* using log directory 'd:/Rcompile/CRANpkg/local/4.5/ICAMS.Rcheck'
* using R Under development (unstable) (2024-11-07 r87302 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 13.3.0
    GNU Fortran (GCC) 13.3.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* checking for file 'ICAMS/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'ICAMS' version '2.3.12'
* package encoding: UTF-8
* 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 'ICAMS' can be installed ... OK
* checking installed package size ... OK
* checking package 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 ... [12s] OK
* checking whether the package can be loaded with stated dependencies ... [12s] OK
* checking whether the package can be unloaded cleanly ... [12s] OK
* checking whether the namespace can be loaded with stated dependencies ... [11s] OK
* checking whether the namespace can be unloaded cleanly ... [12s] OK
* checking loading without being on the library search path ... [12s] 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 ... [38s] OK
* checking Rd files ... [2s] OK
* checking Rd metadata ... OK
* checking Rd cross-references ... NOTE
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  AnnotateDBSVCF.Rd: BSgenome
  AnnotateSBSVCF.Rd: BSgenome
  GeneExpressionData.Rd: data.table
  ICAMS.Rd: BSgenome
  MutectVCFFilesToCatalog.Rd: BSgenome
  MutectVCFFilesToCatalogAndPlotToPdf.Rd: BSgenome
  MutectVCFFilesToZipFile.Rd: BSgenome
  NormalizeGenomeArg.Rd: BSgenome
  PlotTransBiasGeneExp.Rd: data.table
  PlotTransBiasGeneExpToPdf.Rd: data.table
  StrelkaSBSVCFFilesToCatalog.Rd: BSgenome
  StrelkaSBSVCFFilesToCatalogAndPlotToPdf.Rd: BSgenome
  StrelkaSBSVCFFilesToZipFile.Rd: BSgenome
  VCFsToCatalogs.Rd: BSgenome
  VCFsToCatalogsAndPlotToPdf.Rd: BSgenome
  VCFsToDBSCatalogs.Rd: BSgenome
  VCFsToSBSCatalogs.Rd: BSgenome
  VCFsToZipFile.Rd: BSgenome
  revc.Rd: reverseComplement
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 contents of 'data' directory ... OK
* checking data for non-ASCII characters ... [2s] OK
* checking LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking R/sysdata.rda ... OK
* checking examples ... [63s] OK
* checking for unstated dependencies in 'tests' ... OK
* checking tests ... [184s] OK
  Running 'testthat.R' [184s]
* checking PDF version of manual ... [29s] OK
* checking HTML version of manual ... [26s] OK
* DONE
Status: 1 NOTE