• using R Under development (unstable) (2024-12-19 r87451)
• using platform: x86_64-pc-linux-gnu
• R was compiled by     gcc-14 (Debian 14.2.0-8) 14.2.0     GNU Fortran (Debian 14.2.0-8) 14.2.0
• 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 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 ... [10s/11s] OK
• checking whether the package can be loaded with stated dependencies ... [10s/11s] OK
• checking whether the package can be unloaded cleanly ... [10s/11s] OK
• checking whether the namespace can be loaded with stated dependencies ... [10s/11s] OK
• checking whether the namespace can be unloaded cleanly ... [11s/13s] OK
• checking loading without being on the library search path ... [10s/11s] 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 ... [61s/72s] 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:   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/1s] OK
• checking LazyData ... OK
• checking data for ASCII and uncompressed saves ... OK
• checking R/sysdata.rda ... OK
• checking examples ... [31s/30s] OK
• checking for unstated dependencies in ‘tests’ ... OK
• checking tests ... [237s/217s] OK   Running ‘testthat.R’ [237s/216s]
• checking PDF version of manual ... [8s/10s] OK
• checking HTML version of manual ... [4s/7s] OK
• checking for non-standard things in the check directory ... OK
• DONE

Status: 1 NOTE