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### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:preciseTAD.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings preciseTAD_1.9.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/preciseTAD.Rcheck’
* using R Under development (unstable) (2023-01-14 r83615)
* using platform: aarch64-unknown-linux-gnu (64-bit)
* R was compiled by
    gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
    GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
* running under: Ubuntu 22.04.1 LTS
* using session charset: UTF-8
* checking for file ‘preciseTAD/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘preciseTAD’ version ‘1.9.0’
* 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 ‘preciseTAD’ 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 ... NOTE
Found the following CITATION file in a non-standard place:
  CITATION.cff
Most likely ‘inst/CITATION’ should be used instead.
* 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... ERROR
Running examples in ‘preciseTAD-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: TADrandomForest
> ### Title: A wrapper function passed to 'caret::train' to apply a random
> ###   forest classification algorithm built and tested on user-defined
> ###   binned domain data from 'createTADdata'.
> ### Aliases: TADrandomForest
> 
> ### ** Examples
> 
> # Read in ARROWHEAD-called TADs at 5kb
> data(arrowhead_gm12878_5kb)
> 
> # Extract unique boundaries
> bounds.GR <- extractBoundaries(domains.mat = arrowhead_gm12878_5kb,
+                                filter = FALSE,
+                                CHR = c("CHR21", "CHR22"),
+                                resolution = 5000)
> 
> # Read in GRangesList of 26 TFBS
> data(tfbsList)
> 
> # Create the binned data matrix for CHR1 (training) and CHR22 (testing)
> # using 5 kb binning, distance-type predictors from 26 different TFBS from
> # the GM12878 cell line, and random under-sampling
> tadData <- createTADdata(bounds.GR = bounds.GR,
+                          resolution = 5000,
+                          genomicElements.GR = tfbsList,
+                          featureType = "distance",
+                          resampling = "rus",
+                          trainCHR = "CHR21",
+                          predictCHR = "CHR22")
> 
> # Perform random forest using TADrandomForest by tuning mtry over 10 values
> # using 3-fold CV
> tadModel <- TADrandomForest(trainData = tadData[[1]],
+                             testData = tadData[[2]],
+                             tuneParams = list(mtry = c(2,5,8,10,13,16,18,21,24,26),
+                                             ntree = 500,
+                                             nodesize = 1),
+                             cvFolds = 3,
+                             cvMetric = "Accuracy",
+                             verbose = TRUE,
+                             model = TRUE,
+                             importances = TRUE,
+                             impMeasure = "MDA",
+                             performances = TRUE)
Loading required package: ggplot2
Loading required package: lattice
+ Fold1: mtry= 2, ntree=500, nodesize=1 
- Fold1: mtry= 2, ntree=500, nodesize=1 
+ Fold1: mtry= 5, ntree=500, nodesize=1 
- Fold1: mtry= 5, ntree=500, nodesize=1 
+ Fold1: mtry= 8, ntree=500, nodesize=1 
- Fold1: mtry= 8, ntree=500, nodesize=1 
+ Fold1: mtry=10, ntree=500, nodesize=1 
- Fold1: mtry=10, ntree=500, nodesize=1 
+ Fold1: mtry=13, ntree=500, nodesize=1 
- Fold1: mtry=13, ntree=500, nodesize=1 
+ Fold1: mtry=16, ntree=500, nodesize=1 
- Fold1: mtry=16, ntree=500, nodesize=1 
+ Fold1: mtry=18, ntree=500, nodesize=1 
- Fold1: mtry=18, ntree=500, nodesize=1 
+ Fold1: mtry=21, ntree=500, nodesize=1 
- Fold1: mtry=21, ntree=500, nodesize=1 
+ Fold1: mtry=24, ntree=500, nodesize=1 
- Fold1: mtry=24, ntree=500, nodesize=1 
+ Fold1: mtry=26, ntree=500, nodesize=1 
- Fold1: mtry=26, ntree=500, nodesize=1 
+ Fold2: mtry= 2, ntree=500, nodesize=1 
- Fold2: mtry= 2, ntree=500, nodesize=1 
+ Fold2: mtry= 5, ntree=500, nodesize=1 
- Fold2: mtry= 5, ntree=500, nodesize=1 
+ Fold2: mtry= 8, ntree=500, nodesize=1 
- Fold2: mtry= 8, ntree=500, nodesize=1 
+ Fold2: mtry=10, ntree=500, nodesize=1 
- Fold2: mtry=10, ntree=500, nodesize=1 
+ Fold2: mtry=13, ntree=500, nodesize=1 
- Fold2: mtry=13, ntree=500, nodesize=1 
+ Fold2: mtry=16, ntree=500, nodesize=1 
- Fold2: mtry=16, ntree=500, nodesize=1 
+ Fold2: mtry=18, ntree=500, nodesize=1 
- Fold2: mtry=18, ntree=500, nodesize=1 
+ Fold2: mtry=21, ntree=500, nodesize=1 
- Fold2: mtry=21, ntree=500, nodesize=1 
+ Fold2: mtry=24, ntree=500, nodesize=1 
- Fold2: mtry=24, ntree=500, nodesize=1 
+ Fold2: mtry=26, ntree=500, nodesize=1 
- Fold2: mtry=26, ntree=500, nodesize=1 
+ Fold3: mtry= 2, ntree=500, nodesize=1 
- Fold3: mtry= 2, ntree=500, nodesize=1 
+ Fold3: mtry= 5, ntree=500, nodesize=1 
- Fold3: mtry= 5, ntree=500, nodesize=1 
+ Fold3: mtry= 8, ntree=500, nodesize=1 
- Fold3: mtry= 8, ntree=500, nodesize=1 
+ Fold3: mtry=10, ntree=500, nodesize=1 
- Fold3: mtry=10, ntree=500, nodesize=1 
+ Fold3: mtry=13, ntree=500, nodesize=1 
- Fold3: mtry=13, ntree=500, nodesize=1 
+ Fold3: mtry=16, ntree=500, nodesize=1 
Killed
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 ERROR
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  - Fold3: mtry=21, ntree=500, nodesize=1 
  + Fold3: mtry=24, ntree=500, nodesize=1 
  - Fold3: mtry=24, ntree=500, nodesize=1 
  + Fold3: mtry=26, ntree=500, nodesize=1 
  - Fold3: mtry=26, ntree=500, nodesize=1 
  Aggregating results
  Selecting tuning parameters
  Fitting mtry = 2, ntree = 500, nodesize = 1 on full training set
  +(rfe) fit Fold1 size: 26 
  -(rfe) fit Fold1 size: 26 
  +(rfe) imp Fold1 
  -(rfe) imp Fold1 
  +(rfe) fit Fold1 size: 16 
  -(rfe) fit Fold1 size: 16 
  Killed
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
  ‘preciseTAD.Rmd’ using ‘UTF-8’... OK
 NONE
* checking re-building of vignette outputs ... ERROR
Error(s) in re-building vignettes:
  ...
--- re-building ‘preciseTAD.Rmd’ using rmarkdown
Killed

* checking PDF version of manual ... OK
* DONE

Status: 3 ERRORs, 1 NOTE
See
  ‘/home/biocbuild/bbs-3.17-bioc/meat/preciseTAD.Rcheck/00check.log’
for details.

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### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL preciseTAD
###
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* installing to library ‘/home/biocbuild/bbs-3.17-bioc/R/library’
* installing *source* package ‘preciseTAD’ ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
*** copying figures
** 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 (preciseTAD)

R Under development (unstable) (2023-01-14 r83615) -- "Unsuffered Consequences"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: aarch64-unknown-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(preciseTAD)

> 
> test_check("preciseTAD")
+ Fold1: mtry= 2, ntree=500, nodesize=1 
- Fold1: mtry= 2, ntree=500, nodesize=1 
+ Fold1: mtry= 5, ntree=500, nodesize=1 
- Fold1: mtry= 5, ntree=500, nodesize=1 
+ Fold1: mtry= 8, ntree=500, nodesize=1 
- Fold1: mtry= 8, ntree=500, nodesize=1 
+ Fold1: mtry=10, ntree=500, nodesize=1 
- Fold1: mtry=10, ntree=500, nodesize=1 
+ Fold1: mtry=13, ntree=500, nodesize=1 
- Fold1: mtry=13, ntree=500, nodesize=1 
+ Fold1: mtry=16, ntree=500, nodesize=1 
- Fold1: mtry=16, ntree=500, nodesize=1 
+ Fold1: mtry=18, ntree=500, nodesize=1 
- Fold1: mtry=18, ntree=500, nodesize=1 
+ Fold1: mtry=21, ntree=500, nodesize=1 
- Fold1: mtry=21, ntree=500, nodesize=1 
+ Fold1: mtry=24, ntree=500, nodesize=1 
- Fold1: mtry=24, ntree=500, nodesize=1 
+ Fold1: mtry=26, ntree=500, nodesize=1 
- Fold1: mtry=26, ntree=500, nodesize=1 
+ Fold2: mtry= 2, ntree=500, nodesize=1 
- Fold2: mtry= 2, ntree=500, nodesize=1 
+ Fold2: mtry= 5, ntree=500, nodesize=1 
- Fold2: mtry= 5, ntree=500, nodesize=1 
+ Fold2: mtry= 8, ntree=500, nodesize=1 
- Fold2: mtry= 8, ntree=500, nodesize=1 
+ Fold2: mtry=10, ntree=500, nodesize=1 
- Fold2: mtry=10, ntree=500, nodesize=1 
+ Fold2: mtry=13, ntree=500, nodesize=1 
- Fold2: mtry=13, ntree=500, nodesize=1 
+ Fold2: mtry=16, ntree=500, nodesize=1 
- Fold2: mtry=16, ntree=500, nodesize=1 
+ Fold2: mtry=18, ntree=500, nodesize=1 
- Fold2: mtry=18, ntree=500, nodesize=1 
+ Fold2: mtry=21, ntree=500, nodesize=1 
- Fold2: mtry=21, ntree=500, nodesize=1 
+ Fold2: mtry=24, ntree=500, nodesize=1 
- Fold2: mtry=24, ntree=500, nodesize=1 
+ Fold2: mtry=26, ntree=500, nodesize=1 
- Fold2: mtry=26, ntree=500, nodesize=1 
+ Fold3: mtry= 2, ntree=500, nodesize=1 
- Fold3: mtry= 2, ntree=500, nodesize=1 
+ Fold3: mtry= 5, ntree=500, nodesize=1 
- Fold3: mtry= 5, ntree=500, nodesize=1 
+ Fold3: mtry= 8, ntree=500, nodesize=1 
- Fold3: mtry= 8, ntree=500, nodesize=1 
+ Fold3: mtry=10, ntree=500, nodesize=1 
- Fold3: mtry=10, ntree=500, nodesize=1 
+ Fold3: mtry=13, ntree=500, nodesize=1 
- Fold3: mtry=13, ntree=500, nodesize=1 
+ Fold3: mtry=16, ntree=500, nodesize=1 
- Fold3: mtry=16, ntree=500, nodesize=1 
+ Fold3: mtry=18, ntree=500, nodesize=1 
- Fold3: mtry=18, ntree=500, nodesize=1 
+ Fold3: mtry=21, ntree=500, nodesize=1 
- Fold3: mtry=21, ntree=500, nodesize=1 
+ Fold3: mtry=24, ntree=500, nodesize=1 
- Fold3: mtry=24, ntree=500, nodesize=1 
+ Fold3: mtry=26, ntree=500, nodesize=1 
- Fold3: mtry=26, ntree=500, nodesize=1 
Aggregating results
Selecting tuning parameters
Fitting mtry = 2, ntree = 500, nodesize = 1 on full training set
+(rfe) fit Fold1 size: 26 
-(rfe) fit Fold1 size: 26 
+(rfe) imp Fold1 
-(rfe) imp Fold1 
+(rfe) fit Fold1 size: 16 
-(rfe) fit Fold1 size: 16 
Killed