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This page was generated on 2024-05-07 11:32:46 -0400 (Tue, 07 May 2024).

HostnameOSArch (*)R versionInstalled pkgs
kjohnson3macOS 13.6.5 Venturaarm644.4.0 (2024-04-24) -- "Puppy Cup" 4461
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Package 2095/2300HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
structToolbox 1.16.0  (landing page)
Gavin Rhys Lloyd
Snapshot Date: 2024-05-06 14:00:02 -0400 (Mon, 06 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)
kjohnson3macOS 13.6.5 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:
- 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: 2024-05-07 01:19:20 -0400 (Tue, 07 May 2024)
EndedAt: 2024-05-07 01:21:50 -0400 (Tue, 07 May 2024)
EllapsedTime: 149.7 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_1.16.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.19-bioc-mac-arm64/meat/structToolbox.Rcheck’
* using R version 4.4.0 (2024-04-24)
* using platform: aarch64-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 Ventura 13.6.5
* 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
* 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-arm64/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 (2024-04-24) -- "Puppy Cup"
Copyright (C) 2024 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 156 ]

[ FAIL 0 | WARN 6 | SKIP 0 | PASS 156 ]
> 
> proc.time()
   user  system elapsed 
 47.242   0.483  47.723 

Example timings

structToolbox.Rcheck/structToolbox-Ex.timings

nameusersystemelapsed
ANOVA0.0670.0010.069
AUC0.8570.0070.863
DFA0.0560.0000.056
DatasetExperiment_boxplot0.2950.0100.305
DatasetExperiment_dist0.4540.0150.469
DatasetExperiment_factor_boxplot0.0560.0010.057
DatasetExperiment_heatmap0.1250.0100.135
HCA0.0180.0000.017
HSD0.0810.0030.086
HSDEM0.1630.0100.173
MTBLS79_DatasetExperiment000
OPLSDA0.0030.0000.003
OPLSR0.0050.0010.006
PCA0.0010.0000.002
PLSDA0.0080.0010.009
PLSR0.0030.0010.003
SVM0.0080.0010.009
as_data_frame0.0380.0030.042
autoscale0.0210.0020.024
balanced_accuracy0.4930.0060.499
blank_filter0.1120.0040.117
blank_filter_hist000
bootstrap0.010.000.01
calculate0.0010.0000.002
chart_plot0.0080.0000.008
classical_lsq0.0840.0010.085
compare_dist1.5050.0691.575
confounders_clsq0.8250.0090.835
confounders_lsq_barchart0.8520.0050.858
confounders_lsq_boxplot0.8350.0040.846
constant_sum_norm0.0040.0000.004
corr_coef0.0710.0000.071
dfa_scores_plot0.2050.0020.207
dratio_filter0.0810.0020.083
equal_split0.0350.0000.036
feature_boxplot0.0090.0010.009
feature_profile0.1150.0040.120
feature_profile_array0.1330.0010.134
filter_by_name0.0090.0000.009
filter_na_count0.3250.0180.342
filter_smeta0.0180.0000.018
fisher_exact2.5670.0182.586
fold_change2.8570.0112.868
fold_change_int4.6520.0034.655
fold_change_plot0.0030.0000.004
forward_selection_by_rank1.8680.0531.920
fs_line1.6840.0281.712
glog_opt_plot0.1340.0010.135
glog_transform0.0770.0000.077
grid_search_1d1.3830.0611.445
gs_line0.0010.0000.000
hca_dendrogram000
kfold_xval0.9270.0070.935
kfoldxcv_grid1.0210.0081.032
kfoldxcv_metric0.0010.0000.001
knn_impute0.0030.0000.004
kw_p_hist0.0010.0000.000
kw_rank_sum0.0230.0000.024
linear_model0.0080.0000.008
log_transform0.0040.0000.004
mean_centre0.0000.0000.001
mean_of_medians0.0330.0000.034
mixed_effect0.0520.0010.054
model_apply0.0060.0000.007
model_predict0.0220.0010.023
model_reverse0.0120.0000.013
model_train0.0140.0010.014
mv_boxplot0.0790.0000.080
mv_feature_filter0.0340.0000.034
mv_feature_filter_hist0.0010.0000.000
mv_histogram0.0740.0010.075
mv_sample_filter0.0050.0010.005
mv_sample_filter_hist0.0010.0000.000
nroot_transform0.0040.0000.004
ontology_cache000
pairs_filter0.0050.0000.005
pareto_scale0.0160.0010.016
pca_biplot0.0060.0000.006
pca_correlation_plot0.0030.0000.003
pca_dstat_plot0.0040.0000.004
pca_loadings_plot0.0040.0000.004
pca_scores_plot0.1490.0020.152
pca_scree_plot0.0030.0000.004
permutation_test0.0050.0000.005
permutation_test_plot0.0010.0000.001
permute_sample_order0.0040.0000.004
pls_regcoeff_plot0.1010.0010.102
pls_scores_plot0.1980.0010.199
pls_vip_plot0.1030.0010.107
plsda_feature_importance_plot0.1710.0010.172
plsda_predicted_plot0.1290.0020.130
plsda_roc_plot0.3390.0030.342
plsr_cook_dist0.0040.0000.004
plsr_prediction_plot0.0030.0000.003
plsr_qq_plot0.0040.0000.004
plsr_residual_hist0.0030.0000.003
pqn_norm0.0980.0010.099
pqn_norm_hist000
prop_na0.0050.0000.005
r_squared0.0010.0000.000
resample0.0060.0000.007
resample_chart0.0010.0000.001
rsd_filter0.0060.0000.006
rsd_filter_hist000
run0.0090.0000.009
sb_corr0.0090.0010.010
scatter_chart0.0940.0000.094
split_data0.0040.0000.005
stratified_split0.0350.0000.035
svm_plot_2d0.1990.0050.210
tSNE0.0090.0010.009
tSNE_scatter0.0030.0000.003
tic_chart0.0620.0010.062
ttest0.0050.0000.006
vec_norm000
wilcox_p_hist000
wilcox_test0.0080.0000.008