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### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:BubbleTree.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings BubbleTree_2.29.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/BubbleTree.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 ‘BubbleTree/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘BubbleTree’ version ‘2.29.0’
* 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 ‘BubbleTree’ can be installed ... OK
* checking installed package size ... NOTE
  installed size is 23.8Mb
  sub-directories of 1Mb or more:
    data  23.4Mb
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ...Warning in person1(given = given[[i]], family = family[[i]], middle = middle[[i]],  :
  It is recommended to use ‘given’ instead of ‘middle’.
 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 ... NOTE
annoByOverlap,Annotate: no visible binding for global variable
  'queryHits'
Undefined global functions or variables:
  queryHits
* 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 data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... ERROR
Running examples in ‘BubbleTree-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: makeRBD
> ### Title: makeRBD
> ### Aliases: makeRBD makeRBD,RBD-method makeRBD
> 
> ### ** Examples
> 
> 
> # load sample files
> load(system.file("data", "cnv.gr.rda", package="BubbleTree"))
> load(system.file("data", "snp.gr.rda", package="BubbleTree"))
> 
> # load annotations
> load(system.file("data", "centromere.dat.rda", package="BubbleTree"))
> load(system.file("data", "cyto.gr.rda", package="BubbleTree"))
> load(system.file("data", "cancer.genes.minus2.rda", package="BubbleTree"))
> load(system.file("data", "vol.genes.rda", package="BubbleTree"))
> load(system.file("data", "gene.uni.clean.gr.rda", package="BubbleTree"))
> 
> 
> # initialize RBD object
> r <- new("RBD", unimodal.kurtosis=-0.1)
> 
> # create new RBD object with GenomicRanges objects for SNPs and CNVs
> rbd <- makeRBD(r, snp.gr, cnv.gr)
> head(rbd)
  seqnames    start      end    width strand seg.id num.mark     lrr   kurtosis
1     chr1    65625  2066855  2001231      *      1      548  0.1997  0.1830119
2     chr1  2075796 38489397 36413602      *      2     5284 -0.4146 -1.9020390
3     chr1 38511244 39761601  1250358      *      3       72 -0.0511 -2.0000000
4     chr1 39763396 39982177   218782      *      4      112  0.0401 -0.9912620
5     chr1 39988109 43905367  3917259      *      5      601  0.0372 -1.4809979
6     chr1 43905709 44128685   222977      *      6       53  0.2822 -2.0000000
      hds     hds.sd het.cnt   seg.size
1 0.01220 0.05007095      71 0.24809178
2 0.35600 0.06296830     501 2.39218420
3 0.15555 0.03471894       2 0.03259600
4 0.12060 0.06761821       4 0.05070489
5 0.14560 0.06186714      47 0.27208605
6 0.07280 0.05176022       2 0.02399428
> 
> # create a new prediction
> btreepredictor <- new("BTreePredictor", rbd=rbd, max.ploidy=6, prev.grid=seq(0.2,1, by=0.01))
> pred <- btpredict(btreepredictor)
> 
> # create rbd plot
> btreeplotter <- new("BTreePlotter", max.ploidy=5, max.size=10)
> btree <- drawBTree(btreeplotter, pred@rbd)
Warning in drawBTree(btreeplotter, pred@rbd) :
  More ploidy might be suggested: 1.6, 1.6, 2.2, 1.7, 1.9, 1.5, 1.7, 2.2, 1.9, 2.1, 1.7

> print(btree)
> 
> # create rbd.adj plot
> btreeplotter <- new("BTreePlotter", branch.col="gray50")
> btree <- drawBTree(btreeplotter, pred@rbd.adj)
Warning in drawBTree(btreeplotter, pred@rbd.adj) :
  More ploidy might be suggested: 1.8, 1.9, 2.1, 2, 2.2, 2.9, 2.3, 2.6, 1.8, 1.9, 2, 2.3, 3, 2.6, 2.9, 2.3

> print(btree)
Killed
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
  ‘BubbleTree-vignette.Rmd’ using ‘UTF-8’... OK
 NONE
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 1 ERROR, 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.17-bioc/meat/BubbleTree.Rcheck/00check.log’
for details.

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### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL BubbleTree
###
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* installing to library ‘/home/biocbuild/bbs-3.17-bioc/R/library’
* installing *source* package ‘BubbleTree’ ...
** using staged installation
Warning in person1(given = given[[i]], family = family[[i]], middle = middle[[i]],  :
  It is recommended to use ‘given’ instead of ‘middle’.
** R
** data
** 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 (BubbleTree)