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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:preciseTAD.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings preciseTAD_1.16.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/preciseTAD.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 ‘preciseTAD/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘preciseTAD’ version ‘1.16.0’
* 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 ‘preciseTAD’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
License stub is invalid DCF.
* 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 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 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 ... OK
Examples with CPU (user + system) or elapsed time > 5s
                  user system elapsed
preciseTAD      45.856  3.077  49.058
TADrandomForest 19.221  0.799  20.243
TADrfe          10.819  0.447  11.390
* 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: 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.20-bioc/meat/preciseTAD.Rcheck/00check.log’
for details.

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### Running command:
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###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL preciseTAD
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/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 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(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 
+(rfe) fit Fold1 size:  8 
-(rfe) fit Fold1 size:  8 
+(rfe) fit Fold1 size:  4 
-(rfe) fit Fold1 size:  4 
+(rfe) fit Fold1 size:  2 
-(rfe) fit Fold1 size:  2 
+(rfe) fit Fold2 size: 26 
-(rfe) fit Fold2 size: 26 
+(rfe) imp Fold2 
-(rfe) imp Fold2 
+(rfe) fit Fold2 size: 16 
-(rfe) fit Fold2 size: 16 
+(rfe) fit Fold2 size:  8 
-(rfe) fit Fold2 size:  8 
+(rfe) fit Fold2 size:  4 
-(rfe) fit Fold2 size:  4 
+(rfe) fit Fold2 size:  2 
-(rfe) fit Fold2 size:  2 
+(rfe) fit Fold3 size: 26 
-(rfe) fit Fold3 size: 26 
+(rfe) imp Fold3 
-(rfe) imp Fold3 
+(rfe) fit Fold3 size: 16 
-(rfe) fit Fold3 size: 16 
+(rfe) fit Fold3 size:  8 
-(rfe) fit Fold3 size:  8 
+(rfe) fit Fold3 size:  4 
-(rfe) fit Fold3 size:  4 
+(rfe) fit Fold3 size:  2 
-(rfe) fit Fold3 size:  2 
+(rfe) fit Fold4 size: 26 
-(rfe) fit Fold4 size: 26 
+(rfe) imp Fold4 
-(rfe) imp Fold4 
+(rfe) fit Fold4 size: 16 
-(rfe) fit Fold4 size: 16 
+(rfe) fit Fold4 size:  8 
-(rfe) fit Fold4 size:  8 
+(rfe) fit Fold4 size:  4 
-(rfe) fit Fold4 size:  4 
+(rfe) fit Fold4 size:  2 
-(rfe) fit Fold4 size:  2 
+(rfe) fit Fold5 size: 26 
-(rfe) fit Fold5 size: 26 
+(rfe) imp Fold5 
-(rfe) imp Fold5 
+(rfe) fit Fold5 size: 16 
-(rfe) fit Fold5 size: 16 
+(rfe) fit Fold5 size:  8 
-(rfe) fit Fold5 size:  8 
+(rfe) fit Fold5 size:  4 
-(rfe) fit Fold5 size:  4 
+(rfe) fit Fold5 size:  2 
-(rfe) fit Fold5 size:  2 
+ Fold1: mtry=2, ntree=500, nodesize=1 
- Fold1: mtry=2, ntree=500, nodesize=1 
+ Fold2: mtry=2, ntree=500, nodesize=1 
- Fold2: mtry=2, ntree=500, nodesize=1 
+ Fold3: mtry=2, ntree=500, nodesize=1 
- Fold3: mtry=2, ntree=500, nodesize=1 
Aggregating results
Fitting final model on full training set
[1] "Establishing bp resolution test data using a distance type feature space"
[1] "Establishing probability vector"
[1] "Determining optimal combination of epsilon neighborhood (eps) and minimum number of points (MinPts)"
[1] "Initializing DBSCAN for MinPts=3 and eps=10000"
[1] "    preciseTAD identified 13 PTBRs"
[1] "    Establishing PTBPs"
[1] "        Cluster 1 out of 13"
[1] "        Cluster 2 out of 13"
[1] "        Cluster 3 out of 13"
[1] "        Cluster 4 out of 13"
[1] "        Cluster 5 out of 13"
[1] "        Cluster 6 out of 13"
[1] "        Cluster 7 out of 13"
[1] "        Cluster 8 out of 13"
[1] "        Cluster 9 out of 13"
[1] "        Cluster 10 out of 13"
[1] "        Cluster 11 out of 13"
[1] "        Cluster 12 out of 13"
[1] "        Cluster 13 out of 13"
[1] "Optimal combination of MinPts and eps is = (3, 10000)"
[1] "preciseTAD identified a total of 12897 base pairs whose predictive probability was equal to or exceeded a threshold of 1"
[1] "Initializing DBSCAN for MinPts = 3 and eps = 10000"
[1] "preciseTAD identified 13 PTBRs"
[1] "Establishing PTBPs"
[1] "Cluster 1 out of 13"
[1] "Cluster 2 out of 13"
[1] "Cluster 3 out of 13"
[1] "Cluster 4 out of 13"
[1] "Cluster 5 out of 13"
[1] "Cluster 6 out of 13"
[1] "Cluster 7 out of 13"
[1] "Cluster 8 out of 13"
[1] "Cluster 9 out of 13"
[1] "Cluster 10 out of 13"
[1] "Cluster 11 out of 13"
[1] "Cluster 12 out of 13"
[1] "Cluster 13 out of 13"
+ Fold1: mtry=2, ntree=500, nodesize=1 
- Fold1: mtry=2, ntree=500, nodesize=1 
+ Fold2: mtry=2, ntree=500, nodesize=1 
- Fold2: mtry=2, ntree=500, nodesize=1 
+ Fold3: mtry=2, ntree=500, nodesize=1 
- Fold3: mtry=2, ntree=500, nodesize=1 
Aggregating results
Fitting final model on full training set
[1] "Establishing bp resolution test data using a distance type feature space"
[1] "Establishing probability vector"
[1] "Determining optimal combination of epsilon neighborhood (eps) and minimum number of points (MinPts)"
[1] "Initializing DBSCAN for MinPts=1000 and eps=5000"
[1] "    preciseTAD identified 14 PTBRs"
[1] "    Establishing PTBPs"
[1] "        Cluster 1 out of 14"
[1] "        Cluster 2 out of 14"
[1] "        Cluster 3 out of 14"
[1] "        Cluster 4 out of 14"
[1] "        Cluster 5 out of 14"
[1] "        Cluster 6 out of 14"
[1] "        Cluster 7 out of 14"
[1] "        Cluster 8 out of 14"
[1] "        Cluster 9 out of 14"
[1] "        Cluster 10 out of 14"
[1] "        Cluster 11 out of 14"
[1] "        Cluster 12 out of 14"
[1] "        Cluster 13 out of 14"
[1] "        Cluster 14 out of 14"
[1] "Optimal combination of MinPts and eps is = (1000, 5000)"
[1] "preciseTAD identified a total of 59929 base pairs whose predictive probability was equal to or exceeded a threshold of 0.99"
[1] "Initializing DBSCAN for MinPts = 1000 and eps = 5000"
[1] "preciseTAD identified 14 PTBRs"
[1] "Establishing PTBPs"
[1] "Cluster 1 out of 14"
[1] "Cluster 2 out of 14"
[1] "Cluster 3 out of 14"
[1] "Cluster 4 out of 14"
[1] "Cluster 5 out of 14"
[1] "Cluster 6 out of 14"
[1] "Cluster 7 out of 14"
[1] "Cluster 8 out of 14"
[1] "Cluster 9 out of 14"
[1] "Cluster 10 out of 14"
[1] "Cluster 11 out of 14"
[1] "Cluster 12 out of 14"
[1] "Cluster 13 out of 14"
[1] "Cluster 14 out of 14"
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 17 ]
> 
> proc.time()
   user  system elapsed 
161.715  10.264 221.908