* using log directory ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/aroma.affymetrix.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.affymetrix/DESCRIPTION’ ... OK
* this is package ‘aroma.affymetrix’ version ‘3.2.2’
* checking package namespace information ... OK
* checking package dependencies ... INFO
Packages suggested but not available for checking: 'oligo', 'pdInfoBuilder'
* 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.affymetrix’ can be installed ... OK
See 'https://www.r-project.org/nosvn/R.check/r-devel-linux-x86_64-debian-gcc/aroma.affymetrix-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 ... [73s/85s] OK
* checking Rd files ... [2s/2s] 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:
  SmoothMultiarrayModel.Rd: ChromosomalModel,
    CopyNumberSegmentationModel
  byPath.AffymetrixFileSet.Rd: GenericDataFile
  calculateBaseline.ChipEffectSet.Rd: getAverageFile
  doCRMAv1.Rd: Verbose
  doCRMAv2.Rd: Verbose
  doFIRMA.Rd: Verbose
  doGCRMA.Rd: Verbose
  doRMA.Rd: Verbose
  justRMA.Rd: Verbose
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Package unavailable to check Rd xrefs: ‘oligo’
* 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 ... [1s/1s] OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ... [17s/20s] OK
  Running ‘001.setupExampleData,annotationData.R’ [7s/8s]
  Running ‘002.setupExampleData,rawData.R’ [1s/1s]
  Running ‘AffymetrixCdfFile.R’ [4s/5s]
  Running ‘AffymetrixCelFile.R’ [1s/1s]
  Running ‘AffymetrixCelSet.R’ [4s/5s]
* checking PDF version of manual ... [17s/20s] OK
* checking HTML version of manual ... [11s/17s] OK
* checking for non-standard things in the check directory ... OK
* DONE
Status: 1 NOTE