* using log directory ‘/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/ICAMS.Rcheck’
* using R Under development (unstable) (2025-02-26 r87830)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    Debian clang version 19.1.7 (1+b1)
    Debian flang-new version 19.1.7 (1+b1)
* running under: Debian GNU/Linux trixie/sid
* 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 executable files ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘ICAMS’ can be installed ... OK
See 'https://www.r-project.org/nosvn/R.check/r-devel-linux-x86_64-debian-clang/ICAMS-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 ... [14s/18s] OK
* checking whether the package can be loaded with stated dependencies ... [14s/16s] OK
* checking whether the package can be unloaded cleanly ... [14s/17s] OK
* checking whether the namespace can be loaded with stated dependencies ... [15s/18s] OK
* checking whether the namespace can be unloaded cleanly ... [15s/20s] OK
* checking loading without being on the library search path ... [15s/22s] 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 ... [86s/104s] OK
* checking Rd files ... [1s/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:
  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 ... [1s/2s] OK
* checking LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking R/sysdata.rda ... OK
* checking examples ... [56s/50s] OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ... [392s/281s] OK
  Running ‘testthat.R’ [392s/280s]
* checking PDF version of manual ... [10s/14s] OK
* checking HTML version of manual ... [6s/11s] OK
* checking for non-standard things in the check directory ... OK
* DONE
Status: 1 NOTE