| Back to Multiple platform build/check report for BioC 3.18: simplified long |
|
This page was generated on 2024-04-17 11:36:26 -0400 (Wed, 17 Apr 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.3.3 (2024-02-29) -- "Angel Food Cake" | 4676 |
| palomino4 | Windows Server 2022 Datacenter | x64 | 4.3.3 (2024-02-29 ucrt) -- "Angel Food Cake" | 4414 |
| merida1 | macOS 12.7.1 Monterey | x86_64 | 4.3.3 (2024-02-29) -- "Angel Food Cake" | 4437 |
| 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 2070/2266 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| structToolbox 1.14.0 (landing page) Gavin Rhys Lloyd
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK |  | ||||||||
| palomino4 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| merida1 | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson1 | macOS 13.6.1 Ventura / arm64 | see weekly results here | ||||||||||||
|
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: 1.14.0 |
| Command: /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD check --install=check:structToolbox.install-out.txt --library=/home/biocbuild/bbs-3.18-bioc/R/site-library --timings structToolbox_1.14.0.tar.gz |
| StartedAt: 2024-04-16 04:30:31 -0400 (Tue, 16 Apr 2024) |
| EndedAt: 2024-04-16 04:59:34 -0400 (Tue, 16 Apr 2024) |
| EllapsedTime: 1743.2 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: structToolbox.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD check --install=check:structToolbox.install-out.txt --library=/home/biocbuild/bbs-3.18-bioc/R/site-library --timings structToolbox_1.14.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.18-bioc/meat/structToolbox.Rcheck’
* using R version 4.3.3 (2024-02-29)
* using platform: x86_64-pc-linux-gnu (64-bit)
* 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 ‘1.14.0’
* 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 R 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 17.122 0.096 17.218
fold_change 10.238 0.132 10.370
fisher_exact 9.709 0.088 9.797
fs_line 6.415 0.128 6.543
forward_selection_by_rank 5.600 0.088 5.688
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’
OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
‘data_analysis_omics_using_the_structtoolbox.Rmd’ using ‘UTF-8’... OK
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-3.18-bioc/R/bin/R CMD INSTALL structToolbox ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.18-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 4.3.3 (2024-02-29) -- "Angel Food Cake"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)
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 156 ]
[ FAIL 0 | WARN 6 | SKIP 0 | PASS 156 ]
>
> proc.time()
user system elapsed
171.184 1.600 172.770
structToolbox.Rcheck/structToolbox-Ex.timings
| name | user | system | elapsed | |
| ANOVA | 0.188 | 0.001 | 0.188 | |
| AUC | 1.839 | 0.091 | 1.931 | |
| DFA | 0.176 | 0.000 | 0.176 | |
| DatasetExperiment_boxplot | 1.375 | 0.096 | 1.471 | |
| DatasetExperiment_dist | 1.188 | 0.048 | 1.236 | |
| DatasetExperiment_factor_boxplot | 0.188 | 0.001 | 0.188 | |
| DatasetExperiment_heatmap | 0.365 | 0.004 | 0.368 | |
| HCA | 0.051 | 0.000 | 0.050 | |
| HSD | 0.239 | 0.000 | 0.241 | |
| HSDEM | 0.313 | 0.000 | 0.313 | |
| MTBLS79_DatasetExperiment | 0.001 | 0.000 | 0.001 | |
| OPLSDA | 0.005 | 0.000 | 0.005 | |
| OPLSR | 0.010 | 0.000 | 0.009 | |
| PCA | 0.004 | 0.000 | 0.004 | |
| PLSDA | 0.017 | 0.000 | 0.017 | |
| PLSR | 0.004 | 0.000 | 0.004 | |
| SVM | 0.010 | 0.000 | 0.009 | |
| as_data_frame | 0.109 | 0.000 | 0.109 | |
| autoscale | 0.059 | 0.000 | 0.059 | |
| balanced_accuracy | 2.247 | 0.052 | 2.299 | |
| blank_filter | 0.318 | 0.008 | 0.326 | |
| blank_filter_hist | 0.001 | 0.000 | 0.001 | |
| bootstrap | 0.005 | 0.000 | 0.005 | |
| calculate | 0.004 | 0.000 | 0.004 | |
| chart_plot | 0.026 | 0.000 | 0.026 | |
| classical_lsq | 0.250 | 0.008 | 0.258 | |
| compare_dist | 4.083 | 0.136 | 4.218 | |
| confounders_clsq | 2.562 | 0.040 | 2.602 | |
| confounders_lsq_barchart | 2.723 | 0.040 | 2.764 | |
| confounders_lsq_boxplot | 2.725 | 0.016 | 2.742 | |
| constant_sum_norm | 0.005 | 0.000 | 0.005 | |
| corr_coef | 0.257 | 0.000 | 0.256 | |
| dfa_scores_plot | 0.620 | 0.000 | 0.619 | |
| dratio_filter | 0.262 | 0.008 | 0.270 | |
| equal_split | 0.099 | 0.004 | 0.103 | |
| feature_boxplot | 0.015 | 0.000 | 0.015 | |
| feature_profile | 0.347 | 0.004 | 0.352 | |
| feature_profile_array | 0.447 | 0.012 | 0.460 | |
| filter_by_name | 0.029 | 0.000 | 0.030 | |
| filter_na_count | 0.966 | 0.012 | 0.978 | |
| filter_smeta | 0.065 | 0.000 | 0.065 | |
| fisher_exact | 9.709 | 0.088 | 9.797 | |
| fold_change | 10.238 | 0.132 | 10.370 | |
| fold_change_int | 17.122 | 0.096 | 17.218 | |
| fold_change_plot | 0.001 | 0.004 | 0.004 | |
| forward_selection_by_rank | 5.600 | 0.088 | 5.688 | |
| fs_line | 6.415 | 0.128 | 6.543 | |
| glog_opt_plot | 0.444 | 0.008 | 0.452 | |
| glog_transform | 0.291 | 0.000 | 0.291 | |
| grid_search_1d | 3.873 | 0.032 | 3.905 | |
| gs_line | 0 | 0 | 0 | |
| hca_dendrogram | 0 | 0 | 0 | |
| kfold_xval | 3.167 | 0.016 | 3.183 | |
| kfoldxcv_grid | 3.467 | 0.004 | 3.470 | |
| kfoldxcv_metric | 0.001 | 0.000 | 0.001 | |
| knn_impute | 0.006 | 0.000 | 0.006 | |
| kw_p_hist | 0.001 | 0.000 | 0.001 | |
| kw_rank_sum | 0.063 | 0.000 | 0.063 | |
| linear_model | 0.023 | 0.000 | 0.023 | |
| log_transform | 0.004 | 0.000 | 0.004 | |
| mean_centre | 0.001 | 0.000 | 0.001 | |
| mean_of_medians | 0.11 | 0.00 | 0.11 | |
| mixed_effect | 0.156 | 0.000 | 0.156 | |
| model_apply | 0.022 | 0.000 | 0.022 | |
| model_predict | 0.045 | 0.004 | 0.049 | |
| model_reverse | 0.037 | 0.000 | 0.037 | |
| model_train | 0.044 | 0.000 | 0.044 | |
| mv_boxplot | 0.237 | 0.000 | 0.238 | |
| mv_feature_filter | 0.095 | 0.000 | 0.095 | |
| mv_feature_filter_hist | 0 | 0 | 0 | |
| mv_histogram | 0.239 | 0.008 | 0.246 | |
| mv_sample_filter | 0.005 | 0.000 | 0.005 | |
| mv_sample_filter_hist | 0.000 | 0.000 | 0.001 | |
| nroot_transform | 0.004 | 0.000 | 0.004 | |
| ontology_cache | 0 | 0 | 0 | |
| pairs_filter | 0.005 | 0.000 | 0.004 | |
| pareto_scale | 0.052 | 0.004 | 0.056 | |
| pca_biplot | 0.004 | 0.004 | 0.008 | |
| pca_correlation_plot | 0.003 | 0.000 | 0.003 | |
| pca_dstat_plot | 0.004 | 0.000 | 0.004 | |
| pca_loadings_plot | 0.004 | 0.000 | 0.004 | |
| pca_scores_plot | 0.475 | 0.012 | 0.488 | |
| pca_scree_plot | 0.004 | 0.000 | 0.005 | |
| permutation_test | 0.005 | 0.000 | 0.005 | |
| permutation_test_plot | 0.002 | 0.000 | 0.002 | |
| permute_sample_order | 0.003 | 0.000 | 0.004 | |
| pls_regcoeff_plot | 0.304 | 0.000 | 0.304 | |
| pls_scores_plot | 0.600 | 0.000 | 0.599 | |
| pls_vip_plot | 0.332 | 0.000 | 0.332 | |
| plsda_feature_importance_plot | 0.519 | 0.000 | 0.520 | |
| plsda_predicted_plot | 0.404 | 0.000 | 0.404 | |
| plsda_roc_plot | 0.993 | 0.000 | 0.994 | |
| plsr_cook_dist | 0.004 | 0.000 | 0.004 | |
| plsr_prediction_plot | 0.004 | 0.000 | 0.003 | |
| plsr_qq_plot | 0.004 | 0.000 | 0.003 | |
| plsr_residual_hist | 0.004 | 0.000 | 0.004 | |
| pqn_norm | 0.309 | 0.000 | 0.309 | |
| pqn_norm_hist | 0.000 | 0.000 | 0.001 | |
| prop_na | 0.001 | 0.004 | 0.005 | |
| r_squared | 0.001 | 0.000 | 0.000 | |
| resample | 0.008 | 0.000 | 0.007 | |
| resample_chart | 0.003 | 0.000 | 0.003 | |
| rsd_filter | 0.006 | 0.000 | 0.007 | |
| rsd_filter_hist | 0.000 | 0.000 | 0.001 | |
| run | 0.026 | 0.000 | 0.027 | |
| sb_corr | 0.012 | 0.000 | 0.013 | |
| scatter_chart | 0.315 | 0.000 | 0.315 | |
| split_data | 0.004 | 0.000 | 0.004 | |
| stratified_split | 0.099 | 0.000 | 0.099 | |
| svm_plot_2d | 0.612 | 0.000 | 0.612 | |
| tSNE | 0.012 | 0.000 | 0.012 | |
| tSNE_scatter | 0.005 | 0.000 | 0.004 | |
| tic_chart | 0.189 | 0.000 | 0.188 | |
| ttest | 0.009 | 0.000 | 0.008 | |
| vec_norm | 0.001 | 0.000 | 0.000 | |
| wilcox_p_hist | 0 | 0 | 0 | |
| wilcox_test | 0.008 | 0.000 | 0.008 | |