Back to Multiple platform build/check report for BioC 3.21: simplified long |
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This page was generated on 2025-10-16 11:41 -0400 (Thu, 16 Oct 2025).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4833 |
merida1 | macOS 12.7.6 Monterey | x86_64 | 4.5.1 RC (2025-06-05 r88288) -- "Great Square Root" | 4614 |
kjohnson1 | macOS 13.7.5 Ventura | arm64 | 4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" | 4555 |
kunpeng2 | Linux (openEuler 24.03 LTS) | aarch64 | R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" | 4586 |
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 24.04.3 LTS) / x86_64 | OK | OK | OK | ![]() | ||||||||
merida1 | macOS 12.7.6 Monterey / x86_64 | OK | OK | OK | OK | ![]() | ||||||||
kjohnson1 | macOS 13.7.5 Ventura / arm64 | OK | OK | OK | OK | ![]() | ||||||||
kunpeng2 | Linux (openEuler 24.03 LTS) / aarch64 | OK | OK | ERROR | ||||||||||
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: 1.16.0 |
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_1.16.0.tar.gz |
StartedAt: 2025-10-14 06:20:09 -0000 (Tue, 14 Oct 2025) |
EndedAt: 2025-10-14 06:39:53 -0000 (Tue, 14 Oct 2025) |
EllapsedTime: 1183.4 seconds |
RetCode: 1 |
Status: ERROR |
CheckDir: autonomics.Rcheck |
Warnings: NA |
############################################################################## ############################################################################## ### ### 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_1.16.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/autonomics.Rcheck’ * using R Under development (unstable) (2025-02-19 r87757) * 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-SP1) * 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 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_rnaseq_counts 51.093 1.333 59.358 fit_linmod 47.704 0.143 48.306 plot_exprs_per_coef 36.951 0.067 39.297 plot_exprs 36.232 0.128 36.727 default_formula 25.493 0.453 27.382 analyze 23.973 0.387 24.723 read_metabolon 22.463 0.163 23.061 read_somascan 22.271 0.102 23.894 plot_summary 21.837 0.128 23.437 plot_volcano 20.081 0.116 21.060 plot_densities 14.180 0.052 14.271 fcluster 13.475 0.035 14.351 ftype 12.073 0.092 12.788 plot_sample_nas 10.828 0.143 11.596 biplot_covariates 9.822 0.100 10.151 extract_coef_features 9.842 0.015 10.674 read_fragpipe 8.752 0.056 9.020 plot_subgroup_points 8.420 0.028 8.984 log2transform 7.750 0.067 7.984 code 7.507 0.150 7.887 fit_survival 7.645 0.004 7.952 reset_fit 7.155 0.027 7.463 plot_violins 6.749 0.107 7.736 biplot 6.502 0.216 6.735 subtract_baseline 6.669 0.040 6.921 biplot_corrections 6.172 0.135 6.329 plot_joint_density 5.846 0.028 5.990 plot_survival 5.467 0.020 5.989 impute 5.066 0.020 5.100 modelvar 4.957 0.072 5.039 read_diann_proteingroups 4.946 0.031 5.216 annotate_uniprot_rest 0.118 0.028 7.410 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘testthat.R’ ERROR Running the tests in ‘tests/testthat.R’ failed. Last 13 lines of output: [1] nonexistent attr(,"class") [1] "vector_with_cause" "logical" Backtrace: ▆ 1. ├─autonomics::.read_rnaseq_counts(file, sfile = sfile, by.y = "rna_id") at test-8_fit.R:76:9 2. │ └─object %<>% ... 3. └─autonomics::merge_sample_file(...) 4. └─autonomics:::assert_all_are_existing_files(sfile) 5. └─autonomics:::assert_engine(...) 6. └─autonomics:::give_feedback(handler_type, msg, predicate_name) [ FAIL 1 | WARN 4 | SKIP 0 | PASS 157 ] Error: Test failures Execution halted * 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: 1 ERROR, 2 NOTEs See ‘/home/biocbuild/bbs-3.21-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-devel_2025-02-19/site-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.fail
R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" 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 1 | WARN 4 | SKIP 0 | PASS 157 ] ══ Failed tests ════════════════════════════════════════════════════════════════ ── Error ('test-8_fit.R:76:9'): fit: mcclain21 ─────────────────────────────── <assertionError/assertionCondition/simpleError/error/condition> Error in `merge_sample_file(., sfile = sfile, by.x = "sample_id", by.y = by.y)`: is_existing_file : Some or all of the files specified by sfile do not exist. /home/biocbuild/.cache/R/autonomics/datasets/mcclain21/GSE161731_counts_key.csv.gz FALSE attr(,"cause") [1] nonexistent attr(,"class") [1] "vector_with_cause" "logical" Backtrace: ▆ 1. ├─autonomics::.read_rnaseq_counts(file, sfile = sfile, by.y = "rna_id") at test-8_fit.R:76:9 2. │ └─object %<>% ... 3. └─autonomics::merge_sample_file(...) 4. └─autonomics:::assert_all_are_existing_files(sfile) 5. └─autonomics:::assert_engine(...) 6. └─autonomics:::give_feedback(handler_type, msg, predicate_name) [ FAIL 1 | WARN 4 | SKIP 0 | PASS 157 ] Error: Test failures Execution halted
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 | 0.000 | 0.000 | 0.001 | |
X | 2.012 | 0.151 | 2.170 | |
abstract_fit | 2.513 | 0.096 | 2.617 | |
add_adjusted_pvalues | 0.793 | 0.016 | 0.814 | |
add_assay_means | 0.491 | 0.020 | 0.512 | |
add_facetvars | 2.228 | 0.052 | 2.286 | |
add_opentargets_by_uniprot | 0.520 | 0.015 | 0.541 | |
add_psp | 0.686 | 0.008 | 0.699 | |
add_smiles | 0.662 | 0.012 | 0.676 | |
analysis | 0.536 | 0.020 | 0.557 | |
analyze | 23.973 | 0.387 | 24.723 | |
annotate_maxquant | 1.213 | 0.044 | 1.301 | |
annotate_uniprot_rest | 0.118 | 0.028 | 7.410 | |
assert_is_valid_sumexp | 0.743 | 0.060 | 0.804 | |
bin | 0.570 | 0.028 | 0.600 | |
biplot | 6.502 | 0.216 | 6.735 | |
biplot_corrections | 6.172 | 0.135 | 6.329 | |
biplot_covariates | 9.822 | 0.100 | 10.151 | |
block2lme | 0.004 | 0.000 | 0.004 | |
center | 2.573 | 0.008 | 3.044 | |
code | 7.507 | 0.150 | 7.887 | |
coefs | 1.060 | 0.024 | 1.210 | |
collapsed_entrezg_to_symbol | 0.001 | 0.000 | 0.000 | |
contrast_subgroup_cols | 0.726 | 0.008 | 0.735 | |
count_in | 0.001 | 0.000 | 0.001 | |
counts | 0.448 | 0.004 | 0.459 | |
counts2cpm | 0.395 | 0.000 | 0.396 | |
counts2tpm | 0.387 | 0.000 | 0.388 | |
cpm | 0.447 | 0.000 | 0.748 | |
create_design | 0.904 | 0.012 | 0.971 | |
default_formula | 25.493 | 0.453 | 27.382 | |
default_geom | 0.712 | 0.003 | 0.717 | |
default_sfile | 0.002 | 0.000 | 0.002 | |
demultiplex | 0.02 | 0.00 | 0.02 | |
dequantify | 0.000 | 0.003 | 0.003 | |
dequantify_compounddiscoverer | 0.001 | 0.000 | 0.002 | |
dot-coxph | 0.556 | 0.005 | 0.718 | |
dot-merge | 0.021 | 0.004 | 0.024 | |
dot-read_maxquant_proteingroups | 0.134 | 0.003 | 0.138 | |
download_data | 0.001 | 0.000 | 0.000 | |
download_gtf | 0 | 0 | 0 | |
download_mcclain21 | 0.000 | 0.001 | 0.006 | |
dt2mat | 0.004 | 0.000 | 0.004 | |
enrichment | 2.613 | 0.000 | 2.759 | |
entrezg_to_symbol | 0 | 0 | 0 | |
extract_coef_features | 9.842 | 0.015 | 10.674 | |
extract_rectangle | 0.152 | 0.005 | 0.158 | |
fcluster | 13.475 | 0.035 | 14.351 | |
fcor | 2.090 | 0.008 | 2.112 | |
fdata | 0.852 | 0.000 | 0.858 | |
fdr2p | 1.350 | 0.056 | 1.450 | |
filter_exprs_replicated_in_some_subgroup | 1.319 | 0.004 | 1.619 | |
filter_features | 0.685 | 0.008 | 0.695 | |
filter_medoid | 0.960 | 0.004 | 0.997 | |
filter_samples | 0.727 | 0.003 | 0.821 | |
fit_linmod | 47.704 | 0.143 | 48.306 | |
fit_survival | 7.645 | 0.004 | 7.952 | |
fitcoefs | 1.211 | 0.052 | 1.268 | |
fits | 1.030 | 0.008 | 1.040 | |
fix_xlgenes | 0.002 | 0.000 | 0.002 | |
flevels | 0.589 | 0.004 | 0.594 | |
fnames | 0.62 | 0.00 | 0.72 | |
formula2str | 0 | 0 | 0 | |
ftype | 12.073 | 0.092 | 12.788 | |
fvalues | 0.550 | 0.000 | 0.551 | |
fvars | 0.587 | 0.000 | 0.588 | |
genome_to_orgdb | 0.001 | 0.000 | 0.001 | |
group_by_level | 0.001 | 0.000 | 0.001 | |
guess_compounddiscoverer_quantity | 0.002 | 0.000 | 0.001 | |
guess_fitsep | 0.643 | 0.004 | 0.921 | |
guess_maxquant_quantity | 0.007 | 0.000 | 0.007 | |
guess_sep | 0.695 | 0.000 | 0.696 | |
has_multiple_levels | 0.072 | 0.000 | 0.072 | |
hdlproteins | 0.061 | 0.012 | 0.085 | |
impute | 5.066 | 0.020 | 5.100 | |
invert_subgroups | 0.903 | 0.008 | 0.912 | |
is_collapsed_subset | 0.001 | 0.000 | 0.001 | |
is_correlation_matrix | 0.002 | 0.000 | 0.001 | |
is_diann_report | 0.211 | 0.012 | 0.336 | |
is_fastadt | 0.082 | 0.000 | 0.099 | |
is_file | 0.001 | 0.000 | 0.000 | |
is_fraction | 0.002 | 0.000 | 0.002 | |
is_imputed | 0.985 | 0.000 | 0.989 | |
is_positive_number | 0.002 | 0.000 | 0.002 | |
is_scalar_subset | 0.459 | 0.000 | 0.460 | |
is_sig | 2.365 | 0.000 | 2.374 | |
is_valid_formula | 0.057 | 0.000 | 0.057 | |
keep_connected_blocks | 0.695 | 0.000 | 0.700 | |
keep_connected_features | 0.944 | 0.019 | 0.967 | |
keep_replicated_features | 1.100 | 0.020 | 1.125 | |
label2index | 0.001 | 0.000 | 0.001 | |
list2mat | 0.001 | 0.000 | 0.001 | |
log2counts | 0.418 | 0.004 | 0.423 | |
log2cpm | 0.402 | 0.000 | 0.402 | |
log2diffs | 0.455 | 0.008 | 0.464 | |
log2proteins | 0.406 | 0.000 | 0.407 | |
log2sites | 0.454 | 0.008 | 0.469 | |
log2tpm | 0.406 | 0.000 | 0.407 | |
log2transform | 7.750 | 0.067 | 7.984 | |
logical2factor | 0.001 | 0.000 | 0.002 | |
make_alpha_palette | 0.660 | 0.004 | 0.666 | |
make_colors | 0.011 | 0.000 | 0.011 | |
make_volcano_dt | 1.188 | 0.004 | 1.205 | |
map_fvalues | 0.561 | 0.004 | 0.566 | |
matrix2sumexp | 1.387 | 0.000 | 1.473 | |
merge_sample_file | 0.574 | 0.004 | 0.580 | |
merge_sdata | 0.720 | 0.019 | 0.742 | |
message_df | 0.002 | 0.000 | 0.002 | |
model_coefs | 0.991 | 0.004 | 0.997 | |
modelvar | 4.957 | 0.072 | 5.039 | |
order_on_p | 1.606 | 0.020 | 1.631 | |
pca | 4.798 | 0.012 | 4.997 | |
pg_to_canonical | 0.007 | 0.000 | 0.008 | |
plot_coef_densities | 1.862 | 0.008 | 1.873 | |
plot_contrast_venn | 3.377 | 0.040 | 3.425 | |
plot_contrastogram | 3.948 | 0.020 | 4.080 | |
plot_data | 2.223 | 0.008 | 2.531 | |
plot_densities | 14.180 | 0.052 | 14.271 | |
plot_design | 1.040 | 0.015 | 1.057 | |
plot_exprs | 36.232 | 0.128 | 36.727 | |
plot_exprs_per_coef | 36.951 | 0.067 | 39.297 | |
plot_fit_summary | 3.260 | 0.072 | 3.439 | |
plot_heatmap | 3.353 | 0.020 | 3.403 | |
plot_joint_density | 5.846 | 0.028 | 5.990 | |
plot_matrix | 0.725 | 0.036 | 0.799 | |
plot_sample_nas | 10.828 | 0.143 | 11.596 | |
plot_subgroup_points | 8.420 | 0.028 | 8.984 | |
plot_summary | 21.837 | 0.128 | 23.437 | |
plot_survival | 5.467 | 0.020 | 5.989 | |
plot_venn | 0.005 | 0.000 | 0.006 | |
plot_venn_heatmap | 0.031 | 0.000 | 0.031 | |
plot_violins | 6.749 | 0.107 | 7.736 | |
plot_volcano | 20.081 | 0.116 | 21.060 | |
preprocess_rnaseq_counts | 0.423 | 0.000 | 0.438 | |
pull_columns | 0.003 | 0.000 | 0.003 | |
read_affymetrix | 0 | 0 | 0 | |
read_diann_proteingroups | 4.946 | 0.031 | 5.216 | |
read_fragpipe | 8.752 | 0.056 | 9.020 | |
read_maxquant_phosphosites | 2.011 | 0.012 | 2.123 | |
read_maxquant_proteingroups | 1.678 | 0.044 | 1.789 | |
read_metabolon | 22.463 | 0.163 | 23.061 | |
read_msigdt | 0.001 | 0.000 | 0.001 | |
read_olink | 1.893 | 0.052 | 2.111 | |
read_rectangles | 0.228 | 0.000 | 0.233 | |
read_rnaseq_counts | 51.093 | 1.333 | 59.358 | |
read_salmon | 0 | 0 | 0 | |
read_somascan | 22.271 | 0.102 | 23.894 | |
read_uniprotdt | 0.379 | 0.008 | 0.393 | |
reset_fit | 7.155 | 0.027 | 7.463 | |
rm_diann_contaminants | 1.521 | 0.008 | 1.691 | |
rm_missing_in_some_samples | 0.769 | 0.011 | 0.870 | |
rm_unmatched_samples | 0.792 | 0.000 | 0.884 | |
scaledlibsizes | 0.380 | 0.004 | 0.385 | |
scoremat | 1.356 | 0.008 | 1.618 | |
slevels | 0.524 | 0.008 | 0.532 | |
snames | 0.571 | 0.024 | 0.607 | |
split_extract_fixed | 0.642 | 0.032 | 0.676 | |
split_samples | 1.580 | 0.028 | 1.613 | |
stri_any_regex | 0 | 0 | 0 | |
stri_detect_fixed_in_collapsed | 0.417 | 0.004 | 0.422 | |
subgroup_matrix | 0.686 | 0.012 | 0.699 | |
subtract_baseline | 6.669 | 0.040 | 6.921 | |
sumexp_to_longdt | 2.515 | 0.019 | 2.587 | |
sumexp_to_tsv | 0.678 | 0.004 | 0.685 | |
sumexplist_to_longdt | 2.047 | 0.000 | 2.088 | |
summarize_fit | 2.308 | 0.005 | 2.705 | |
svalues | 0.534 | 0.000 | 0.552 | |
svars | 0.497 | 0.012 | 0.511 | |
systematic_nas | 0.803 | 0.000 | 0.870 | |
tag_features | 1.301 | 0.055 | 1.451 | |
tag_hdlproteins | 0.774 | 0.027 | 0.830 | |
taxon2org | 0.000 | 0.001 | 0.002 | |
tpm | 0.424 | 0.009 | 0.439 | |
uncollapse | 0.038 | 0.000 | 0.038 | |
values | 0.552 | 0.003 | 0.556 | |
varlevels_dont_clash | 0.029 | 0.000 | 0.029 | |
venn_detects | 0.807 | 0.004 | 0.812 | |
weights | 0.425 | 0.000 | 0.425 | |
write_xl | 0.947 | 0.008 | 0.957 | |
zero_to_na | 0.002 | 0.000 | 0.002 | |