##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:plotgardener.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings plotgardener_1.11.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'F:/biocbuild/bbs-3.20-bioc/meat/plotgardener.Rcheck'
* using R version 4.4.0 RC (2024-04-16 r86468 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 'plotgardener/DESCRIPTION' ... OK
* this is package 'plotgardener' version '1.11.0'
* 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 'plotgardener' can be installed ... OK
* used C++ compiler: 'G__~1.EXE (GCC) 13.2.0'
* 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 whether startup messages can be suppressed ... 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
pgParams: no visible binding for global variable 'width'
pgParams: no visible binding for global variable 'strand'
Undefined global functions or variables:
  strand width
* checking Rd files ... NOTE
checkRd: (-1) annoDomains.Rd:28-29: Lost braces in \itemize; meant \describe ?
checkRd: (-1) annoDomains.Rd:30-31: Lost braces in \itemize; meant \describe ?
checkRd: (-1) annoDomains.Rd:32-33: Lost braces in \itemize; meant \describe ?
checkRd: (-1) annoDomains.Rd:34-35: Lost braces in \itemize; meant \describe ?
checkRd: (-1) annoGenomeLabel.Rd:47: Lost braces in \itemize; meant \describe ?
checkRd: (-1) annoGenomeLabel.Rd:48-49: Lost braces in \itemize; meant \describe ?
checkRd: (-1) annoGenomeLabel.Rd:50-51: Lost braces in \itemize; meant \describe ?
checkRd: (-1) annoGenomeLabel.Rd:69: Lost braces in \itemize; meant \describe ?
checkRd: (-1) annoGenomeLabel.Rd:70-72: Lost braces in \itemize; meant \describe ?
checkRd: (-1) annoHeatmapLegend.Rd:33: Lost braces in \itemize; meant \describe ?
checkRd: (-1) annoHeatmapLegend.Rd:34: Lost braces in \itemize; meant \describe ?
checkRd: (-1) annoPixels.Rd:30: Lost braces in \itemize; meant \describe ?
checkRd: (-1) annoPixels.Rd:31: Lost braces in \itemize; meant \describe ?
checkRd: (-1) annoPixels.Rd:32: Lost braces in \itemize; meant \describe ?
checkRd: (-1) annoPixels.Rd:39-40: Lost braces in \itemize; meant \describe ?
checkRd: (-1) annoPixels.Rd:41-42: Lost braces in \itemize; meant \describe ?
checkRd: (-1) annoPixels.Rd:43-44: Lost braces in \itemize; meant \describe ?
checkRd: (-1) annoPixels.Rd:45-46: Lost braces in \itemize; meant \describe ?
checkRd: (-1) annoSegments.Rd:64: Lost braces in \itemize; meant \describe ?
checkRd: (-1) annoSegments.Rd:65: Lost braces in \itemize; meant \describe ?
checkRd: (-1) annoSegments.Rd:66: Lost braces in \itemize; meant \describe ?
checkRd: (-1) annoXaxis.Rd:31: Lost braces in \itemize; meant \describe ?
checkRd: (-1) annoXaxis.Rd:32: Lost braces in \itemize; meant \describe ?
checkRd: (-1) annoYaxis.Rd:31: Lost braces in \itemize; meant \describe ?
checkRd: (-1) annoYaxis.Rd:32: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plotGenomeLabel.Rd:58: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plotGenomeLabel.Rd:59-60: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plotGenomeLabel.Rd:61-62: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plotGenomeLabel.Rd:80: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plotGenomeLabel.Rd:81-83: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plotHicRectangle.Rd:53: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plotHicRectangle.Rd:54: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plotHicRectangle.Rd:55: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plotHicSquare.Rd:57: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plotHicSquare.Rd:58: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plotHicSquare.Rd:59: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plotHicSquare.Rd:96: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plotHicSquare.Rd:97: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plotHicSquare.Rd:98: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plotHicTriangle.Rd:53: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plotHicTriangle.Rd:54: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plotHicTriangle.Rd:55: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plotIdeogram.Rd:40: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plotIdeogram.Rd:41: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plotLegend.Rd:42: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plotLegend.Rd:43: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plotManhattan.Rd:45: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plotManhattan.Rd:46-47: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plotManhattan.Rd:48-49: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plotManhattan.Rd:50-51: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plotMultiSignal.Rd:103-104: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plotMultiSignal.Rd:105-106: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plotPairs.Rd:58: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plotPairs.Rd:59: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plotPairsArches.Rd:56: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plotPairsArches.Rd:57: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plotPairsArches.Rd:79: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plotPairsArches.Rd:80: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plotRanges.Rd:62: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plotRanges.Rd:63: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plotRanges.Rd:70: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plotRanges.Rd:71: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plotSegments.Rd:68: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plotSegments.Rd:69: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plotSegments.Rd:70: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plotSignal.Rd:104: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plotSignal.Rd:105: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plotTranscripts.Rd:88: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plotTranscripts.Rd:89: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plotTranscripts.Rd:90: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plotTranscripts.Rd:91-92: Lost braces in \itemize; meant \describe ?
checkRd: (-1) readBigwig.Rd:29: Lost braces in \itemize; meant \describe ?
checkRd: (-1) readBigwig.Rd:30: Lost braces in \itemize; meant \describe ?
checkRd: (-1) readBigwig.Rd:31: Lost braces in \itemize; meant \describe ?
checkRd: (-1) readHic.Rd:54: Lost braces in \itemize; meant \describe ?
checkRd: (-1) readHic.Rd:55: Lost braces in \itemize; meant \describe ?
checkRd: (-1) readHic.Rd:68: Lost braces in \itemize; meant \describe ?
checkRd: (-1) readHic.Rd:69: Lost braces in \itemize; meant \describe ?
checkRd: (-1) readHic.Rd:70: Lost braces in \itemize; meant \describe ?
* 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 R/sysdata.rda ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... NOTE
Note: information on .o files for x64 is not available
File 'F:/biocbuild/bbs-3.20-bioc/R/library/plotgardener/libs/x64/plotgardener.dll':
  Found '_exit', possibly from '_exit' (C)
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
  Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs nor [v]sprintf. The detected symbols are linked into
the code but might come from libraries and not actually be called.

See 'Writing portable packages' in the 'Writing R Extensions' manual.
* checking files in 'vignettes' ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
               user system elapsed
plotRaster    12.17   0.83   13.01
plotGenes      5.84   0.16    6.00
annoZoomLines  5.63   0.32    5.95
* 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: 3 NOTEs
See
  'F:/biocbuild/bbs-3.20-bioc/meat/plotgardener.Rcheck/00check.log'
for details.