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### Running command:
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###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:R3CPET.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings R3CPET_1.31.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/R3CPET.Rcheck’
* using R Under development (unstable) (2023-01-10 r83596)
* using platform: aarch64-apple-darwin20 (64-bit)
* R was compiled by
    Apple clang version 13.0.0 (clang-1300.0.29.3)
    GNU Fortran (GCC) 12.0.1 20220312 (experimental)
* running under: macOS Monterey 12.6.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘R3CPET/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘R3CPET’ version ‘1.31.0’
* 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 ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘R3CPET’ can be installed ... WARNING
Found the following significant warnings:
  state.cpp:171:7: warning: 'random_shuffle<std::__wrap_iter<DocState **>>' is deprecated [-Wdeprecated-declarations]
  state.cpp:173:12: warning: 'random_shuffle<std::__wrap_iter<WordInfo *>>' is deprecated [-Wdeprecated-declarations]
See ‘/Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/R3CPET.Rcheck/00install.out’ for details.
* used C compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
* used C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
* used SDK: ‘MacOSX13.0.sdk’
* checking installed package size ... NOTE
  installed size is  6.1Mb
  sub-directories of 1Mb or more:
    data      3.0Mb
    example   1.0Mb
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Package listed in more than one of Depends, Imports, Suggests, Enhances:
  ‘methods’
A package should be listed in only one of these fields.
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* 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
Namespace in Imports field not imported from: 'BiocGenerics'
  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
.GetClusterInfo: no visible binding for global variable
  'TxDb.Hsapiens.UCSC.hg19.knownGene'
.GetClusterInfo: no visible global function definition for 'toTable'
.GetClusterInfo: no visible binding for global variable
  'org.Hs.egUCSCKG'
.GetClusterInfo: no visible global function definition for 'select'
.GetClusterInfo: no visible binding for global variable 'org.Hs.eg.db'
.formatDAVIDResult: no visible global function definition for
  'formatGeneReportFull'
.formatDAVIDResult: no visible global function definition for
  'formatGeneReport'
.formatDAVIDResult: no visible global function definition for
  'formatList'
.formatDAVIDResult: no visible global function definition for
  'formatGene2Gene'
.formatDAVIDResult: no visible global function definition for
  'formatAnnotationReport'
.get.NetworksGenes: no visible global function definition for
  'annotatePeakInBatch'
.plot.sota: no visible global function definition for 'legend'
.plot.sota: no visible global function definition for 'lines'
EnsemblToHGNC: no visible global function definition for 'useMart'
EnsemblToHGNC: no visible global function definition for 'useDataset'
EnsemblToHGNC: no visible global function definition for 'getBM'
EntrezToHGNC: no visible global function definition for 'useMart'
EntrezToHGNC: no visible global function definition for 'useDataset'
EntrezToHGNC: no visible global function definition for 'getBM'
RunHLDA: no visible binding for global variable '_R3CPET_RunHLDA'
createServer,ChiapetExperimentData-NetworkCollection-ChromMaintainers:
  no visible global function definition for 'runApp'
plot3CPETRes,ChromMaintainers: no visible global function definition
  for 'plotCurves'
plot3CPETRes,ChromMaintainers: no visible global function definition
  for 'plotAvgCurves'
Undefined global functions or variables:
  TxDb.Hsapiens.UCSC.hg19.knownGene _R3CPET_RunHLDA annotatePeakInBatch
  formatAnnotationReport formatGene2Gene formatGeneReport
  formatGeneReportFull formatList getBM legend lines org.Hs.eg.db
  org.Hs.egUCSCKG plotAvgCurves plotCurves runApp select toTable
  useDataset useMart
Consider adding
  importFrom("graphics", "legend", "lines")
to your NAMESPACE file.
* checking Rd files ... WARNING
checkRd: (5) ChiapetExperimentData-class.Rd:109-124: \item in \describe must have non-empty label
checkRd: (5) ChiapetExperimentData-class.Rd:125-128: \item in \describe must have non-empty label
checkRd: (5) ChiapetExperimentData-class.Rd:129-132: \item in \describe must have non-empty label
* 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking use of PKG_*FLAGS in Makefiles ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘tests.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: 2 WARNINGs, 5 NOTEs
See
  ‘/Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/R3CPET.Rcheck/00check.log’
for details.