##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:GeomxTools.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings GeomxTools_2.0.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.14-bioc/meat/GeomxTools.Rcheck'
* using R version 4.1.3 (2022-03-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'GeomxTools/DESCRIPTION' ... OK
* this is package 'GeomxTools' version '2.0.0'
* 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 'GeomxTools' can be installed ... OK
* checking installed package size ... NOTE
  installed size is 12.7Mb
  sub-directories of 1Mb or more:
    extdata  11.7Mb
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... NOTE
License components which are templates and need '+ file LICENSE':
  MIT
* checking top-level files ... NOTE
File
  LICENSE
is not mentioned in the DESCRIPTION file.
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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
aggregateCounts: no visible binding for global variable 'TargetName'
hkNorm: no visible binding for global variable 'TargetName'
mixedModelDE: multiple local function definitions for 'deFunc' with
  different formal arguments
setGrubbsFlags: no visible binding for global variable 'TargetName'
setGrubbsFlags : <anonymous>: no visible binding for global variable
  'Module'
setProbeRatioFlags: no visible binding for global variable 'TargetName'
subtractBackground : <anonymous>: no visible binding for global
  variable 'Module'
setSignatureFuncs<-,NanoStringGeoMxSet-character: no visible global
  function definition for 'setSigFuncs<-'
signatureScores,NanoStringGeoMxSet: no visible global function
  definition for 'assayDataElement2'
signatureScores,NanoStringGeoMxSet: no visible global function
  definition for '.sigCalc'
Undefined global functions or variables:
  .sigCalc Module TargetName assayDataElement2 setSigFuncs<-
* 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 ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                                      user system elapsed
readNanoStringGeoMxSet               40.31   0.75   41.06
setBioProbeQCFlags                   34.70   0.03   34.74
setQCFlags-NanoStringGeoMxSet-method 32.41   0.05   32.46
NanoStringGeoMxSet-class             19.92   0.53   30.39
writeNanoStringGeoMxSet              14.83   0.35   19.89
aggregateCounts                      14.41   0.15   15.13
mixedModelDE                         14.27   0.05   35.24
readDccFile                           6.33   0.08    6.41
readPKCFile                           5.91   0.04    5.95
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                                      user system elapsed
setQCFlags-NanoStringGeoMxSet-method 42.57   0.03   42.61
setBioProbeQCFlags                   41.76   0.02   41.79
readNanoStringGeoMxSet               40.05   0.78   40.83
NanoStringGeoMxSet-class             17.89   0.35   20.86
writeNanoStringGeoMxSet              17.92   0.23   21.34
aggregateCounts                      15.97   0.09   16.08
mixedModelDE                         14.78   0.10   39.75
readPKCFile                           5.59   0.05    5.64
readDccFile                           5.27   0.03    5.29
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'testthat.R'
 OK
** running tests for arch 'x64' ...
  Running 'testthat.R'
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in 'inst/doc' ... 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
  'C:/Users/biocbuild/bbs-3.14-bioc/meat/GeomxTools.Rcheck/00check.log'
for details.