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### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:PureCN.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings PureCN_2.17.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.23-bioc/meat/PureCN.Rcheck’
* using R Under development (unstable) (2026-01-15 r89304)
* using platform: aarch64-apple-darwin20
* R was compiled by
    Apple clang version 16.0.0 (clang-1600.0.26.6)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Ventura 13.7.8
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘PureCN/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘PureCN’ version ‘2.17.0’
* 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 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                                user system elapsed
callAmplificationsInLowPurity 15.532  0.133  16.943
segmentationPSCBS             14.850  0.163  16.141
filterIntervals                9.072  0.165  10.094
runAbsoluteCN                  6.570  0.122   7.090
annotateTargets                6.357  0.258   6.989
segmentationHclust             5.767  0.101   6.493
* 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 running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 ERROR
See
  ‘/Users/biocbuild/bbs-3.23-bioc/meat/PureCN.Rcheck/00check.log’
for details.

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### Running command:
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###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL PureCN
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library’
* installing *source* package ‘PureCN’ ...
** this is package ‘PureCN’ version ‘2.17.0’
** 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 Under development (unstable) (2026-01-15 r89304) -- "Unsuffered Consequences"
Copyright (C) 2026 The R Foundation for Statistical Computing
Platform: aarch64-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(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: closing unused connection 4 (/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/PureCN/extdata/example_allelic_counts_empty.tsv) 
2: In UseMethod("isUrl") :
  closing unused connection 4 (/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/PureCN/extdata/example_gatk4_denoised_cr.tsv.gz)
3: In is.numeric(trim) :
  closing unused connection 4 (/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpgulwGa/file105a871a6e0c3.tsv)
Setting multi-figure configuration
Setting multi-figure configuration
Setting multi-figure configuration
Setting multi-figure configuration
sh: gatk: command 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