| Back to Multiple platform build/check report for BioC 3.17 |
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This page was generated on 2023-04-12 10:55:32 -0400 (Wed, 12 Apr 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 22.04.1 LTS) | x86_64 | 4.3.0 alpha (2023-04-03 r84154) | 4547 |
| nebbiolo2 | Linux (Ubuntu 20.04.5 LTS) | x86_64 | R Under development (unstable) (2023-02-14 r83833) -- "Unsuffered Consequences" | 4333 |
| 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 | ||||
|
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. Note: If "R CMD check" recently failed on the Linux builder over a missing dependency, add the missing dependency to "Suggests" in your DESCRIPTION file. See the Renviron.bioc for details. |
| Package 2013/2207 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| structToolbox 1.11.0 (landing page) Gavin Rhys Lloyd
| nebbiolo1 | Linux (Ubuntu 22.04.1 LTS) / x86_64 | OK | OK | OK | |||||||||
| nebbiolo2 | Linux (Ubuntu 20.04.5 LTS) / x86_64 | OK | OK | OK | ||||||||||
| Package: structToolbox |
| Version: 1.11.0 |
| Command: /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:structToolbox.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/site-library --timings structToolbox_1.11.0.tar.gz |
| StartedAt: 2023-04-11 23:57:31 -0400 (Tue, 11 Apr 2023) |
| EndedAt: 2023-04-12 00:16:07 -0400 (Wed, 12 Apr 2023) |
| EllapsedTime: 1116.0 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: structToolbox.Rcheck |
| Warnings: 0 |
##############################################################################
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###
### Running command:
###
### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:structToolbox.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/site-library --timings structToolbox_1.11.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/structToolbox.Rcheck’
* using R version 4.3.0 alpha (2023-04-03 r84154)
* using platform: x86_64-pc-linux-gnu (64-bit)
* R was compiled by
gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
* running under: Ubuntu 22.04.2 LTS
* using session charset: UTF-8
* checking for file ‘structToolbox/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘structToolbox’ version ‘1.11.0’
* 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 17.142 0.124 17.266
fisher_exact 10.471 0.152 10.623
fold_change 9.794 0.064 9.857
fs_line 5.645 0.024 5.670
forward_selection_by_rank 5.516 0.112 5.628
* 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
NONE
* 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-3.17-bioc/R/bin/R CMD INSTALL structToolbox ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.17-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 4.3.0 alpha (2023-04-03 r84154)
Copyright (C) 2023 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 7 | SKIP 0 | PASS 124 ]
[ FAIL 0 | WARN 7 | SKIP 0 | PASS 124 ]
>
> proc.time()
user system elapsed
167.030 1.645 168.668
structToolbox.Rcheck/structToolbox-Ex.timings
| name | user | system | elapsed | |
| ANOVA | 0.224 | 0.012 | 0.236 | |
| AUC | 2.665 | 0.268 | 2.934 | |
| DFA | 0.182 | 0.001 | 0.183 | |
| DatasetExperiment_boxplot | 0.804 | 0.039 | 0.844 | |
| DatasetExperiment_dist | 1.925 | 0.084 | 2.009 | |
| DatasetExperiment_factor_boxplot | 0.194 | 0.000 | 0.195 | |
| DatasetExperiment_heatmap | 0.273 | 0.003 | 0.277 | |
| HCA | 0.054 | 0.001 | 0.054 | |
| HSD | 0.401 | 0.015 | 0.417 | |
| HSDEM | 0.309 | 0.004 | 0.313 | |
| MTBLS79_DatasetExperiment | 0.001 | 0.000 | 0.001 | |
| PCA | 0.004 | 0.000 | 0.004 | |
| PLSDA | 0.013 | 0.000 | 0.014 | |
| PLSR | 0.001 | 0.004 | 0.004 | |
| SVM | 0.01 | 0.00 | 0.01 | |
| as_data_frame | 0.117 | 0.004 | 0.122 | |
| autoscale | 0.065 | 0.000 | 0.065 | |
| balanced_accuracy | 1.817 | 0.067 | 1.885 | |
| blank_filter | 0.381 | 0.012 | 0.392 | |
| blank_filter_hist | 0.001 | 0.000 | 0.001 | |
| bootstrap | 0.007 | 0.000 | 0.006 | |
| calculate | 0.002 | 0.003 | 0.006 | |
| chart_plot | 0.030 | 0.000 | 0.031 | |
| classical_lsq | 0.282 | 0.016 | 0.298 | |
| compare_dist | 4.625 | 0.120 | 4.744 | |
| confounders_clsq | 2.877 | 0.056 | 2.933 | |
| confounders_lsq_barchart | 2.964 | 0.008 | 2.971 | |
| confounders_lsq_boxplot | 2.823 | 0.024 | 2.847 | |
| constant_sum_norm | 0.004 | 0.000 | 0.004 | |
| corr_coef | 0.233 | 0.007 | 0.240 | |
| dfa_scores_plot | 0.630 | 0.036 | 0.666 | |
| dratio_filter | 0.541 | 0.024 | 0.565 | |
| equal_split | 0.108 | 0.000 | 0.108 | |
| feature_boxplot | 0.017 | 0.000 | 0.017 | |
| feature_profile | 0.382 | 0.000 | 0.382 | |
| feature_profile_array | 0.525 | 0.004 | 0.529 | |
| filter_by_name | 0.026 | 0.000 | 0.026 | |
| filter_na_count | 0.906 | 0.016 | 0.922 | |
| filter_smeta | 0.056 | 0.000 | 0.056 | |
| fisher_exact | 10.471 | 0.152 | 10.623 | |
| fold_change | 9.794 | 0.064 | 9.857 | |
| fold_change_int | 17.142 | 0.124 | 17.266 | |
| fold_change_plot | 0.004 | 0.000 | 0.003 | |
| forward_selection_by_rank | 5.516 | 0.112 | 5.628 | |
| fs_line | 5.645 | 0.024 | 5.670 | |
| glog_opt_plot | 0.468 | 0.004 | 0.472 | |
| glog_transform | 0.254 | 0.000 | 0.254 | |
| grid_search_1d | 4.578 | 0.072 | 4.650 | |
| gs_line | 0.001 | 0.000 | 0.001 | |
| hca_dendrogram | 0 | 0 | 0 | |
| kfold_xval | 3.149 | 0.008 | 3.157 | |
| kfoldxcv_grid | 3.475 | 0.059 | 3.533 | |
| kfoldxcv_metric | 0.001 | 0.000 | 0.001 | |
| knn_impute | 0.002 | 0.004 | 0.006 | |
| kw_p_hist | 0.001 | 0.000 | 0.000 | |
| kw_rank_sum | 0.065 | 0.000 | 0.065 | |
| linear_model | 0.022 | 0.000 | 0.022 | |
| log_transform | 0.004 | 0.000 | 0.004 | |
| mean_centre | 0.001 | 0.000 | 0.001 | |
| mean_of_medians | 0.106 | 0.000 | 0.106 | |
| mixed_effect | 0.138 | 0.004 | 0.142 | |
| model_apply | 0.017 | 0.004 | 0.022 | |
| model_predict | 0.049 | 0.000 | 0.049 | |
| model_reverse | 0.048 | 0.004 | 0.052 | |
| model_train | 0.046 | 0.000 | 0.046 | |
| mv_boxplot | 0.25 | 0.00 | 0.25 | |
| mv_feature_filter | 0.097 | 0.000 | 0.097 | |
| mv_feature_filter_hist | 0.001 | 0.000 | 0.001 | |
| mv_histogram | 0.232 | 0.000 | 0.232 | |
| mv_sample_filter | 0.006 | 0.000 | 0.006 | |
| mv_sample_filter_hist | 0.001 | 0.000 | 0.001 | |
| nroot_transform | 0.001 | 0.003 | 0.004 | |
| ontology_cache | 0.001 | 0.000 | 0.000 | |
| pairs_filter | 0.005 | 0.000 | 0.005 | |
| pareto_scale | 0.052 | 0.000 | 0.051 | |
| pca_biplot | 0.008 | 0.000 | 0.007 | |
| pca_correlation_plot | 0.004 | 0.000 | 0.004 | |
| pca_dstat_plot | 0.005 | 0.000 | 0.005 | |
| pca_loadings_plot | 0.005 | 0.000 | 0.004 | |
| pca_scores_plot | 0.5 | 0.0 | 0.5 | |
| pca_scree_plot | 0 | 0 | 0 | |
| permutation_test | 0.005 | 0.000 | 0.005 | |
| permutation_test_plot | 0.002 | 0.000 | 0.002 | |
| permute_sample_order | 0.004 | 0.000 | 0.003 | |
| pls_regcoeff_plot | 0.318 | 0.000 | 0.318 | |
| pls_scores_plot | 0.634 | 0.000 | 0.633 | |
| pls_vip_plot | 0.354 | 0.000 | 0.354 | |
| plsda_feature_importance_plot | 0.555 | 0.000 | 0.555 | |
| plsda_predicted_plot | 0.473 | 0.031 | 0.504 | |
| plsda_roc_plot | 0.996 | 0.008 | 1.003 | |
| plsr_cook_dist | 0.004 | 0.000 | 0.004 | |
| plsr_prediction_plot | 0.004 | 0.000 | 0.004 | |
| plsr_qq_plot | 0.004 | 0.000 | 0.004 | |
| plsr_residual_hist | 0.003 | 0.000 | 0.003 | |
| pqn_norm | 0.324 | 0.000 | 0.324 | |
| pqn_norm_hist | 0.001 | 0.000 | 0.001 | |
| prop_na | 0.005 | 0.000 | 0.005 | |
| r_squared | 0.000 | 0.001 | 0.001 | |
| resample | 0.006 | 0.002 | 0.008 | |
| resample_chart | 0.003 | 0.000 | 0.003 | |
| rsd_filter | 0.007 | 0.000 | 0.007 | |
| rsd_filter_hist | 0.001 | 0.000 | 0.001 | |
| run | 0.029 | 0.000 | 0.029 | |
| sb_corr | 0.014 | 0.000 | 0.014 | |
| scatter_chart | 0.351 | 0.004 | 0.354 | |
| split_data | 0.004 | 0.000 | 0.004 | |
| stratified_split | 0.103 | 0.000 | 0.103 | |
| svm_plot_2d | 0.639 | 0.016 | 0.655 | |
| tSNE | 0.011 | 0.000 | 0.011 | |
| tSNE_scatter | 0.004 | 0.000 | 0.004 | |
| tic_chart | 0.222 | 0.000 | 0.222 | |
| ttest | 0.009 | 0.000 | 0.009 | |
| vec_norm | 0.000 | 0.000 | 0.001 | |
| wilcox_p_hist | 0.001 | 0.000 | 0.001 | |
| wilcox_test | 0.009 | 0.000 | 0.008 | |