Back to Multiple platform build/check report for BioC 3.19:   simplified   long
ABCDEFGHIJKLMNOPQR[S]TUVWXYZ

This page was generated on 2024-05-04 11:40:04 -0400 (Sat, 04 May 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_644.4.0 beta (2024-04-15 r86425) -- "Puppy Cup" 4753
palomino3Windows Server 2022 Datacenterx644.4.0 beta (2024-04-15 r86425 ucrt) -- "Puppy Cup" 4486
lconwaymacOS 12.7.1 Montereyx86_644.4.0 beta (2024-04-14 r86421) -- "Puppy Cup" 4519
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch644.4.0 beta (2024-04-15 r86425) -- "Puppy Cup" 4479
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

Package 2095/2300HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
structToolbox 1.16.0  (landing page)
Gavin Rhys Lloyd
Snapshot Date: 2024-05-03 14:00:19 -0400 (Fri, 03 May 2024)
git_url: https://git.bioconductor.org/packages/structToolbox
git_branch: RELEASE_3_19
git_last_commit: daf3d2f
git_last_commit_date: 2024-04-30 11:20:29 -0400 (Tue, 30 Apr 2024)
nebbiolo1Linux (Ubuntu 22.04.3 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
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  OK    OK    OK  
kjohnson3macOS 13.6.5 Ventura / arm64see weekly results here

CHECK results for structToolbox on lconway


To the developers/maintainers of the structToolbox package:
- 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 Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results


Summary

Package: structToolbox
Version: 1.16.0
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_1.16.0.tar.gz
StartedAt: 2024-05-04 01:17:00 -0400 (Sat, 04 May 2024)
EndedAt: 2024-05-04 01:26:42 -0400 (Sat, 04 May 2024)
EllapsedTime: 582.6 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_1.16.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/structToolbox.Rcheck’
* using R version 4.4.0 beta (2024-04-14 r86421)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘structToolbox/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘structToolbox’ version ‘1.16.0’
* 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 code 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           22.170  0.240  22.598
fold_change               13.142  0.138  13.383
fisher_exact              13.112  0.167  13.412
fs_line                    7.321  0.235   7.646
forward_selection_by_rank  6.905  0.145   7.114
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... 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/4.4-x86_64/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 4.4.0 beta (2024-04-14 r86421) -- "Puppy Cup"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20

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 6 | SKIP 0 | PASS 156 ]

[ FAIL 0 | WARN 6 | SKIP 0 | PASS 156 ]
> 
> proc.time()
   user  system elapsed 
219.338   3.524 224.822 

Example timings

structToolbox.Rcheck/structToolbox-Ex.timings

nameusersystemelapsed
ANOVA0.2710.0110.286
AUC2.5710.1442.738
DFA0.2550.0030.259
DatasetExperiment_boxplot1.6510.0641.731
DatasetExperiment_dist1.4350.0921.541
DatasetExperiment_factor_boxplot0.2670.0030.273
DatasetExperiment_heatmap0.5120.0210.539
HCA0.0800.0020.083
HSD0.3650.0160.391
HSDEM0.5610.0380.604
MTBLS79_DatasetExperiment0.0020.0010.002
OPLSDA0.0160.0010.020
OPLSR0.0190.0010.020
PCA0.0060.0000.007
PLSDA0.0370.0040.044
PLSR0.0110.0020.013
SVM0.0350.0040.038
as_data_frame0.1900.0110.201
autoscale0.0990.0020.102
balanced_accuracy2.1620.0302.214
blank_filter0.4250.0270.458
blank_filter_hist0.0010.0000.001
bootstrap0.0230.0000.023
calculate0.0070.0000.008
chart_plot0.0360.0020.038
classical_lsq0.3730.0070.383
compare_dist4.5010.2724.838
confounders_clsq3.8550.0653.957
confounders_lsq_barchart3.9980.0504.086
confounders_lsq_boxplot3.6900.0423.771
constant_sum_norm0.0180.0010.018
corr_coef0.3520.0040.380
dfa_scores_plot0.9080.0130.928
dratio_filter0.3290.0090.339
equal_split0.1610.0030.166
feature_boxplot0.0430.0020.046
feature_profile0.4810.0110.497
feature_profile_array0.5140.0060.523
filter_by_name0.0340.0010.035
filter_na_count1.2050.0511.265
filter_smeta0.0820.0020.084
fisher_exact13.112 0.16713.412
fold_change13.142 0.13813.383
fold_change_int22.170 0.24022.598
fold_change_plot0.0150.0000.016
forward_selection_by_rank6.9050.1457.114
fs_line7.3210.2357.646
glog_opt_plot0.5780.0080.592
glog_transform0.3450.0040.352
grid_search_1d4.1370.1424.319
gs_line0.0010.0000.001
hca_dendrogram0.0010.0000.001
kfold_xval4.0030.0554.093
kfoldxcv_grid4.6270.0684.750
kfoldxcv_metric0.0010.0000.001
knn_impute0.0140.0010.014
kw_p_hist0.0000.0000.001
kw_rank_sum0.1050.0020.110
linear_model0.0340.0010.035
log_transform0.0170.0010.017
mean_centre0.0040.0010.005
mean_of_medians0.1670.0020.171
mixed_effect0.2420.0050.253
model_apply0.0390.0020.040
model_predict0.0810.0020.083
model_reverse0.0560.0010.057
model_train0.0620.0020.064
mv_boxplot0.3440.0120.358
mv_feature_filter0.1710.0040.179
mv_feature_filter_hist0.0010.0010.001
mv_histogram0.3130.0070.325
mv_sample_filter0.0160.0010.018
mv_sample_filter_hist0.0010.0010.001
nroot_transform0.0180.0000.019
ontology_cache0.0000.0010.001
pairs_filter0.0180.0000.019
pareto_scale0.0760.0010.078
pca_biplot0.0300.0000.031
pca_correlation_plot0.0170.0000.017
pca_dstat_plot0.0210.0000.021
pca_loadings_plot0.0220.0000.022
pca_scores_plot0.6800.0120.704
pca_scree_plot0.0140.0000.015
permutation_test0.0180.0000.019
permutation_test_plot0.0040.0000.005
permute_sample_order0.0200.0010.020
pls_regcoeff_plot0.4460.0090.463
pls_scores_plot1.6280.0771.729
pls_vip_plot0.4530.0080.469
plsda_feature_importance_plot0.6770.0140.702
plsda_predicted_plot0.5380.0100.557
plsda_roc_plot1.3040.0221.341
plsr_cook_dist0.0150.0010.016
plsr_prediction_plot0.0140.0010.016
plsr_qq_plot0.0160.0000.018
plsr_residual_hist0.0270.0010.028
pqn_norm0.4280.0070.441
pqn_norm_hist0.0010.0010.001
prop_na0.0190.0010.020
r_squared0.0010.0010.002
resample0.0270.0010.028
resample_chart0.0030.0000.003
rsd_filter0.0200.0010.022
rsd_filter_hist0.0010.0000.001
run0.0380.0010.039
sb_corr0.0430.0020.046
scatter_chart0.4040.0070.418
split_data0.0170.0010.018
stratified_split0.1690.0030.175
svm_plot_2d0.7550.0240.789
tSNE0.0420.0010.043
tSNE_scatter0.0170.0010.018
tic_chart0.2590.0050.268
ttest0.0230.0010.025
vec_norm0.0010.0010.001
wilcox_p_hist0.0010.0000.002
wilcox_test0.0310.0010.032