Gavin Rhys Lloyd
| Snapshot Date: 2024-03-27 14:00:18 -0400 (Wed, 27 Mar 2024) |
| git_url: https://git.bioconductor.org/packages/structToolbox |
| git_branch: devel |
| git_last_commit: 55546c0 |
| git_last_commit_date: 2024-02-02 05:50:50 -0400 (Fri, 02 Feb 2024) |
| Back to Multiple platform build/check report for BioC 3.19: simplified long |
|
This page was generated on 2024-03-28 11:41:24 -0400 (Thu, 28 Mar 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | R Under development (unstable) (2024-03-18 r86148) -- "Unsuffered Consequences" | 4708 |
| palomino3 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2024-03-16 r86144 ucrt) -- "Unsuffered Consequences" | 4446 |
| lconway | macOS 12.7.1 Monterey | x86_64 | R Under development (unstable) (2024-03-18 r86148) -- "Unsuffered Consequences" | 4471 |
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | R Under development (unstable) (2024-03-19 r86153) -- "Unsuffered Consequences" | 4426 |
| 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 2067/2270 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| structToolbox 1.15.1 (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 | | ||||||||
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | OK | ||||||||||
|
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. - See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host. |
| Package: structToolbox |
| Version: 1.15.1 |
| Command: /home/biocbuild/R/R-4.4-devel-2024.03.20/bin/R CMD check --install=check:structToolbox.install-out.txt --library=/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library --no-vignettes --timings structToolbox_1.15.1.tar.gz |
| StartedAt: 2024-03-28 10:08:31 -0000 (Thu, 28 Mar 2024) |
| EndedAt: 2024-03-28 10:19:27 -0000 (Thu, 28 Mar 2024) |
| EllapsedTime: 656.3 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: structToolbox.Rcheck |
| Warnings: 0 |
##############################################################################
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###
### Running command:
###
### /home/biocbuild/R/R-4.4-devel-2024.03.20/bin/R CMD check --install=check:structToolbox.install-out.txt --library=/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library --no-vignettes --timings structToolbox_1.15.1.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/structToolbox.Rcheck’
* using R Under development (unstable) (2024-03-19 r86153)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
gcc (GCC) 10.3.1
GNU Fortran (GCC) 10.3.1
* running under: openEuler 22.03 (LTS-SP1)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘structToolbox/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘structToolbox’ version ‘1.15.1’
* 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 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 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 27.138 0.084 27.273
fold_change 17.636 0.024 17.693
fisher_exact 14.253 0.116 14.394
fs_line 10.408 0.103 10.532
forward_selection_by_rank 9.241 0.064 9.324
compare_dist 6.132 0.068 6.210
grid_search_1d 5.949 0.064 6.023
kfoldxcv_grid 5.256 0.012 5.277
* 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: ### ### /home/biocbuild/R/R-4.4-devel-2024.03.20/bin/R CMD INSTALL structToolbox ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-4.4-devel-2024.03.20/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) (2024-03-19 r86153) -- "Unsuffered Consequences"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-unknown-linux-gnu
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
259.810 2.433 262.814
structToolbox.Rcheck/structToolbox-Ex.timings
| name | user | system | elapsed | |
| ANOVA | 0.299 | 0.000 | 0.300 | |
| AUC | 2.867 | 0.144 | 3.017 | |
| DFA | 0.283 | 0.000 | 0.284 | |
| DatasetExperiment_boxplot | 1.074 | 0.008 | 1.084 | |
| DatasetExperiment_dist | 2.503 | 0.068 | 2.576 | |
| DatasetExperiment_factor_boxplot | 0.298 | 0.000 | 0.298 | |
| DatasetExperiment_heatmap | 0.542 | 0.004 | 0.547 | |
| HCA | 0.091 | 0.000 | 0.092 | |
| HSD | 0.417 | 0.035 | 0.457 | |
| HSDEM | 0.468 | 0.000 | 0.469 | |
| MTBLS79_DatasetExperiment | 0.001 | 0.000 | 0.001 | |
| OPLSDA | 0.015 | 0.000 | 0.015 | |
| OPLSR | 0.021 | 0.000 | 0.021 | |
| PCA | 0.006 | 0.000 | 0.006 | |
| PLSDA | 0.036 | 0.000 | 0.036 | |
| PLSR | 0.014 | 0.000 | 0.014 | |
| SVM | 0.042 | 0.000 | 0.042 | |
| as_data_frame | 0.178 | 0.004 | 0.182 | |
| autoscale | 0.111 | 0.004 | 0.116 | |
| balanced_accuracy | 2.550 | 0.012 | 2.566 | |
| blank_filter | 0.503 | 0.012 | 0.517 | |
| blank_filter_hist | 0.001 | 0.000 | 0.001 | |
| bootstrap | 0.021 | 0.004 | 0.026 | |
| calculate | 0.007 | 0.000 | 0.008 | |
| chart_plot | 0.041 | 0.000 | 0.040 | |
| classical_lsq | 0.458 | 0.008 | 0.467 | |
| compare_dist | 6.132 | 0.068 | 6.210 | |
| confounders_clsq | 4.288 | 0.052 | 4.347 | |
| confounders_lsq_barchart | 4.484 | 0.024 | 4.515 | |
| confounders_lsq_boxplot | 4.452 | 0.020 | 4.481 | |
| constant_sum_norm | 0.016 | 0.003 | 0.020 | |
| corr_coef | 0.4 | 0.0 | 0.4 | |
| dfa_scores_plot | 1.023 | 0.000 | 1.025 | |
| dratio_filter | 0.485 | 0.004 | 0.490 | |
| equal_split | 0.185 | 0.000 | 0.186 | |
| feature_boxplot | 0.046 | 0.000 | 0.045 | |
| feature_profile | 0.548 | 0.000 | 0.549 | |
| feature_profile_array | 0.704 | 0.000 | 0.705 | |
| filter_by_name | 0.045 | 0.000 | 0.044 | |
| filter_na_count | 1.589 | 0.008 | 1.600 | |
| filter_smeta | 0.092 | 0.000 | 0.093 | |
| fisher_exact | 14.253 | 0.116 | 14.394 | |
| fold_change | 17.636 | 0.024 | 17.693 | |
| fold_change_int | 27.138 | 0.084 | 27.273 | |
| fold_change_plot | 0.018 | 0.000 | 0.017 | |
| forward_selection_by_rank | 9.241 | 0.064 | 9.324 | |
| fs_line | 10.408 | 0.103 | 10.532 | |
| glog_opt_plot | 0.733 | 0.000 | 0.734 | |
| glog_transform | 0.394 | 0.004 | 0.399 | |
| grid_search_1d | 5.949 | 0.064 | 6.023 | |
| gs_line | 0.001 | 0.000 | 0.001 | |
| hca_dendrogram | 0.001 | 0.000 | 0.001 | |
| kfold_xval | 4.864 | 0.000 | 4.872 | |
| kfoldxcv_grid | 5.256 | 0.012 | 5.277 | |
| kfoldxcv_metric | 0.001 | 0.000 | 0.001 | |
| knn_impute | 0.014 | 0.004 | 0.017 | |
| kw_p_hist | 0.001 | 0.000 | 0.001 | |
| kw_rank_sum | 0.117 | 0.000 | 0.118 | |
| linear_model | 0.041 | 0.000 | 0.041 | |
| log_transform | 0.019 | 0.000 | 0.020 | |
| mean_centre | 0.004 | 0.000 | 0.004 | |
| mean_of_medians | 0.178 | 0.000 | 0.178 | |
| mixed_effect | 0.236 | 0.004 | 0.240 | |
| model_apply | 0.032 | 0.000 | 0.033 | |
| model_predict | 0.073 | 0.004 | 0.078 | |
| model_reverse | 0.060 | 0.000 | 0.061 | |
| model_train | 0.071 | 0.000 | 0.071 | |
| mv_boxplot | 0.404 | 0.000 | 0.404 | |
| mv_feature_filter | 0.162 | 0.000 | 0.162 | |
| mv_feature_filter_hist | 0.001 | 0.000 | 0.000 | |
| mv_histogram | 0.361 | 0.000 | 0.362 | |
| mv_sample_filter | 0.021 | 0.000 | 0.021 | |
| mv_sample_filter_hist | 0.001 | 0.000 | 0.001 | |
| nroot_transform | 0.018 | 0.000 | 0.019 | |
| ontology_cache | 0.000 | 0.000 | 0.001 | |
| pairs_filter | 0.040 | 0.000 | 0.041 | |
| pareto_scale | 0.078 | 0.000 | 0.078 | |
| pca_biplot | 0.028 | 0.000 | 0.027 | |
| pca_correlation_plot | 0.016 | 0.000 | 0.016 | |
| pca_dstat_plot | 0.019 | 0.000 | 0.020 | |
| pca_loadings_plot | 0.02 | 0.00 | 0.02 | |
| pca_scores_plot | 0.740 | 0.000 | 0.741 | |
| pca_scree_plot | 0.016 | 0.000 | 0.015 | |
| permutation_test | 0.025 | 0.000 | 0.024 | |
| permutation_test_plot | 0.003 | 0.000 | 0.004 | |
| permute_sample_order | 0.021 | 0.000 | 0.021 | |
| pls_regcoeff_plot | 0.492 | 0.000 | 0.493 | |
| pls_scores_plot | 0.937 | 0.000 | 0.939 | |
| pls_vip_plot | 0.516 | 0.008 | 0.525 | |
| plsda_feature_importance_plot | 0.825 | 0.000 | 0.827 | |
| plsda_predicted_plot | 0.636 | 0.000 | 0.638 | |
| plsda_roc_plot | 1.695 | 0.000 | 1.699 | |
| plsr_cook_dist | 0.013 | 0.003 | 0.016 | |
| plsr_prediction_plot | 0.016 | 0.000 | 0.015 | |
| plsr_qq_plot | 0.016 | 0.000 | 0.015 | |
| plsr_residual_hist | 0.016 | 0.000 | 0.016 | |
| pqn_norm | 0.484 | 0.004 | 0.489 | |
| pqn_norm_hist | 0.001 | 0.000 | 0.001 | |
| prop_na | 0.021 | 0.004 | 0.024 | |
| r_squared | 0.001 | 0.000 | 0.001 | |
| resample | 0.032 | 0.000 | 0.033 | |
| resample_chart | 0.004 | 0.000 | 0.004 | |
| rsd_filter | 0.029 | 0.000 | 0.028 | |
| rsd_filter_hist | 0.001 | 0.000 | 0.001 | |
| run | 0.040 | 0.000 | 0.041 | |
| sb_corr | 0.043 | 0.004 | 0.047 | |
| scatter_chart | 0.461 | 0.020 | 0.481 | |
| split_data | 0.015 | 0.004 | 0.019 | |
| stratified_split | 0.175 | 0.000 | 0.175 | |
| svm_plot_2d | 0.865 | 0.004 | 0.870 | |
| tSNE | 0.043 | 0.000 | 0.043 | |
| tSNE_scatter | 0.016 | 0.000 | 0.016 | |
| tic_chart | 0.274 | 0.000 | 0.274 | |
| ttest | 0.027 | 0.000 | 0.027 | |
| vec_norm | 0.001 | 0.000 | 0.001 | |
| wilcox_p_hist | 0.001 | 0.000 | 0.001 | |
| wilcox_test | 0.034 | 0.000 | 0.034 | |