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This page was generated on 2022-01-21 13:05:48 -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 nebbiolo2


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: /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD check --install=check:structToolbox.install-out.txt --library=/home/biocbuild/bbs-3.14-bioc/R/library --no-vignettes --timings structToolbox_1.6.0.tar.gz
StartedAt: 2022-01-20 09:45:08 -0500 (Thu, 20 Jan 2022)
EndedAt: 2022-01-20 09:51:56 -0500 (Thu, 20 Jan 2022)
EllapsedTime: 408.3 seconds
RetCode: 0
Status:   OK  
CheckDir: structToolbox.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD check --install=check:structToolbox.install-out.txt --library=/home/biocbuild/bbs-3.14-bioc/R/library --no-vignettes --timings structToolbox_1.6.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.14-bioc/meat/structToolbox.Rcheck’
* using R version 4.1.2 (2021-11-01)
* 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 ‘1.6.0’
* 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           15.229  0.000  15.229
fold_change                9.432  0.388   9.819
fisher_exact               7.409  0.016   7.424
fs_line                    5.323  0.016   5.339
forward_selection_by_rank  5.096  0.048   5.143
* 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-3.14-bioc/R/bin/R CMD INSTALL structToolbox
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.14-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 4.1.2 (2021-11-01) -- "Bird Hippie"
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 121 ]
> 
> proc.time()
   user  system elapsed 
170.822   1.112 171.917 

Example timings

structToolbox.Rcheck/structToolbox-Ex.timings

nameusersystemelapsed
ANOVA0.1970.0000.197
AUC1.8630.0241.887
DFA0.2560.0120.268
DatasetExperiment_boxplot1.2040.0201.224
DatasetExperiment_dist1.1170.0401.157
DatasetExperiment_factor_boxplot0.1750.0000.176
DatasetExperiment_heatmap0.9440.0000.944
HCA0.0750.0080.082
HSD0.3650.0080.374
HSDEM0.3670.0160.383
MTBLS79_DatasetExperiment0.0030.0000.003
PCA0.0040.0000.005
PLSDA0.0080.0040.012
PLSR0.0060.0000.006
SVM0.0080.0040.011
as_data_frame0.1270.0360.163
autoscale0.0820.0160.098
balanced_accuracy1.6380.0321.670
blank_filter0.3830.0040.387
blank_filter_hist0.0000.0000.001
bootstrap0.0040.0000.004
calculate0.0040.0000.004
chart_plot0.0300.0040.034
classical_lsq0.3130.0000.313
compare_dist3.2800.0923.372
confounders_clsq3.3150.0243.339
confounders_lsq_barchart3.7440.2964.039
confounders_lsq_boxplot3.5060.3083.814
constant_sum_norm0.0050.0000.004
corr_coef0.2090.0040.213
dfa_scores_plot0.5110.0080.519
dratio_filter0.5000.0400.539
feature_boxplot0.0110.0040.015
feature_profile0.3400.0120.352
feature_profile_array0.4320.0160.448
filter_by_name0.030.000.03
filter_na_count0.8560.0120.868
filter_smeta0.0600.0000.059
fisher_exact7.4090.0167.424
fold_change9.4320.3889.819
fold_change_int15.229 0.00015.229
fold_change_plot0.0040.0000.003
forward_selection_by_rank5.0960.0485.143
fs_line5.3230.0165.339
glog_opt_plot0.4940.0000.495
glog_transform0.3590.0000.359
grid_search_1d4.4560.0004.457
gs_line000
hca_dendrogram000
kfold_xval3.2360.0123.248
kfoldxcv_grid3.4570.0123.469
kfoldxcv_metric000
knn_impute0.0050.0000.005
kw_p_hist0.0010.0000.001
kw_rank_sum0.0790.0000.079
linear_model0.0310.0000.031
log_transform0.0040.0000.004
mean_centre0.0020.0000.002
mean_of_medians0.1390.0000.139
mixed_effect0.150.000.15
model_apply0.0320.0000.032
model_predict0.0660.0000.066
model_reverse0.0470.0000.047
model_train0.060.000.06
mv_boxplot0.2330.0000.233
mv_feature_filter0.1460.0000.146
mv_feature_filter_hist0.0010.0000.001
mv_histogram0.1870.0000.187
mv_sample_filter0.0050.0000.005
mv_sample_filter_hist000
nroot_transform0.0040.0000.004
ontology_cache0.0000.0000.001
pairs_filter0.0010.0040.005
pareto_scale0.070.000.07
pca_biplot0.0080.0000.007
pca_correlation_plot0.0040.0000.004
pca_dstat_plot0.0040.0000.005
pca_loadings_plot0.0010.0040.005
pca_scores_plot0.4950.0000.495
pca_scree_plot0.0010.0000.001
permutation_test0.0050.0000.006
permutation_test_plot0.0030.0000.003
permute_sample_order0.0040.0000.004
plsda_predicted_plot0.3290.0000.328
plsda_regcoeff_plot0.2380.0000.238
plsda_roc_plot0.5880.0000.588
plsda_scores_plot0.4130.0000.413
plsda_vip_plot0.2640.0000.265
plsda_vip_summary_plot0.4390.0000.439
plsr_cook_dist0.0010.0000.001
plsr_prediction_plot0.0010.0000.001
plsr_qq_plot0.0010.0000.001
plsr_residual_hist0.0000.0000.001
pqn_norm0.4610.0000.461
pqn_norm_hist000
prop_na0.0040.0000.005
r_squared0.0010.0000.001
rsd_filter0.0060.0000.006
rsd_filter_hist000
run0.0350.0000.035
sb_corr0.0110.0000.011
split_data0.0040.0000.004
stratified_split0.1420.0000.142
svm_plot_2d0.6510.0000.651
tSNE0.0110.0000.011
tSNE_scatter0.0040.0000.004
tic_chart0.1880.0000.187
ttest0.0090.0000.008
vec_norm0.0010.0000.001
wilcox_p_hist000
wilcox_test0.0080.0000.008