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### Running command:
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###   E:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:DegNorm.install-out.txt --library=E:\biocbuild\bbs-3.19-bioc\R\library --no-vignettes --timings DegNorm_1.14.0.tar.gz
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* using log directory 'E:/biocbuild/bbs-3.19-bioc/meat/DegNorm.Rcheck'
* using R version 4.4.1 (2024-06-14 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 13.2.0
    GNU Fortran (GCC) 13.2.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'DegNorm/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'DegNorm' version '1.14.0'
* 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 'DegNorm' can be installed ... OK
* used C++ compiler: 'G__~1.EXE (GCC) 13.2.0'
* checking C++ specification ... NOTE
  Specified C++11: please drop specification unless essential
* checking installed package size ... NOTE
  installed size is  8.9Mb
  sub-directories of 1Mb or more:
    doc       4.9Mb
    extdata   2.1Mb
    libs      1.2Mb
* checking package directory ... OK
* checking 'build' 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 ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... 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 ... OK
* checking Rd files ... NOTE
checkRd: (-1) PlotFunctions.Rd:30: Lost braces
    30 | \code{plot_corr}{ plots the correlation matrix of DI scores between samples.}
       |                 ^
checkRd: (-1) PlotFunctions.Rd:31-34: Lost braces
    31 | \code{plot_heatmap}{ plots the heatmap of DI  scores. Left is ploted in 
       |                    ^
checkRd: (-1) PlotFunctions.Rd:35: Lost braces
    35 | \code{plot_boxplot}{plots the boxplot of DI scores by samples.}
       |                    ^
checkRd: (-1) plot_coverage.Rd:31-32: Lost braces
    31 | \code{plot_coverage}{outputs the coverage curves before- and after-degradation 
       |                     ^
checkRd: (-1) summary_CoverageClass.Rd:16: Lost braces
    16 | \item{object}{CoverageClass from code{read_coverage_batch.}
       |                                      ^
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* 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 ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking use of PKG_*FLAGS in Makefiles ... OK
* checking compiled code ... OK
* checking installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                    user system elapsed
read_coverage_batch  5.9   0.20  117.44
degnorm              0.7   0.16   52.22
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 3 NOTEs
See
  'E:/biocbuild/bbs-3.19-bioc/meat/DegNorm.Rcheck/00check.log'
for details.