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This page was generated on 2022-06-24 12:08:13 -0400 (Fri, 24 Jun 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 20.04.4 LTS)x86_644.2.0 (2022-04-22) -- "Vigorous Calisthenics" 4380
palomino3Windows Server 2022 Datacenterx644.2.0 (2022-04-22 ucrt) -- "Vigorous Calisthenics" 4156
merida1macOS 10.14.6 Mojavex86_644.2.0 (2022-04-22) -- "Vigorous Calisthenics" 4221
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

CHECK results for structToolbox on merida1


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? for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 1947/2140HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
structToolbox 1.8.0  (landing page)
Gavin Rhys Lloyd
Snapshot Date: 2022-06-23 13:55:15 -0400 (Thu, 23 Jun 2022)
git_url: https://git.bioconductor.org/packages/structToolbox
git_branch: RELEASE_3_15
git_last_commit: 29adf97
git_last_commit_date: 2022-04-26 12:02:16 -0400 (Tue, 26 Apr 2022)
nebbiolo1Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    NA  

Summary

Package: structToolbox
Version: 1.8.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:structToolbox.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings structToolbox_1.8.0.tar.gz
StartedAt: 2022-06-24 09:38:38 -0400 (Fri, 24 Jun 2022)
EndedAt: 2022-06-24 09:53:51 -0400 (Fri, 24 Jun 2022)
EllapsedTime: 912.6 seconds
RetCode: 0
Status:   OK  
CheckDir: structToolbox.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:structToolbox.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings structToolbox_1.8.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.15-bioc/meat/structToolbox.Rcheck’
* using R version 4.2.0 (2022-04-22)
* using platform: x86_64-apple-darwin17.0 (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 ‘1.8.0’
* 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           41.945  0.113  43.391
fold_change               25.727  0.081  26.436
fisher_exact              21.708  0.096  22.274
forward_selection_by_rank 13.768  0.152  14.083
fs_line                   13.125  0.087  13.353
kfoldxcv_grid              7.859  0.028   7.963
grid_search_1d             7.369  0.149   7.638
kfold_xval                 7.259  0.025   7.356
compare_dist               6.278  0.316   6.654
confounders_lsq_boxplot    6.507  0.019   6.597
confounders_lsq_barchart   6.400  0.018   6.510
confounders_clsq           6.257  0.038   6.365
AUC                        4.738  0.149   5.001
* 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:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL structToolbox
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.2/Resources/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)

Tests output

structToolbox.Rcheck/tests/testthat.Rout


R version 4.2.0 (2022-04-22) -- "Vigorous Calisthenics"
Copyright (C) 2022 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin17.0 (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 
375.945   2.224 381.774 

Example timings

structToolbox.Rcheck/structToolbox-Ex.timings

nameusersystemelapsed
ANOVA0.4150.0080.430
AUC4.7380.1495.001
DFA0.4080.0010.411
DatasetExperiment_boxplot1.2280.0441.309
DatasetExperiment_dist2.3920.1062.519
DatasetExperiment_factor_boxplot0.3720.0030.378
DatasetExperiment_heatmap0.5230.0180.543
HCA0.1200.0050.126
HSD0.8790.0460.933
HSDEM0.7670.0160.786
MTBLS79_DatasetExperiment0.0010.0000.002
PCA0.010.000.01
PLSDA0.0340.0010.035
PLSR0.0120.0000.012
SVM0.0270.0000.028
as_data_frame0.2700.0020.272
autoscale0.1440.0010.145
balanced_accuracy3.8540.0253.904
blank_filter0.7470.0150.773
blank_filter_hist0.0010.0000.002
bootstrap0.0130.0000.013
calculate0.0110.0000.012
chart_plot0.0560.0010.058
classical_lsq0.5980.0020.604
compare_dist6.2780.3166.654
confounders_clsq6.2570.0386.365
confounders_lsq_barchart6.4000.0186.510
confounders_lsq_boxplot6.5070.0196.597
constant_sum_norm0.0090.0000.010
corr_coef0.5450.0020.560
dfa_scores_plot1.1240.0061.168
dratio_filter1.5540.0351.619
equal_split0.2360.0020.238
feature_boxplot0.0360.0010.036
feature_profile0.8210.0070.840
feature_profile_array1.0790.0371.122
filter_by_name0.0540.0000.054
filter_na_count2.5260.0482.598
filter_smeta0.1370.0000.138
fisher_exact21.708 0.09622.274
fold_change25.727 0.08126.436
fold_change_int41.945 0.11343.391
fold_change_plot0.0080.0000.009
forward_selection_by_rank13.768 0.15214.083
fs_line13.125 0.08713.353
glog_opt_plot1.0910.0041.109
glog_transform0.6570.0020.674
grid_search_1d7.3690.1497.638
gs_line0.0010.0000.001
hca_dendrogram0.0010.0000.001
kfold_xval7.2590.0257.356
kfoldxcv_grid7.8590.0287.963
kfoldxcv_metric0.0010.0000.002
knn_impute0.0120.0000.012
kw_p_hist0.0010.0000.001
kw_rank_sum0.1510.0010.151
linear_model0.0470.0010.047
log_transform0.010.000.01
mean_centre0.0030.0010.004
mean_of_medians0.2520.0010.253
mixed_effect0.2950.0010.296
model_apply0.0440.0010.045
model_predict0.1130.0010.114
model_reverse0.0880.0000.089
model_train0.1100.0010.110
mv_boxplot0.4970.0030.500
mv_feature_filter0.2160.0010.217
mv_feature_filter_hist0.0010.0000.001
mv_histogram0.4450.0020.447
mv_sample_filter0.0090.0000.010
mv_sample_filter_hist0.0010.0000.001
nroot_transform0.0090.0000.010
ontology_cache0.0000.0000.001
pairs_filter0.0130.0000.013
pareto_scale0.1170.0010.118
pca_biplot0.0190.0000.019
pca_correlation_plot0.0050.0000.005
pca_dstat_plot0.0100.0000.011
pca_loadings_plot0.0120.0000.011
pca_scores_plot1.0740.0061.081
pca_scree_plot0.0020.0000.001
permutation_test0.0120.0000.012
permutation_test_plot0.0060.0000.005
permute_sample_order0.0090.0000.009
pls_regcoeff_plot0.6770.0030.681
pls_scores_plot1.4160.0041.427
pls_vip_plot0.7320.0050.742
plsda_feature_importance_plot1.1330.0081.145
plsda_predicted_plot0.9690.0040.982
plsda_roc_plot2.5650.0082.580
plsr_cook_dist0.0070.0000.007
plsr_prediction_plot0.0090.0000.008
plsr_qq_plot0.0080.0010.008
plsr_residual_hist0.0090.0000.008
pqn_norm0.7830.0020.788
pqn_norm_hist0.0010.0000.001
prop_na0.0130.0000.013
r_squared0.0010.0000.002
resample0.020.000.02
resample_chart0.0060.0000.006
rsd_filter0.0170.0000.017
rsd_filter_hist0.0010.0000.001
run0.0610.0010.062
sb_corr0.0320.0010.031
scatter_chart0.7080.0040.720
split_data0.0080.0010.008
stratified_split0.2320.0010.233
svm_plot_2d1.3260.0141.349
tSNE0.0280.0000.029
tSNE_scatter0.0090.0000.010
tic_chart0.4530.0020.460
ttest0.0220.0000.022
vec_norm0.0010.0000.002
wilcox_p_hist0.0010.0000.001
wilcox_test0.0200.0000.021