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This page was generated on 2024-12-23 11:44 -0500 (Mon, 23 Dec 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.1 LTS)x86_64R Under development (unstable) (2024-10-21 r87258) -- "Unsuffered Consequences" 4754
palomino7Windows Server 2022 Datacenterx64R Under development (unstable) (2024-10-26 r87273 ucrt) -- "Unsuffered Consequences" 4472
lconwaymacOS 12.7.1 Montereyx86_64R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" 4426
kjohnson3macOS 13.7.1 Venturaarm64R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" 4381
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch64R Under development (unstable) (2024-11-24 r87369) -- "Unsuffered Consequences" 4372
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 2064/2274HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
structToolbox 1.19.0  (landing page)
Gavin Rhys Lloyd
Snapshot Date: 2024-12-22 13:40 -0500 (Sun, 22 Dec 2024)
git_url: https://git.bioconductor.org/packages/structToolbox
git_branch: devel
git_last_commit: 4622d2f
git_last_commit_date: 2024-10-29 10:43:04 -0500 (Tue, 29 Oct 2024)
nebbiolo1Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino7Windows Server 2022 Datacenter / x64  OK    ERROR  skippedskipped
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 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: 1.19.0
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_1.19.0.tar.gz
StartedAt: 2024-12-22 23:37:30 -0500 (Sun, 22 Dec 2024)
EndedAt: 2024-12-22 23:46:32 -0500 (Sun, 22 Dec 2024)
EllapsedTime: 541.5 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_1.19.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/structToolbox.Rcheck’
* using R Under development (unstable) (2024-11-20 r87352)
* 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 ‘1.19.0’
* 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
Examples with CPU (user + system) or elapsed time > 5s
                            user system elapsed
fold_change_int           18.875  0.108  19.117
fold_change               14.059  0.083  14.255
fisher_exact              12.820  0.083  13.000
forward_selection_by_rank  7.121  0.147   7.319
fs_line                    6.382  0.119   6.546
* 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’ ...
** 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) (2024-11-20 r87352) -- "Unsuffered Consequences"
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 
204.357   2.466 208.003 

Example timings

structToolbox.Rcheck/structToolbox-Ex.timings

nameusersystemelapsed
ANOVA0.2900.0120.307
AUC2.3350.1082.464
DFA0.2560.0020.261
DatasetExperiment_boxplot1.5820.0471.648
DatasetExperiment_dist1.3600.0961.474
DatasetExperiment_factor_boxplot0.2300.0030.240
DatasetExperiment_heatmap0.4210.0210.444
HCA0.0700.0030.074
HSD0.3210.0210.360
HSDEM0.5060.0260.540
MTBLS79_DatasetExperiment0.0010.0000.001
OPLSDA0.010.000.01
OPLSR0.0180.0000.021
PCA0.0050.0000.005
PLSDA0.0240.0010.025
PLSR0.0110.0010.012
SVM0.0320.0010.033
as_data_frame0.1340.0010.138
autoscale0.0760.0020.078
balanced_accuracy2.0780.0232.119
blank_filter0.4160.0250.449
blank_filter_hist0.0010.0010.001
bootstrap0.0210.0000.022
calculate0.0060.0010.006
chart_plot0.0310.0030.033
classical_lsq0.3770.0050.384
compare_dist4.6990.2564.994
confounders_clsq3.4130.0353.470
confounders_lsq_barchart3.5310.0313.588
confounders_lsq_boxplot3.6640.0283.712
constant_sum_norm0.0190.0000.020
corr_coef0.3540.0040.359
dfa_scores_plot0.9640.0100.987
dratio_filter0.3200.0080.329
equal_split0.1790.0020.186
feature_boxplot0.0410.0020.045
feature_profile0.4670.0100.480
feature_profile_array0.5590.0080.572
filter_by_name0.0400.0010.042
filter_na_count1.2810.0701.516
filter_smeta0.0960.0050.105
fisher_exact12.820 0.08313.000
fold_change14.059 0.08314.255
fold_change_int18.875 0.10819.117
fold_change_plot0.0160.0000.017
forward_selection_by_rank7.1210.1477.319
fs_line6.3820.1196.546
glog_opt_plot0.5370.0070.547
glog_transform0.3440.0030.350
grid_search_1d3.6260.1113.758
gs_line0.0010.0000.001
hca_dendrogram0.0010.0000.001
kfold_xval3.7450.0323.793
kfoldxcv_grid4.2450.0364.300
kfoldxcv_metric0.0010.0000.002
knn_impute0.0120.0010.013
kw_p_hist0.0010.0000.001
kw_rank_sum0.0960.0010.098
linear_model0.0330.0010.034
log_transform0.0160.0010.016
mean_centre0.0040.0010.005
mean_of_medians0.1470.0040.152
mixed_effect0.1950.0030.200
model_apply0.0280.0010.028
model_predict0.0510.0010.052
model_reverse0.0460.0010.047
model_train0.0550.0000.057
mv_boxplot0.3240.0050.329
mv_feature_filter0.1340.0020.137
mv_feature_filter_hist0.0010.0000.001
mv_histogram0.2760.0040.282
mv_sample_filter0.0150.0010.016
mv_sample_filter_hist0.0010.0000.001
nroot_transform0.0140.0000.014
ontology_cache0.0000.0000.001
pairs_filter0.0230.0000.023
pareto_scale0.0660.0010.067
pca_biplot0.0250.0000.024
pca_correlation_plot0.0160.0000.016
pca_dstat_plot0.0150.0000.016
pca_loadings_plot0.0170.0000.018
pca_scores_plot0.6320.0070.642
pca_scree_plot0.0120.0000.013
permutation_test0.0210.0010.021
permutation_test_plot0.0030.0000.003
permute_sample_order0.0150.0000.015
pls_regcoeff_plot0.4060.0060.415
pls_scores_plot0.7980.0090.814
pls_vip_plot0.4700.0090.482
plsda_feature_importance_plot0.7130.0120.728
plsda_predicted_plot0.4830.0050.490
plsda_roc_plot1.2620.0121.279
plsr_cook_dist0.0130.0000.015
plsr_prediction_plot0.0130.0000.013
plsr_qq_plot0.0120.0010.012
plsr_residual_hist0.0160.0010.016
pqn_norm0.3900.0030.393
pqn_norm_hist0.0010.0010.001
prop_na0.0200.0010.021
r_squared0.0010.0000.001
resample0.0260.0010.026
resample_chart0.0040.0010.004
rsd_filter0.0210.0010.023
rsd_filter_hist0.0010.0000.001
run0.0350.0010.037
sb_corr0.0380.0010.039
scatter_chart0.3870.0050.396
split_data0.0180.0000.019
stratified_split0.1490.0020.152
svm_plot_2d0.7380.0160.757
tSNE0.0310.0010.033
tSNE_scatter0.0130.0000.014
tic_chart0.2220.0030.227
ttest0.0270.0000.028
vec_norm0.0010.0000.001
wilcox_p_hist0.0010.0010.001
wilcox_test0.0230.0010.025