| Back to Multiple platform build/check report for BioC 3.11 |
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This page was generated on 2020-10-17 11:59:44 -0400 (Sat, 17 Oct 2020).
| TO THE DEVELOPERS/MAINTAINERS OF THE structToolbox PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 1753/1905 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| structToolbox 1.0.1 Gavin Rhys Lloyd
| malbec2 | Linux (Ubuntu 18.04.4 LTS) / x86_64 | OK | OK | OK | |||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | NA | |||||||
| machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | [ OK ] | OK |
| Package: structToolbox |
| Version: 1.0.1 |
| Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:structToolbox.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings structToolbox_1.0.1.tar.gz |
| StartedAt: 2020-10-17 05:43:38 -0400 (Sat, 17 Oct 2020) |
| EndedAt: 2020-10-17 05:52:30 -0400 (Sat, 17 Oct 2020) |
| EllapsedTime: 531.1 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: structToolbox.Rcheck |
| Warnings: 0 |
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### Running command:
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### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:structToolbox.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings structToolbox_1.0.1.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.11-bioc/meat/structToolbox.Rcheck’
* using R version 4.0.3 (2020-10-10)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘structToolbox/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘structToolbox’ version ‘1.0.1’
* 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 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 17.168 0.043 17.229
fisher_exact 8.841 0.023 8.870
fs_line 8.023 0.076 8.110
forward_selection_byrank 7.359 0.089 7.457
fold_change 7.046 0.034 7.086
compare_dist 5.634 0.304 5.955
* 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 ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: OK
structToolbox.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL structToolbox ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library’ * installing *source* package ‘structToolbox’ ... ** using staged installation ** R ** 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 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin17.0 (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")
══ testthat results ═══════════════════════════════════════════════════════════
[ OK: 95 | SKIPPED: 0 | WARNINGS: 2 | FAILED: 0 ]
>
> proc.time()
user system elapsed
192.035 1.132 193.345
structToolbox.Rcheck/structToolbox-Ex.timings
| name | user | system | elapsed | |
| ANOVA | 0.657 | 0.033 | 0.694 | |
| AUC | 2.022 | 0.082 | 2.105 | |
| DFA | 0.318 | 0.001 | 0.319 | |
| DatasetExperiment_boxplot | 0.856 | 0.036 | 0.893 | |
| DatasetExperiment_dist | 2.011 | 0.114 | 2.126 | |
| DatasetExperiment_factor_barchart | 0.285 | 0.002 | 0.287 | |
| DatasetExperiment_heatmap | 0.003 | 0.001 | 0.003 | |
| HCA | 0.062 | 0.001 | 0.062 | |
| HSD | 0.631 | 0.031 | 0.667 | |
| HSDEM | 0.514 | 0.018 | 0.532 | |
| MTBLS79_DatasetExperiment | 0.002 | 0.001 | 0.003 | |
| PCA | 0.003 | 0.000 | 0.004 | |
| PLSDA | 0.002 | 0.000 | 0.003 | |
| PLSR | 0.004 | 0.000 | 0.004 | |
| SVM | 0.008 | 0.001 | 0.009 | |
| as_data_frame | 0.205 | 0.002 | 0.209 | |
| autoscale | 0.100 | 0.001 | 0.101 | |
| balanced_accuracy | 1.927 | 0.013 | 1.940 | |
| blank_filter | 0.543 | 0.014 | 0.558 | |
| blank_filter_hist | 0.000 | 0.001 | 0.001 | |
| bootstrap | 1.380 | 0.002 | 1.382 | |
| calculate | 0.007 | 0.001 | 0.008 | |
| chart_plot | 0.034 | 0.002 | 0.035 | |
| classical_lsq | 0.237 | 0.000 | 0.238 | |
| compare_dist | 5.634 | 0.304 | 5.955 | |
| confounders_clsq | 3.403 | 0.007 | 3.412 | |
| confounders_lsq_barchart | 3.208 | 0.008 | 3.219 | |
| confounders_lsq_boxplot | 3.180 | 0.009 | 3.194 | |
| constant_sum_norm | 0.002 | 0.000 | 0.002 | |
| corr_coef | 0.231 | 0.002 | 0.232 | |
| dfa_scores_plot | 0.763 | 0.003 | 0.766 | |
| dratio_filter | 1.279 | 0.028 | 1.310 | |
| feature_boxplot | 0.015 | 0.001 | 0.015 | |
| feature_profile | 0.745 | 0.014 | 0.760 | |
| filter_by_name | 0.03 | 0.00 | 0.03 | |
| filter_na_count | 1.414 | 0.049 | 1.469 | |
| filter_smeta | 0.079 | 0.000 | 0.079 | |
| fisher_exact | 8.841 | 0.023 | 8.870 | |
| fold_change | 7.046 | 0.034 | 7.086 | |
| fold_change_int | 17.168 | 0.043 | 17.229 | |
| fold_change_plot | 0.002 | 0.001 | 0.002 | |
| forward_selection_byrank | 7.359 | 0.089 | 7.457 | |
| fs_line | 8.023 | 0.076 | 8.110 | |
| glog_opt_plot | 0.801 | 0.007 | 0.810 | |
| glog_transform | 0.473 | 0.004 | 0.478 | |
| grid_search_1d | 4.889 | 0.104 | 4.997 | |
| gs_line | 0.001 | 0.000 | 0.001 | |
| hca_dendrogram | 0.001 | 0.000 | 0.001 | |
| kfold_xval | 3.115 | 0.010 | 3.132 | |
| kfoldxcv_grid | 3.611 | 0.011 | 3.629 | |
| kfoldxcv_metric | 0.002 | 0.000 | 0.002 | |
| knn_impute | 0.003 | 0.000 | 0.003 | |
| kw_p_hist | 0.001 | 0.000 | 0.001 | |
| kw_rank_sum | 0.091 | 0.000 | 0.091 | |
| linear_model | 0.022 | 0.000 | 0.022 | |
| log_transform | 0.003 | 0.000 | 0.003 | |
| mean_centre | 0.001 | 0.000 | 0.000 | |
| mean_of_medians | 0.121 | 0.001 | 0.122 | |
| mixed_effect | 0.230 | 0.000 | 0.231 | |
| model_apply | 0.031 | 0.000 | 0.031 | |
| model_predict | 0.074 | 0.001 | 0.075 | |
| model_reverse | 0.030 | 0.001 | 0.031 | |
| model_train | 0.070 | 0.001 | 0.071 | |
| mv_boxplot | 0.450 | 0.007 | 0.459 | |
| mv_feature_filter | 0.180 | 0.001 | 0.180 | |
| mv_feature_filter_hist | 0.001 | 0.001 | 0.001 | |
| mv_histogram | 0.399 | 0.002 | 0.401 | |
| mv_sample_filter | 0.004 | 0.000 | 0.004 | |
| mv_sample_filter_hist | 0.001 | 0.001 | 0.002 | |
| nroot_transform | 0.003 | 0.000 | 0.004 | |
| pairs_filter | 0.004 | 0.000 | 0.004 | |
| pareto_scale | 0.087 | 0.000 | 0.088 | |
| pca_biplot_plot | 0.006 | 0.000 | 0.006 | |
| pca_correlation_plot | 0.003 | 0.001 | 0.003 | |
| pca_dstat_plot | 0.003 | 0.000 | 0.004 | |
| pca_loadings_plot | 0.003 | 0.000 | 0.004 | |
| pca_scores_plot | 0.570 | 0.004 | 0.577 | |
| pca_scree_plot | 0.001 | 0.000 | 0.002 | |
| permutation_test | 0.003 | 0.000 | 0.003 | |
| permutation_test_plot | 0.001 | 0.000 | 0.002 | |
| permute_sample_order | 0.002 | 0.000 | 0.002 | |
| plsda_predicted_plot | 0.520 | 0.005 | 0.526 | |
| plsda_regcoeff_plot | 0.338 | 0.002 | 0.341 | |
| plsda_roc_plot | 0.805 | 0.003 | 0.808 | |
| plsda_scores_plot | 0.533 | 0.003 | 0.537 | |
| plsda_vip_plot | 0.335 | 0.002 | 0.337 | |
| plsr_cook_dist | 0.001 | 0.000 | 0.002 | |
| plsr_prediction_plot | 0.001 | 0.000 | 0.001 | |
| plsr_qq_plot | 0.001 | 0.000 | 0.001 | |
| plsr_residual_hist | 0.000 | 0.000 | 0.001 | |
| pqn_norm | 1.066 | 0.004 | 1.072 | |
| pqn_norm_hist | 0.001 | 0.001 | 0.001 | |
| prop_na | 0.006 | 0.000 | 0.006 | |
| r_squared | 0.001 | 0.000 | 0.002 | |
| rsd_filter | 0.005 | 0.000 | 0.006 | |
| rsd_filter_hist | 0.001 | 0.000 | 0.001 | |
| run | 0.035 | 0.000 | 0.035 | |
| sb_corr | 0.009 | 0.000 | 0.010 | |
| split_data | 0.003 | 0.001 | 0.003 | |
| stratified_split | 0.145 | 0.001 | 0.146 | |
| svm_plot_2d | 0.860 | 0.008 | 0.870 | |
| tSNE | 0.002 | 0.001 | 0.002 | |
| tSNE_scatter | 0.001 | 0.000 | 0.002 | |
| ttest | 0.007 | 0.000 | 0.006 | |
| vec_norm | 0.001 | 0.000 | 0.001 | |
| wilcox_p_hist | 0.000 | 0.000 | 0.001 | |
| wilcox_test | 0.004 | 0.000 | 0.005 | |