* using log directory ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/aroma.core.Rcheck’
* using R Under development (unstable) (2025-02-25 r87824)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc-14 (Debian 14.2.0-16) 14.2.0
    GNU Fortran (Debian 14.2.0-16) 14.2.0
* running under: Debian GNU/Linux trixie/sid
* using session charset: UTF-8
* checking for file ‘aroma.core/DESCRIPTION’ ... OK
* this is package ‘aroma.core’ version ‘3.3.1’
* checking package namespace information ... OK
* checking package dependencies ... INFO
Packages suggested but not available for checking:
  'sfit', 'expectile', 'HaarSeg', 'mpcbs'
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for executable files ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking serialization versions ... OK
* checking whether package ‘aroma.core’ can be installed ... OK
See 'https://www.r-project.org/nosvn/R.check/r-devel-linux-x86_64-debian-gcc/aroma.core-00install.html' for details.
* checking package directory ... OK
* checking for future file timestamps ... 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 ... [1s/1s] OK
* checking whether the package can be loaded with stated dependencies ... [1s/1s] OK
* checking whether the package can be unloaded cleanly ... [1s/1s] OK
* checking whether the namespace can be loaded with stated dependencies ... [1s/1s] OK
* checking whether the namespace can be unloaded cleanly ... [1s/1s] OK
* checking loading without being on the library search path ... [1s/1s] OK
* checking whether startup messages can be suppressed ... [1s/1s] OK
* checking use of S3 registration ... 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 ... [42s/53s] OK
* checking Rd files ... [1s/1s] OK
* checking Rd metadata ... OK
* checking Rd line widths ... OK
* checking Rd cross-references ... NOTE
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  writeDataFrame.AromaUnitSignalBinaryFile.Rd: TabularTextFile
  writeDataFrame.AromaUnitSignalBinarySet.Rd: TabularTextFileSet
  writeDataFrame.AromaUnitTabularBinaryFile.Rd: TabularTextFile
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 examples ... [4s/5s] OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ... [18s/22s] OK
  Running ‘PairedPSCNData,SEG.R’ [0s/0s]
  Running ‘PairedPSCNData.R’ [0s/0s]
  Running ‘RawCopyNumbers,states.R’ [1s/2s]
  Running ‘RawCopyNumbers.R’ [1s/2s]
  Running ‘RawGenomicSignals.R’ [1s/1s]
  Running ‘RawGenomicSignals.SEG,MP.R’ [1s/1s]
  Running ‘RawGenomicSignals.SEG.R’ [1s/1s]
  Running ‘RichDataFrame.R’ [1s/1s]
  Running ‘SegmentedCopyNumbers.R’ [2s/2s]
  Running ‘aromaSettings.R’ [1s/1s]
  Running ‘binScatter.R’ [2s/2s]
  Running ‘colBinnedSmoothing.R’ [1s/1s]
  Running ‘colKernelSmoothing.R’ [1s/1s]
  Running ‘fitGenotypeCone.R’ [1s/1s]
  Running ‘fitMultiDimensionalCone.R’ [1s/1s]
  Running ‘matrixBlockPolish.R’ [1s/1s]
  Running ‘mergeBoxplotStats.R’ [1s/1s]
* checking PDF version of manual ... [13s/16s] OK
* checking HTML version of manual ... [5s/8s] OK
* checking for non-standard things in the check directory ... OK
* DONE
Status: 1 NOTE