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### Running command:
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###   F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:Moonlight2R.install-out.txt --library=F:\biocbuild\bbs-3.19-bioc\R\library --no-vignettes --timings Moonlight2R_1.2.0.tar.gz
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* using log directory 'F:/biocbuild/bbs-3.19-bioc/meat/Moonlight2R.Rcheck'
* using R version 4.4.1 (2024-06-14 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 'Moonlight2R/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'Moonlight2R' version '1.2.0'
* 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 'Moonlight2R' can be installed ... OK
* 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 ... OK
* 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 ... 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 ... 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 ... ERROR
Running examples in 'Moonlight2R-Ex.R' failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: LiftMAF
> ### Title: LiftMAF
> ### Aliases: LiftMAF
> 
> ### ** Examples
> 
> data(dataMAF)
> dataMAF_example <- dataMAF[1,]
> LiftMAF(dataMAF_example, Current_Build = 'GRCh38')
Error: Corrupt Cache: index file
  See AnnotationHub's TroubleshootingTheHubs vignette section on corrupt cache
  cache: F:\biocbuild\AnnotationHub_cache
  filename: annotationhub.index.rds
Execution halted
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
  Running 'testthat.R'
 ERROR
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
  Error: Corrupt Cache: index file
    See AnnotationHub's TroubleshootingTheHubs vignette section on corrupt cache
    cache: F:\biocbuild\AnnotationHub_cache
    filename: annotationhub.index.rds
  Backtrace:
      ▆
   1. └─Moonlight2R::DMA(...) at test-DMA.R:14:1
   2.   └─Moonlight2R::LiftMAF(Infile = mut_only, Current_Build = "GRCh38")
   3.     └─AnnotationHub::AnnotationHub()
   4.       └─AnnotationHub::.Hub(...)
   5.         └─AnnotationHub:::.db_create_index(hub)
  
  [ FAIL 1 | WARN 1 | SKIP 0 | PASS 46 ]
  Error: Test failures
  Execution halted
* 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: 2 ERRORs
See
  'F:/biocbuild/bbs-3.19-bioc/meat/Moonlight2R.Rcheck/00check.log'
for details.