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### Running command:
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###   /home/biocbuild/R/R/bin/R CMD check --install=check:PureCN.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings PureCN_2.14.1.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/PureCN.Rcheck’
* using R Under development (unstable) (2025-02-19 r87757)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
    aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0
    GNU Fortran (GCC) 14.2.0
* running under: openEuler 24.03 (LTS-SP1)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘PureCN/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘PureCN’ version ‘2.14.1’
* checking package namespace information ... OK
* checking package dependencies ... INFO
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 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 ... ERROR
Running examples in ‘PureCN-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: segmentationPSCBS
> ### Title: PSCBS segmentation
> ### Aliases: segmentationPSCBS
> 
> ### ** Examples
> 
> 
> normal.coverage.file <- system.file("extdata", "example_normal_tiny.txt",
+     package = "PureCN")
> tumor.coverage.file <- system.file("extdata", "example_tumor_tiny.txt",
+     package = "PureCN")
> vcf.file <- system.file("extdata", "example.vcf.gz",
+     package = "PureCN")
> 
> # The max.candidate.solutions, max.ploidy and test.purity parameters are set to
> # non-default values to speed-up this example.  This is not a good idea for real
> # samples.
>  ret <-runAbsoluteCN(normal.coverage.file = normal.coverage.file,
+      tumor.coverage.file = tumor.coverage.file, vcf.file = vcf.file,
+      sampleid = "Sample1",  genome = "hg19",
+      fun.segmentation = segmentationPSCBS, max.ploidy = 4,
+      test.purity = seq(0.3, 0.7, by = 0.05), max.candidate.solutions = 1)
INFO [2025-10-14 13:02:05] ------------------------------------------------------------
INFO [2025-10-14 13:02:05] PureCN 2.14.1
INFO [2025-10-14 13:02:05] ------------------------------------------------------------
INFO [2025-10-14 13:02:05] Arguments: -normal.coverage.file /home/biocbuild/R/R-devel_2025-02-19/site-library/PureCN/extdata/example_normal_tiny.txt -tumor.coverage.file /home/biocbuild/R/R-devel_2025-02-19/site-library/PureCN/extdata/example_tumor_tiny.txt -vcf.file /home/biocbuild/R/R-devel_2025-02-19/site-library/PureCN/extdata/example.vcf.gz -genome hg19 -sampleid Sample1 -max.ploidy 4 -test.purity 0.3,0.35,0.4,0.45,0.5,0.55,0.6,0.65,0.7 -max.candidate.solutions 1 -fun.segmentation <data>
INFO [2025-10-14 13:02:05] Loading coverage files...
INFO [2025-10-14 13:02:05] Mean target coverages: 109X (tumor) 102X (normal).
WARN [2025-10-14 13:02:05] Allosome coverage missing, cannot determine sex.
WARN [2025-10-14 13:02:05] Allosome coverage missing, cannot determine sex.
INFO [2025-10-14 13:02:05] Removing 9 intervals with missing log.ratio.
INFO [2025-10-14 13:02:05] Removing 1 small (< 5bp) intervals.
INFO [2025-10-14 13:02:05] Removing 1 intervals with low total coverage in normal (< 150.00 reads).
WARN [2025-10-14 13:02:05] No normalDB provided. Provide one for better results.
INFO [2025-10-14 13:02:05] Removing 73 low count (< 100 total reads) intervals.
INFO [2025-10-14 13:02:05] Removing 1 low coverage (< 15.0000X) intervals.
INFO [2025-10-14 13:02:05] Using 411 intervals (411 on-target, 0 off-target).
INFO [2025-10-14 13:02:05] No off-target intervals. If this is hybrid-capture data, consider adding them.
INFO [2025-10-14 13:02:05] No interval.file provided. Cannot check for any GC-biases.
INFO [2025-10-14 13:02:05] Loading VCF...
INFO [2025-10-14 13:02:06] Found 127 variants in VCF file.
INFO [2025-10-14 13:02:06] 127 (100.0%) variants annotated as likely germline (DB INFO flag).
INFO [2025-10-14 13:02:06] LIB-02240e4 is tumor in VCF file.
INFO [2025-10-14 13:02:06] No homozygous variants in VCF, provide unfiltered VCF.
INFO [2025-10-14 13:02:06] Removing 1 non heterozygous (in matched normal) germline SNPs.
INFO [2025-10-14 13:02:06] Removing 0 low quality variants with non-offset BQ < 25.
INFO [2025-10-14 13:02:06] Base quality scores range from 29 to 35 (offset by 1)
INFO [2025-10-14 13:02:06] Minimum number of supporting reads ranges from 2 to 5, depending on coverage and BQS.
INFO [2025-10-14 13:02:07] Removing 1 variants with AF < 0.030 or AF >= 1.000 or insufficient supporting reads or depth < 15.
INFO [2025-10-14 13:02:07] Total size of targeted genomic region: 0.11Mb (0.16Mb with 50bp padding).
INFO [2025-10-14 13:02:07] 23.1% of targets contain variants.
INFO [2025-10-14 13:02:07] Removing 4 variants outside intervals.
INFO [2025-10-14 13:02:07] Found SOMATIC annotation in VCF.
INFO [2025-10-14 13:02:07] Setting somatic prior probabilities for somatic variants to 0.999000 or to 0.000100 otherwise.
INFO [2025-10-14 13:02:08] Found SOMATIC annotation in VCF. Setting mapping bias to 0.972.
INFO [2025-10-14 13:02:08] Excluding 0 novel or poor quality variants from segmentation.
INFO [2025-10-14 13:02:08] Sample sex: ?
INFO [2025-10-14 13:02:08] Segmenting data...
INFO [2025-10-14 13:02:08] MAPD of 121 allelic fractions: 0.15 (0.15 adjusted).
INFO [2025-10-14 13:02:08] Using unweighted PSCBS.
INFO [2025-10-14 13:02:08] Setting undo.SD parameter to 0.750000.
Error in nbrOfSegments(fit, splitters = TRUE) : 
  could not find function "nbrOfSegments"
Calls: runAbsoluteCN ... eval -> eval -> value -> value.Future -> signalConditions
Execution halted
Examples with CPU (user + system) or elapsed time > 5s
                                user system elapsed
callAmplificationsInLowPurity 67.776  0.558  68.524
filterIntervals               34.407  0.191  34.686
runAbsoluteCN                 30.527  0.191  30.797
segmentationHclust            26.423  0.064  26.556
findFocal                     18.859  0.108  19.022
segmentationCBS               14.010  0.036  14.084
annotateTargets                8.081  0.650   8.755
* 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:
   11. │         └─listenv:::as.list.listenv(fitList)
   12. │           └─base::mget(vars[ok], envir = x, inherits = FALSE)
   13. └─base::local(...)
   14.   └─base::eval.parent(substitute(eval(quote(expr), envir)))
   15.     └─base::eval(expr, p)
   16.       └─base::eval(expr, p)
   17.         └─base::eval(...)
   18.           └─base::eval(...)
   19.             ├─future::value(future)
   20.             └─future:::value.Future(future)
   21.               └─future:::signalConditions(...)
  
  [ FAIL 1 | WARN 12 | SKIP 2 | PASS 398 ]
  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: 2 ERRORs
See
  ‘/home/biocbuild/bbs-3.21-bioc/meat/PureCN.Rcheck/00check.log’
for details.