##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:EpiTxDb.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings EpiTxDb_1.19.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/EpiTxDb.Rcheck’
* using R Under development (unstable) (2024-11-20 r87352)
* using platform: x86_64-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 Monterey 12.7.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘EpiTxDb/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘EpiTxDb’ version ‘1.19.0’
* package encoding: UTF-8
* 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 ‘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 ‘/Users/biocbuild/bbs-3.21-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
  ‘/Users/biocbuild/bbs-3.21-bioc/meat/EpiTxDb.Rcheck/00check.log’
for details.

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL EpiTxDb
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library’
* installing *source* package ‘EpiTxDb’ ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
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’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
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’
** testing if installed package can be loaded from final location
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’
** testing if installed package keeps a record of temporary installation path
* DONE (EpiTxDb)

R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

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Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(testthat)
> library(EpiTxDb)
Loading required package: AnnotationDbi
Loading required package: stats4
Loading required package: BiocGenerics
Loading required package: generics

Attaching package: 'generics'

The following objects are masked from 'package:base':

    as.difftime, as.factor, as.ordered, intersect, is.element, setdiff,
    setequal, union


Attaching package: 'BiocGenerics'

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append,
    as.data.frame, basename, cbind, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, is.unsorted, lapply,
    mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int,
    rank, rbind, rownames, sapply, saveRDS, table, tapply, unique,
    unsplit, which.max, which.min

Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Loading required package: IRanges
Loading required package: S4Vectors

Attaching package: 'S4Vectors'

The following object is masked from 'package:utils':

    findMatches

The following objects are masked from 'package:base':

    I, expand.grid, unname

Loading required package: Modstrings
Loading required package: Biostrings
Loading required package: XVector
Loading required package: GenomeInfoDb

Attaching package: 'Biostrings'

The following object is masked from 'package:base':

    strsplit

There were 19 warnings (use warnings() to see them)
> library(RSQLite)
> 
> test_check("EpiTxDb")
Error in x$.self$finalize() : attempt to apply non-function
[ FAIL 0 | WARN 0 | SKIP 1 | PASS 257 ]

══ Skipped tests (1) ═══════════════════════════════════════════════════════════
• On CRAN (1): 'test-4makeEpiTxDbFromtRNAdb.R:7:5'

[ FAIL 0 | WARN 0 | SKIP 1 | PASS 257 ]
> 
> proc.time()
   user  system elapsed 
 20.778   1.083  24.222