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### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:PureCN.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings PureCN_2.16.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/PureCN.Rcheck’
* using R version 4.5.2 (2025-10-31)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
    GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.3 LTS
* using session charset: UTF-8
* checking for file ‘PureCN/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘PureCN’ version ‘2.16.0’
* checking package namespace information ... OK
* checking package dependencies ... INFO
Package which this enhances but not available for checking: ‘genomicsdb’

Imports includes 21 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
* 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 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 loading without being on the library search path ... 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 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
callAmplificationsInLowPurity 46.581  0.253  46.840
segmentationPSCBS             42.078  0.164  42.243
filterIntervals               23.086  0.062  23.140
runAbsoluteCN                 18.174  0.049  18.225
segmentationHclust            16.199  0.078  16.277
findFocal                     13.114  0.199  13.314
annotateTargets               11.569  0.462  12.032
segmentationCBS                9.177  0.018   9.196
* 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:
  ── Failure ('test_preprocessIntervals.R:140:5'): Offtarget settings work as expected ──
  Expected `... <- NULL` to produce output.
  ── Failure ('test_readCoverageFile.R:21:5'): Overlapping intervals were merged and warned ──
  Expected `coverage <- readCoverageFile(tumor.overlapping.coverage.file)` to produce output.
  ── Failure ('test_readSegmentationFile.R:26:5'): Missing values raise warning ──
  Expected `readSegmentationFile(seg.file, "SC_9030.tumour.recalibrated")` to produce output.
  ── Failure ('test_runAbsoluteCN.R:50:5'): VCF is not necessary to produce output ──
  Expected output from `... <- NULL` to match regexp "Insufficient number of variants".
  Actual output:
  ✖ │ Setting multi-figure configuration
  
  [ FAIL 17 | WARN 12 | SKIP 2 | PASS 388 ]
  Error:
  ! Test failures.
  Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 1 ERROR
See
  ‘/home/biocbuild/bbs-3.22-bioc/meat/PureCN.Rcheck/00check.log’
for details.

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### Running command:
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###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD INSTALL PureCN
###
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* installing to library ‘/home/biocbuild/bbs-3.22-bioc/R/site-library’
* installing *source* package ‘PureCN’ ...
** this is package ‘PureCN’ version ‘2.16.0’
** 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 version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu

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
Loading required package: generics

Attaching package: 'generics'

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

    as.difftime, as.factor, as.ordered, intersect, is.element, setdiff,
    setequal, union


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, is.unsorted, lapply,
    mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int,
    rank, rbind, rownames, sapply, saveRDS, table, tapply, 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: Seqinfo
Loading required package: GenomicRanges
Loading required package: stats4
Loading required package: S4Vectors

Attaching package: 'S4Vectors'

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

    findMatches

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

    I, expand.grid, unname

Loading required package: IRanges
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")
Saving _problems/test_createCurationFile-84.R
Saving _problems/test_createNormalDatabase-46.R
Saving _problems/test_createNormalDatabase-56.R
Saving _problems/test_filterVcf-52.R
Saving _problems/test_filterVcf-56.R
Saving _problems/test_filterVcf-86.R
Saving _problems/test_filterVcf-96.R
Saving _problems/test_filterVcf-105.R
Saving _problems/test_filterVcf-140.R
Saving _problems/test_getSexFromCoverage-14.R
Saving _problems/test_getSexFromCoverage-20.R
Saving _problems/test_preprocessIntervals-119.R
Saving _problems/test_preprocessIntervals-124.R
Saving _problems/test_preprocessIntervals-143.R
Error in read.table(file = file, header = header, sep = sep, quote = quote,  : 
  no lines available in input
Saving _problems/test_readCoverageFile-22.R
Saving _problems/test_readSegmentationFile-27.R
Setting multi-figure configuration
Saving _problems/test_runAbsoluteCN-59.R
Error in FileForFormat(resource(con), fileFormat(con)) : 
  Format 'txt' unsupported
In addition: Warning messages:
1: In for (i in seq_len(n)) { :
  closing unused connection 4 (/home/biocbuild/bbs-3.22-bioc/R/site-library/PureCN/extdata/example_allelic_counts_empty.tsv)
2: In for (i in seq_len(n)) { :
  closing unused connection 5 (/tmp/Rtmp4xpgzy/fileb7e7370b53a0.tsv)
3: In for (i in seq_len(n)) { :
  closing unused connection 4 (/home/biocbuild/bbs-3.22-bioc/R/site-library/PureCN/extdata/example_gatk4_denoised_cr.tsv.gz)
Setting multi-figure configuration
Setting multi-figure configuration
Setting multi-figure configuration
Setting multi-figure configuration
sh: 1: gatk: not found
Failed with error:  'there is no package called 'genomicsdb''
[ FAIL 17 | WARN 12 | SKIP 2 | PASS 388 ]

══ Skipped tests (2) ═══════════════════════════════════════════════════════════
• gatk binary > 4.1.7.0 required (1): 'test_segmentation.R:25:4'
• genomicsdb required (1): 'test_setMappingBiasVcf.R:45:5'

══ Failed tests ════════════════════════════════════════════════════════════════
── Failure ('test_createCurationFile.R:84:5'): warning occurs with missing curation file ──
Expected `retx <- readCurationFile(file.rds)` to produce output.
── Failure ('test_createNormalDatabase.R:45:5'): Exceptions happen with wrong input ──
Expected `correctCoverageBias(...)` to produce output.
── Failure ('test_createNormalDatabase.R:55:5'): Exceptions happen with wrong input ──
Expected `createNormalDatabase(...)` to produce output.
── Failure ('test_filterVcf.R:51:5'): M2 VCF with POP_AF flag is annotated with DB flag ──
Expected `filterVcfMuTect(vcf.m2, use.somatic.status = FALSE)` to produce output.
── Failure ('test_filterVcf.R:55:5'): M2 VCF with POP_AF flag is annotated with DB flag ──
Expected `vcf.m2 <- PureCN:::.readAndCheckVcf(output.file, "hg38")` to produce output.
── Failure ('test_filterVcf.R:86:5'): issue 109 is fixed ───────────────────────
Expected `x <- PureCN:::.readAndCheckVcf(vcf.file)` to produce output.
── Failure ('test_filterVcf.R:95:6'): Missing FA does not cause crash ──────────
Expected `x <- PureCN:::.readAndCheckVcf(vcf, "hg19")` to produce output.
── Failure ('test_filterVcf.R:105:5'): issue 184 is fixed ──────────────────────
Expected `x <- PureCN:::.getTumorIdInVcf(vcf.184)` to produce output.
── Failure ('test_filterVcf.R:139:5'): issue 320 ───────────────────────────────
Expected `x <- filterVcfBasic(vcf, use.somatic.status = FALSE, min.base.quality = 34)` to produce output.
── Failure ('test_getSexFromCoverage.R:14:5'): Warning with missing coverage data ──
Expected `getSexFromCoverage(coverage)` to produce output.
── Failure ('test_getSexFromCoverage.R:20:5'): Warning with missing coverage data in file ──
Expected `getSexFromCoverage(coverage)` to produce output.
── Failure ('test_preprocessIntervals.R:117:5'): Offtarget settings work as expected ──
Expected `gcMap <- preprocessIntervals(intervals, reference.file, mappability = mappability4)` to produce output.
── Failure ('test_preprocessIntervals.R:122:5'): Offtarget settings work as expected ──
Expected `... <- NULL` to produce output.
── Failure ('test_preprocessIntervals.R:140:5'): Offtarget settings work as expected ──
Expected `... <- NULL` to produce output.
── Failure ('test_readCoverageFile.R:21:5'): Overlapping intervals were merged and warned ──
Expected `coverage <- readCoverageFile(tumor.overlapping.coverage.file)` to produce output.
── Failure ('test_readSegmentationFile.R:26:5'): Missing values raise warning ──
Expected `readSegmentationFile(seg.file, "SC_9030.tumour.recalibrated")` to produce output.
── Failure ('test_runAbsoluteCN.R:50:5'): VCF is not necessary to produce output ──
Expected output from `... <- NULL` to match regexp "Insufficient number of variants".
Actual output:
✖ │ Setting multi-figure configuration

[ FAIL 17 | WARN 12 | SKIP 2 | PASS 388 ]
Error:
! Test failures.
Execution halted