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This page was generated on 2025-03-17 11:39 -0400 (Mon, 17 Mar 2025).

HostnameOSArch (*)R versionInstalled pkgs
palomino7Windows Server 2022 Datacenterx64R Under development (unstable) (2025-03-01 r87860 ucrt) -- "Unsuffered Consequences" 4545
lconwaymacOS 12.7.1 Montereyx86_64R Under development (unstable) (2025-03-02 r87868) -- "Unsuffered Consequences" 4576
kjohnson3macOS 13.7.1 Venturaarm64R Under development (unstable) (2025-03-02 r87868) -- "Unsuffered Consequences" 4528
kunpeng2Linux (openEuler 24.03 LTS)aarch64R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" 4459
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 2096/2313HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
structToolbox 1.19.2  (landing page)
Gavin Rhys Lloyd
Snapshot Date: 2025-03-16 13:40 -0400 (Sun, 16 Mar 2025)
git_url: https://git.bioconductor.org/packages/structToolbox
git_branch: devel
git_last_commit: 4fab996
git_last_commit_date: 2025-02-19 06:09:45 -0400 (Wed, 19 Feb 2025)
palomino7Windows 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
kjohnson3macOS 13.7.1 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published
kunpeng2Linux (openEuler 24.03 LTS) / aarch64  OK    OK    OK  


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: 1.19.2
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_1.19.2.tar.gz
StartedAt: 2025-03-17 00:07:27 -0400 (Mon, 17 Mar 2025)
EndedAt: 2025-03-17 00:16:24 -0400 (Mon, 17 Mar 2025)
EllapsedTime: 536.8 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_1.19.2.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/structToolbox.Rcheck’
* using R Under development (unstable) (2025-03-02 r87868)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 14.2.0
* 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 ‘1.19.2’
* 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           17.821  0.104  18.033
fold_change               12.724  0.104  12.915
fisher_exact              12.015  0.079  12.188
forward_selection_by_rank  7.201  0.138   7.386
fs_line                    7.084  0.124   7.247
* 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/4.5-x86_64/Resources/library’
* installing *source* package ‘structToolbox’ ...
** this is package ‘structToolbox’ version ‘1.19.2’
** 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 Under development (unstable) (2025-03-02 r87868) -- "Unsuffered Consequences"
Copyright (C) 2025 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 
203.795   2.652 208.219 

Example timings

structToolbox.Rcheck/structToolbox-Ex.timings

nameusersystemelapsed
ANOVA0.3240.0130.339
AUC2.2650.1162.397
DFA0.2460.0030.253
DatasetExperiment_boxplot1.5340.0601.606
DatasetExperiment_dist2.0880.1102.215
DatasetExperiment_factor_boxplot0.3000.0030.306
DatasetExperiment_heatmap0.4800.0280.514
HCA0.0750.0060.081
HSD0.3330.0180.358
HSDEM0.5430.0240.571
MTBLS79_DatasetExperiment0.0010.0000.001
OPLSDA0.0110.0010.011
OPLSR0.0190.0000.019
PCA0.0060.0000.007
PLSDA0.0260.0000.026
PLSR0.0080.0010.008
SVM0.0250.0010.026
as_data_frame0.1500.0020.152
autoscale0.0960.0010.096
balanced_accuracy2.1450.0242.184
blank_filter0.4390.0250.465
blank_filter_hist0.0010.0010.001
bootstrap0.0260.0010.027
calculate0.0070.0010.008
chart_plot0.0330.0010.034
classical_lsq0.3920.0050.401
compare_dist4.3920.2704.709
confounders_clsq3.5110.0343.567
confounders_lsq_barchart3.6850.0283.731
confounders_lsq_boxplot3.6630.0263.711
constant_sum_norm0.0160.0000.017
corr_coef0.3250.0030.331
dfa_scores_plot0.8470.0070.858
dratio_filter0.3120.0080.322
equal_split0.1550.0020.157
feature_boxplot0.0330.0010.034
feature_profile0.4490.0100.464
feature_profile_array0.5210.0050.527
filter_by_name0.0370.0010.038
filter_na_count1.2190.0531.285
filter_smeta0.0750.0010.077
fisher_exact12.015 0.07912.188
fold_change12.724 0.10412.915
fold_change_int17.821 0.10418.033
fold_change_plot0.0140.0010.016
forward_selection_by_rank7.2010.1387.386
fs_line7.0840.1247.247
glog_opt_plot0.5350.0050.544
glog_transform0.3340.0030.341
grid_search_1d3.8310.1564.012
gs_line0.0010.0000.001
hca_dendrogram0.0000.0000.001
kfold_xval3.7670.0303.813
kfoldxcv_grid4.3690.0374.429
kfoldxcv_metric0.0010.0000.002
knn_impute0.0140.0000.015
kw_p_hist0.0010.0000.001
kw_rank_sum0.0830.0000.084
linear_model0.0300.0000.031
log_transform0.0160.0000.016
mean_centre0.0040.0000.004
mean_of_medians0.1510.0010.152
mixed_effect0.1950.0020.200
model_apply0.0240.0010.025
model_predict0.0650.0010.066
model_reverse0.0480.0000.049
model_train0.0610.0000.061
mv_boxplot0.3420.0150.358
mv_feature_filter0.1470.0030.151
mv_feature_filter_hist0.0010.0000.001
mv_histogram0.2940.0040.300
mv_sample_filter0.0210.0010.021
mv_sample_filter_hist0.0000.0010.001
nroot_transform0.0180.0000.018
ontology_cache000
pairs_filter0.0210.0000.021
pareto_scale0.0710.0010.073
pca_biplot0.0270.0010.028
pca_correlation_plot0.0130.0010.013
pca_dstat_plot0.0160.0000.016
pca_loadings_plot0.0200.0000.021
pca_scores_plot0.6600.0100.677
pca_scree_plot0.0150.0000.015
permutation_test0.0190.0000.019
permutation_test_plot0.0030.0000.004
permute_sample_order0.0180.0010.018
pls_regcoeff_plot0.4420.0080.455
pls_scores_plot0.8090.0070.822
pls_vip_plot0.3830.0040.389
plsda_feature_importance_plot0.6530.0080.664
plsda_predicted_plot0.5410.0070.552
plsda_roc_plot1.3610.0141.383
plsr_cook_dist0.0150.0000.015
plsr_prediction_plot0.0120.0000.013
plsr_qq_plot0.0130.0010.013
plsr_residual_hist0.0130.0010.012
pqn_norm0.3960.0050.403
pqn_norm_hist0.0010.0000.001
prop_na0.0180.0010.020
r_squared0.0010.0010.001
resample0.0420.0010.044
resample_chart0.0050.0000.006
rsd_filter0.0240.0010.024
rsd_filter_hist0.0010.0000.002
run0.0380.0010.039
sb_corr0.0300.0000.031
scatter_chart0.3430.0030.348
split_data0.0120.0000.011
stratified_split0.1540.0010.158
svm_plot_2d0.7940.0190.819
tSNE0.0360.0010.037
tSNE_scatter0.0160.0000.017
tic_chart0.2290.0020.232
ttest0.0250.0000.025
vec_norm0.0020.0000.001
wilcox_p_hist0.0010.0010.000
wilcox_test0.0240.0000.024