Back to Multiple platform build/check report for BioC 3.22: simplified long |
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This page was generated on 2025-09-23 12:03 -0400 (Tue, 23 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" | 4816 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4605 |
kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4549 |
taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4560 |
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 1.17.0 (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: /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: 2025-09-22 21:02:59 -0400 (Mon, 22 Sep 2025) |
EndedAt: 2025-09-22 21:22:31 -0400 (Mon, 22 Sep 2025) |
EllapsedTime: 1171.4 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_1.17.0.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 ‘1.17.0’ * 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 396.194 2.085 102.968 rm_diann_contaminants 104.492 1.242 23.687 read_rnaseq_counts 44.614 1.860 38.257 fit_linmod 42.926 0.265 32.202 ftype 39.204 0.150 9.229 plot_exprs 28.728 0.056 25.191 default_formula 26.375 0.301 17.358 plot_exprs_per_coef 24.915 0.032 24.864 plot_contrastogram 19.639 0.058 3.312 read_somascan 17.873 0.136 17.467 analyze 16.275 0.238 16.389 read_metabolon 15.821 0.331 16.056 plot_summary 15.266 0.098 15.261 plot_volcano 14.163 0.020 14.096 plot_densities 12.094 0.115 9.967 read_olink 11.916 0.042 1.787 is_diann_report 8.706 0.107 0.696 fcluster 8.731 0.043 8.623 read_fragpipe 7.644 0.266 5.928 plot_subgroup_points 7.121 0.095 5.647 plot_sample_nas 6.792 0.035 6.803 biplot_covariates 6.518 0.031 6.518 extract_coef_features 6.369 0.022 6.359 subtract_baseline 6.167 0.115 5.145 log2transform 5.850 0.117 5.968 fit_survival 5.372 0.078 5.433 code 5.147 0.035 5.145 plot_joint_density 4.874 0.153 5.005 * 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 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 283.527 9.179 222.726
autonomics.Rcheck/autonomics-Ex.timings
name | user | system | elapsed | |
AUTONOMICS_DATASETS | 0 | 0 | 0 | |
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 | 1.464 | 0.140 | 1.579 | |
abstract_fit | 1.669 | 0.050 | 1.694 | |
add_adjusted_pvalues | 0.545 | 0.011 | 0.557 | |
add_assay_means | 0.350 | 0.004 | 0.354 | |
add_facetvars | 1.507 | 0.020 | 1.507 | |
add_opentargets_by_uniprot | 0.381 | 0.009 | 0.393 | |
add_psp | 0.515 | 0.009 | 0.525 | |
add_smiles | 0.433 | 0.005 | 0.418 | |
analysis | 0.374 | 0.001 | 0.376 | |
analyze | 16.275 | 0.238 | 16.389 | |
annotate_maxquant | 0.849 | 0.030 | 0.879 | |
annotate_uniprot_rest | 0.335 | 0.030 | 2.120 | |
assert_is_valid_sumexp | 0.561 | 0.007 | 0.529 | |
bin | 0.378 | 0.013 | 0.391 | |
biplot | 4.355 | 0.089 | 4.406 | |
biplot_corrections | 4.390 | 0.128 | 4.479 | |
biplot_covariates | 6.518 | 0.031 | 6.518 | |
block2lme | 0.002 | 0.001 | 0.003 | |
center | 1.737 | 0.003 | 1.741 | |
code | 5.147 | 0.035 | 5.145 | |
coefs | 0.783 | 0.006 | 0.751 | |
collapsed_entrezg_to_symbol | 0.000 | 0.001 | 0.000 | |
contrast_subgroup_cols | 0.551 | 0.045 | 0.573 | |
count_in | 0.001 | 0.000 | 0.001 | |
counts | 0.314 | 0.021 | 0.334 | |
counts2cpm | 0.291 | 0.005 | 0.296 | |
counts2tpm | 0.26 | 0.00 | 0.26 | |
cpm | 0.350 | 0.003 | 0.353 | |
create_design | 0.640 | 0.009 | 0.616 | |
default_formula | 26.375 | 0.301 | 17.358 | |
default_geom | 0.488 | 0.004 | 0.470 | |
default_sfile | 0.001 | 0.000 | 0.001 | |
demultiplex | 0.012 | 0.001 | 0.013 | |
dequantify | 0.002 | 0.000 | 0.002 | |
dequantify_compounddiscoverer | 0.001 | 0.000 | 0.000 | |
dot-coxph | 0.372 | 0.006 | 0.378 | |
dot-merge | 0.016 | 0.000 | 0.017 | |
dot-read_maxquant_proteingroups | 0.106 | 0.004 | 0.110 | |
download_data | 0 | 0 | 0 | |
download_gtf | 0 | 0 | 0 | |
download_mcclain21 | 0 | 0 | 0 | |
dt2mat | 0.003 | 0.000 | 0.002 | |
enrichment | 1.731 | 0.001 | 1.732 | |
entrezg_to_symbol | 0 | 0 | 0 | |
extract_coef_features | 6.369 | 0.022 | 6.359 | |
extract_rectangle | 0.102 | 0.005 | 0.108 | |
fcluster | 8.731 | 0.043 | 8.623 | |
fcor | 1.379 | 0.005 | 1.384 | |
fdata | 0.589 | 0.047 | 0.636 | |
fdr2p | 0.923 | 0.015 | 0.917 | |
filter_exprs_replicated_in_some_subgroup | 0.951 | 0.006 | 0.902 | |
filter_features | 0.502 | 0.006 | 0.488 | |
filter_medoid | 0.619 | 0.004 | 0.625 | |
filter_samples | 0.515 | 0.011 | 0.498 | |
fit_linmod | 42.926 | 0.265 | 32.202 | |
fit_survival | 5.372 | 0.078 | 5.433 | |
fitcoefs | 0.844 | 0.005 | 0.827 | |
fits | 0.706 | 0.006 | 0.690 | |
fix_xlgenes | 0.002 | 0.000 | 0.002 | |
flevels | 0.367 | 0.001 | 0.369 | |
fnames | 0.468 | 0.003 | 0.471 | |
formula2str | 0 | 0 | 0 | |
ftype | 39.204 | 0.150 | 9.229 | |
fvalues | 0.387 | 0.002 | 0.388 | |
fvars | 0.408 | 0.002 | 0.409 | |
genome_to_orgdb | 0.001 | 0.000 | 0.000 | |
group_by_level | 0.001 | 0.000 | 0.001 | |
guess_compounddiscoverer_quantity | 0.001 | 0.000 | 0.002 | |
guess_fitsep | 0.460 | 0.005 | 0.465 | |
guess_maxquant_quantity | 0.005 | 0.001 | 0.006 | |
guess_sep | 0.542 | 0.010 | 0.521 | |
has_multiple_levels | 0.054 | 0.000 | 0.054 | |
hdlproteins | 0.042 | 0.008 | 0.052 | |
impute | 3.564 | 0.011 | 3.575 | |
invert_subgroups | 0.659 | 0.000 | 0.658 | |
is_collapsed_subset | 0 | 0 | 0 | |
is_correlation_matrix | 0.000 | 0.001 | 0.001 | |
is_diann_report | 8.706 | 0.107 | 0.696 | |
is_fastadt | 0.065 | 0.001 | 0.066 | |
is_file | 0.000 | 0.001 | 0.001 | |
is_fraction | 0.002 | 0.000 | 0.002 | |
is_imputed | 0.725 | 0.003 | 0.729 | |
is_positive_number | 0.001 | 0.000 | 0.002 | |
is_scalar_subset | 0.351 | 0.003 | 0.355 | |
is_sig | 1.791 | 0.004 | 1.796 | |
is_valid_formula | 0.042 | 0.000 | 0.044 | |
keep_connected_blocks | 0.842 | 0.011 | 0.526 | |
keep_connected_features | 2.696 | 0.014 | 0.808 | |
keep_replicated_features | 0.894 | 0.011 | 0.841 | |
label2index | 0.001 | 0.000 | 0.000 | |
list2mat | 0.001 | 0.000 | 0.001 | |
log2counts | 0.316 | 0.000 | 0.316 | |
log2cpm | 0.348 | 0.000 | 0.348 | |
log2diffs | 0.317 | 0.001 | 0.317 | |
log2proteins | 0.388 | 0.000 | 0.388 | |
log2sites | 0.307 | 0.002 | 0.308 | |
log2tpm | 0.336 | 0.000 | 0.336 | |
log2transform | 5.850 | 0.117 | 5.968 | |
logical2factor | 0.001 | 0.000 | 0.002 | |
make_alpha_palette | 0.509 | 0.008 | 0.495 | |
make_colors | 0.01 | 0.00 | 0.01 | |
make_volcano_dt | 0.874 | 0.001 | 0.876 | |
map_fvalues | 0.355 | 0.002 | 0.357 | |
matrix2sumexp | 0.989 | 0.006 | 0.973 | |
merge_sample_file | 0.418 | 0.002 | 0.420 | |
merge_sdata | 0.549 | 0.005 | 0.531 | |
message_df | 0.002 | 0.000 | 0.002 | |
model_coefs | 0.697 | 0.010 | 0.687 | |
modelvar | 3.561 | 0.036 | 3.541 | |
order_on_p | 1.175 | 0.008 | 1.162 | |
pca | 3.461 | 0.009 | 3.448 | |
pg_to_canonical | 0.005 | 0.000 | 0.005 | |
plot_coef_densities | 1.318 | 0.005 | 1.302 | |
plot_contrast_venn | 2.442 | 0.034 | 2.395 | |
plot_contrastogram | 19.639 | 0.058 | 3.312 | |
plot_data | 1.582 | 0.006 | 1.566 | |
plot_densities | 12.094 | 0.115 | 9.967 | |
plot_design | 0.738 | 0.003 | 0.741 | |
plot_exprs | 28.728 | 0.056 | 25.191 | |
plot_exprs_per_coef | 24.915 | 0.032 | 24.864 | |
plot_fit_summary | 2.212 | 0.010 | 2.124 | |
plot_heatmap | 2.293 | 0.005 | 2.300 | |
plot_joint_density | 4.874 | 0.153 | 5.005 | |
plot_matrix | 0.461 | 0.010 | 0.436 | |
plot_sample_nas | 6.792 | 0.035 | 6.803 | |
plot_subgroup_points | 7.121 | 0.095 | 5.647 | |
plot_summary | 15.266 | 0.098 | 15.261 | |
plot_survival | 4.117 | 0.028 | 4.162 | |
plot_venn | 0.005 | 0.000 | 0.005 | |
plot_venn_heatmap | 0.023 | 0.000 | 0.023 | |
plot_violins | 4.715 | 0.053 | 4.745 | |
plot_volcano | 14.163 | 0.020 | 14.096 | |
preprocess_rnaseq_counts | 0.338 | 0.002 | 0.339 | |
pull_columns | 0.002 | 0.000 | 0.002 | |
read_affymetrix | 0 | 0 | 0 | |
read_diann_proteingroups | 396.194 | 2.085 | 102.968 | |
read_fragpipe | 7.644 | 0.266 | 5.928 | |
read_maxquant_phosphosites | 1.650 | 0.025 | 1.679 | |
read_maxquant_proteingroups | 1.150 | 0.019 | 1.169 | |
read_metabolon | 15.821 | 0.331 | 16.056 | |
read_msigdt | 0.001 | 0.000 | 0.000 | |
read_olink | 11.916 | 0.042 | 1.787 | |
read_rectangles | 0.172 | 0.010 | 0.182 | |
read_rnaseq_counts | 44.614 | 1.860 | 38.257 | |
read_salmon | 0 | 0 | 0 | |
read_somascan | 17.873 | 0.136 | 17.467 | |
read_uniprotdt | 0.280 | 0.003 | 0.283 | |
reset_fit | 4.928 | 0.008 | 4.842 | |
rm_diann_contaminants | 104.492 | 1.242 | 23.687 | |
rm_missing_in_some_samples | 0.488 | 0.068 | 0.532 | |
rm_unmatched_samples | 0.652 | 0.095 | 0.747 | |
scaledlibsizes | 0.271 | 0.006 | 0.277 | |
scoremat | 0.970 | 0.022 | 0.967 | |
slevels | 0.383 | 0.006 | 0.390 | |
snames | 0.468 | 0.020 | 0.488 | |
split_extract_fixed | 0.486 | 0.032 | 0.494 | |
split_samples | 1.301 | 0.075 | 1.360 | |
stri_any_regex | 0.000 | 0.000 | 0.001 | |
stri_detect_fixed_in_collapsed | 0.359 | 0.014 | 0.374 | |
subgroup_matrix | 0.619 | 0.039 | 0.628 | |
subtract_baseline | 6.167 | 0.115 | 5.145 | |
sumexp_to_longdt | 2.032 | 0.094 | 2.073 | |
sumexp_to_tsv | 0.442 | 0.008 | 0.450 | |
sumexplist_to_longdt | 1.377 | 0.019 | 1.396 | |
summarize_fit | 1.772 | 0.015 | 1.720 | |
svalues | 0.402 | 0.006 | 0.407 | |
svars | 0.400 | 0.004 | 0.404 | |
systematic_nas | 0.624 | 0.022 | 0.646 | |
tag_features | 1.052 | 0.013 | 1.066 | |
tag_hdlproteins | 0.583 | 0.016 | 0.599 | |
taxon2org | 0.000 | 0.001 | 0.001 | |
tpm | 0.304 | 0.003 | 0.308 | |
uncollapse | 0.027 | 0.000 | 0.027 | |
values | 0.391 | 0.011 | 0.402 | |
varlevels_dont_clash | 0.021 | 0.001 | 0.022 | |
venn_detects | 0.571 | 0.001 | 0.572 | |
weights | 0.288 | 0.000 | 0.288 | |
write_xl | 0.979 | 0.056 | 1.012 | |
zero_to_na | 0.001 | 0.000 | 0.001 | |