##############################################################################
##############################################################################
###
### Running command:
###
###   E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:AneuFinder.install-out.txt --library=E:\biocbuild\bbs-3.21-bioc\R\library --no-vignettes --timings AneuFinder_1.35.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'E:/biocbuild/bbs-3.21-bioc/meat/AneuFinder.Rcheck'
* using R Under development (unstable) (2024-10-26 r87273 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 13.2.0
    GNU Fortran (GCC) 13.2.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'AneuFinder/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'AneuFinder' version '1.35.0'
* 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 whether package 'AneuFinder' can be installed ... OK
* used C++ compiler: 'G__~1.EXE (GCC) 13.3.0'
* 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 whether startup messages can be suppressed ... 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
Aneufinder: multiple local function definitions for 'parallel.helper'
  with different formal arguments
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... NOTE
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  Aneufinder.Rd: GRanges-class
  DNAcopy.findCNVs.Rd: GRanges-class
  HMM.findCNVs.Rd: GRanges-class, GRangesList
  aneuBiHMM.Rd: GRanges-class
  aneuHMM.Rd: GRanges-class
  annotateBreakpoints.Rd: GRanges-class
  bam2GRanges.Rd: GRanges-class
  bed2GRanges.Rd: GRanges-class
  bi.edivisive.findCNVs.Rd: e.divisive, GRanges-class
  biDNAcopy.findCNVs.Rd: GRanges-class
  biHMM.findCNVs.Rd: GRanges-class, GRangesList
  binReads.Rd: GRanges-class, GenomicRanges, GRangesList
  binned.data.Rd: GRanges-class
  blacklist.Rd: GRanges-class
  clusterByQuality.Rd: mclust
  clusterHMMs.Rd: GRanges-class
  edivisive.findCNVs.Rd: e.divisive, GRanges-class
  estimateComplexity.Rd: GRanges-class
  export.Rd: GRanges-class
  filterSegments.Rd: GRanges-class
  findCNVs.Rd: GRanges-class
  findCNVs.strandseq.Rd: GRanges-class
  findHotspots.Rd: GRanges-class
  fixedWidthBins.Rd: GRanges-class, GRangesList
  getBreakpoints.Rd: GRanges-class
  getQC.Rd: GRanges-class
  getSCEcoordinates.Rd: GRanges-class
  heatmapGenomewide.Rd: GRanges-class
  hotspotter.Rd: GRanges-class
  hotspotter.variable.Rd: GRanges-class
  importBed.Rd: GRanges-class
  karyotypeMeasures.Rd: GRanges-class
  loadFromFiles.Rd: GRanges-class, GRangesList
  mergeStrandseqFiles.Rd: GRanges-class
  plot.GRanges.Rd: GRanges-class
  plot.GRangesList.Rd: GRangesList
  plotHeterogeneity.Rd: GRanges-class
  plot_pca.Rd: GRanges-class
  refineBreakpoints.Rd: GRanges-class
  subsetByCNVprofile.Rd: GRanges-class
  transCoord.Rd: GRanges-class
  variableWidthBins.Rd: GRanges-class, GRangesList
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
* 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 line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... NOTE
Note: information on .o files for x64 is not available
File 'E:/biocbuild/bbs-3.21-bioc/R/library/AneuFinder/libs/x64/AneuFinder.dll':
  Found '_exit', possibly from '_exit' (C)
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
  Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs nor [v]sprintf. The detected symbols are linked into
the code but might come from libraries and not actually be called.

See 'Writing portable packages' in the 'Writing R Extensions' manual.
* 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
simulateReads             214.11   6.75  221.02
correctGC                 167.36   3.23  171.98
refineBreakpoints          59.19   1.02   60.20
heatmapAneuploidies        57.64   0.42   58.09
plotHeterogeneity          35.65   0.63   36.28
heatmapGenomewideClusters  30.89   0.37   31.27
karyotypeMeasures          29.99   0.42   30.40
heatmapGenomewide          28.45   0.55   29.78
annotateBreakpoints        18.65   0.56   22.47
getBreakpoints             12.06   0.64   12.71
consensusSegments          10.25   0.17   10.42
getSCEcoordinates           7.62   0.56    8.97
findCNVs.strandseq          6.70   0.46    7.15
subsetByCNVprofile          6.99   0.04    7.03
variableWidthBins           5.42   0.19    5.61
findCNVs                    4.77   0.43    5.21
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
  Running 'testthat.R'
 OK
* 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: 3 NOTEs
See
  'E:/biocbuild/bbs-3.21-bioc/meat/AneuFinder.Rcheck/00check.log'
for details.