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### Running command:
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###   F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:EpiTxDb.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings EpiTxDb_1.17.0.tar.gz
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* using log directory 'F:/biocbuild/bbs-3.20-bioc/meat/EpiTxDb.Rcheck'
* using R version 4.4.0 RC (2024-04-16 r86468 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 13.2.0
    GNU Fortran (GCC) 13.2.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'EpiTxDb/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'EpiTxDb' version '1.17.0'
* 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 whether package 'EpiTxDb' can be installed ... WARNING
Found the following significant warnings:
  Warning: replacing previous import 'GenomicFeatures::makeTxDbPackage' by 'txdbmaker::makeTxDbPackage' when loading 'EpiTxDb'
  Warning: replacing previous import 'GenomicFeatures::supportedUCSCFeatureDbTables' by 'txdbmaker::supportedUCSCFeatureDbTables' when loading 'EpiTxDb'
  Warning: replacing previous import 'GenomicFeatures::makeTxDbFromGFF' by 'txdbmaker::makeTxDbFromGFF' when loading 'EpiTxDb'
  Warning: replacing previous import 'GenomicFeatures::makeTxDbPackageFromBiomart' by 'txdbmaker::makeTxDbPackageFromBiomart' when loading 'EpiTxDb'
  Warning: replacing previous import 'GenomicFeatures::supportedMiRBaseBuildValues' by 'txdbmaker::supportedMiRBaseBuildValues' when loading 'EpiTxDb'
  Warning: replacing previous import 'GenomicFeatures::supportedUCSCFeatureDbTracks' by 'txdbmaker::supportedUCSCFeatureDbTracks' when loading 'EpiTxDb'
  Warning: replacing previous import 'GenomicFeatures::browseUCSCtrack' by 'txdbmaker::browseUCSCtrack' when loading 'EpiTxDb'
  Warning: replacing previous import 'GenomicFeatures::getChromInfoFromBiomart' by 'txdbmaker::getChromInfoFromBiomart' when loading 'EpiTxDb'
  Warning: replacing previous import 'GenomicFeatures::makeTxDbFromGRanges' by 'txdbmaker::makeTxDbFromGRanges' when loading 'EpiTxDb'
  Warning: replacing previous import 'GenomicFeatures::supportedUCSCtables' by 'txdbmaker::supportedUCSCtables' when loading 'EpiTxDb'
  Warning: replacing previous import 'GenomicFeatures::makeTxDbFromBiomart' by 'txdbmaker::makeTxDbFromBiomart' when loading 'EpiTxDb'
  Warning: replacing previous import 'GenomicFeatures::UCSCFeatureDbTableSchema' by 'txdbmaker::UCSCFeatureDbTableSchema' when loading 'EpiTxDb'
  Warning: replacing previous import 'GenomicFeatures::makeTxDbFromEnsembl' by 'txdbmaker::makeTxDbFromEnsembl' when loading 'EpiTxDb'
  Warning: replacing previous import 'GenomicFeatures::makeTxDb' by 'txdbmaker::makeTxDb' when loading 'EpiTxDb'
  Warning: replacing previous import 'GenomicFeatures::makeFDbPackageFromUCSC' by 'txdbmaker::makeFDbPackageFromUCSC' when loading 'EpiTxDb'
  Warning: replacing previous import 'GenomicFeatures::makeTxDbFromUCSC' by 'txdbmaker::makeTxDbFromUCSC' when loading 'EpiTxDb'
  Warning: replacing previous import 'GenomicFeatures::makeTxDbPackageFromUCSC' by 'txdbmaker::makeTxDbPackageFromUCSC' when loading 'EpiTxDb'
  Warning: replacing previous import 'GenomicFeatures::makePackageName' by 'txdbmaker::makePackageName' when loading 'EpiTxDb'
  Warning: replacing previous import 'GenomicFeatures::makeFeatureDbFromUCSC' by 'txdbmaker::makeFeatureDbFromUCSC' when loading 'EpiTxDb'
See 'F:/biocbuild/bbs-3.20-bioc/meat/EpiTxDb.Rcheck/00install.out' for details.
* 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 dependencies in R code ... NOTE
Unexported objects imported by ':::' calls:
  'AnnotationDbi:::.getMetaValue'
  'AnnotationDbi:::.valid.metadata.table'
  'AnnotationDbi:::.valid.table.colnames' 'AnnotationDbi:::dbEasyQuery'
  'AnnotationDbi:::dbQuery' 'AnnotationDbi:::smartKeys'
  'BiocGenerics:::replaceSlots'
  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 ... OK
* checking Rd files ... NOTE
checkRd: (-1) makeEpiTxDb.Rd:20: Lost braces in \itemize; meant \describe ?
checkRd: (-1) makeEpiTxDb.Rd:21-23: Lost braces in \itemize; meant \describe ?
checkRd: (-1) makeEpiTxDb.Rd:24-25: Lost braces in \itemize; meant \describe ?
checkRd: (-1) makeEpiTxDb.Rd:26-27: Lost braces in \itemize; meant \describe ?
checkRd: (-1) makeEpiTxDb.Rd:28-29: Lost braces in \itemize; meant \describe ?
checkRd: (-1) makeEpiTxDb.Rd:30-31: Lost braces in \itemize; meant \describe ?
checkRd: (-1) makeEpiTxDb.Rd:32: Lost braces in \itemize; meant \describe ?
checkRd: (-1) makeEpiTxDb.Rd:33-34: Lost braces in \itemize; meant \describe ?
checkRd: (-1) makeEpiTxDb.Rd:43-44: Lost braces in \itemize; meant \describe ?
checkRd: (-1) makeEpiTxDb.Rd:45-46: Lost braces in \itemize; meant \describe ?
checkRd: (-1) makeEpiTxDb.Rd:47-49: Lost braces in \itemize; meant \describe ?
checkRd: (-1) makeEpiTxDb.Rd:50-51: Lost braces in \itemize; meant \describe ?
checkRd: (-1) makeEpiTxDb.Rd:52-53: Lost braces in \itemize; meant \describe ?
checkRd: (-1) makeEpiTxDb.Rd:54-55: Lost braces in \itemize; meant \describe ?
checkRd: (-1) makeEpiTxDb.Rd:62-63: Lost braces in \itemize; meant \describe ?
checkRd: (-1) makeEpiTxDb.Rd:64-66: Lost braces in \itemize; meant \describe ?
checkRd: (-1) makeEpiTxDb.Rd:67-69: Lost braces in \itemize; meant \describe ?
checkRd: (-1) makeEpiTxDb.Rd:70-71: Lost braces in \itemize; meant \describe ?
checkRd: (-1) makeEpiTxDb.Rd:72-73: Lost braces in \itemize; meant \describe ?
checkRd: (-1) makeEpiTxDb.Rd:74-75: Lost braces in \itemize; meant \describe ?
checkRd: (-1) makeEpiTxDb.Rd:82-83: Lost braces in \itemize; meant \describe ?
checkRd: (-1) makeEpiTxDb.Rd:84-85: Lost braces in \itemize; meant \describe ?
checkRd: (-1) makeEpiTxDb.Rd:86-88: Lost braces in \itemize; meant \describe ?
checkRd: (-1) makeEpiTxDb.Rd:94: Lost braces in \itemize; meant \describe ?
checkRd: (-1) makeEpiTxDb.Rd:95: Lost braces in \itemize; meant \describe ?
* 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 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 ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 WARNING, 2 NOTEs
See
  'F:/biocbuild/bbs-3.20-bioc/meat/EpiTxDb.Rcheck/00check.log'
for details.