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### Running command:
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###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:oligoClasses.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings oligoClasses_1.68.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/oligoClasses.Rcheck’
* using R version 4.4.1 (2024-06-14)
* using platform: aarch64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Ventura 13.6.7
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘oligoClasses/DESCRIPTION’ ... OK
* this is package ‘oligoClasses’ version ‘1.68.0’
* 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'
 NOTE
Packages which this enhances but not available for checking:
  'doMPI', 'doRedis'
* 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 ‘oligoClasses’ can be installed ... OK
* checking installed package size ... OK
* checking package 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 whether startup messages can be suppressed ... OK
* checking dependencies in R code ... NOTE
Namespace in Imports field not imported from: ‘RSQLite’
  All declared Imports should be used.
Unexported object imported by a ':::' call: ‘Biobase:::assayDataEnvLock’
  See the note in ?`:::` about the use of this operator.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
getSequenceLengths: no visible binding for global variable ‘seqlengths’
chromosome,gSetList: no visible global function definition for
  ‘chromosomeList’
coerce,CNSet-CopyNumberSet: no visible global function definition for
  ‘totalCopynumber’
geometry,FeatureSet: no visible global function definition for ‘getPD’
Undefined global functions or variables:
  chromosomeList getPD seqlengths totalCopynumber
* checking Rd files ... WARNING
checkRd: (-1) AlleleSet-methods.Rd:51: Lost braces in \itemize; meant \describe ?
checkRd: (-1) AlleleSet-methods.Rd:52: Lost braces in \itemize; meant \describe ?
checkRd: (-1) AlleleSet-methods.Rd:53: Lost braces in \itemize; meant \describe ?
checkRd: (-1) AlleleSet-methods.Rd:54: Lost braces in \itemize; meant \describe ?
checkRd: (-1) AlleleSet-methods.Rd:55: Lost braces in \itemize; meant \describe ?
checkRd: (-1) AlleleSet-methods.Rd:56: Lost braces in \itemize; meant \describe ?
checkRd: (5) BeadStudioSet-class.Rd:52: \item in \describe must have non-empty label
checkRd: (5) BeadStudioSet-class.Rd:53-54: \item in \describe must have non-empty label
checkRd: (5) BeadStudioSet-class.Rd:55-57: \item in \describe must have non-empty label
checkRd: (5) BeadStudioSet-class.Rd:58: \item in \describe must have non-empty label
checkRd: (5) BeadStudioSet-class.Rd:59-60: \item in \describe must have non-empty label
checkRd: (5) BeadStudioSet-class.Rd:63: \item in \describe must have non-empty label
checkRd: (5) BeadStudioSet-class.Rd:64-65: \item in \describe must have non-empty label
checkRd: (5) BeadStudioSet-class.Rd:66-67: \item in \describe must have non-empty label
checkRd: (5) BeadStudioSet-class.Rd:68: \item in \describe must have non-empty label
checkRd: (5) BeadStudioSetList-class.Rd:44-58: \item in \describe must have non-empty label
checkRd: (5) BeadStudioSetList-class.Rd:64-69: \item in \describe must have non-empty label
checkRd: (5) BeadStudioSetList-class.Rd:71-78: \item in \describe must have non-empty label
checkRd: (5) CNSet-class.Rd:85-86: \item in \describe must have non-empty label
checkRd: (5) CNSet-class.Rd:88-89: \item in \describe must have non-empty label
checkRd: (5) CNSet-class.Rd:91-93: \item in \describe must have non-empty label
checkRd: (5) CNSet-class.Rd:96-98: \item in \describe must have non-empty label
checkRd: (5) CNSet-class.Rd:100-101: \item in \describe must have non-empty label
checkRd: (5) CNSet-class.Rd:103-105: \item in \describe must have non-empty label
checkRd: (5) CNSet-class.Rd:107: \item in \describe must have non-empty label
checkRd: (5) CNSet-class.Rd:109: \item in \describe must have non-empty label
checkRd: (5) CNSet-class.Rd:113: \item in \describe must have non-empty label
checkRd: (5) CNSet-class.Rd:115-116: \item in \describe must have non-empty label
checkRd: (5) CNSet-class.Rd:118: \item in \describe must have non-empty label
checkRd: (5) CNSet-class.Rd:120-121: \item in \describe must have non-empty label
checkRd: (5) CNSet-class.Rd:124-126: \item in \describe must have non-empty label
checkRd: (5) CNSet-class.Rd:131-132: \item in \describe must have non-empty label
checkRd: (5) CNSet-class.Rd:135-136: \item in \describe must have non-empty label
checkRd: (5) CNSet-class.Rd:138: \item in \describe must have non-empty label
checkRd: (5) CNSet-class.Rd:140-142: \item in \describe must have non-empty label
checkRd: (5) CNSet-class.Rd:144-145: \item in \describe must have non-empty label
checkRd: (5) CNSet-class.Rd:147-148: \item in \describe must have non-empty label
checkRd: (5) CNSet-class.Rd:150-151: \item in \describe must have non-empty label
checkRd: (5) CNSet-class.Rd:153: \item in \describe must have non-empty label
checkRd: (5) GRanges-methods.Rd:28-38: \item in \describe must have non-empty label
checkRd: (5) GRanges-methods.Rd:49-60: \item in \describe must have non-empty label
checkRd: (5) GRanges-methods.Rd:62-67: \item in \describe must have non-empty label
checkRd: (5) GRanges-methods.Rd:69-75: \item in \describe must have non-empty label
checkRd: (5) GRanges-methods.Rd:77-85: \item in \describe must have non-empty label
checkRd: (5) GenomeAnnotatedDataFrame-class.Rd:35-42: \item in \describe must have non-empty label
checkRd: (5) GenomeAnnotatedDataFrame-class.Rd:44-54: \item in \describe must have non-empty label
checkRd: (5) GenomeAnnotatedDataFrame-class.Rd:56-61: \item in \describe must have non-empty label
checkRd: (5) GenomeAnnotatedDataFrame-class.Rd:68-73: \item in \describe must have non-empty label
checkRd: (5) GenomeAnnotatedDataFrame-class.Rd:75-81: \item in \describe must have non-empty label
checkRd: (5) GenomeAnnotatedDataFrame-class.Rd:84-89: \item in \describe must have non-empty label
checkRd: (5) GenomeAnnotatedDataFrame-class.Rd:91-100: \item in \describe must have non-empty label
checkRd: (5) SnpSet2-class.Rd:55-60: \item in \describe must have non-empty label
checkRd: (5) SnpSet2-class.Rd:62-67: \item in \describe must have non-empty label
checkRd: (5) SnpSet2-class.Rd:69-73: \item in \describe must have non-empty label
checkRd: (5) chromosome-methods.Rd:44-45: \item in \describe must have non-empty label
checkRd: (5) gSet-class.Rd:43-44: \item in \describe must have non-empty label
checkRd: (5) gSet-class.Rd:45-46: \item in \describe must have non-empty label
checkRd: (5) gSet-class.Rd:47-49: \item in \describe must have non-empty label
checkRd: (5) gSet-class.Rd:50-52: \item in \describe must have non-empty label
checkRd: (5) gSet-class.Rd:53-59: \item in \describe must have non-empty label
checkRd: (5) gSet-class.Rd:61-66: \item in \describe must have non-empty label
checkRd: (5) gSet-class.Rd:69-70: \item in \describe must have non-empty label
checkRd: (5) gSet-class.Rd:72-77: \item in \describe must have non-empty label
checkRd: (5) gSet-class.Rd:79-80: \item in \describe must have non-empty label
checkRd: (5) gSet-class.Rd:81-86: \item in \describe must have non-empty label
checkRd: (5) gSetList-class.Rd:51-56: \item in \describe must have non-empty label
checkRd: (5) gSetList-class.Rd:58-64: \item in \describe must have non-empty label
checkRd: (5) gSetList-class.Rd:66-71: \item in \describe must have non-empty label
checkRd: (5) gSetList-class.Rd:74-79: \item in \describe must have non-empty label
checkRd: (5) gSetList-class.Rd:89-99: \item in \describe must have non-empty label
checkRd: (5) oligoSnpSet-methods.Rd:28-39: \item in \describe must have non-empty label
checkRd: (5) oligoSnpSet-methods.Rd:41-46: \item in \describe must have non-empty label
checkRd: (5) oligoSnpSet-methods.Rd:48-54: \item in \describe must have non-empty label
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... WARNING
Undocumented S4 methods:
  generic '[' and siglist 'CNSet,ANY,ANY,ANY'
  generic '[' and siglist 'gSetList,ANY,ANY,ANY'
All user-level objects in a package (including S4 classes and methods)
should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* 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 data for ASCII and uncompressed saves ... OK
* checking line endings in Makefiles ... OK
* checking for GNU extensions in Makefiles ... OK
* checking include directives in Makefiles ... OK
* checking files in ‘vignettes’ ... WARNING
Files in the 'vignettes' directory but no files in 'inst/doc':
  ‘scriptsForExampleData/CreateExampleData.R’
Package has no Sweave vignette sources and no VignetteBuilder field.
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘doRUnit.R’
 OK
* checking package vignettes ... NOTE
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
* checking PDF version of manual ... OK
* DONE

Status: 3 WARNINGs, 4 NOTEs
See
  ‘/Users/biocbuild/bbs-3.20-bioc/meat/oligoClasses.Rcheck/00check.log’
for details.