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This page was generated on 2021-10-15 15:05:54 -0400 (Fri, 15 Oct 2021).

CHECK results for structToolbox on nebbiolo1

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.
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raw results

Package 1864/2041HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
structToolbox 1.4.3  (landing page)
Gavin Rhys Lloyd
Snapshot Date: 2021-10-14 04:50:12 -0400 (Thu, 14 Oct 2021)
git_url: https://git.bioconductor.org/packages/structToolbox
git_branch: RELEASE_3_13
git_last_commit: 1af2d87
git_last_commit_date: 2021-09-17 08:51:56 -0400 (Fri, 17 Sep 2021)
nebbiolo1Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: structToolbox
Version: 1.4.3
Command: /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:structToolbox.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings structToolbox_1.4.3.tar.gz
StartedAt: 2021-10-14 11:47:25 -0400 (Thu, 14 Oct 2021)
EndedAt: 2021-10-14 11:53:47 -0400 (Thu, 14 Oct 2021)
EllapsedTime: 381.1 seconds
RetCode: 0
Status:   OK  
CheckDir: structToolbox.Rcheck
Warnings: 0

Command output

##############################################################################
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### Running command:
###
###   /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:structToolbox.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings structToolbox_1.4.3.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.13-bioc/meat/structToolbox.Rcheck’
* using R version 4.1.1 (2021-08-10)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘structToolbox/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘structToolbox’ version ‘1.4.3’
* 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           13.016  0.008  13.023
fisher_exact               6.416  0.004   6.423
fold_change                5.685  0.000   5.684
forward_selection_by_rank  5.160  0.028   5.188
fs_line                    5.150  0.000   5.150
* 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


Installation output

structToolbox.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD INSTALL structToolbox
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.13-bioc/R/library’
* installing *source* package ‘structToolbox’ ...
** using staged installation
** R
** 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)

Tests output

structToolbox.Rcheck/tests/testthat.Rout


R version 4.1.1 (2021-08-10) -- "Kick Things"
Copyright (C) 2021 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 2 | SKIP 0 | PASS 106 ]
> 
> proc.time()
   user  system elapsed 
153.938   0.967 154.898 

Example timings

structToolbox.Rcheck/structToolbox-Ex.timings

nameusersystemelapsed
ANOVA0.4420.0510.493
AUC2.2280.1642.392
DFA0.2260.0100.236
DatasetExperiment_boxplot0.6090.0330.641
DatasetExperiment_dist1.7600.0161.776
DatasetExperiment_factor_boxplot0.1670.0000.167
DatasetExperiment_heatmap0.1540.0070.161
HCA0.0590.0010.059
HSD0.4450.0110.459
HSDEM0.4100.0080.418
MTBLS79_DatasetExperiment0.0030.0000.003
PCA0.0020.0000.002
PLSDA0.0000.0020.001
PLSR0.0000.0020.002
SVM0.0040.0000.004
as_data_frame0.1370.0030.141
autoscale0.0900.0000.091
balanced_accuracy1.6410.0001.641
blank_filter0.3220.0120.334
blank_filter_hist000
calculate0.0040.0000.005
chart_plot0.0270.0040.032
classical_lsq0.2470.0000.247
compare_dist4.7370.0434.780
confounders_clsq2.6000.0122.613
confounders_lsq_barchart2.8570.0002.857
confounders_lsq_boxplot2.6260.0002.626
constant_sum_norm0.0020.0000.002
corr_coef0.1780.0000.177
dfa_scores_plot0.5120.0040.516
dratio_filter0.4620.0000.462
feature_boxplot0.0090.0000.008
feature_profile0.3230.0000.323
feature_profile_array0.4150.0000.415
filter_by_name0.0270.0000.026
filter_na_count0.6530.0000.653
filter_smeta0.0490.0000.049
fisher_exact6.4160.0046.423
fold_change5.6850.0005.684
fold_change_int13.016 0.00813.023
fold_change_plot0.0020.0000.002
forward_selection_by_rank5.1600.0285.188
fs_line5.150.005.15
glog_opt_plot0.5280.0000.528
glog_transform0.3580.0000.358
grid_search_1d4.2220.0164.239
gs_line0.0010.0000.001
hca_dendrogram0.0000.0010.000
kfold_xval2.7250.0022.728
kfoldxcv_grid2.9810.0002.982
kfoldxcv_metric0.0010.0000.000
knn_impute0.0020.0000.002
kw_p_hist0.0000.0000.001
kw_rank_sum0.0620.0000.062
linear_model0.0260.0000.025
log_transform0.0010.0000.002
mean_centre000
mean_of_medians0.1280.0000.129
mixed_effect0.1330.0000.134
model_apply0.0280.0000.027
model_predict0.0540.0000.054
model_reverse0.0250.0000.024
model_train0.0510.0000.051
mv_boxplot0.2020.0030.207
mv_feature_filter0.1160.0000.115
mv_feature_filter_hist0.0010.0000.000
mv_histogram0.1740.0000.175
mv_sample_filter0.0020.0000.002
mv_sample_filter_hist0.0000.0000.001
nroot_transform0.0010.0000.002
pairs_filter0.0020.0000.002
pareto_scale0.0630.0000.062
pca_biplot0.0040.0000.003
pca_correlation_plot0.0020.0000.001
pca_dstat_plot0.0020.0000.002
pca_loadings_plot0.0020.0000.002
pca_scores_plot0.3850.0000.385
pca_scree_plot0.0000.0010.000
permutation_test0.0010.0010.002
permutation_test_plot0.0010.0000.001
permute_sample_order0.0010.0000.002
plsda_predicted_plot0.290.000.29
plsda_regcoeff_plot0.2140.0000.213
plsda_roc_plot0.4150.0000.415
plsda_scores_plot0.3510.0000.350
plsda_vip_plot0.2620.0000.262
plsda_vip_summary_plot0.3990.0000.398
plsr_cook_dist0.0010.0000.001
plsr_prediction_plot0.0000.0000.001
plsr_qq_plot000
plsr_residual_hist000
pqn_norm0.3990.0000.400
pqn_norm_hist0.0010.0000.000
prop_na0.0000.0030.002
r_squared0.0000.0010.001
rsd_filter0.0020.0000.003
rsd_filter_hist0.0010.0000.001
run0.0300.0000.031
sb_corr0.0040.0000.005
split_data0.0010.0000.002
stratified_split0.1110.0000.112
svm_plot_2d0.6350.0230.660
tSNE0.0020.0030.005
tSNE_scatter0.0000.0020.002
tic_chart0.1460.0010.147
ttest0.0030.0000.003
vec_norm0.0010.0000.001
wilcox_p_hist0.0000.0000.001
wilcox_test0.0030.0000.004