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### Running command:
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###   C:\Users\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:CNVMetrics.install-out.txt --library=C:\Users\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings CNVMetrics_1.9.0.tar.gz
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* using log directory 'C:/Users/biocbuild/bbs-3.20-bioc/meat/CNVMetrics.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 'CNVMetrics/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'CNVMetrics' version '1.9.0'
* 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 'CNVMetrics' can be installed ... OK
* checking installed package size ... OK
* 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) CNVMetrics-package.Rd:23-24: Lost braces
    23 |     \item \code{\link{calculateOverlapMetric}} {for calculating metric
       |                                                ^
checkRd: (-1) CNVMetrics-package.Rd:25-26: Lost braces
    25 |     \item \code{\link{calculateLog2ratioMetric}} {for calculating metric
       |                                                  ^
checkRd: (-1) CNVMetrics-package.Rd:27: Lost braces; missing escapes or markup?
    27 |     \item \code{\link{processSim}} {for generating simulations}
       |                                    ^
checkRd: (-1) CNVMetrics-package.Rd:28: Lost braces; missing escapes or markup?
    28 |     \item \code{\link{plotMetric}} {for plotting metrics}
       |                                    ^
checkRd: (-1) calculateLog2ratioMetric.Rd:42-47: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) calculateLog2ratioMetric.Rd:52-53: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) calculateLog2ratioMetric.Rd:54-56: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) calculateOneLog2valueMetricT.Rd:37: Lost braces
    37 | that have to be excluded for the metric calculation or code{NULL}.}
       |                                                            ^
checkRd: (-1) calculateOneLog2valueMetricT.Rd:42-49: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) calculateOneOverlapMetricT.Rd:33-40: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) calculateOverlapMetric.Rd:39-44: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) calculateOverlapMetric.Rd:50-51: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) calculateOverlapMetric.Rd:52-54: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) processSim.Rd:27-28: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) processSim.Rd:29: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) processSim.Rd:30-31: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) processSim.Rd:32: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) processSim.Rd:33-34: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) processSim.Rd:35-36: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) simChr.Rd:26: Lost braces
    26 | a code{list} containing one entry per simulation. Each entry is
       |       ^
checkRd: (-1) simChr.Rd:29: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) simChr.Rd:30: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) simChr.Rd:31-33: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) simChr.Rd:34-36: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) simChr.Rd:37-38: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) simChr.Rd:39-40: Lost braces in \itemize; \value handles \item{}{} directly
* 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 files in 'vignettes' ... OK
* checking examples ... OK
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
  Running 'testthat.R'
 OK
* 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: 1 NOTE
See
  'C:/Users/biocbuild/bbs-3.20-bioc/meat/CNVMetrics.Rcheck/00check.log'
for details.