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### Running command:
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###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:bioCancer.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings bioCancer_1.28.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/bioCancer.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: aarch64-apple-darwin20 (64-bit)
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.6.7
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘bioCancer/DESCRIPTION’ ... OK
* this is package ‘bioCancer’ version ‘1.28.0’
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘bioCancer’ can be installed ... OK
* checking installed package size ... NOTE
  installed size is  5.6Mb
  sub-directories of 1Mb or more:
    app       3.3Mb
    extdata   1.6Mb
* 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 ... NOTE
Problems with news in ‘NEWS’:
  Cannot process chunk/lines:
    metamorphosis: bioCancer is a radiant.data extension
  Cannot process chunk/lines:
    reduce size of package by half 14 -> 7 mb
  Cannot process chunk/lines:
    improve Reactome_ui functions
  Cannot process chunk/lines:
    add switch button to ui_circomics
  Cannot process chunk/lines:
    improve circomics functions
  Cannot process chunk/lines:
    delete commented files and figures
  Cannot process chunk/lines:
    cleanup ui_radiant, /Rbis, /quant, /bioCancer
  Cannot process chunk/lines:
    switchButton
  Cannot process chunk/lines:
    data.row.names(row.names, rowsi, i) :
  Cannot process chunk/lines:
    some row.names duplicated: 11,12,13,14 --> row.names NOT used
  Cannot process chunk/lines:
    dplyr::mutate_each() is deprecated
  Cannot process chunk/lines:
    dply::summarise_each() is deprecated
  Cannot process chunk/lines:
    replace BiocStyle by prettydoc
  Cannot process chunk/lines:
    Warning in formals(fun) : argument is not a function
  Cannot process chunk/lines:
    Warning in body(fun) : argument is not a function
  Cannot process chunk/lines:
    Fix setting plot size
  Cannot process chunk/lines:
    Change the color rang of Circular layout plot as in standards
  Cannot process chunk/lines:
    update Correlation Methods
  Cannot process chunk/lines:
    replace .libPath() by path.package('bioCancer') in portal.R file
* checking R 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
Namespaces in Imports field not imported from:
  ‘AlgDesign’ ‘GO.db’ ‘R.methodsS3’ ‘import’ ‘methods’ ‘org.Bt.eg.db’
  ‘shinythemes’
  All declared Imports should be used.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
getGenesClassification: no visible global function definition for ‘new’
Undefined global functions or variables:
  new
Consider adding
  importFrom("methods", "new")
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 ... NOTE
S3 methods shown with full name in documentation object 'getCancerStudies.CGDS':
  ‘getCancerStudies.CGDS’

S3 methods shown with full name in documentation object 'getCaseLists.CGDS':
  ‘getCaseLists.CGDS’

S3 methods shown with full name in documentation object 'getClinicalData.CGDS':
  ‘getClinicalData.CGDS’

S3 methods shown with full name in documentation object 'getGeneticProfiles.CGDS':
  ‘getGeneticProfiles.CGDS’

S3 methods shown with full name in documentation object 'getMutationData.CGDS':
  ‘getMutationData.CGDS’

S3 methods shown with full name in documentation object 'getProfileData.CGDS':
  ‘getProfileData.CGDS’

S3 methods shown with full name in documentation object 'processURL.CGDS':
  ‘processURL.CGDS’

S3 methods shown with full name in documentation object 'setVerbose.CGDS':
  ‘setVerbose.CGDS’

S3 methods shown with full name in documentation object 'test.CGDS':
  ‘test.CGDS’

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 ... OK
* checking LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  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: 5 NOTEs
See
  ‘/Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/bioCancer.Rcheck/00check.log’
for details.