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

This page was generated on 2024-05-04 11:37:15 -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 nebbiolo1


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: /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:structToolbox.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings structToolbox_1.16.0.tar.gz
StartedAt: 2024-05-04 04:09:59 -0400 (Sat, 04 May 2024)
EndedAt: 2024-05-04 04:27:45 -0400 (Sat, 04 May 2024)
EllapsedTime: 1066.8 seconds
RetCode: 0
Status:   OK  
CheckDir: structToolbox.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:structToolbox.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings structToolbox_1.16.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/structToolbox.Rcheck’
* using R version 4.4.0 beta (2024-04-15 r86425)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
    GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
* running under: Ubuntu 22.04.4 LTS
* using session charset: UTF-8
* 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 loading without being on the library search path ... 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           18.548  0.156  18.704
fold_change               10.112  0.124  10.236
fisher_exact               9.574  0.132   9.706
fs_line                    6.711  0.136   6.848
forward_selection_by_rank  5.792  0.072   5.864
* 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 re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: OK


Installation output

structToolbox.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD INSTALL structToolbox
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.19-bioc/R/site-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 (2024-04-15 r86425) -- "Puppy Cup"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu

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 
167.245   1.686 168.921 

Example timings

structToolbox.Rcheck/structToolbox-Ex.timings

nameusersystemelapsed
ANOVA0.1950.0000.196
AUC1.7610.2191.981
DFA0.1780.0040.182
DatasetExperiment_boxplot0.8220.0320.854
DatasetExperiment_dist2.4790.1092.587
DatasetExperiment_factor_boxplot0.2020.0000.201
DatasetExperiment_heatmap0.3850.0000.385
HCA0.0670.0000.067
HSD0.2990.0070.311
HSDEM0.3610.0000.361
MTBLS79_DatasetExperiment0.0010.0000.001
OPLSDA0.0110.0000.011
OPLSR0.0140.0000.014
PCA0.0040.0000.004
PLSDA0.0240.0000.024
PLSR0.0090.0000.009
SVM0.0260.0000.026
as_data_frame0.1210.0000.121
autoscale0.0730.0030.076
balanced_accuracy1.7680.0281.796
blank_filter0.3230.0200.343
blank_filter_hist0.0010.0000.001
bootstrap0.0160.0000.017
calculate0.0010.0030.005
chart_plot0.0270.0000.027
classical_lsq0.2890.0120.301
compare_dist3.7160.2323.949
confounders_clsq2.6930.0572.749
confounders_lsq_barchart2.7930.0672.861
confounders_lsq_boxplot2.7320.0332.764
constant_sum_norm0.0140.0000.014
corr_coef0.2570.0000.257
dfa_scores_plot0.6750.0030.679
dratio_filter0.2680.0000.268
equal_split0.1110.0030.115
feature_boxplot0.0290.0000.030
feature_profile0.3480.0150.365
feature_profile_array0.4310.0240.455
filter_by_name0.0280.0000.029
filter_na_count0.8900.0190.910
filter_smeta0.0530.0000.054
fisher_exact9.5740.1329.706
fold_change10.112 0.12410.236
fold_change_int18.548 0.15618.704
fold_change_plot0.010.000.01
forward_selection_by_rank5.7920.0725.864
fs_line6.7110.1366.848
glog_opt_plot0.4160.0000.416
glog_transform0.2640.0000.264
grid_search_1d3.3010.0283.330
gs_line0.0010.0000.001
hca_dendrogram0.0010.0000.001
kfold_xval3.1830.0043.188
kfoldxcv_grid3.3680.0163.384
kfoldxcv_metric0.0010.0000.001
knn_impute0.0110.0000.012
kw_p_hist0.0010.0000.001
kw_rank_sum0.0750.0000.074
linear_model0.0270.0000.026
log_transform0.0140.0000.013
mean_centre0.0040.0000.003
mean_of_medians0.1130.0000.112
mixed_effect0.1600.0000.159
model_apply0.0220.0000.022
model_predict0.0510.0000.051
model_reverse0.0380.0000.038
model_train0.0460.0000.046
mv_boxplot0.2510.0040.256
mv_feature_filter0.1020.0000.102
mv_feature_filter_hist0.0010.0000.001
mv_histogram0.2180.0000.218
mv_sample_filter0.0140.0000.015
mv_sample_filter_hist0.0010.0000.000
nroot_transform0.0120.0000.012
ontology_cache000
pairs_filter0.0140.0000.015
pareto_scale0.0510.0000.051
pca_biplot0.0180.0000.018
pca_correlation_plot0.010.000.01
pca_dstat_plot0.0130.0000.012
pca_loadings_plot0.0130.0000.013
pca_scores_plot0.4930.0000.494
pca_scree_plot0.0070.0040.010
permutation_test0.0160.0000.016
permutation_test_plot0.0020.0000.003
permute_sample_order0.0110.0030.013
pls_regcoeff_plot0.3040.0040.308
pls_scores_plot0.6270.0000.626
pls_vip_plot0.3170.0040.320
plsda_feature_importance_plot0.5630.0040.567
plsda_predicted_plot0.4040.0000.404
plsda_roc_plot1.0030.0201.024
plsr_cook_dist0.0120.0000.012
plsr_prediction_plot0.0080.0030.011
plsr_qq_plot0.0030.0080.011
plsr_residual_hist0.010.000.01
pqn_norm0.3160.0040.319
pqn_norm_hist0.0010.0000.001
prop_na0.0140.0000.015
r_squared0.0010.0000.001
resample0.0210.0000.021
resample_chart0.0030.0000.003
rsd_filter0.0190.0000.019
rsd_filter_hist0.0010.0000.001
run0.0260.0000.026
sb_corr0.0290.0000.029
scatter_chart0.3070.0000.307
split_data0.0130.0000.013
stratified_split0.110.000.11
svm_plot_2d0.5950.0040.599
tSNE0.0240.0040.028
tSNE_scatter0.0120.0000.012
tic_chart0.1930.0040.197
ttest0.0180.0000.018
vec_norm0.0010.0000.001
wilcox_p_hist000
wilcox_test0.0230.0000.023