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This page was generated on 2024-11-20 12:07 -0500 (Wed, 20 Nov 2024).

HostnameOSArch (*)R versionInstalled pkgs
teran2Linux (Ubuntu 24.04.1 LTS)x86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4481
nebbiolo2Linux (Ubuntu 24.04.1 LTS)x86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4479
palomino8Windows Server 2022 Datacenterx644.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" 4359
lconwaymacOS 12.7.1 Montereyx86_644.4.1 (2024-06-14) -- "Race for Your Life" 4539
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: 2024-11-19 13:40 -0500 (Tue, 19 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
nebbiolo2Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    OK  
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
kunpeng2Linux (openEuler 22.03 LTS-SP1) / 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: 1.18.0
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: 2024-11-20 03:10:55 -0500 (Wed, 20 Nov 2024)
EndedAt: 2024-11-20 03:20:56 -0500 (Wed, 20 Nov 2024)
EllapsedTime: 601.4 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: 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 ...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
Examples with CPU (user + system) or elapsed time > 5s
                  user system elapsed
fold_change_int 12.986  0.041  13.070
fold_change      9.235  0.064   9.343
fisher_exact     8.270  0.041   8.342
fs_line          5.423  0.110   5.549
* 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 4.4.1 (2024-06-14) -- "Race for Your Life"
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 
138.059   1.501 140.143 

Example timings

structToolbox.Rcheck/structToolbox-Ex.timings

nameusersystemelapsed
ANOVA0.1860.0060.194
AUC1.6410.0781.723
DFA0.1650.0010.165
DatasetExperiment_boxplot1.2500.0531.306
DatasetExperiment_dist1.0280.0801.113
DatasetExperiment_factor_boxplot0.1820.0040.188
DatasetExperiment_heatmap0.3290.0150.346
HCA0.0600.0030.063
HSD0.2460.0170.296
HSDEM0.4190.0200.447
MTBLS79_DatasetExperiment0.0010.0000.001
OPLSDA0.0090.0000.009
OPLSR0.0120.0000.012
PCA0.0040.0000.003
PLSDA0.020.000.02
PLSR0.0070.0010.008
SVM0.0210.0010.022
as_data_frame0.1020.0010.104
autoscale0.0620.0010.063
balanced_accuracy1.4430.0131.462
blank_filter0.3060.0160.326
blank_filter_hist0.0010.0000.001
bootstrap0.0140.0000.014
calculate0.0050.0000.005
chart_plot0.0220.0000.024
classical_lsq0.2660.0020.270
compare_dist3.5220.2403.777
confounders_clsq2.3910.0182.419
confounders_lsq_barchart2.7080.0242.746
confounders_lsq_boxplot2.4960.0192.524
constant_sum_norm0.0120.0000.012
corr_coef0.2310.0020.235
dfa_scores_plot0.5660.0060.574
dratio_filter0.2120.0050.217
equal_split0.1080.0010.109
feature_boxplot0.0260.0000.028
feature_profile0.3040.0060.310
feature_profile_array0.3910.0060.400
filter_by_name0.0250.0000.026
filter_na_count0.8200.0460.869
filter_smeta0.0510.0010.052
fisher_exact8.2700.0418.342
fold_change9.2350.0649.343
fold_change_int12.986 0.04113.070
fold_change_plot0.0470.0220.070
forward_selection_by_rank4.8730.0964.985
fs_line5.4230.1105.549
glog_opt_plot0.3620.0030.367
glog_transform0.2160.0010.217
grid_search_1d3.1760.1083.293
gs_line0.0010.0010.000
hca_dendrogram0.0010.0000.001
kfold_xval2.5900.0162.611
kfoldxcv_grid2.8500.0212.882
kfoldxcv_metric0.0000.0000.001
knn_impute0.0100.0010.010
kw_p_hist0.0010.0000.001
kw_rank_sum0.0640.0010.064
linear_model0.0230.0000.023
log_transform0.0110.0000.011
mean_centre0.0030.0000.002
mean_of_medians0.1060.0060.112
mixed_effect0.1350.0010.138
model_apply0.0170.0000.019
model_predict0.0420.0000.042
model_reverse0.0310.0010.032
model_train0.0390.0010.039
mv_boxplot0.2130.0020.216
mv_feature_filter0.1020.0030.105
mv_feature_filter_hist0.0010.0000.001
mv_histogram0.1870.0010.189
mv_sample_filter0.0120.0000.012
mv_sample_filter_hist0.0010.0000.001
nroot_transform0.0100.0010.010
ontology_cache0.0000.0000.001
pairs_filter0.0130.0000.013
pareto_scale0.0460.0010.046
pca_biplot0.0160.0000.016
pca_correlation_plot0.0090.0000.009
pca_dstat_plot0.0110.0000.011
pca_loadings_plot0.0110.0000.011
pca_scores_plot0.4120.0060.418
pca_scree_plot0.0090.0010.009
permutation_test0.0140.0000.014
permutation_test_plot0.0020.0000.002
permute_sample_order0.0110.0010.012
pls_regcoeff_plot0.2730.0030.276
pls_scores_plot0.5220.0030.526
pls_vip_plot0.3100.0190.330
plsda_feature_importance_plot0.4730.0070.481
plsda_predicted_plot0.3350.0030.338
plsda_roc_plot0.8600.0050.866
plsr_cook_dist0.0090.0000.009
plsr_prediction_plot0.0090.0010.009
plsr_qq_plot0.0080.0000.008
plsr_residual_hist0.0080.0000.008
pqn_norm0.2520.0010.253
pqn_norm_hist0.0010.0000.000
prop_na0.0130.0000.013
r_squared0.0000.0000.001
resample0.0180.0010.019
resample_chart0.0020.0000.003
rsd_filter0.0160.0000.017
rsd_filter_hist0.0010.0010.001
run0.0230.0010.023
sb_corr0.0260.0010.026
scatter_chart0.2610.0030.265
split_data0.0100.0000.011
stratified_split0.0950.0010.095
svm_plot_2d0.5060.0130.524
tSNE0.0230.0010.024
tSNE_scatter0.0090.0010.011
tic_chart0.1580.0030.162
ttest0.0170.0000.017
vec_norm0.0010.0000.001
wilcox_p_hist0.0010.0010.000
wilcox_test0.0190.0000.019