##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:ddCt.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings ddCt_1.62.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'F:/biocbuild/bbs-3.20-bioc/meat/ddCt.Rcheck'
* using R version 4.4.2 (2024-10-31 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
* using option '--no-vignettes'
* checking for file 'ddCt/DESCRIPTION' ... OK
* this is package 'ddCt' version '1.62.0'
* 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 'ddCt' 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 ... NOTE
barploterrbar: no visible global function definition for 'par'
barploterrbar: no visible global function definition for 'layout'
barploterrbar: no visible global function definition for 'barplot'
barploterrbar: no visible global function definition for 'segments'
ddCtErrBarchart: no visible global function definition for 'as.formula'
ddCtReport: no visible global function definition for 'write.table'
na.mad: no visible global function definition for 'mad'
na.median: no visible global function definition for 'median'
na.sd: no visible global function definition for 'sd'
replaceNames: no visible global function definition for 'na.omit'
ddCtWithEExec,InputFrame: no visible global function definition for
  'deriv'
ddCtWithEExec,InputFrame: no visible global function definition for
  'as.formula'
elistWrite,ddCtExpression-character: no visible global function
  definition for 'write.table'
readRawData,QuantStudioReader-character: no visible global function
  definition for 'read.table'
readRawData,SDMReader-character: no visible global function definition
  for 'read.table'
readRawData,TSVReader-character: no visible global function definition
  for 'read.table'
Undefined global functions or variables:
  as.formula barplot deriv layout mad median na.omit par read.table sd
  segments write.table
Consider adding
  importFrom("graphics", "barplot", "layout", "par", "segments")
  importFrom("stats", "as.formula", "deriv", "mad", "median", "na.omit",
             "sd")
  importFrom("utils", "read.table", "write.table")
to your NAMESPACE file.
* checking Rd files ... WARNING
checkRd: (7) InputFrame.Rd:18: Invalid URL: mailto: jitao_david.zhang@roche.com
checkRd: (-1) SDMFrame-class.Rd:83: Escaped LaTeX specials: \$
checkRd: (7) SDMFrame-class.Rd:172: Invalid email address: mailto:r.biczok@dkfz.de
checkRd: (7) SDMFrame-class.Rd:173: Invalid email address: mailto:jitao_david.zhang@roche.com
checkRd: (-1) ddCtAbsolute.Rd:30: Escaped LaTeX specials: \_
checkRd: (-1) ddCtExpression-class.Rd:97: Lost braces; missing escapes or markup?
    97 |         "character")}: {writes ddCtExpression object into a file}
       |                        ^
checkRd: (7) ddCtExpression-class.Rd:101: Invalid email address: mailto:r.biczok@dkfz.de
checkRd: (7) ddCtExpression-methods.Rd:59: Invalid email address: mailto:r.biczok@dkfz.de
* 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 sizes of PDF files under 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ... OK
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
  Running 'testthat.R'
  Running 'unit.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 WARNING, 1 NOTE
See
  'F:/biocbuild/bbs-3.20-bioc/meat/ddCt.Rcheck/00check.log'
for details.