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This page was generated on 2024-12-23 12:07 -0500 (Mon, 23 Dec 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.1 LTS)x86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4744
palomino8Windows Server 2022 Datacenterx644.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" 4487
merida1macOS 12.7.5 Montereyx86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4515
kjohnson1macOS 13.6.6 Venturaarm644.4.2 (2024-10-31) -- "Pile of Leaves" 4467
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 2079/2289HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
structToolbox 1.18.0  (landing page)
Gavin Rhys Lloyd
Snapshot Date: 2024-12-19 13:00 -0500 (Thu, 19 Dec 2024)
git_url: https://git.bioconductor.org/packages/structToolbox
git_branch: RELEASE_3_20
git_last_commit: 6758b3b
git_last_commit_date: 2024-10-29 10:43:03 -0500 (Tue, 29 Oct 2024)
nebbiolo2Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino8Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 12.7.5 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.6 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published


CHECK results for structToolbox on merida1

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: 1.18.0
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_1.18.0.tar.gz
StartedAt: 2024-12-20 10:25:04 -0500 (Fri, 20 Dec 2024)
EndedAt: 2024-12-20 10:43:35 -0500 (Fri, 20 Dec 2024)
EllapsedTime: 1110.8 seconds
RetCode: 0
Status:   OK  
CheckDir: structToolbox.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### 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_1.18.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/structToolbox.Rcheck’
* using R version 4.4.2 (2024-10-31)
* 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 12.7.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘structToolbox/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘structToolbox’ version ‘1.18.0’
* 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           40.764  0.184  46.580
fold_change               28.681  0.166  31.347
fisher_exact              23.552  0.081  23.980
fs_line                   15.742  0.186  18.724
forward_selection_by_rank 14.558  0.139  16.613
kfoldxcv_grid              8.962  0.054  10.150
grid_search_1d             8.636  0.130   9.907
kfold_xval                 8.279  0.046   9.408
compare_dist               7.807  0.271   8.639
confounders_lsq_barchart   7.524  0.049   7.953
confounders_clsq           7.389  0.060   8.139
confounders_lsq_boxplot    7.289  0.034   7.613
AUC                        5.193  0.263   6.228
balanced_accuracy          4.377  0.033   5.073
* 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 4.4.2 (2024-10-31) -- "Pile of Leaves"
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 166 ]

[ FAIL 0 | WARN 6 | SKIP 0 | PASS 166 ]
> 
> proc.time()
   user  system elapsed 
446.367   3.697 461.595 

Example timings

structToolbox.Rcheck/structToolbox-Ex.timings

nameusersystemelapsed
ANOVA0.5180.0110.596
AUC5.1930.2636.228
DFA0.5070.0040.573
DatasetExperiment_boxplot2.3700.0742.790
DatasetExperiment_dist1.8950.1072.283
DatasetExperiment_factor_boxplot0.4990.0050.579
DatasetExperiment_heatmap1.0030.0381.183
HCA0.1700.0170.204
HSD0.7200.0260.993
HSDEM0.9250.0361.095
MTBLS79_DatasetExperiment0.0030.0010.003
OPLSDA0.0290.0010.036
OPLSR0.0400.0020.049
PCA0.0110.0010.013
PLSDA0.0660.0010.077
PLSR0.0240.0010.027
SVM0.0740.0010.086
as_data_frame0.3180.0030.360
autoscale0.1870.0020.216
balanced_accuracy4.3770.0335.073
blank_filter0.8170.0270.940
blank_filter_hist0.0020.0010.004
bootstrap0.0440.0010.052
calculate0.0110.0010.012
chart_plot0.0620.0030.070
classical_lsq0.7580.0040.846
compare_dist7.8070.2718.639
confounders_clsq7.3890.0608.139
confounders_lsq_barchart7.5240.0497.953
confounders_lsq_boxplot7.2890.0347.613
constant_sum_norm0.0340.0010.035
corr_coef0.6430.0050.696
dfa_scores_plot1.7200.0111.851
dratio_filter0.7450.0200.831
equal_split0.2860.0020.289
feature_boxplot0.0740.0010.075
feature_profile0.9480.0151.017
feature_profile_array1.1200.0111.140
filter_by_name0.0760.0010.079
filter_na_count2.8920.0933.120
filter_smeta0.1640.0020.169
fisher_exact23.552 0.08123.980
fold_change28.681 0.16631.347
fold_change_int40.764 0.18446.580
fold_change_plot0.0300.0000.033
forward_selection_by_rank14.558 0.13916.613
fs_line15.742 0.18618.724
glog_opt_plot1.1880.0081.378
glog_transform0.7190.0040.828
grid_search_1d8.6360.1309.907
gs_line0.0020.0000.002
hca_dendrogram0.0010.0000.001
kfold_xval8.2790.0469.408
kfoldxcv_grid 8.962 0.05410.150
kfoldxcv_metric0.0020.0000.002
knn_impute0.0310.0010.035
kw_p_hist0.0010.0010.002
kw_rank_sum0.1880.0020.207
linear_model0.0670.0020.081
log_transform0.0340.0010.038
mean_centre0.0080.0000.008
mean_of_medians0.3180.0030.363
mixed_effect0.3870.0030.423
model_apply0.0540.0020.059
model_predict0.1300.0010.142
model_reverse0.1030.0010.113
model_train0.1250.0020.138
mv_boxplot0.6490.0050.738
mv_feature_filter0.3050.0070.344
mv_feature_filter_hist0.0010.0010.002
mv_histogram0.5940.0370.675
mv_sample_filter0.0240.0010.026
mv_sample_filter_hist0.0010.0000.002
nroot_transform0.0180.0000.018
ontology_cache0.0010.0010.002
pairs_filter0.0290.0010.030
pareto_scale0.0810.0020.115
pca_biplot0.0460.0010.049
pca_correlation_plot0.0240.0010.027
pca_dstat_plot0.0350.0000.042
pca_loadings_plot0.0370.0010.040
pca_scores_plot1.0650.0221.674
pca_scree_plot0.0170.0010.029
permutation_test0.0220.0010.023
permutation_test_plot0.0040.0010.015
permute_sample_order0.0220.0010.022
pls_regcoeff_plot0.5540.0080.575
pls_scores_plot1.5530.0292.166
pls_vip_plot0.9250.0361.159
plsda_feature_importance_plot1.3370.0201.461
plsda_predicted_plot0.7750.0110.817
plsda_roc_plot2.6580.0342.946
plsr_cook_dist0.0270.0010.029
plsr_prediction_plot0.0280.0010.029
plsr_qq_plot0.0280.0010.030
plsr_residual_hist0.0280.0010.032
pqn_norm0.8820.0060.956
pqn_norm_hist0.0020.0000.002
prop_na0.0430.0010.051
r_squared0.0020.0010.002
resample0.0620.0010.070
resample_chart0.0070.0010.008
rsd_filter0.0500.0020.057
rsd_filter_hist0.0020.0000.003
run0.0710.0020.082
sb_corr0.0900.0020.107
scatter_chart0.8380.0080.929
split_data0.0350.0010.041
stratified_split0.3080.0040.345
svm_plot_2d1.5310.0381.757
tSNE0.0780.0020.087
tSNE_scatter0.0290.0010.034
tic_chart0.4890.0050.535
ttest0.0580.0010.067
vec_norm0.0010.0000.003
wilcox_p_hist0.0020.0010.003
wilcox_test0.0630.0010.069