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### Running command:
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###   /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:frmaTools.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings frmaTools_1.59.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/frmaTools.Rcheck’
* using R Under development (unstable) (2024-10-21 r87258)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0
    GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0
* running under: Ubuntu 24.04.1 LTS
* using session charset: UTF-8
* checking for file ‘frmaTools/DESCRIPTION’ ... OK
* this is package ‘frmaTools’ version ‘1.59.0’
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
  cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
 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 for sufficient/correct file permissions ... 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 loading without being on the library search path ... 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                 user system elapsed
convertPlatform 6.002  0.231   6.238
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.21-bioc/meat/frmaTools.Rcheck/00check.log’
for details.