| Back to Multiple platform build/check report for BioC 3.19: simplified long |
|
This page was generated on 2024-05-18 11:37:26 -0400 (Sat, 18 May 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4751 |
| palomino3 | Windows Server 2022 Datacenter | x64 | 4.4.0 (2024-04-24 ucrt) -- "Puppy Cup" | 4485 |
| lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4515 |
| 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 2095/2300 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| structToolbox 1.16.0 (landing page) Gavin Rhys Lloyd
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK |  | ||||||||
| palomino3 | 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 | 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: 1.16.0 |
| Command: F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:structToolbox.install-out.txt --library=F:\biocbuild\bbs-3.19-bioc\R\library --no-vignettes --timings structToolbox_1.16.0.tar.gz |
| StartedAt: 2024-05-18 07:12:13 -0400 (Sat, 18 May 2024) |
| EndedAt: 2024-05-18 07:21:50 -0400 (Sat, 18 May 2024) |
| EllapsedTime: 576.5 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: structToolbox.Rcheck |
| Warnings: 0 |
##############################################################################
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###
### Running command:
###
### F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:structToolbox.install-out.txt --library=F:\biocbuild\bbs-3.19-bioc\R\library --no-vignettes --timings structToolbox_1.16.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory 'F:/biocbuild/bbs-3.19-bioc/meat/structToolbox.Rcheck'
* using R version 4.4.0 (2024-04-24 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
gcc.exe (GCC) 13.2.0
GNU Fortran (GCC) 13.2.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'structToolbox/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'structToolbox' version '1.16.0'
* 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 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 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 19.67 0.14 19.83
fold_change 14.11 0.08 14.19
fisher_exact 13.44 0.17 13.62
forward_selection_by_rank 7.00 0.16 7.17
fs_line 6.57 0.17 6.74
* 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: ### ### F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD INSTALL structToolbox ### ############################################################################## ############################################################################## * installing to library 'F:/biocbuild/bbs-3.19-bioc/R/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 4.4.0 (2024-04-24 ucrt) -- "Puppy Cup"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64
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
215.57 3.85 219.50
structToolbox.Rcheck/structToolbox-Ex.timings
| name | user | system | elapsed | |
| ANOVA | 0.31 | 0.02 | 0.33 | |
| AUC | 2.73 | 0.26 | 3.03 | |
| DFA | 0.29 | 0.02 | 0.32 | |
| DatasetExperiment_boxplot | 1.75 | 0.05 | 1.79 | |
| DatasetExperiment_dist | 1.53 | 0.08 | 1.61 | |
| DatasetExperiment_factor_boxplot | 0.28 | 0.01 | 0.30 | |
| DatasetExperiment_heatmap | 0.57 | 0.03 | 0.59 | |
| HCA | 0.11 | 0.00 | 0.11 | |
| HSD | 0.34 | 0.03 | 0.52 | |
| HSDEM | 0.55 | 0.03 | 0.76 | |
| MTBLS79_DatasetExperiment | 0 | 0 | 0 | |
| OPLSDA | 0.01 | 0.00 | 0.02 | |
| OPLSR | 0.02 | 0.00 | 0.02 | |
| PCA | 0.01 | 0.00 | 0.01 | |
| PLSDA | 0.04 | 0.00 | 0.03 | |
| PLSR | 0 | 0 | 0 | |
| SVM | 0.03 | 0.00 | 0.03 | |
| as_data_frame | 0.20 | 0.02 | 0.22 | |
| autoscale | 0.11 | 0.00 | 0.11 | |
| balanced_accuracy | 2.23 | 0.03 | 2.27 | |
| blank_filter | 0.47 | 0.00 | 0.48 | |
| blank_filter_hist | 0 | 0 | 0 | |
| bootstrap | 0.03 | 0.00 | 0.03 | |
| calculate | 0 | 0 | 0 | |
| chart_plot | 0.03 | 0.00 | 0.03 | |
| classical_lsq | 0.3 | 0.0 | 0.3 | |
| compare_dist | 4.22 | 0.27 | 4.50 | |
| confounders_clsq | 3.66 | 0.09 | 3.75 | |
| confounders_lsq_barchart | 3.51 | 0.02 | 3.53 | |
| confounders_lsq_boxplot | 3.17 | 0.04 | 3.22 | |
| constant_sum_norm | 0.02 | 0.00 | 0.02 | |
| corr_coef | 0.33 | 0.00 | 0.32 | |
| dfa_scores_plot | 0.87 | 0.01 | 0.89 | |
| dratio_filter | 0.28 | 0.02 | 0.30 | |
| equal_split | 0.19 | 0.00 | 0.19 | |
| feature_boxplot | 0.05 | 0.00 | 0.05 | |
| feature_profile | 0.58 | 0.00 | 0.58 | |
| feature_profile_array | 0.53 | 0.00 | 0.53 | |
| filter_by_name | 0.03 | 0.00 | 0.03 | |
| filter_na_count | 0.94 | 0.04 | 0.98 | |
| filter_smeta | 0.06 | 0.00 | 0.07 | |
| fisher_exact | 13.44 | 0.17 | 13.62 | |
| fold_change | 14.11 | 0.08 | 14.19 | |
| fold_change_int | 19.67 | 0.14 | 19.83 | |
| fold_change_plot | 0.01 | 0.00 | 0.01 | |
| forward_selection_by_rank | 7.00 | 0.16 | 7.17 | |
| fs_line | 6.57 | 0.17 | 6.74 | |
| glog_opt_plot | 0.43 | 0.00 | 0.44 | |
| glog_transform | 0.38 | 0.00 | 0.37 | |
| grid_search_1d | 4.45 | 0.16 | 4.61 | |
| gs_line | 0 | 0 | 0 | |
| hca_dendrogram | 0 | 0 | 0 | |
| kfold_xval | 3.97 | 0.06 | 4.03 | |
| kfoldxcv_grid | 4.40 | 0.08 | 4.48 | |
| kfoldxcv_metric | 0 | 0 | 0 | |
| knn_impute | 0.02 | 0.00 | 0.01 | |
| kw_p_hist | 0 | 0 | 0 | |
| kw_rank_sum | 0.08 | 0.00 | 0.08 | |
| linear_model | 0.03 | 0.00 | 0.03 | |
| log_transform | 0.01 | 0.00 | 0.02 | |
| mean_centre | 0 | 0 | 0 | |
| mean_of_medians | 0.17 | 0.00 | 0.17 | |
| mixed_effect | 0.23 | 0.00 | 0.24 | |
| model_apply | 0.02 | 0.00 | 0.01 | |
| model_predict | 0.08 | 0.00 | 0.08 | |
| model_reverse | 0.06 | 0.00 | 0.07 | |
| model_train | 0.06 | 0.00 | 0.06 | |
| mv_boxplot | 0.27 | 0.02 | 0.28 | |
| mv_feature_filter | 0.12 | 0.00 | 0.13 | |
| mv_feature_filter_hist | 0 | 0 | 0 | |
| mv_histogram | 0.22 | 0.03 | 0.25 | |
| mv_sample_filter | 0.02 | 0.00 | 0.02 | |
| mv_sample_filter_hist | 0 | 0 | 0 | |
| nroot_transform | 0.01 | 0.00 | 0.01 | |
| ontology_cache | 0 | 0 | 0 | |
| pairs_filter | 0.02 | 0.00 | 0.02 | |
| pareto_scale | 0.06 | 0.00 | 0.06 | |
| pca_biplot | 0.02 | 0.00 | 0.01 | |
| pca_correlation_plot | 0.00 | 0.01 | 0.02 | |
| pca_dstat_plot | 0.01 | 0.00 | 0.02 | |
| pca_loadings_plot | 0.02 | 0.00 | 0.01 | |
| pca_scores_plot | 0.5 | 0.0 | 0.5 | |
| pca_scree_plot | 0.01 | 0.00 | 0.02 | |
| permutation_test | 0.04 | 0.00 | 0.03 | |
| permutation_test_plot | 0 | 0 | 0 | |
| permute_sample_order | 0.01 | 0.00 | 0.01 | |
| pls_regcoeff_plot | 0.53 | 0.00 | 0.54 | |
| pls_scores_plot | 0.94 | 0.03 | 0.96 | |
| pls_vip_plot | 0.52 | 0.00 | 0.52 | |
| plsda_feature_importance_plot | 0.73 | 0.03 | 0.77 | |
| plsda_predicted_plot | 0.42 | 0.02 | 0.43 | |
| plsda_roc_plot | 1.44 | 0.00 | 1.44 | |
| plsr_cook_dist | 0.02 | 0.00 | 0.02 | |
| plsr_prediction_plot | 0.01 | 0.00 | 0.01 | |
| plsr_qq_plot | 0 | 0 | 0 | |
| plsr_residual_hist | 0.02 | 0.00 | 0.02 | |
| pqn_norm | 0.36 | 0.00 | 0.36 | |
| pqn_norm_hist | 0 | 0 | 0 | |
| prop_na | 0.01 | 0.00 | 0.01 | |
| r_squared | 0 | 0 | 0 | |
| resample | 0.03 | 0.00 | 0.03 | |
| resample_chart | 0 | 0 | 0 | |
| rsd_filter | 0.03 | 0.00 | 0.03 | |
| rsd_filter_hist | 0 | 0 | 0 | |
| run | 0.05 | 0.00 | 0.05 | |
| sb_corr | 0.05 | 0.00 | 0.05 | |
| scatter_chart | 0.4 | 0.0 | 0.4 | |
| split_data | 0.02 | 0.00 | 0.02 | |
| stratified_split | 0.12 | 0.00 | 0.13 | |
| svm_plot_2d | 0.63 | 0.06 | 0.79 | |
| tSNE | 0.03 | 0.00 | 0.03 | |
| tSNE_scatter | 0 | 0 | 0 | |
| tic_chart | 0.2 | 0.0 | 0.2 | |
| ttest | 0 | 0 | 0 | |
| vec_norm | 0 | 0 | 0 | |
| wilcox_p_hist | 0 | 0 | 0 | |
| wilcox_test | 0.04 | 0.00 | 0.03 | |