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### Running command:
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###   F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:ontoProc.install-out.txt --library=F:\biocbuild\bbs-3.19-bioc\R\library --no-vignettes --timings ontoProc_1.26.0.tar.gz
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* using log directory 'F:/biocbuild/bbs-3.19-bioc/meat/ontoProc.Rcheck'
* using R version 4.4.0 (2024-04-24 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 'ontoProc/DESCRIPTION' ... OK
* this is package 'ontoProc' version '1.26.0'
* 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 'ontoProc' can be installed ... OK
* checking installed package size ... NOTE
  installed size is 10.0Mb
  sub-directories of 1Mb or more:
    app       1.9Mb
    data      1.8Mb
    ontoRda   2.8Mb
    owl       2.9Mb
* 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
CLfeat : prupdate: no visible binding for global variable 'PROSYM'
CLfeat : prupdate: no visible binding for global variable 'PRID'
CLfeat : prupdate: no visible binding for global variable 'SYMBOL'
ctmarks : server: no visible binding for global variable 'text'
ctmarks : server: no visible binding for global variable 'packDesc2022'
ctmarks : server: no visible binding for global variable 'packDesc2021'
ctmarks: no visible binding for global variable 'cumu'
dropStop: no visible binding for global variable 'stopWords'
getOnto: no visible binding for global variable 'rdatadateadded'
getOnto: no visible binding for global variable 'title'
getOnto: no visible binding for global variable 'description'
ldfToTerm: no visible binding for global variable 'PROSYM'
sym2CellOnto: no visible binding for global variable 'PROSYM'
sym2CellOnto: no visible binding for global variable 'SYMBOL'
Undefined global functions or variables:
  PRID PROSYM SYMBOL cumu description packDesc2021 packDesc2022
  rdatadateadded stopWords text title
Consider adding
  importFrom("graphics", "text", "title")
to your NAMESPACE file.
* checking Rd files ... OK
* 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 ... NOTE
S3 methods shown with full name in Rd file 'plot.owlents.Rd':
  'plot.owlents'

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of 'data' directory ... OK
* checking data for non-ASCII characters ... NOTE
  Note: found 162 marked UTF-8 strings
* checking data for ASCII and uncompressed saves ... OK
* checking files in 'vignettes' ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                                  user system elapsed
sym2CellOnto                     54.34   3.44   71.53
CLfeats                          30.76   4.16   42.87
siblings_TAG                     28.15   4.31   41.90
plot.owlents                     18.31   0.39   19.67
fastGrep                         15.54   1.61   22.06
ancestors                        14.82   1.67   21.18
getLeavesFromTerm                14.98   1.36   16.56
owl2cache                        14.37   0.37   15.34
common_classes                   12.57   2.02   16.39
nomenCheckup                     13.15   1.28   14.53
cleanCLOnames                    12.37   1.23   14.74
selectFromMap                    10.80   1.64   12.56
TermSet-class                     9.45   1.28   13.49
secLevGen                         9.22   1.33   10.72
getOnto                           8.69   1.24   10.03
mapOneNaive                       8.14   1.30    9.53
make_graphNEL_from_ontology_plot  8.09   1.10    9.30
findCommonAncestors               7.85   1.26    9.19
liberalMap                        7.53   1.26    8.93
onto_plot2                        7.10   1.45    8.78
setup_entities                    5.14   0.08    5.25
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
  Running 'test.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: 4 NOTEs
See
  'F:/biocbuild/bbs-3.19-bioc/meat/ontoProc.Rcheck/00check.log'
for details.