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This page was generated on 2025-02-11 11:44 -0500 (Tue, 11 Feb 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.1 LTS)x86_64R Under development (unstable) (2025-01-20 r87609) -- "Unsuffered Consequences" 4719
palomino7Windows Server 2022 Datacenterx64R Under development (unstable) (2025-01-21 r87610 ucrt) -- "Unsuffered Consequences" 4480
lconwaymacOS 12.7.1 Montereyx86_64R Under development (unstable) (2025-01-22 r87618) -- "Unsuffered Consequences" 4491
kjohnson3macOS 13.7.1 Venturaarm64R Under development (unstable) (2025-01-20 r87609) -- "Unsuffered Consequences" 4444
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 2083/2295HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
structToolbox 1.19.1  (landing page)
Gavin Rhys Lloyd
Snapshot Date: 2025-02-10 13:40 -0500 (Mon, 10 Feb 2025)
git_url: https://git.bioconductor.org/packages/structToolbox
git_branch: devel
git_last_commit: 6714233
git_last_commit_date: 2025-01-28 04:25:47 -0500 (Tue, 28 Jan 2025)
nebbiolo1Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
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


CHECK results for structToolbox on kjohnson3

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: 1.19.1
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_1.19.1.tar.gz
StartedAt: 2025-02-10 21:39:43 -0500 (Mon, 10 Feb 2025)
EndedAt: 2025-02-10 21:42:20 -0500 (Mon, 10 Feb 2025)
EllapsedTime: 156.8 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_1.19.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/structToolbox.Rcheck’
* using R Under development (unstable) (2025-01-20 r87609)
* using platform: aarch64-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 Ventura 13.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘structToolbox/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘structToolbox’ version ‘1.19.1’
* 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
* 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-arm64/Resources/library’
* installing *source* package ‘structToolbox’ ...
** this is package ‘structToolbox’ version ‘1.19.1’
** 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) (2025-01-20 r87609) -- "Unsuffered Consequences"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: aarch64-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 
 52.661   0.583  53.366 

Example timings

structToolbox.Rcheck/structToolbox-Ex.timings

nameusersystemelapsed
ANOVA0.0670.0010.069
AUC0.5770.0210.598
DFA0.0570.0010.058
DatasetExperiment_boxplot0.6080.0120.620
DatasetExperiment_dist0.4890.0250.513
DatasetExperiment_factor_boxplot0.060.000.06
DatasetExperiment_heatmap0.1240.0090.133
HCA0.0240.0020.027
HSD0.0810.0040.087
HSDEM0.1430.0070.150
MTBLS79_DatasetExperiment0.0010.0000.000
OPLSDA0.0030.0000.003
OPLSR0.0040.0000.004
PCA0.0010.0000.001
PLSDA0.0070.0000.007
PLSR0.0020.0000.003
SVM0.0080.0010.008
as_data_frame0.0360.0000.036
autoscale0.0280.0010.029
balanced_accuracy0.5060.0150.522
blank_filter0.1070.0070.113
blank_filter_hist0.0000.0000.001
bootstrap0.0050.0000.005
calculate0.0010.0000.002
chart_plot0.0080.0010.008
classical_lsq0.0890.0010.089
compare_dist1.5120.0681.581
confounders_clsq0.8460.0050.852
confounders_lsq_barchart0.8610.0050.876
confounders_lsq_boxplot0.8380.0050.904
constant_sum_norm0.0050.0000.007
corr_coef0.0780.0010.083
dfa_scores_plot0.2130.0020.219
dratio_filter0.0810.0020.084
equal_split0.0350.0000.036
feature_boxplot0.0090.0010.009
feature_profile0.1170.0030.125
feature_profile_array0.1350.0030.148
filter_by_name0.0090.0010.009
filter_na_count0.3630.0230.422
filter_smeta0.0170.0000.017
fisher_exact2.7750.0102.803
fold_change3.2290.0103.258
fold_change_int4.5420.0054.547
fold_change_plot0.0040.0000.004
forward_selection_by_rank2.0200.0552.087
fs_line1.7520.0401.800
glog_opt_plot0.1320.0010.133
glog_transform0.0930.0030.096
grid_search_1d1.1060.0521.162
gs_line000
hca_dendrogram0.0000.0000.001
kfold_xval0.9010.0080.908
kfoldxcv_grid1.0320.0081.040
kfoldxcv_metric000
knn_impute0.0030.0000.004
kw_p_hist0.0010.0000.000
kw_rank_sum0.0220.0010.022
linear_model0.0070.0000.008
log_transform0.0040.0000.004
mean_centre0.0000.0010.001
mean_of_medians0.0330.0000.033
mixed_effect0.0510.0010.051
model_apply0.0060.0000.006
model_predict0.0160.0000.016
model_reverse0.0120.0000.012
model_train0.0140.0000.014
mv_boxplot0.0880.0030.090
mv_feature_filter0.0330.0000.034
mv_feature_filter_hist0.0010.0000.001
mv_histogram0.0770.0010.078
mv_sample_filter0.0050.0010.005
mv_sample_filter_hist000
nroot_transform0.0040.0000.005
ontology_cache000
pairs_filter0.0040.0000.005
pareto_scale0.0160.0000.016
pca_biplot0.0050.0000.006
pca_correlation_plot0.0030.0000.003
pca_dstat_plot0.0040.0000.003
pca_loadings_plot0.0040.0000.004
pca_scores_plot0.1570.0010.158
pca_scree_plot0.0030.0000.004
permutation_test0.0050.0000.005
permutation_test_plot0.0010.0000.000
permute_sample_order0.0040.0000.004
pls_regcoeff_plot0.1100.0020.113
pls_scores_plot0.1980.0020.200
pls_vip_plot0.1010.0010.103
plsda_feature_importance_plot0.1770.0070.188
plsda_predicted_plot0.1330.0020.135
plsda_roc_plot0.3370.0040.344
plsr_cook_dist0.0040.0000.004
plsr_prediction_plot0.0030.0000.003
plsr_qq_plot0.0040.0000.003
plsr_residual_hist0.0030.0000.003
pqn_norm0.1010.0000.107
pqn_norm_hist0.0010.0000.000
prop_na0.0050.0000.005
r_squared000
resample0.0070.0000.007
resample_chart0.0010.0000.001
rsd_filter0.0050.0000.006
rsd_filter_hist0.0010.0000.000
run0.0080.0000.009
sb_corr0.010.000.01
scatter_chart0.0970.0010.098
split_data0.0050.0000.004
stratified_split0.0390.0010.040
svm_plot_2d0.2010.0070.208
tSNE0.010.000.01
tSNE_scatter0.0040.0010.004
tic_chart0.0670.0010.069
ttest0.0060.0010.006
vec_norm000
wilcox_p_hist000
wilcox_test0.0070.0000.007