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### Running command:
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###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:Moonlight2R.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings Moonlight2R_1.3.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/Moonlight2R.Rcheck’
* using R version 4.4.0 RC (2024-04-16 r86468)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
    GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
* running under: Ubuntu 22.04.4 LTS
* using session charset: UTF-8
* checking for file ‘Moonlight2R/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘Moonlight2R’ version ‘1.3.0’
* 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 for sufficient/correct file permissions ... 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 loading without being on the library search path ... 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')
loading from cache
require(“rtracklayer”)
Error: failed to load resource
  name: AH14108
  title: hg38ToHg19.over.chain.gz
  reason: expected 11 elements in header, got 1, on line 1
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:
       ▆
    1. └─Moonlight2R::DMA(...) at test-DMA.R:14:1
    2.   └─Moonlight2R::LiftMAF(Infile = mut_only, Current_Build = "GRCh38")
    3.     ├─ah[["AH14108"]]
    4.     └─ah[["AH14108"]]
    5.       └─AnnotationHub (local) .local(x, i, j = j, ...)
    6.         └─AnnotationHub:::.Hub_get1(x[idx], force = force, verbose = verbose)
    7.           └─base::tryCatch(...)
    8.             └─base (local) tryCatchList(expr, classes, parentenv, handlers)
    9.               └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
   10.                 └─value[[3L]](cond)
  
  [ 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 re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 2 ERRORs
See
  ‘/home/biocbuild/bbs-3.20-bioc/meat/Moonlight2R.Rcheck/00check.log’
for details.