Gavin Rhys Lloyd
| Snapshot Date: 2022-03-17 13:55:23 -0400 (Thu, 17 Mar 2022) |
| git_url: https://git.bioconductor.org/packages/structToolbox |
| git_branch: master |
| git_last_commit: afe7d71 |
| git_last_commit_date: 2022-02-28 09:27:17 -0400 (Mon, 28 Feb 2022) |
| Back to Multiple platform build/check report for BioC 3.15 |
|
This page was generated on 2022-03-18 11:08:48 -0400 (Fri, 18 Mar 2022).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 20.04.4 LTS) | x86_64 | R Under development (unstable) (2022-02-17 r81757) -- "Unsuffered Consequences" | 4334 |
| riesling1 | Windows Server 2019 Standard | x64 | R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences" | 4097 |
| palomino3 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2022-02-17 r81757 ucrt) -- "Unsuffered Consequences" | 4083 |
| merida1 | macOS 10.14.6 Mojave | x86_64 | R Under development (unstable) (2022-03-02 r81842) -- "Unsuffered Consequences" | 4134 |
| 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: - Please 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 How and When does the builder pull? When will my changes propagate? here for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 1902/2090 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| structToolbox 1.7.2 (landing page) Gavin Rhys Lloyd
| nebbiolo1 | Linux (Ubuntu 20.04.4 LTS) / x86_64 | OK | OK | OK | | ||||||||
| riesling1 | Windows Server 2019 Standard / x64 | OK | OK | OK | OK | |||||||||
| palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| merida1 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | | ||||||||
| Package: structToolbox |
| Version: 1.7.2 |
| Command: D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:structToolbox.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings structToolbox_1.7.2.tar.gz |
| StartedAt: 2022-03-17 20:24:31 -0400 (Thu, 17 Mar 2022) |
| EndedAt: 2022-03-17 20:30:49 -0400 (Thu, 17 Mar 2022) |
| EllapsedTime: 378.2 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: structToolbox.Rcheck |
| Warnings: 0 |
##############################################################################
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###
### Running command:
###
### D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:structToolbox.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings structToolbox_1.7.2.tar.gz
###
##############################################################################
##############################################################################
* using log directory 'D:/biocbuild/bbs-3.15-bioc/meat/structToolbox.Rcheck'
* using R Under development (unstable) (2021-11-21 r81221)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'structToolbox/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'structToolbox' version '1.7.2'
* 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 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 14.94 0.01 14.95
fold_change 7.75 0.05 7.80
fisher_exact 7.62 0.00 7.63
fs_line 6.23 0.18 6.41
* 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
##############################################################################
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###
### Running command:
###
### D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL structToolbox
###
##############################################################################
##############################################################################
* installing to library 'D:/biocbuild/bbs-3.15-bioc/R/library'
* installing *source* package 'structToolbox' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'structToolbox'
finding HTML links ... done
ANOVA html
AUC html
DFA html
DatasetExperiment_boxplot html
DatasetExperiment_dist html
DatasetExperiment_factor_boxplot html
DatasetExperiment_heatmap html
HCA html
HSD html
HSDEM html
MTBLS79_DatasetExperiment html
PCA html
PLSDA html
PLSR html
SVM html
as_data_frame html
autoscale html
balanced_accuracy html
blank_filter html
blank_filter_hist html
bootstrap html
calculate html
chart_plot html
classical_lsq html
compare_dist html
confounders_clsq html
confounders_lsq_barchart html
confounders_lsq_boxplot html
constant_sum_norm html
corr_coef html
dfa_scores_plot html
dratio_filter html
equal_split html
feature_boxplot html
feature_profile html
feature_profile_array html
filter_by_name html
filter_na_count html
filter_smeta html
fisher_exact html
fold_change html
fold_change_int html
fold_change_plot html
forward_selection_by_rank html
fs_line html
glog_opt_plot html
glog_transform html
grid_search_1d html
gs_line html
hca_dendrogram html
kfold_xval html
kfoldxcv_grid html
kfoldxcv_metric html
knn_impute html
kw_p_hist html
kw_rank_sum html
linear_model html
log_transform html
mean_centre html
mean_of_medians html
mixed_effect html
model_apply html
model_predict html
model_reverse html
model_train html
mv_boxplot html
mv_feature_filter html
mv_feature_filter_hist html
mv_histogram html
mv_sample_filter html
mv_sample_filter_hist html
nroot_transform html
ontology_cache html
pairs_filter html
pareto_scale html
pca_biplot html
pca_correlation_plot html
pca_dstat_plot html
pca_loadings_plot html
pca_scores_plot html
pca_scree_plot html
permutation_test html
permutation_test_plot html
permute_sample_order html
pls_regcoeff_plot html
pls_scores_plot html
pls_vip_plot html
plsda_feature_importance_plot html
plsda_predicted_plot html
plsda_roc_plot html
plsr_cook_dist html
plsr_prediction_plot html
plsr_qq_plot html
plsr_residual_hist html
pqn_norm html
pqn_norm_hist html
prop_na html
r_squared html
resample html
resample_chart html
rsd_filter html
rsd_filter_hist html
run html
sb_corr html
scatter_chart html
split_data html
stratified_split html
structToolbox html
svm_plot_2d html
tSNE html
tSNE_scatter html
tic_chart html
ttest html
vec_norm html
wilcox_p_hist html
wilcox_test html
** 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)
Making 'packages.html' ... done
structToolbox.Rcheck/tests/testthat.Rout
R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (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 2 | SKIP 0 | PASS 124 ]
[ FAIL 0 | WARN 2 | SKIP 0 | PASS 124 ]
>
> proc.time()
user system elapsed
150.10 1.73 151.84
structToolbox.Rcheck/structToolbox-Ex.timings
| name | user | system | elapsed | |
| ANOVA | 0.13 | 0.00 | 0.13 | |
| AUC | 1.28 | 0.08 | 1.36 | |
| DFA | 0.14 | 0.00 | 0.14 | |
| DatasetExperiment_boxplot | 1.04 | 0.02 | 1.06 | |
| DatasetExperiment_dist | 0.9 | 0.1 | 1.0 | |
| DatasetExperiment_factor_boxplot | 0.12 | 0.00 | 0.12 | |
| DatasetExperiment_heatmap | 0.20 | 0.00 | 0.21 | |
| HCA | 0.05 | 0.02 | 0.06 | |
| HSD | 0.29 | 0.09 | 0.35 | |
| HSDEM | 0.82 | 0.05 | 0.86 | |
| MTBLS79_DatasetExperiment | 0 | 0 | 0 | |
| PCA | 0 | 0 | 0 | |
| PLSDA | 0.01 | 0.00 | 0.02 | |
| PLSR | 0.02 | 0.00 | 0.02 | |
| SVM | 0 | 0 | 0 | |
| as_data_frame | 0.07 | 0.00 | 0.07 | |
| autoscale | 0.03 | 0.00 | 0.03 | |
| balanced_accuracy | 1.49 | 0.03 | 1.52 | |
| blank_filter | 0.25 | 0.00 | 0.25 | |
| blank_filter_hist | 0 | 0 | 0 | |
| bootstrap | 0.01 | 0.00 | 0.01 | |
| calculate | 0 | 0 | 0 | |
| chart_plot | 0.02 | 0.00 | 0.02 | |
| classical_lsq | 0.2 | 0.0 | 0.2 | |
| compare_dist | 3.53 | 0.41 | 3.94 | |
| confounders_clsq | 2.10 | 0.01 | 2.11 | |
| confounders_lsq_barchart | 2.26 | 0.00 | 2.26 | |
| confounders_lsq_boxplot | 2.55 | 0.00 | 2.55 | |
| constant_sum_norm | 0.01 | 0.00 | 0.02 | |
| corr_coef | 0.27 | 0.00 | 0.26 | |
| dfa_scores_plot | 0.58 | 0.00 | 0.58 | |
| dratio_filter | 0.67 | 0.00 | 0.68 | |
| equal_split | 0.13 | 0.00 | 0.12 | |
| feature_boxplot | 0.02 | 0.00 | 0.01 | |
| feature_profile | 0.46 | 0.00 | 0.47 | |
| feature_profile_array | 0.57 | 0.03 | 0.60 | |
| filter_by_name | 0.03 | 0.00 | 0.03 | |
| filter_na_count | 1.19 | 0.08 | 1.26 | |
| filter_smeta | 0.03 | 0.00 | 0.03 | |
| fisher_exact | 7.62 | 0.00 | 7.63 | |
| fold_change | 7.75 | 0.05 | 7.80 | |
| fold_change_int | 14.94 | 0.01 | 14.95 | |
| fold_change_plot | 0 | 0 | 0 | |
| forward_selection_by_rank | 4.69 | 0.20 | 4.89 | |
| fs_line | 6.23 | 0.18 | 6.41 | |
| glog_opt_plot | 0.53 | 0.00 | 0.53 | |
| glog_transform | 0.31 | 0.00 | 0.31 | |
| grid_search_1d | 3.33 | 0.20 | 3.53 | |
| gs_line | 0 | 0 | 0 | |
| hca_dendrogram | 0 | 0 | 0 | |
| kfold_xval | 2.19 | 0.02 | 2.20 | |
| kfoldxcv_grid | 2.41 | 0.00 | 2.41 | |
| kfoldxcv_metric | 0 | 0 | 0 | |
| knn_impute | 0.01 | 0.00 | 0.02 | |
| kw_p_hist | 0 | 0 | 0 | |
| kw_rank_sum | 0.05 | 0.00 | 0.04 | |
| linear_model | 0.01 | 0.00 | 0.02 | |
| log_transform | 0 | 0 | 0 | |
| mean_centre | 0 | 0 | 0 | |
| mean_of_medians | 0.08 | 0.00 | 0.08 | |
| mixed_effect | 0.14 | 0.00 | 0.14 | |
| model_apply | 0.01 | 0.00 | 0.02 | |
| model_predict | 0.05 | 0.00 | 0.04 | |
| model_reverse | 0.03 | 0.00 | 0.04 | |
| model_train | 0.03 | 0.00 | 0.03 | |
| mv_boxplot | 0.19 | 0.00 | 0.18 | |
| mv_feature_filter | 0.08 | 0.00 | 0.08 | |
| mv_feature_filter_hist | 0 | 0 | 0 | |
| mv_histogram | 0.16 | 0.00 | 0.16 | |
| mv_sample_filter | 0 | 0 | 0 | |
| mv_sample_filter_hist | 0 | 0 | 0 | |
| nroot_transform | 0 | 0 | 0 | |
| ontology_cache | 0 | 0 | 0 | |
| pairs_filter | 0 | 0 | 0 | |
| pareto_scale | 0.04 | 0.00 | 0.05 | |
| pca_biplot | 0.02 | 0.00 | 0.02 | |
| pca_correlation_plot | 0 | 0 | 0 | |
| pca_dstat_plot | 0.01 | 0.00 | 0.01 | |
| pca_loadings_plot | 0 | 0 | 0 | |
| pca_scores_plot | 0.41 | 0.00 | 0.41 | |
| pca_scree_plot | 0 | 0 | 0 | |
| permutation_test | 0 | 0 | 0 | |
| permutation_test_plot | 0 | 0 | 0 | |
| permute_sample_order | 0.02 | 0.00 | 0.01 | |
| pls_regcoeff_plot | 0.21 | 0.00 | 0.22 | |
| pls_scores_plot | 0.55 | 0.00 | 0.55 | |
| pls_vip_plot | 0.25 | 0.00 | 0.25 | |
| plsda_feature_importance_plot | 0.41 | 0.00 | 0.41 | |
| plsda_predicted_plot | 0.31 | 0.00 | 0.31 | |
| plsda_roc_plot | 0.71 | 0.00 | 0.72 | |
| plsr_cook_dist | 0 | 0 | 0 | |
| plsr_prediction_plot | 0 | 0 | 0 | |
| plsr_qq_plot | 0 | 0 | 0 | |
| plsr_residual_hist | 0.02 | 0.00 | 0.02 | |
| pqn_norm | 0.23 | 0.00 | 0.23 | |
| pqn_norm_hist | 0 | 0 | 0 | |
| prop_na | 0.02 | 0.00 | 0.02 | |
| r_squared | 0 | 0 | 0 | |
| resample | 0 | 0 | 0 | |
| resample_chart | 0 | 0 | 0 | |
| rsd_filter | 0.02 | 0.00 | 0.01 | |
| rsd_filter_hist | 0 | 0 | 0 | |
| run | 0.01 | 0.00 | 0.02 | |
| sb_corr | 0.02 | 0.00 | 0.02 | |
| scatter_chart | 0.22 | 0.00 | 0.21 | |
| split_data | 0.01 | 0.00 | 0.02 | |
| stratified_split | 0.08 | 0.00 | 0.08 | |
| svm_plot_2d | 0.5 | 0.0 | 0.5 | |
| tSNE | 0.02 | 0.00 | 0.01 | |
| tSNE_scatter | 0 | 0 | 0 | |
| tic_chart | 0.15 | 0.00 | 0.16 | |
| ttest | 0.02 | 0.00 | 0.02 | |
| vec_norm | 0 | 0 | 0 | |
| wilcox_p_hist | 0 | 0 | 0 | |
| wilcox_test | 0 | 0 | 0 | |