Back to Multiple platform build/check report for BioC 3.22: simplified long |
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This page was generated on 2025-09-02 12:04 -0400 (Tue, 02 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" | 4824 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4615 |
kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" | 4562 |
taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4541 |
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 2106/2320 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
structToolbox 1.21.0 (landing page) Gavin Rhys Lloyd
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | NA | NA | |||||||||
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 structToolbox package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/structToolbox.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: structToolbox |
Version: 1.21.0 |
Command: /home/biocbuild/R/R/bin/R CMD check --install=check:structToolbox.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings structToolbox_1.21.0.tar.gz |
StartedAt: 2025-09-02 12:05:59 -0000 (Tue, 02 Sep 2025) |
EndedAt: 2025-09-02 12:18:09 -0000 (Tue, 02 Sep 2025) |
EllapsedTime: 730.7 seconds |
RetCode: 0 |
Status: OK |
CheckDir: structToolbox.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD check --install=check:structToolbox.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings structToolbox_1.21.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/structToolbox.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 ‘structToolbox/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘structToolbox’ version ‘1.21.0’ * package encoding: UTF-8 * checking package namespace information ... OK * checking package dependencies ... OK * checking if this is a source package ... OK * checking if there is a namespace ... OK * checking for hidden files and directories ... OK * checking for portable file names ... OK * checking for sufficient/correct file permissions ... OK * checking whether package ‘structToolbox’ 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 ... OK * 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 R/sysdata.rda ... OK * checking files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed fold_change_int 24.366 0.046 24.850 fold_change 17.795 0.092 18.221 fisher_exact 14.451 0.104 16.499 fs_line 8.971 0.012 9.010 forward_selection_by_rank 8.731 0.124 8.886 kfoldxcv_grid 5.539 0.001 5.557 compare_dist 5.283 0.117 6.425 grid_search_1d 5.132 0.012 5.160 kfold_xval 5.008 0.008 5.033 confounders_lsq_barchart 4.556 0.024 7.239 confounders_lsq_boxplot 4.522 0.004 5.630 confounders_clsq 4.212 0.037 5.255 * 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: OK
structToolbox.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD INSTALL structToolbox ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-4.5.0/site-library’ * installing *source* package ‘structToolbox’ ... ** this is package ‘structToolbox’ version ‘1.21.0’ ** 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 (structToolbox)
structToolbox.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(ggplot2) > library(structToolbox) Loading required package: struct > > test_check("structToolbox") [ FAIL 0 | WARN 6 | SKIP 0 | PASS 166 ] [ FAIL 0 | WARN 6 | SKIP 0 | PASS 166 ] > > proc.time() user system elapsed 257.350 1.913 260.268
structToolbox.Rcheck/structToolbox-Ex.timings
name | user | system | elapsed | |
ANOVA | 0.301 | 0.011 | 0.339 | |
AUC | 3.434 | 0.184 | 4.300 | |
DFA | 0.293 | 0.000 | 0.590 | |
DatasetExperiment_boxplot | 0.958 | 0.013 | 1.947 | |
DatasetExperiment_dist | 1.385 | 0.084 | 2.464 | |
DatasetExperiment_factor_boxplot | 0.295 | 0.000 | 0.321 | |
DatasetExperiment_heatmap | 0.522 | 0.000 | 0.542 | |
HCA | 0.080 | 0.000 | 0.082 | |
HSD | 0.387 | 0.007 | 0.568 | |
HSDEM | 0.369 | 0.000 | 0.370 | |
MTBLS79_DatasetExperiment | 0.001 | 0.000 | 0.001 | |
OPLSDA | 0.015 | 0.000 | 0.015 | |
OPLSR | 0.012 | 0.000 | 0.011 | |
PCA | 0.006 | 0.000 | 0.006 | |
PLSDA | 0.016 | 0.000 | 0.016 | |
PLSR | 0.014 | 0.000 | 0.014 | |
SVM | 0.026 | 0.004 | 0.030 | |
as_data_frame | 0.164 | 0.000 | 0.164 | |
autoscale | 0.096 | 0.004 | 0.100 | |
balanced_accuracy | 3.225 | 0.036 | 3.640 | |
blank_filter | 0.485 | 0.019 | 0.556 | |
blank_filter_hist | 0.001 | 0.000 | 0.001 | |
bootstrap | 0.012 | 0.004 | 0.018 | |
calculate | 0.007 | 0.000 | 0.007 | |
chart_plot | 0.038 | 0.000 | 0.042 | |
classical_lsq | 0.408 | 0.004 | 0.424 | |
compare_dist | 5.283 | 0.117 | 6.425 | |
confounders_clsq | 4.212 | 0.037 | 5.255 | |
confounders_lsq_barchart | 4.556 | 0.024 | 7.239 | |
confounders_lsq_boxplot | 4.522 | 0.004 | 5.630 | |
constant_sum_norm | 0.011 | 0.000 | 0.017 | |
corr_coef | 0.383 | 0.000 | 0.384 | |
dfa_scores_plot | 1.016 | 0.012 | 1.034 | |
dratio_filter | 0.427 | 0.012 | 0.440 | |
equal_split | 0.191 | 0.012 | 0.404 | |
feature_boxplot | 0.039 | 0.000 | 0.079 | |
feature_profile | 0.533 | 0.008 | 1.084 | |
feature_profile_array | 0.656 | 0.000 | 0.978 | |
filter_by_name | 0.039 | 0.003 | 0.044 | |
filter_na_count | 1.470 | 0.040 | 2.541 | |
filter_smeta | 0.082 | 0.000 | 0.087 | |
fisher_exact | 14.451 | 0.104 | 16.499 | |
fold_change | 17.795 | 0.092 | 18.221 | |
fold_change_int | 24.366 | 0.046 | 24.850 | |
fold_change_plot | 0.01 | 0.00 | 0.01 | |
forward_selection_by_rank | 8.731 | 0.124 | 8.886 | |
fs_line | 8.971 | 0.012 | 9.010 | |
glog_opt_plot | 0.698 | 0.000 | 0.700 | |
glog_transform | 0.438 | 0.000 | 0.441 | |
grid_search_1d | 5.132 | 0.012 | 5.160 | |
gs_line | 0.001 | 0.000 | 0.001 | |
hca_dendrogram | 0.001 | 0.000 | 0.001 | |
kfold_xval | 5.008 | 0.008 | 5.033 | |
kfoldxcv_grid | 5.539 | 0.001 | 5.557 | |
kfoldxcv_metric | 0.000 | 0.000 | 0.001 | |
knn_impute | 0.018 | 0.000 | 0.018 | |
kw_p_hist | 0.001 | 0.000 | 0.001 | |
kw_rank_sum | 0.106 | 0.000 | 0.106 | |
linear_model | 0.042 | 0.000 | 0.042 | |
log_transform | 0.009 | 0.000 | 0.010 | |
mean_centre | 0.004 | 0.000 | 0.005 | |
mean_of_medians | 0.166 | 0.000 | 0.167 | |
mixed_effect | 0.237 | 0.000 | 0.240 | |
model_apply | 0.037 | 0.000 | 0.037 | |
model_predict | 0.084 | 0.000 | 0.084 | |
model_reverse | 0.039 | 0.000 | 0.038 | |
model_train | 0.077 | 0.000 | 0.076 | |
mv_boxplot | 0.412 | 0.000 | 0.414 | |
mv_feature_filter | 0.153 | 0.000 | 0.153 | |
mv_feature_filter_hist | 0.001 | 0.000 | 0.001 | |
mv_histogram | 0.337 | 0.000 | 0.337 | |
mv_sample_filter | 0.008 | 0.004 | 0.012 | |
mv_sample_filter_hist | 0.001 | 0.000 | 0.001 | |
nroot_transform | 0.009 | 0.000 | 0.009 | |
ontology_cache | 0 | 0 | 0 | |
pairs_filter | 0.013 | 0.000 | 0.013 | |
pareto_scale | 0.082 | 0.000 | 0.082 | |
pca_biplot | 0.022 | 0.000 | 0.022 | |
pca_correlation_plot | 0.009 | 0.000 | 0.010 | |
pca_dstat_plot | 0.009 | 0.004 | 0.013 | |
pca_loadings_plot | 0.014 | 0.000 | 0.013 | |
pca_scores_plot | 0.767 | 0.000 | 0.769 | |
pca_scree_plot | 0.009 | 0.000 | 0.009 | |
permutation_test | 0.014 | 0.000 | 0.014 | |
permutation_test_plot | 0.004 | 0.000 | 0.004 | |
permute_sample_order | 0.01 | 0.00 | 0.01 | |
pls_regcoeff_plot | 0.488 | 0.000 | 0.490 | |
pls_scores_plot | 1.026 | 0.000 | 1.030 | |
pls_vip_plot | 0.524 | 0.004 | 0.529 | |
plsda_feature_importance_plot | 0.886 | 0.016 | 0.906 | |
plsda_predicted_plot | 0.654 | 0.008 | 0.665 | |
plsda_roc_plot | 1.718 | 0.004 | 1.727 | |
plsr_cook_dist | 0.010 | 0.000 | 0.009 | |
plsr_prediction_plot | 0.009 | 0.000 | 0.010 | |
plsr_qq_plot | 0.01 | 0.00 | 0.01 | |
plsr_residual_hist | 0.010 | 0.000 | 0.009 | |
pqn_norm | 0.537 | 0.000 | 0.538 | |
pqn_norm_hist | 0.001 | 0.000 | 0.000 | |
prop_na | 0.014 | 0.000 | 0.014 | |
r_squared | 0.000 | 0.000 | 0.001 | |
resample | 0.022 | 0.000 | 0.023 | |
resample_chart | 0.004 | 0.000 | 0.004 | |
rsd_filter | 0.02 | 0.00 | 0.02 | |
rsd_filter_hist | 0.001 | 0.000 | 0.001 | |
run | 0.043 | 0.000 | 0.042 | |
sb_corr | 0.038 | 0.000 | 0.037 | |
scatter_chart | 0.503 | 0.000 | 0.504 | |
split_data | 0.01 | 0.00 | 0.01 | |
stratified_split | 0.171 | 0.000 | 0.172 | |
svm_plot_2d | 1.601 | 0.067 | 1.682 | |
tSNE | 0.034 | 0.000 | 0.034 | |
tSNE_scatter | 0.011 | 0.000 | 0.010 | |
tic_chart | 0.285 | 0.000 | 0.285 | |
ttest | 0.029 | 0.000 | 0.029 | |
vec_norm | 0.001 | 0.000 | 0.001 | |
wilcox_p_hist | 0.001 | 0.000 | 0.001 | |
wilcox_test | 0.024 | 0.000 | 0.024 | |