Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-08-27 11:40 -0400 (Tue, 27 Aug 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4703 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4440 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4472 |
kjohnson3 | macOS 13.6.5 Ventura | arm64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4421 |
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4415 |
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 2050/2255 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
structToolbox 1.17.3 (landing page) Gavin Rhys Lloyd
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | ![]() | ||||||||
palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | ![]() | ||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | ![]() | ||||||||
kjohnson3 | macOS 13.6.5 Ventura / arm64 | OK | OK | OK | OK | ![]() | ||||||||
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / 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. |
Package: structToolbox |
Version: 1.17.3 |
Command: /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:structToolbox.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings structToolbox_1.17.3.tar.gz |
StartedAt: 2024-08-27 04:25:13 -0400 (Tue, 27 Aug 2024) |
EndedAt: 2024-08-27 04:43:07 -0400 (Tue, 27 Aug 2024) |
EllapsedTime: 1073.9 seconds |
RetCode: 0 |
Status: OK |
CheckDir: structToolbox.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:structToolbox.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings structToolbox_1.17.3.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/structToolbox.Rcheck’ * using R version 4.4.1 (2024-06-14) * using platform: x86_64-pc-linux-gnu * R was compiled by gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 * running under: Ubuntu 22.04.4 LTS * using session charset: UTF-8 * checking for file ‘structToolbox/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘structToolbox’ version ‘1.17.3’ * 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 14.791 0.084 14.874 fold_change 10.895 0.144 11.039 fisher_exact 9.442 0.108 9.550 forward_selection_by_rank 6.565 0.156 6.720 fs_line 5.749 0.080 5.829 * 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: OK
structToolbox.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD INSTALL structToolbox ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.20-bioc/R/site-library’ * installing *source* package ‘structToolbox’ ... ** 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 4.4.1 (2024-06-14) -- "Race for Your Life" Copyright (C) 2024 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(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 169.076 1.584 170.661
structToolbox.Rcheck/structToolbox-Ex.timings
name | user | system | elapsed | |
ANOVA | 0.201 | 0.017 | 0.217 | |
AUC | 1.830 | 0.127 | 1.958 | |
DFA | 0.176 | 0.001 | 0.176 | |
DatasetExperiment_boxplot | 1.543 | 0.111 | 1.655 | |
DatasetExperiment_dist | 1.212 | 0.044 | 1.256 | |
DatasetExperiment_factor_boxplot | 0.185 | 0.001 | 0.185 | |
DatasetExperiment_heatmap | 0.361 | 0.004 | 0.365 | |
HCA | 0.059 | 0.000 | 0.060 | |
HSD | 0.254 | 0.004 | 0.263 | |
HSDEM | 0.341 | 0.004 | 0.345 | |
MTBLS79_DatasetExperiment | 0.001 | 0.000 | 0.001 | |
OPLSDA | 0.011 | 0.000 | 0.011 | |
OPLSR | 0.014 | 0.000 | 0.015 | |
PCA | 0.005 | 0.000 | 0.004 | |
PLSDA | 0.025 | 0.000 | 0.025 | |
PLSR | 0.009 | 0.000 | 0.010 | |
SVM | 0.049 | 0.000 | 0.050 | |
as_data_frame | 0.110 | 0.000 | 0.111 | |
autoscale | 0.068 | 0.000 | 0.068 | |
balanced_accuracy | 1.641 | 0.016 | 1.657 | |
blank_filter | 0.346 | 0.000 | 0.345 | |
blank_filter_hist | 0.001 | 0.000 | 0.001 | |
bootstrap | 0.017 | 0.000 | 0.017 | |
calculate | 0.004 | 0.000 | 0.005 | |
chart_plot | 0.026 | 0.000 | 0.026 | |
classical_lsq | 0.314 | 0.008 | 0.321 | |
compare_dist | 3.483 | 0.136 | 3.619 | |
confounders_clsq | 2.686 | 0.024 | 2.711 | |
confounders_lsq_barchart | 2.772 | 0.096 | 2.868 | |
confounders_lsq_boxplot | 2.772 | 0.004 | 2.776 | |
constant_sum_norm | 0.013 | 0.000 | 0.013 | |
corr_coef | 0.259 | 0.008 | 0.267 | |
dfa_scores_plot | 0.660 | 0.004 | 0.664 | |
dratio_filter | 0.258 | 0.004 | 0.262 | |
equal_split | 0.115 | 0.000 | 0.115 | |
feature_boxplot | 0.028 | 0.000 | 0.029 | |
feature_profile | 0.349 | 0.008 | 0.356 | |
feature_profile_array | 0.413 | 0.000 | 0.413 | |
filter_by_name | 0.029 | 0.000 | 0.029 | |
filter_na_count | 0.931 | 0.032 | 0.962 | |
filter_smeta | 0.054 | 0.000 | 0.054 | |
fisher_exact | 9.442 | 0.108 | 9.550 | |
fold_change | 10.895 | 0.144 | 11.039 | |
fold_change_int | 14.791 | 0.084 | 14.874 | |
fold_change_plot | 0.012 | 0.000 | 0.012 | |
forward_selection_by_rank | 6.565 | 0.156 | 6.720 | |
fs_line | 5.749 | 0.080 | 5.829 | |
glog_opt_plot | 0.417 | 0.004 | 0.420 | |
glog_transform | 0.271 | 0.000 | 0.271 | |
grid_search_1d | 3.233 | 0.040 | 3.273 | |
gs_line | 0.001 | 0.000 | 0.001 | |
hca_dendrogram | 0.001 | 0.000 | 0.001 | |
kfold_xval | 3.149 | 0.008 | 3.157 | |
kfoldxcv_grid | 3.414 | 0.028 | 3.442 | |
kfoldxcv_metric | 0.001 | 0.000 | 0.001 | |
knn_impute | 0.011 | 0.000 | 0.011 | |
kw_p_hist | 0.001 | 0.000 | 0.001 | |
kw_rank_sum | 0.077 | 0.000 | 0.077 | |
linear_model | 0.027 | 0.000 | 0.027 | |
log_transform | 0.013 | 0.000 | 0.013 | |
mean_centre | 0.003 | 0.000 | 0.003 | |
mean_of_medians | 0.116 | 0.000 | 0.116 | |
mixed_effect | 0.174 | 0.000 | 0.174 | |
model_apply | 0.018 | 0.004 | 0.022 | |
model_predict | 0.051 | 0.000 | 0.051 | |
model_reverse | 0.039 | 0.000 | 0.039 | |
model_train | 0.045 | 0.000 | 0.045 | |
mv_boxplot | 0.246 | 0.004 | 0.250 | |
mv_feature_filter | 0.111 | 0.000 | 0.111 | |
mv_feature_filter_hist | 0.001 | 0.000 | 0.001 | |
mv_histogram | 0.253 | 0.004 | 0.257 | |
mv_sample_filter | 0.016 | 0.000 | 0.016 | |
mv_sample_filter_hist | 0.001 | 0.000 | 0.001 | |
nroot_transform | 0.014 | 0.000 | 0.014 | |
ontology_cache | 0 | 0 | 0 | |
pairs_filter | 0.014 | 0.000 | 0.014 | |
pareto_scale | 0.053 | 0.000 | 0.053 | |
pca_biplot | 0.019 | 0.000 | 0.019 | |
pca_correlation_plot | 0.01 | 0.00 | 0.01 | |
pca_dstat_plot | 0.012 | 0.000 | 0.012 | |
pca_loadings_plot | 0.012 | 0.000 | 0.012 | |
pca_scores_plot | 0.481 | 0.000 | 0.481 | |
pca_scree_plot | 0.012 | 0.000 | 0.012 | |
permutation_test | 0.017 | 0.000 | 0.017 | |
permutation_test_plot | 0.003 | 0.000 | 0.003 | |
permute_sample_order | 0.026 | 0.000 | 0.026 | |
pls_regcoeff_plot | 0.317 | 0.000 | 0.317 | |
pls_scores_plot | 0.630 | 0.000 | 0.629 | |
pls_vip_plot | 0.328 | 0.000 | 0.328 | |
plsda_feature_importance_plot | 0.535 | 0.004 | 0.540 | |
plsda_predicted_plot | 0.42 | 0.00 | 0.42 | |
plsda_roc_plot | 0.985 | 0.052 | 1.037 | |
plsr_cook_dist | 0.011 | 0.000 | 0.011 | |
plsr_prediction_plot | 0.011 | 0.000 | 0.011 | |
plsr_qq_plot | 0.011 | 0.000 | 0.011 | |
plsr_residual_hist | 0.011 | 0.000 | 0.011 | |
pqn_norm | 0.311 | 0.000 | 0.311 | |
pqn_norm_hist | 0.001 | 0.000 | 0.001 | |
prop_na | 0.016 | 0.000 | 0.016 | |
r_squared | 0.001 | 0.000 | 0.001 | |
resample | 0.030 | 0.004 | 0.034 | |
resample_chart | 0.003 | 0.000 | 0.003 | |
rsd_filter | 0.019 | 0.000 | 0.019 | |
rsd_filter_hist | 0.001 | 0.000 | 0.001 | |
run | 0.026 | 0.000 | 0.026 | |
sb_corr | 0.030 | 0.000 | 0.029 | |
scatter_chart | 0.3 | 0.0 | 0.3 | |
split_data | 0.013 | 0.000 | 0.013 | |
stratified_split | 0.112 | 0.000 | 0.112 | |
svm_plot_2d | 0.598 | 0.000 | 0.598 | |
tSNE | 0.027 | 0.000 | 0.028 | |
tSNE_scatter | 0.011 | 0.000 | 0.011 | |
tic_chart | 0.184 | 0.004 | 0.188 | |
ttest | 0.02 | 0.00 | 0.02 | |
vec_norm | 0.001 | 0.000 | 0.001 | |
wilcox_p_hist | 0 | 0 | 0 | |
wilcox_test | 0.022 | 0.000 | 0.022 | |