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###
### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:PureCN.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings PureCN_2.5.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/PureCN.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 ‘PureCN/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘PureCN’ version ‘2.5.0’
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Package which this enhances but not available for checking: ‘genomicsdb’
* 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 ‘PureCN’ 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 ... NOTE
Killed
* 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 data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... ERROR
Running examples in ‘PureCN-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: callAmplificationsInLowPurity
> ### Title: Calling of amplifications in low purity samples
> ### Aliases: callAmplificationsInLowPurity
> 
> ### ** Examples
> 
> 
> data(purecn.example.output)
> normal.coverage.file <- system.file("extdata", "example_normal.txt.gz", 
+     package = "PureCN")
> normal2.coverage.file <- system.file("extdata", "example_normal2.txt.gz", 
+     package = "PureCN")
> normal.coverage.files <- c(normal.coverage.file, normal2.coverage.file)
> normalDB <- createNormalDatabase(normal.coverage.files)
INFO [2023-02-07 12:16:05] 576 on-target bins with low coverage in all samples.
WARN [2023-02-07 12:16:05] You are likely not using the correct baits file!
WARN [2023-02-07 12:16:05] Allosome coverage missing, cannot determine sex.
WARN [2023-02-07 12:16:05] Allosome coverage missing, cannot determine sex.
INFO [2023-02-07 12:16:05] Processing on-target regions...
INFO [2023-02-07 12:16:06] Removing 930 intervals with low coverage in normalDB.
INFO [2023-02-07 12:16:06] Removing 1 intervals with zero coverage in more than 3% of normalDB.
> callAmplificationsInLowPurity(purecn.example.output, normalDB)["EIF2A", ]
INFO [2023-02-07 12:16:09] Tumor/normal noise ratio: 19.041
WARN [2023-02-07 12:16:09] Extensive noise in tumor compared to normals.
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:
  > 
  > test_check("PureCN")
  WARN [2023-02-07 12:16:41] Attempted adding gene symbols to intervals. Heuristics have been used to pick symbols for overlapping genes.
  WARN [2023-02-07 12:16:41] Chromosome naming style of txdb file (UCSC) was different from interval file (Ensembl).
  WARN [2023-02-07 12:16:48] Attempted adding gene symbols to intervals. Heuristics have been used to pick symbols for overlapping genes.
  FATAL [2023-02-07 12:16:52] tumor.coverage.file and interval.file do not align. 
  
  FATAL [2023-02-07 12:16:52]  
  
  FATAL [2023-02-07 12:16:52] This is most likely a user error due to invalid input data or 
  
  FATAL [2023-02-07 12:16:52] parameters (PureCN 2.5.0). 
  
  WARN [2023-02-07 12:16:53] Cannot find all contig lengths while exporting interval file.
  Killed
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
  ‘Quick.Rmd’ using ‘UTF-8’... OK
  ‘PureCN.Rnw’... OK
 NONE
* checking re-building of vignette outputs ... ERROR
Error(s) in re-building vignettes:
  ...
--- re-building ‘Quick.Rmd’ using rmarkdown
--- finished re-building ‘Quick.Rmd’

--- re-building ‘PureCN.Rnw’ using knitr
Killed
SUMMARY: processing the following file failed:
  ‘PureCN.Rnw’

Error: Vignette re-building failed.
Execution halted

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

Status: 3 ERRORs, 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.17-bioc/meat/PureCN.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL PureCN
###
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* installing to library ‘/home/biocbuild/bbs-3.17-bioc/R/library’
* installing *source* package ‘PureCN’ ...
** using staged installation
** 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 (PureCN)

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(PureCN)
Loading required package: DNAcopy
Loading required package: VariantAnnotation
Loading required package: BiocGenerics

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append,
    as.data.frame, basename, cbind, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
    pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
    tapply, union, unique, unsplit, which.max, which.min

Loading required package: MatrixGenerics
Loading required package: matrixStats

Attaching package: 'MatrixGenerics'

The following objects are masked from 'package:matrixStats':

    colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse,
    colCounts, colCummaxs, colCummins, colCumprods, colCumsums,
    colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs,
    colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats,
    colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds,
    colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads,
    colWeightedMeans, colWeightedMedians, colWeightedSds,
    colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet,
    rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods,
    rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps,
    rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins,
    rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks,
    rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars,
    rowWeightedMads, rowWeightedMeans, rowWeightedMedians,
    rowWeightedSds, rowWeightedVars

Loading required package: GenomeInfoDb
Loading required package: S4Vectors
Loading required package: stats4

Attaching package: 'S4Vectors'

The following objects are masked from 'package:base':

    I, expand.grid, unname

Loading required package: IRanges
Loading required package: GenomicRanges
Loading required package: SummarizedExperiment
Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.


Attaching package: 'Biobase'

The following object is masked from 'package:MatrixGenerics':

    rowMedians

The following objects are masked from 'package:matrixStats':

    anyMissing, rowMedians

Loading required package: Rsamtools
Loading required package: Biostrings
Loading required package: XVector

Attaching package: 'Biostrings'

The following object is masked from 'package:base':

    strsplit


Attaching package: 'VariantAnnotation'

The following object is masked from 'package:base':

    tabulate

> 
> test_check("PureCN")
WARN [2023-02-07 12:16:41] Attempted adding gene symbols to intervals. Heuristics have been used to pick symbols for overlapping genes.
WARN [2023-02-07 12:16:41] Chromosome naming style of txdb file (UCSC) was different from interval file (Ensembl).
WARN [2023-02-07 12:16:48] Attempted adding gene symbols to intervals. Heuristics have been used to pick symbols for overlapping genes.
FATAL [2023-02-07 12:16:52] tumor.coverage.file and interval.file do not align. 

FATAL [2023-02-07 12:16:52]  

FATAL [2023-02-07 12:16:52] This is most likely a user error due to invalid input data or 

FATAL [2023-02-07 12:16:52] parameters (PureCN 2.5.0). 

WARN [2023-02-07 12:16:53] Cannot find all contig lengths while exporting interval file.
Killed