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This page was generated on 2022-06-27 11:10:10 -0400 (Mon, 27 Jun 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 20.04.4 LTS)x86_644.2.0 (2022-04-22) -- "Vigorous Calisthenics" 4380
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 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? 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: 2022-06-26 13:55:11 -0400 (Sun, 26 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

Summary

Package: structToolbox
Version: 1.8.0
Command: /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD check --install=check:structToolbox.install-out.txt --library=/home/biocbuild/bbs-3.15-bioc/R/library --no-vignettes --timings structToolbox_1.8.0.tar.gz
StartedAt: 2022-06-26 22:10:19 -0400 (Sun, 26 Jun 2022)
EndedAt: 2022-06-26 22:17:20 -0400 (Sun, 26 Jun 2022)
EllapsedTime: 421.9 seconds
RetCode: 0
Status:   OK  
CheckDir: structToolbox.Rcheck
Warnings: 0

Command output

##############################################################################
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### Running command:
###
###   /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD check --install=check:structToolbox.install-out.txt --library=/home/biocbuild/bbs-3.15-bioc/R/library --no-vignettes --timings structToolbox_1.8.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.15-bioc/meat/structToolbox.Rcheck’
* using R version 4.2.0 (2022-04-22)
* 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 ‘1.8.0’
* 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           17.691  0.143  17.835
fold_change               10.138  0.089  10.225
fisher_exact               9.661  0.079   9.742
fs_line                    7.244  0.176   7.419
forward_selection_by_rank  5.815  0.067   5.883
* 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-3.15-bioc/R/bin/R CMD INSTALL structToolbox
###
##############################################################################
##############################################################################


* installing to library ‘/home/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
** 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-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 124 ]

[ FAIL 0 | WARN 2 | SKIP 0 | PASS 124 ]
> 
> proc.time()
   user  system elapsed 
167.366   2.422 169.778 

Example timings

structToolbox.Rcheck/structToolbox-Ex.timings

nameusersystemelapsed
ANOVA0.3130.0160.329
AUC2.3530.1752.529
DFA0.1670.0190.187
DatasetExperiment_boxplot0.6460.0130.658
DatasetExperiment_dist1.7510.0801.831
DatasetExperiment_factor_boxplot0.1530.0000.153
DatasetExperiment_heatmap0.2210.0070.227
HCA0.0510.0010.051
HSD0.3790.0160.395
HSDEM0.3740.0070.381
MTBLS79_DatasetExperiment0.0010.0010.001
PCA0.0040.0000.005
PLSDA0.0140.0000.015
PLSR0.0040.0000.005
SVM0.010.000.01
as_data_frame0.1140.0000.115
autoscale0.0650.0000.065
balanced_accuracy1.6080.0441.652
blank_filter0.3370.0000.336
blank_filter_hist0.0010.0000.001
bootstrap0.0050.0000.006
calculate0.0050.0000.005
chart_plot0.0450.0000.044
classical_lsq0.2510.0040.255
compare_dist4.0230.1284.152
confounders_clsq2.7660.0392.806
confounders_lsq_barchart2.7870.0512.840
confounders_lsq_boxplot2.7240.0242.749
constant_sum_norm0.0040.0000.004
corr_coef0.2370.0000.237
dfa_scores_plot0.4900.0190.510
dratio_filter0.5300.0330.563
equal_split0.1130.0000.113
feature_boxplot0.0160.0000.016
feature_profile0.3550.0000.355
feature_profile_array0.460.000.46
filter_by_name0.0210.0030.025
filter_na_count0.8550.0480.904
filter_smeta0.0490.0010.049
fisher_exact9.6610.0799.742
fold_change10.138 0.08910.225
fold_change_int17.691 0.14317.835
fold_change_plot0.0040.0000.004
forward_selection_by_rank5.8150.0675.883
fs_line7.2440.1767.419
glog_opt_plot0.4290.0030.433
glog_transform0.2670.0000.268
grid_search_1d3.9710.0684.039
gs_line0.0010.0000.000
hca_dendrogram0.0010.0010.001
kfold_xval3.0110.0113.024
kfoldxcv_grid3.2100.0363.247
kfoldxcv_metric0.0010.0000.001
knn_impute0.0060.0000.006
kw_p_hist0.0010.0010.001
kw_rank_sum0.0620.0000.062
linear_model0.0210.0000.021
log_transform0.0040.0000.004
mean_centre0.0000.0010.001
mean_of_medians0.1010.0020.102
mixed_effect0.1380.0010.137
model_apply0.0210.0000.021
model_predict0.0470.0000.047
model_reverse0.0360.0000.037
model_train0.0440.0000.044
mv_boxplot0.2200.0000.221
mv_feature_filter0.0960.0000.096
mv_feature_filter_hist0.0010.0000.001
mv_histogram0.1870.0000.186
mv_sample_filter0.0050.0000.005
mv_sample_filter_hist000
nroot_transform0.0050.0000.005
ontology_cache0.0000.0000.001
pairs_filter0.0030.0020.005
pareto_scale0.0480.0000.049
pca_biplot0.0040.0030.007
pca_correlation_plot0.0030.0000.003
pca_dstat_plot0.0050.0000.005
pca_loadings_plot0.0050.0000.005
pca_scores_plot0.5580.0040.562
pca_scree_plot0.0010.0000.001
permutation_test0.0060.0000.006
permutation_test_plot0.0020.0000.003
permute_sample_order0.0040.0000.004
pls_regcoeff_plot0.3030.0000.303
pls_scores_plot0.6040.0040.608
pls_vip_plot0.3050.0000.305
plsda_feature_importance_plot0.4970.0000.498
plsda_predicted_plot0.3950.0000.395
plsda_roc_plot0.9540.0040.958
plsr_cook_dist0.0050.0000.005
plsr_prediction_plot0.0040.0000.004
plsr_qq_plot0.0040.0000.004
plsr_residual_hist0.0040.0000.004
pqn_norm0.3430.0000.343
pqn_norm_hist0.0010.0000.000
prop_na0.0050.0000.005
r_squared0.0010.0000.001
resample0.0080.0000.008
resample_chart0.0030.0000.003
rsd_filter0.0060.0000.006
rsd_filter_hist0.0010.0000.000
run0.0220.0040.026
sb_corr0.0120.0000.012
scatter_chart0.2880.0000.289
split_data0.0050.0000.004
stratified_split0.0970.0040.101
svm_plot_2d0.5850.0360.621
tSNE0.0120.0000.012
tSNE_scatter0.0040.0000.005
tic_chart0.2180.0000.218
ttest0.0060.0040.010
vec_norm0.0010.0000.001
wilcox_p_hist0.0000.0010.001
wilcox_test0.0080.0010.010