| Back to Build/check report for BioC 3.18: simplified long |
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This page was generated on 2023-05-10 10:04:42 -0000 (Wed, 10 May 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| kunpeng1 | Linux (Ubuntu 22.04.1 LTS) | aarch64 | R Under development (unstable) (2023-03-12 r83975) -- "Unsuffered Consequences" | 6211 |
| 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 | ||||
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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 2000/2194 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| structToolbox 1.13.0 (landing page) Gavin Rhys Lloyd
| kunpeng1 | Linux (Ubuntu 22.04.1 LTS) / aarch64 | OK | OK | OK | |||||||||
| Package: structToolbox |
| Version: 1.13.0 |
| 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_1.13.0.tar.gz |
| StartedAt: 2023-05-10 06:25:34 -0000 (Wed, 10 May 2023) |
| EndedAt: 2023-05-10 06:51:00 -0000 (Wed, 10 May 2023) |
| EllapsedTime: 1526.6 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_1.13.0.tar.gz
###
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##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/structToolbox.Rcheck’
* using R Under development (unstable) (2023-03-12 r83975)
* using platform: aarch64-unknown-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 ‘1.13.0’
* 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 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 25.294 0.140 25.434
fold_change 16.691 0.140 16.831
fisher_exact 13.386 0.100 13.486
fs_line 9.278 0.064 9.343
forward_selection_by_rank 8.926 0.132 9.058
grid_search_1d 6.677 0.099 6.777
kfoldxcv_grid 5.148 0.084 5.231
compare_dist 4.995 0.156 5.154
* 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-devel_2023-03-12_r83975-bin/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 Under development (unstable) (2023-03-12 r83975) -- "Unsuffered Consequences"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: aarch64-unknown-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
240.451 2.019 242.457
structToolbox.Rcheck/structToolbox-Ex.timings
| name | user | system | elapsed | |
| ANOVA | 0.239 | 0.008 | 0.247 | |
| AUC | 2.487 | 0.160 | 2.648 | |
| DFA | 0.250 | 0.000 | 0.251 | |
| DatasetExperiment_boxplot | 1.715 | 0.056 | 1.771 | |
| DatasetExperiment_dist | 1.655 | 0.008 | 1.663 | |
| DatasetExperiment_factor_boxplot | 0.267 | 0.000 | 0.268 | |
| DatasetExperiment_heatmap | 0.366 | 0.004 | 0.371 | |
| HCA | 0.071 | 0.000 | 0.071 | |
| HSD | 0.504 | 0.019 | 0.529 | |
| HSDEM | 0.471 | 0.012 | 0.484 | |
| MTBLS79_DatasetExperiment | 0.001 | 0.000 | 0.001 | |
| PCA | 0.005 | 0.000 | 0.005 | |
| PLSDA | 0.020 | 0.000 | 0.019 | |
| PLSR | 0.007 | 0.000 | 0.006 | |
| SVM | 0.015 | 0.000 | 0.015 | |
| as_data_frame | 0.194 | 0.004 | 0.199 | |
| autoscale | 0.090 | 0.000 | 0.091 | |
| balanced_accuracy | 3.231 | 0.128 | 3.359 | |
| blank_filter | 0.416 | 0.012 | 0.427 | |
| blank_filter_hist | 0.001 | 0.000 | 0.001 | |
| bootstrap | 0.007 | 0.000 | 0.007 | |
| calculate | 0.007 | 0.000 | 0.006 | |
| chart_plot | 0.035 | 0.000 | 0.035 | |
| classical_lsq | 0.357 | 0.012 | 0.369 | |
| compare_dist | 4.995 | 0.156 | 5.154 | |
| confounders_clsq | 3.811 | 0.016 | 3.827 | |
| confounders_lsq_barchart | 4.032 | 0.036 | 4.068 | |
| confounders_lsq_boxplot | 3.951 | 0.052 | 4.003 | |
| constant_sum_norm | 0.005 | 0.000 | 0.005 | |
| corr_coef | 0.339 | 0.001 | 0.339 | |
| dfa_scores_plot | 0.873 | 0.007 | 0.881 | |
| dratio_filter | 0.812 | 0.024 | 0.836 | |
| equal_split | 0.158 | 0.000 | 0.158 | |
| feature_boxplot | 0.022 | 0.000 | 0.022 | |
| feature_profile | 0.576 | 0.000 | 0.576 | |
| feature_profile_array | 0.729 | 0.004 | 0.733 | |
| filter_by_name | 0.079 | 0.000 | 0.079 | |
| filter_na_count | 1.431 | 0.012 | 1.443 | |
| filter_smeta | 0.074 | 0.004 | 0.078 | |
| fisher_exact | 13.386 | 0.100 | 13.486 | |
| fold_change | 16.691 | 0.140 | 16.831 | |
| fold_change_int | 25.294 | 0.140 | 25.434 | |
| fold_change_plot | 0.006 | 0.000 | 0.006 | |
| forward_selection_by_rank | 8.926 | 0.132 | 9.058 | |
| fs_line | 9.278 | 0.064 | 9.343 | |
| glog_opt_plot | 0.707 | 0.008 | 0.716 | |
| glog_transform | 0.378 | 0.000 | 0.378 | |
| grid_search_1d | 6.677 | 0.099 | 6.777 | |
| gs_line | 0.001 | 0.000 | 0.001 | |
| hca_dendrogram | 0.001 | 0.001 | 0.001 | |
| kfold_xval | 4.641 | 0.006 | 4.649 | |
| kfoldxcv_grid | 5.148 | 0.084 | 5.231 | |
| kfoldxcv_metric | 0.000 | 0.000 | 0.001 | |
| knn_impute | 0.008 | 0.000 | 0.008 | |
| kw_p_hist | 0.001 | 0.000 | 0.000 | |
| kw_rank_sum | 0.088 | 0.000 | 0.088 | |
| linear_model | 0.03 | 0.00 | 0.03 | |
| log_transform | 0.005 | 0.000 | 0.005 | |
| mean_centre | 0.002 | 0.000 | 0.002 | |
| mean_of_medians | 0.145 | 0.000 | 0.145 | |
| mixed_effect | 0.177 | 0.004 | 0.180 | |
| model_apply | 0.025 | 0.004 | 0.030 | |
| model_predict | 0.069 | 0.000 | 0.069 | |
| model_reverse | 0.053 | 0.000 | 0.053 | |
| model_train | 0.065 | 0.000 | 0.064 | |
| mv_boxplot | 0.368 | 0.004 | 0.372 | |
| mv_feature_filter | 0.132 | 0.000 | 0.132 | |
| mv_feature_filter_hist | 0.001 | 0.000 | 0.001 | |
| mv_histogram | 0.323 | 0.000 | 0.323 | |
| mv_sample_filter | 0.007 | 0.000 | 0.006 | |
| mv_sample_filter_hist | 0.001 | 0.000 | 0.001 | |
| nroot_transform | 0.005 | 0.000 | 0.005 | |
| ontology_cache | 0.000 | 0.000 | 0.001 | |
| pairs_filter | 0.007 | 0.000 | 0.007 | |
| pareto_scale | 0.07 | 0.00 | 0.07 | |
| pca_biplot | 0.01 | 0.00 | 0.01 | |
| pca_correlation_plot | 0.005 | 0.000 | 0.005 | |
| pca_dstat_plot | 0.006 | 0.000 | 0.006 | |
| pca_loadings_plot | 0.007 | 0.000 | 0.006 | |
| pca_scores_plot | 0.689 | 0.004 | 0.692 | |
| pca_scree_plot | 0.000 | 0.001 | 0.001 | |
| permutation_test | 0.006 | 0.001 | 0.007 | |
| permutation_test_plot | 0.004 | 0.000 | 0.003 | |
| permute_sample_order | 0.005 | 0.000 | 0.005 | |
| pls_regcoeff_plot | 0.433 | 0.004 | 0.436 | |
| pls_scores_plot | 0.886 | 0.000 | 0.886 | |
| pls_vip_plot | 1.379 | 0.028 | 1.408 | |
| plsda_feature_importance_plot | 0.804 | 0.020 | 0.823 | |
| plsda_predicted_plot | 0.655 | 0.032 | 0.688 | |
| plsda_roc_plot | 1.489 | 0.004 | 1.492 | |
| plsr_cook_dist | 0.005 | 0.000 | 0.005 | |
| plsr_prediction_plot | 0.001 | 0.003 | 0.004 | |
| plsr_qq_plot | 0.005 | 0.000 | 0.005 | |
| plsr_residual_hist | 0.004 | 0.000 | 0.005 | |
| pqn_norm | 0.448 | 0.000 | 0.447 | |
| pqn_norm_hist | 0.001 | 0.000 | 0.001 | |
| prop_na | 0.007 | 0.000 | 0.007 | |
| r_squared | 0.001 | 0.000 | 0.001 | |
| resample | 0.010 | 0.000 | 0.011 | |
| resample_chart | 0.003 | 0.000 | 0.003 | |
| rsd_filter | 0.009 | 0.000 | 0.010 | |
| rsd_filter_hist | 0.001 | 0.000 | 0.000 | |
| run | 0.037 | 0.000 | 0.037 | |
| sb_corr | 0.018 | 0.000 | 0.018 | |
| scatter_chart | 0.453 | 0.000 | 0.454 | |
| split_data | 0.005 | 0.000 | 0.005 | |
| stratified_split | 0.155 | 0.000 | 0.154 | |
| svm_plot_2d | 0.797 | 0.008 | 0.805 | |
| tSNE | 0.015 | 0.000 | 0.016 | |
| tSNE_scatter | 0.005 | 0.000 | 0.005 | |
| tic_chart | 0.317 | 0.004 | 0.320 | |
| ttest | 0.012 | 0.000 | 0.012 | |
| vec_norm | 0.001 | 0.000 | 0.001 | |
| wilcox_p_hist | 0.000 | 0.001 | 0.001 | |
| wilcox_test | 0.010 | 0.002 | 0.013 | |