0 | 0 | 0 | |
TAXON_TO_ORGNAME | 0 | 0 | 0 | |
TESTS | 0 | 0 | 0 | |
X | 2.758 | 0.076 | 2.849 | |
abstract_fit | 2.439 | 0.020 | 2.462 | |
add_adjusted_pvalues | 0.799 | 0.012 | 0.816 | |
add_assay_means | 0.484 | 0.016 | 0.500 | |
add_facetvars | 2.116 | 0.015 | 2.133 | |
add_opentargets_by_uniprot | 0.511 | 0.004 | 0.521 | |
add_psp | 0.706 | 0.064 | 0.775 | |
add_smiles | 0.606 | 0.040 | 0.644 | |
analysis | 0.565 | 0.000 | 0.566 | |
analyze | 20.992 | 0.044 | 21.085 | |
annotate_maxquant | 1.271 | 0.028 | 1.305 | |
annotate_uniprot_rest | 0.125 | 0.004 | 5.749 | |
assert_is_valid_sumexp | 0.754 | 0.028 | 0.781 | |
bin | 1.204 | 0.059 | 1.267 | |
biplot | 5.842 | 0.068 | 5.924 | |
biplot_corrections | 4.583 | 0.004 | 4.596 | |
biplot_covariates | 7.360 | 0.024 | 7.398 | |
block2lme | 0.004 | 0.000 | 0.004 | |
center | 1.948 | 0.004 | 1.956 | |
code | 7.522 | 0.008 | 7.547 | |
coefs | 1.122 | 0.012 | 1.134 | |
collapsed_entrezg_to_symbol | 0.001 | 0.000 | 0.001 | |
contrast_subgroup_cols | 0.813 | 0.004 | 0.816 | |
count_in | 0.002 | 0.000 | 0.001 | |
counts | 0.496 | 0.004 | 0.503 | |
counts2cpm | 0.418 | 0.000 | 0.419 | |
counts2tpm | 0.408 | 0.000 | 0.409 | |
cpm | 0.488 | 0.000 | 0.489 | |
create_design | 0.955 | 0.004 | 0.959 | |
default_formula | 24.091 | 0.323 | 24.340 | |
default_geom | 0.707 | 0.004 | 0.710 | |
default_sfile | 0.002 | 0.000 | 0.002 | |
demultiplex | 0.021 | 0.000 | 0.021 | |
dequantify | 0.003 | 0.000 | 0.003 | |
dequantify_compounddiscoverer | 0.002 | 0.000 | 0.001 | |
dot-coxph | 0.549 | 0.008 | 0.560 | |
dot-merge | 0.024 | 0.000 | 0.024 | |
dot-read_maxquant_proteingroups | 0.121 | 0.008 | 0.129 | |
download_data | 0 | 0 | 0 | |
download_gtf | 0.000 | 0.000 | 0.001 | |
download_mcclain21 | 0 | 0 | 0 | |
dt2mat | 0.002 | 0.002 | 0.004 | |
enrichment | 2.672 | 0.008 | 2.688 | |
entrezg_to_symbol | 0.001 | 0.000 | 0.001 | |
extract_coef_features | 9.903 | 0.088 | 10.015 | |
extract_rectangle | 0.159 | 0.000 | 0.159 | |
fcluster | 8.822 | 0.032 | 8.873 | |
fcor | 1.414 | 0.000 | 1.418 | |
fdata | 0.760 | 0.008 | 0.771 | |
fdr2p | 1.370 | 0.004 | 1.376 | |
filter_exprs_replicated_in_some_subgroup | 1.417 | 0.016 | 1.431 | |
filter_features | 0.674 | 0.008 | 0.681 | |
filter_medoid | 1.046 | 0.000 | 1.049 | |
filter_samples | 0.691 | 0.012 | 0.701 | |
fit_linmod | 43.920 | 0.167 | 44.183 | |
fit_survival | 7.028 | 0.032 | 7.077 | |
fitcoefs | 1.245 | 0.012 | 1.256 | |
fits | 1.044 | 0.028 | 1.071 | |
fix_xlgenes | 0.002 | 0.000 | 0.002 | |
flevels | 0.529 | 0.008 | 0.539 | |
fnames | 0.698 | 0.000 | 0.700 | |
formula2str | 0 | 0 | 0 | |
ftype | 12.002 | 0.191 | 12.184 | |
fvalues | 0.554 | 0.004 | 0.560 | |
fvars | 0.535 | 0.000 | 0.537 | |
genome_to_orgdb | 0.001 | 0.000 | 0.001 | |
group_by_level | 0.002 | 0.000 | 0.002 | |
guess_compounddiscoverer_quantity | 0.002 | 0.000 | 0.002 | |
guess_fitsep | 0.677 | 0.004 | 0.684 | |
guess_maxquant_quantity | 0.007 | 0.000 | 0.007 | |
guess_sep | 0.677 | 0.016 | 0.691 | |
has_multiple_levels | 0.077 | 0.004 | 0.082 | |
hdlproteins | 0.050 | 0.020 | 0.083 | |
impute | 4.131 | 0.024 | 4.167 | |
invert_subgroups | 0.918 | 0.004 | 0.925 | |
is_collapsed_subset | 0.001 | 0.000 | 0.000 | |
is_correlation_matrix | 0.002 | 0.000 | 0.001 | |
is_diann_report | 0.302 | 0.020 | 0.312 | |
is_fastadt | 0.096 | 0.000 | 0.096 | |
is_file | 0 | 0 | 0 | |
is_fraction | 0.002 | 0.000 | 0.002 | |
is_imputed | 0.991 | 0.000 | 0.994 | |
is_positive_number | 0.002 | 0.000 | 0.002 | |
is_scalar_subset | 0.434 | 0.000 | 0.434 | |
is_sig | 2.411 | 0.004 | 2.422 | |
is_valid_formula | 0.065 | 0.000 | 0.065 | |
keep_connected_blocks | 0.720 | 0.016 | 0.734 | |
keep_connected_features | 0.890 | 0.004 | 0.904 | |
keep_replicated_features | 1.109 | 0.019 | 1.127 | |
label2index | 0.001 | 0.000 | 0.001 | |
list2mat | 0.001 | 0.000 | 0.000 | |
log2counts | 0.464 | 0.000 | 0.465 | |
log2cpm | 0.446 | 0.000 | 0.448 | |
log2diffs | 0.473 | 0.008 | 0.482 | |
log2proteins | 0.461 | 0.004 | 0.467 | |
log2sites | 0.442 | 0.004 | 0.448 | |
log2tpm | 0.414 | 0.000 | 0.415 | |
log2transform | 5.003 | 0.028 | 5.046 | |
logical2factor | 0.002 | 0.000 | 0.002 | |
make_alpha_palette | 0.712 | 0.008 | 0.719 | |
make_colors | 0.011 | 0.000 | 0.012 | |
make_volcano_dt | 1.248 | 0.000 | 1.251 | |
map_fvalues | 0.546 | 0.000 | 0.547 | |
matrix2sumexp | 1.175 | 0.004 | 1.182 | |
merge_sample_file | 0.585 | 0.000 | 0.586 | |
merge_sdata | 0.739 | 0.004 | 0.743 | |
message_df | 0.003 | 0.000 | 0.003 | |
model_coefs | 0.986 | 0.016 | 1.002 | |
modelvar | 5.271 | 0.008 | 5.288 | |
order_on_p | 1.679 | 0.036 | 1.716 | |
pca | 4.023 | 0.020 | 4.051 | |
pg_to_canonical | 0.008 | 0.000 | 0.009 | |
plot_coef_densities | 1.773 | 0.027 | 1.803 | |
plot_contrast_venn | 3.636 | 0.008 | 3.643 | |
plot_contrastogram | 4.136 | 0.048 | 4.203 | |
plot_data | 1.730 | 0.020 | 1.752 | |
plot_densities | 11.862 | 0.128 | 12.014 | |
plot_design | 0.857 | 0.008 | 0.867 | |
plot_exprs | 33.031 | 0.215 | 33.336 | |
plot_exprs_per_coef | 34.688 | 0.060 | 34.837 | |
plot_fit_summary | 2.842 | 0.032 | 2.877 | |
plot_heatmap | 3.077 | 0.008 | 3.094 | |
plot_joint_density | 3.840 | 0.044 | 3.893 | |
plot_matrix | 0.647 | 0.012 | 0.658 | |
plot_sample_nas | 8.632 | 0.075 | 8.727 | |
plot_subgroup_points | 6.600 | 0.040 | 6.656 | |
plot_summary | 20.927 | 0.036 | 21.011 | |
plot_survival | 5.201 | 0.028 | 5.244 | |
plot_venn | 0.005 | 0.000 | 0.006 | |
plot_venn_heatmap | 0.031 | 0.000 | 0.031 | |
plot_violins | 5.652 | 0.032 | 5.698 | |
plot_volcano | 17.341 | 0.116 | 17.499 | |
preprocess_rnaseq_counts | 0.548 | 0.012 | 0.561 | |
pull_columns | 0.003 | 0.000 | 0.003 | |
read_affymetrix | 0 | 0 | 0 | |
read_diann_proteingroups | 33.451 | 0.506 | 33.692 | |
read_fragpipe | 8.518 | 0.104 | 8.482 | |
read_maxquant_phosphosites | 1.889 | 0.016 | 1.909 | |
read_maxquant_proteingroups | 1.639 | 0.008 | 1.652 | |
read_metabolon | 20.996 | 0.112 | 21.166 | |
read_msigdt | 0.001 | 0.000 | 0.001 | |
read_olink | 1.665 | 0.020 | 1.671 | |
read_rectangles | 0.244 | 0.000 | 0.245 | |
read_rnaseq_counts | 41.754 | 1.426 | 43.343 | |
read_salmon | 0 | 0 | 0 | |
read_somascan | 20.364 | 0.223 | 20.646 | |
read_uniprotdt | 0.376 | 0.008 | 0.385 | |
reset_fit | 7.454 | 0.016 | 7.504 | |
rm_diann_contaminants | 7.568 | 0.084 | 7.565 | |
rm_missing_in_some_samples | 0.746 | 0.032 | 0.777 | |
rm_unmatched_samples | 0.862 | 0.004 | 0.867 | |
scaledlibsizes | 0.427 | 0.000 | 0.428 | |
scoremat | 1.447 | 0.008 | 1.457 | |
slevels | 0.628 | 0.008 | 0.639 | |
snames | 0.537 | 0.004 | 0.542 | |
split_extract_fixed | 0.687 | 0.012 | 0.697 | |
split_samples | 1.635 | 0.019 | 1.657 | |
stri_any_regex | 0.001 | 0.000 | 0.000 | |
stri_detect_fixed_in_collapsed | 0.471 | 0.000 | 0.472 | |
subgroup_matrix | 0.780 | 0.008 | 0.787 | |
subtract_baseline | 6.517 | 0.028 | 6.557 | |
sumexp_to_longdt | 3.620 | 0.092 | 3.714 | |
sumexp_to_tsv | 0.676 | 0.000 | 0.678 | |
sumexplist_to_longdt | 1.939 | 0.020 | 1.965 | |
summarize_fit | 2.279 | 0.004 | 2.283 | |
svalues | 0.564 | 0.000 | 0.565 | |
svars | 0.506 | 0.016 | 0.524 | |
systematic_nas | 0.727 | 0.036 | 0.765 | |
tag_features | 1.301 | 0.020 | 1.324 | |
tag_hdlproteins | 0.692 | 0.016 | 0.710 | |
taxon2org | 0.001 | 0.000 | 0.001 | |
tpm | 0.447 | 0.000 | 0.448 | |
uncollapse | 0.039 | 0.000 | 0.039 | |
values | 0.591 | 0.000 | 0.592 | |
varlevels_dont_clash | 0.028 | 0.000 | 0.027 | |
venn_detects | 0.716 | 0.000 | 0.719 | |
weights | 0.454 | 0.000 | 0.456 | |
write_xl | 0.930 | 0.012 | 0.941 | |
zero_to_na | 0.001 | 0.000 | 0.001 | |