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This page was generated on 2022-01-22 11:06:42 -0500 (Sat, 22 Jan 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 20.04.4 LTS)x86_64R Under development (unstable) (2022-01-05 r81451) -- "Unsuffered Consequences" 4163
riesling1Windows Server 2019 Standardx64R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences" 4058
palomino3Windows Server 2022 Datacenterx64R Under development (unstable) (2021-12-21 r81400 ucrt) -- "Unsuffered Consequences" 4000
merida1macOS 10.14.6 Mojavex86_64R Under development (unstable) (2022-01-05 r81451) -- "Unsuffered Consequences" 4117
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

CHECK results for structToolbox on nebbiolo1


To the developers/maintainers of the structToolbox package:
- Please 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 How and When does the builder pull? When will my changes propagate? here for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 1889/2075HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
structToolbox 1.7.0  (landing page)
Gavin Rhys Lloyd
Snapshot Date: 2022-01-21 13:55:18 -0500 (Fri, 21 Jan 2022)
git_url: https://git.bioconductor.org/packages/structToolbox
git_branch: master
git_last_commit: 0170bda
git_last_commit_date: 2021-10-26 12:57:03 -0500 (Tue, 26 Oct 2021)
nebbiolo1Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
riesling1Windows Server 2019 Standard / x64  OK    OK    NA    NA  
palomino3Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  NO, package depends on 'struct' which is not available
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: structToolbox
Version: 1.7.0
Command: /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD check --install=check:structToolbox.install-out.txt --library=/home/biocbuild/bbs-3.15-bioc/R/library --no-vignettes --timings structToolbox_1.7.0.tar.gz
StartedAt: 2022-01-21 21:17:26 -0500 (Fri, 21 Jan 2022)
EndedAt: 2022-01-21 21:23:32 -0500 (Fri, 21 Jan 2022)
EllapsedTime: 366.0 seconds
RetCode: 0
Status:   OK  
CheckDir: structToolbox.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD check --install=check:structToolbox.install-out.txt --library=/home/biocbuild/bbs-3.15-bioc/R/library --no-vignettes --timings structToolbox_1.7.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.15-bioc/meat/structToolbox.Rcheck’
* using R Under development (unstable) (2022-01-05 r81451)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘structToolbox/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘structToolbox’ version ‘1.7.0’
* 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 R 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           16.819  0.000  16.820
fisher_exact               9.986  0.779  10.766
fold_change                8.889  0.065   8.953
forward_selection_by_rank  4.986  0.059   5.051
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... 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:
###
###   /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD INSTALL structToolbox
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.15-bioc/R/library’
* installing *source* package ‘structToolbox’ ...
** using staged installation
** R
** 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) (2022-01-05 r81451) -- "Unsuffered Consequences"
Copyright (C) 2022 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

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 2 | SKIP 0 | PASS 121 ]

[ FAIL 0 | WARN 2 | SKIP 0 | PASS 121 ]
> 
> proc.time()
   user  system elapsed 
128.146   1.771 129.901 

Example timings

structToolbox.Rcheck/structToolbox-Ex.timings

nameusersystemelapsed
ANOVA0.1660.0040.170
AUC1.2740.0391.312
DFA0.1630.0000.163
DatasetExperiment_boxplot1.2780.0201.298
DatasetExperiment_dist1.1150.0281.142
DatasetExperiment_factor_boxplot0.1520.0000.152
DatasetExperiment_heatmap0.2430.0040.247
HCA0.0440.0030.048
HSD0.3690.0120.383
HSDEM0.4040.0030.407
MTBLS79_DatasetExperiment0.0010.0000.001
PCA0.0040.0000.004
PLSDA0.010.000.01
PLSR0.0050.0000.005
SVM0.010.000.01
as_data_frame0.1120.0000.112
autoscale0.0620.0000.062
balanced_accuracy1.1520.0071.160
blank_filter0.2900.0130.302
blank_filter_hist000
bootstrap0.0050.0000.005
calculate0.0050.0000.005
chart_plot0.0240.0000.024
classical_lsq0.2420.0040.246
compare_dist3.8640.0843.948
confounders_clsq2.5860.0592.646
confounders_lsq_barchart2.6730.0372.709
confounders_lsq_boxplot2.7220.0232.747
constant_sum_norm0.0040.0000.004
corr_coef0.2280.0000.228
dfa_scores_plot0.5080.0120.519
dratio_filter0.5340.0110.545
feature_boxplot0.0150.0010.015
feature_profile0.3510.0000.351
feature_profile_array0.6220.0160.638
filter_by_name0.0290.0000.029
filter_na_count1.9870.2792.266
filter_smeta0.0530.0010.054
fisher_exact 9.986 0.77910.766
fold_change8.8890.0658.953
fold_change_int16.819 0.00016.820
fold_change_plot0.0040.0000.005
forward_selection_by_rank4.9860.0595.051
fs_line4.9520.0084.960
glog_opt_plot0.4660.0040.470
glog_transform0.280.000.28
grid_search_1d4.3920.0244.417
gs_line0.0010.0000.000
hca_dendrogram0.0000.0000.001
kfold_xval3.0590.0003.060
kfoldxcv_grid2.5880.0002.589
kfoldxcv_metric0.0010.0000.001
knn_impute0.0050.0000.006
kw_p_hist0.0010.0000.000
kw_rank_sum0.0640.0000.065
linear_model0.0210.0000.021
log_transform0.0000.0040.004
mean_centre0.0000.0020.001
mean_of_medians0.1020.0010.102
mixed_effect0.1370.0000.137
model_apply0.0170.0040.021
model_predict0.0470.0000.047
model_reverse0.0370.0000.037
model_train0.0420.0000.043
mv_boxplot0.2250.0000.225
mv_feature_filter0.0940.0000.094
mv_feature_filter_hist0.0010.0000.001
mv_histogram0.1890.0000.189
mv_sample_filter0.0050.0000.006
mv_sample_filter_hist0.0000.0000.001
nroot_transform0.0040.0000.004
ontology_cache0.0000.0000.001
pairs_filter0.0020.0030.005
pareto_scale0.0540.0000.053
pca_biplot0.0060.0030.009
pca_correlation_plot0.0040.0000.005
pca_dstat_plot0.0060.0000.006
pca_loadings_plot0.0050.0000.006
pca_scores_plot0.3980.0000.397
pca_scree_plot0.0010.0000.001
permutation_test0.0050.0000.005
permutation_test_plot0.0030.0000.002
permute_sample_order0.0040.0000.004
plsda_predicted_plot0.3250.0000.326
plsda_regcoeff_plot0.2250.0000.225
plsda_roc_plot0.5860.0000.586
plsda_scores_plot0.3590.0000.360
plsda_vip_plot0.2260.0040.230
plsda_vip_summary_plot0.4120.0000.411
plsr_cook_dist0.0010.0000.001
plsr_prediction_plot0.0010.0000.000
plsr_qq_plot0.0010.0000.001
plsr_residual_hist0.0010.0000.001
pqn_norm0.3000.0000.301
pqn_norm_hist0.0010.0000.001
prop_na0.0050.0000.005
r_squared0.0010.0000.000
rsd_filter0.0030.0040.007
rsd_filter_hist0.0000.0000.001
run0.0270.0000.027
sb_corr0.0130.0000.012
split_data0.0050.0000.004
stratified_split0.1030.0000.103
svm_plot_2d0.6160.0040.620
tSNE0.0120.0000.011
tSNE_scatter0.0010.0030.005
tic_chart0.2000.0040.204
ttest0.0080.0000.008
vec_norm0.0010.0000.001
wilcox_p_hist0.0010.0000.001
wilcox_test0.0080.0000.008