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This page was generated on 2022-01-21 13:08:36 -0500 (Fri, 21 Jan 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.1.2 (2021-11-01) -- "Bird Hippie" 4329
tokay2Windows Server 2012 R2 Standardx644.1.2 (2021-11-01) -- "Bird Hippie" 4079
machv2macOS 10.14.6 Mojavex86_644.1.2 (2021-11-01) -- "Bird Hippie" 4140
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 machv2


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.

raw results

Package 1896/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
structToolbox 1.6.0  (landing page)
Gavin Rhys Lloyd
Snapshot Date: 2022-01-20 01:55:04 -0500 (Thu, 20 Jan 2022)
git_url: https://git.bioconductor.org/packages/structToolbox
git_branch: RELEASE_3_14
git_last_commit: 46cf01a
git_last_commit_date: 2021-10-26 12:57:03 -0500 (Tue, 26 Oct 2021)
nebbiolo2Linux (Ubuntu 20.04.4 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: 1.6.0
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_1.6.0.tar.gz
StartedAt: 2022-01-20 18:42:52 -0500 (Thu, 20 Jan 2022)
EndedAt: 2022-01-20 18:55:12 -0500 (Thu, 20 Jan 2022)
EllapsedTime: 740.4 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_1.6.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.14-bioc/meat/structToolbox.Rcheck’
* using R version 4.1.2 (2021-11-01)
* 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 ‘1.6.0’
* 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           30.854  0.087  30.970
fold_change               19.885  0.103  20.004
fisher_exact              13.090  0.027  13.151
fs_line                   11.067  0.148  11.231
forward_selection_by_rank 10.266  0.095  10.373
confounders_lsq_boxplot    6.799  0.036   6.840
confounders_lsq_barchart   6.599  0.021   6.626
kfoldxcv_grid              6.495  0.018   6.516
confounders_clsq           6.170  0.068   6.245
kfold_xval                 6.011  0.015   6.029
grid_search_1d             5.636  0.134   5.778
compare_dist               4.930  0.312   5.253
* 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/4.1/Resources/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 4.1.2 (2021-11-01) -- "Bird Hippie"
Copyright (C) 2021 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 121 ]
> 
> proc.time()
   user  system elapsed 
324.122   1.757 326.145 

Example timings

structToolbox.Rcheck/structToolbox-Ex.timings

nameusersystemelapsed
ANOVA0.3820.0060.389
AUC3.3810.0603.443
DFA0.4900.0010.492
DatasetExperiment_boxplot1.6370.0381.677
DatasetExperiment_dist1.4670.1001.570
DatasetExperiment_factor_boxplot0.2720.0020.275
DatasetExperiment_heatmap0.4130.0140.427
HCA0.1410.0010.142
HSD0.7480.0340.784
HSDEM0.5570.0150.573
MTBLS79_DatasetExperiment0.0050.0000.006
PCA0.0070.0000.008
PLSDA0.0210.0010.021
PLSR0.0110.0010.011
SVM0.0230.0010.023
as_data_frame0.2440.0010.246
autoscale0.1430.0020.145
balanced_accuracy3.2130.0133.233
blank_filter0.6410.0100.651
blank_filter_hist0.0010.0010.001
bootstrap0.0110.0010.012
calculate0.0090.0010.009
chart_plot0.0750.0020.077
classical_lsq0.6150.0040.620
compare_dist4.9300.3125.253
confounders_clsq6.1700.0686.245
confounders_lsq_barchart6.5990.0216.626
confounders_lsq_boxplot6.7990.0366.840
constant_sum_norm0.0050.0000.005
corr_coef0.3980.0030.401
dfa_scores_plot1.1140.0321.147
dratio_filter1.2490.0361.289
feature_boxplot0.0270.0010.027
feature_profile0.6590.0130.674
feature_profile_array0.8480.0340.924
filter_by_name0.0610.0000.061
filter_na_count2.1160.0492.165
filter_smeta0.1150.0010.117
fisher_exact13.090 0.02713.151
fold_change19.885 0.10320.004
fold_change_int30.854 0.08730.970
fold_change_plot0.0060.0000.008
forward_selection_by_rank10.266 0.09510.373
fs_line11.067 0.14811.231
glog_opt_plot1.0750.0041.080
glog_transform0.7370.0010.739
grid_search_1d5.6360.1345.778
gs_line0.0000.0000.001
hca_dendrogram0.0010.0000.001
kfold_xval6.0110.0156.029
kfoldxcv_grid6.4950.0186.516
kfoldxcv_metric0.0010.0000.002
knn_impute0.0090.0000.009
kw_p_hist0.0010.0000.002
kw_rank_sum0.1620.0010.163
linear_model0.0490.0010.049
log_transform0.0080.0000.008
mean_centre0.0030.0000.004
mean_of_medians0.2500.0010.251
mixed_effect0.2110.0010.211
model_apply0.0470.0020.049
model_predict0.1340.0010.135
model_reverse0.1050.0000.106
model_train0.1380.0010.139
mv_boxplot0.3850.0010.386
mv_feature_filter0.2250.0010.227
mv_feature_filter_hist0.0010.0000.002
mv_histogram0.4060.0020.409
mv_sample_filter0.0100.0010.010
mv_sample_filter_hist0.0010.0010.001
nroot_transform0.0060.0000.006
ontology_cache0.0000.0000.001
pairs_filter0.0110.0000.011
pareto_scale0.1430.0010.144
pca_biplot0.0160.0010.016
pca_correlation_plot0.0060.0000.006
pca_dstat_plot0.0120.0000.012
pca_loadings_plot0.0090.0000.009
pca_scores_plot0.8500.0040.885
pca_scree_plot0.0010.0000.001
permutation_test0.0110.0000.012
permutation_test_plot0.0050.0000.006
permute_sample_order0.0090.0000.009
plsda_predicted_plot0.7260.0060.731
plsda_regcoeff_plot0.5220.0030.527
plsda_roc_plot1.2680.0051.273
plsda_scores_plot0.7100.0030.714
plsda_vip_plot0.5310.0040.537
plsda_vip_summary_plot0.8220.0040.826
plsr_cook_dist0.0020.0000.001
plsr_prediction_plot0.0010.0010.001
plsr_qq_plot0.0010.0000.001
plsr_residual_hist0.0000.0000.001
pqn_norm0.7950.0010.796
pqn_norm_hist0.0010.0010.001
prop_na0.0090.0000.009
r_squared0.0010.0000.001
rsd_filter0.0090.0000.009
rsd_filter_hist0.0010.0000.002
run0.0650.0010.065
sb_corr0.0290.0010.030
split_data0.0050.0000.005
stratified_split0.3060.0010.308
svm_plot_2d1.2740.0141.290
tSNE0.0170.0000.017
tSNE_scatter0.0070.0010.007
tic_chart0.2800.0020.282
ttest0.0190.0010.020
vec_norm0.0010.0010.002
wilcox_p_hist0.0010.0000.001
wilcox_test0.020.000.02