• using R Under development (unstable) (2025-01-29 r87668)
• using platform: x86_64-pc-linux-gnu
• R was compiled by     Debian clang version 19.1.6 (1+b1)     Debian flang-new version 19.1.6 (1+b1)
• 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:   'affxparser', '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 the install log 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/2s] OK
• checking whether the package can be loaded with stated dependencies ... [1s/2s] OK
• checking whether the package can be unloaded cleanly ... [1s/2s] OK
• checking whether the namespace can be loaded with stated dependencies ... [1s/2s] OK
• checking whether the namespace can be unloaded cleanly ... [1s/2s] OK
• checking loading without being on the library search path ... [1s/2s] OK
• checking whether startup messages can be suppressed ... [1s/2s] 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 ... [131s/161s] OK
• checking Rd files ... [4s/6s] 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. Packages unavailable to check Rd xrefs: ‘affxparser’, ‘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 ... [2s/2s] OK
• checking for unstated dependencies in ‘tests’ ... OK
• checking tests ... [8s/10s] OK   Running ‘001.setupExampleData,annotationData.R’ [1s/2s]   Running ‘002.setupExampleData,rawData.R’ [1s/2s]   Running ‘AffymetrixCdfFile.R’ [1s/2s]   Running ‘AffymetrixCelFile.R’ [1s/2s]   Running ‘AffymetrixCelSet.R’ [2s/2s]
• checking PDF version of manual ... [25s/32s] OK
• checking HTML version of manual ... [18s/32s] OK
• checking for non-standard things in the check directory ... OK
• DONE

Status: 1 NOTE