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### Running command:
###
###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:convert.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings convert_1.82.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/convert.Rcheck’
* using R version 4.4.1 (2024-06-14)
* 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 ‘convert/DESCRIPTION’ ... OK
* this is package ‘convert’ version ‘1.82.0’
* 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 ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘convert’ 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
Packages in Depends field not imported from:
  ‘Biobase’ ‘limma’ ‘marray’ ‘methods’
  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
coerce,MAList-ExpressionSet: no visible global function definition for
  ‘new’
coerce,MAList-ExpressionSet: no visible global function definition for
  ‘notes<-’
coerce,MAList-marrayNorm: no visible global function definition for
  ‘new’
coerce,RGList-NChannelSet: no visible global function definition for
  ‘new’
coerce,RGList-NChannelSet: no visible binding for global variable ‘df’
coerce,RGList-marrayRaw: no visible global function definition for
  ‘new’
coerce,marrayNorm-ExpressionSet: no visible global function definition
  for ‘new’
coerce,marrayNorm-ExpressionSet: no visible global function definition
  for ‘notes<-’
coerce,marrayNorm-ExpressionSet: no visible global function definition
  for ‘maM’
coerce,marrayNorm-ExpressionSet: no visible global function definition
  for ‘maLabels’
coerce,marrayNorm-ExpressionSet: no visible global function definition
  for ‘maGnames’
coerce,marrayNorm-ExpressionSet: no visible global function definition
  for ‘maInfo’
coerce,marrayNorm-ExpressionSet: no visible global function definition
  for ‘maTargets’
coerce,marrayNorm-MAList: no visible global function definition for
  ‘new’
coerce,marrayNorm-MAList: no visible global function definition for
  ‘getClass’
coerce,marrayRaw-NChannelSet: no visible global function definition for
  ‘maRf’
coerce,marrayRaw-NChannelSet: no visible global function definition for
  ‘maGf’
coerce,marrayRaw-NChannelSet: no visible global function definition for
  ‘maRb’
coerce,marrayRaw-NChannelSet: no visible global function definition for
  ‘maGb’
coerce,marrayRaw-NChannelSet: no visible binding for global variable
  ‘assayDataNew’
coerce,marrayRaw-NChannelSet: no visible global function definition for
  ‘maInfo’
coerce,marrayRaw-NChannelSet: no visible global function definition for
  ‘maTargets’
coerce,marrayRaw-NChannelSet: no visible global function definition for
  ‘new’
coerce,marrayRaw-NChannelSet: no visible global function definition for
  ‘maGnames’
coerce,marrayRaw-NChannelSet: no visible global function definition for
  ‘phenoData<-’
coerce,marrayRaw-NChannelSet: no visible global function definition for
  ‘sampleNames’
coerce,marrayRaw-NChannelSet: no visible global function definition for
  ‘sampleNames<-’
coerce,marrayRaw-NChannelSet: no visible global function definition for
  ‘maLabels’
coerce,marrayRaw-NChannelSet: no visible global function definition for
  ‘featureData<-’
coerce,marrayRaw-NChannelSet: no visible global function definition for
  ‘featureNames<-’
coerce,marrayRaw-RGList: no visible global function definition for
  ‘new’
Undefined global functions or variables:
  assayDataNew df featureData<- featureNames<- getClass maGb maGf
  maGnames maInfo maLabels maM maRb maRf maTargets new notes<-
  phenoData<- sampleNames sampleNames<-
Consider adding
  importFrom("methods", "getClass", "new")
  importFrom("stats", "df")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* 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
* 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: 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.20-bioc/meat/convert.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD INSTALL convert
###
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* installing to library ‘/home/biocbuild/bbs-3.20-bioc/R/site-library’
* installing *source* package ‘convert’ ...
** using staged installation
** R
** 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 (convert)