Back to Multiple platform build/check report for BioC 3.20:   simplified   long
ABCDEFGHIJKLMNOPQR[S]TUVWXYZ

This page was generated on 2024-11-09 21:31 -0500 (Sat, 09 Nov 2024).

HostnameOSArch (*)R versionInstalled pkgs
teran2Linux (Ubuntu 24.04.1 LTS)x86_644.4.1 (2024-06-14) -- "Race for Your Life" 4505
palomino8Windows Server 2022 Datacenterx644.4.1 (2024-06-14 ucrt) -- "Race for Your Life" 4506
lconwaymacOS 12.7.1 Montereyx86_644.4.1 (2024-06-14) -- "Race for Your Life" 4538
kjohnson3macOS 13.6.5 Venturaarm644.4.1 (2024-06-14) -- "Race for Your Life" 4486
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch644.4.1 (2024-06-14) -- "Race for Your Life" 4493
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: 2024-11-08 13:40 -0500 (Fri, 08 Nov 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)
teran2Linux (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
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson3macOS 13.6.5 Ventura / arm64  OK    OK    OK    OK  YES
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  OK    OK    OK  


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: 1.18.0
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: 2024-11-09 14:34:06 -0500 (Sat, 09 Nov 2024)
EndedAt: 2024-11-09 14:40:18 -0500 (Sat, 09 Nov 2024)
EllapsedTime: 371.6 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_1.18.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/structToolbox.Rcheck’
* using R version 4.4.1 (2024-06-14)
* 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 13.6.7
* 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 ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
  cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
 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 4.4.1 (2024-06-14) -- "Race for Your Life"
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 166 ]

[ FAIL 0 | WARN 6 | SKIP 0 | PASS 166 ]
> 
> proc.time()
   user  system elapsed 
 51.467   0.506  51.974 

Example timings

structToolbox.Rcheck/structToolbox-Ex.timings

nameusersystemelapsed
ANOVA0.0660.0020.068
AUC0.5420.0200.563
DFA0.0520.0010.054
DatasetExperiment_boxplot0.5790.0070.587
DatasetExperiment_dist0.4590.0090.469
DatasetExperiment_factor_boxplot0.0570.0010.057
DatasetExperiment_heatmap0.1210.0030.123
HCA0.0190.0000.020
HSD0.0850.0040.091
HSDEM0.1350.0050.141
MTBLS79_DatasetExperiment0.0000.0000.001
OPLSDA0.0030.0000.003
OPLSR0.0040.0010.004
PCA0.0010.0000.001
PLSDA0.0070.0000.007
PLSR0.0020.0000.002
SVM0.0070.0010.008
as_data_frame0.0350.0000.036
autoscale0.0210.0010.021
balanced_accuracy0.4630.0020.466
blank_filter0.1050.0040.112
blank_filter_hist0.0010.0000.000
bootstrap0.0040.0000.005
calculate0.0010.0000.002
chart_plot0.0070.0000.008
classical_lsq0.0840.0010.084
compare_dist1.3800.0811.462
confounders_clsq0.7640.0030.767
confounders_lsq_barchart0.8000.0030.804
confounders_lsq_boxplot0.7830.0040.786
constant_sum_norm0.0040.0000.004
corr_coef0.0700.0010.071
dfa_scores_plot0.1870.0010.188
dratio_filter0.0730.0010.075
equal_split0.0320.0000.033
feature_boxplot0.0080.0000.008
feature_profile0.1020.0010.103
feature_profile_array0.1260.0010.128
filter_by_name0.0080.0000.009
filter_na_count0.3310.0100.342
filter_smeta0.0170.0000.017
fisher_exact2.6130.0022.615
fold_change3.0100.0123.022
fold_change_int4.4170.0054.421
fold_change_plot0.020.000.02
forward_selection_by_rank1.7280.0271.755
fs_line1.9750.0462.022
glog_opt_plot0.1290.0010.131
glog_transform0.0730.0000.074
grid_search_1d1.0540.0361.091
gs_line000
hca_dendrogram0.0000.0000.001
kfold_xval0.9010.0050.906
kfoldxcv_grid0.9650.0060.971
kfoldxcv_metric000
knn_impute0.0030.0010.004
kw_p_hist000
kw_rank_sum0.0210.0000.022
linear_model0.0120.0000.013
log_transform0.0030.0000.004
mean_centre0.0010.0000.001
mean_of_medians0.0340.0000.034
mixed_effect0.0460.0000.047
model_apply0.0070.0010.007
model_predict0.0140.0000.014
model_reverse0.0120.0000.012
model_train0.0140.0000.014
mv_boxplot0.0780.0000.079
mv_feature_filter0.0300.0010.030
mv_feature_filter_hist000
mv_histogram0.0690.0010.070
mv_sample_filter0.0050.0000.005
mv_sample_filter_hist0.0000.0000.001
nroot_transform0.0040.0000.004
ontology_cache0.0010.0000.001
pairs_filter0.0040.0000.004
pareto_scale0.0150.0000.014
pca_biplot0.0050.0000.005
pca_correlation_plot0.0030.0000.003
pca_dstat_plot0.0030.0000.004
pca_loadings_plot0.0040.0000.004
pca_scores_plot0.1350.0020.137
pca_scree_plot0.0030.0000.003
permutation_test0.0050.0000.004
permutation_test_plot0.0010.0000.001
permute_sample_order0.0040.0000.004
pls_regcoeff_plot0.0900.0010.091
pls_scores_plot0.1850.0010.187
pls_vip_plot0.0990.0010.099
plsda_feature_importance_plot0.1610.0020.163
plsda_predicted_plot0.1150.0010.116
plsda_roc_plot0.3180.0030.321
plsr_cook_dist0.0040.0000.003
plsr_prediction_plot0.0030.0000.003
plsr_qq_plot0.0030.0000.003
plsr_residual_hist0.0030.0000.002
pqn_norm0.0870.0000.088
pqn_norm_hist0.0010.0000.000
prop_na0.0040.0000.004
r_squared0.0010.0000.001
resample0.0060.0000.006
resample_chart0.0010.0000.001
rsd_filter0.0090.0010.009
rsd_filter_hist000
run0.010.000.01
sb_corr0.0090.0000.009
scatter_chart0.0900.0000.091
split_data0.0040.0010.004
stratified_split0.0320.0000.032
svm_plot_2d0.1840.0050.190
tSNE0.0090.0010.009
tSNE_scatter0.0030.0000.004
tic_chart0.0560.0010.056
ttest0.0050.0000.005
vec_norm0.0010.0000.000
wilcox_p_hist000
wilcox_test0.0070.0000.007