##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:frmaTools.install-out.txt --library=F:\biocbuild\bbs-3.19-bioc\R\library --no-vignettes --timings frmaTools_1.56.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'F:/biocbuild/bbs-3.19-bioc/meat/frmaTools.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 'frmaTools/DESCRIPTION' ... OK
* this is package 'frmaTools' version '1.56.0'
* 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 ... NOTE
Found the following hidden files and directories:
  inst/VectorPkg-template/data/.dummy.txt
These were most likely included in error. See section 'Package
structure' in the 'Writing R Extensions' manual.
* checking for portable file names ... OK
* checking whether package 'frmaTools' 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 ... NOTE
'library' or 'require' call to 'oligo' in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Package in Depends field not imported from: 'affy'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
convertPlatform: no visible global function definition for
  'cleancdfname'
convertPlatform: no visible global function definition for 'cdfName'
convertPlatform: no visible global function definition for 'probeNames'
convertPlatform: no visible global function definition for 'pmindex'
getFidMetaProbesetCore: no visible global function definition for 'db'
getFidMetaProbesetExtended: no visible global function definition for
  'db'
getFidMetaProbesetFull: no visible global function definition for 'db'
getFidProbeset: no visible global function definition for 'db'
makeMaps: no visible global function definition for 'xy2indices'
makeVectorsAffyBatch: no visible global function definition for
  'ReadAffy'
makeVectorsAffyBatch: no visible global function definition for
  'bg.correct.rma'
makeVectorsAffyBatch: no visible global function definition for 'pm'
makeVectorsAffyBatch: no visible global function definition for
  'probeNames'
makeVectorsAffyBatch: no visible global function definition for
  'pmindex'
makeVectorsAffyBatch: no visible global function definition for
  'packageVersion'
makeVectorsFeatureSet: no visible global function definition for
  'read.celfiles'
makeVectorsFeatureSet: no visible global function definition for
  'backgroundCorrect'
Undefined global functions or variables:
  ReadAffy backgroundCorrect bg.correct.rma cdfName cleancdfname db
  packageVersion pm pmindex probeNames read.celfiles xy2indices
Consider adding
  importFrom("utils", "packageVersion")
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 ... 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
Examples with CPU (user + system) or elapsed time > 5s
                user system elapsed
convertPlatform 8.63   0.35   10.14
* 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-3.19-bioc/meat/frmaTools.Rcheck/00check.log'
for details.

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD INSTALL frmaTools
###
##############################################################################
##############################################################################


* installing to library 'F:/biocbuild/bbs-3.19-bioc/R/library'
* installing *source* package 'frmaTools' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (frmaTools)