• using R version 3.6.2 (2019-12-12)
• using platform: x86_64-apple-darwin15.6.0 (64-bit)
• using session charset: UTF-8
• checking for file ‘ctDNAtools/DESCRIPTION’ ... OK
• this is package ‘ctDNAtools’ version ‘0.4.0’
• package encoding: UTF-8
• checking package namespace information ... OK
• checking package dependencies ... NOTE
  Package suggested but not available for checking: ‘BSgenome.Hsapiens.UCSC.hg19’
• checking if this is a source package ... OK
• checking if there is a namespace ... OK
• checking for executable files ... OK
• checking for hidden files and directories ... OK
• checking for portable file names ... OK
• checking for sufficient/correct file permissions ... OK
• checking whether package ‘ctDNAtools’ can be installed ... [3s/3s] 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 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 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 ... [4s/4s] 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 installed files from ‘inst/doc’ ... OK
• checking files in ‘vignettes’ ... OK
• checking examples ... ERROR
  Running examples in ‘ctDNAtools-Ex.R’ failed
  The error most likely occurred in:
  
  > ### Name: get_mutations_read_counts
  > ### Title: Counts ref and alt reads for a set of mutations
  > ### Aliases: get_mutations_read_counts
  >
  > ### ** Examples
  >
  > data("mutations", package = "ctDNAtools")
  > bamT1 <- system.file("extdata", "T1.bam", package = "ctDNAtools")
  > get_mutations_read_counts(mutations = mutations[1:3, ], bam = bamT1)
  Error in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]) :
    there is no package called ‘GenomeInfoDbData’
  Calls: get_mutations_read_counts ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
  Execution halted
• checking for unstated dependencies in ‘tests’ ... OK
• checking tests ... [4s/4s] ERROR
    Running ‘testthat.R’ [4s/4s]
  Running the tests in ‘tests/testthat.R’ failed.
  Last 13 lines of output:
      5. base::getNamespace(ns)
      6. base::loadNamespace(name)
      9. base::loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]])
     11. base::loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]])
     12. base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
     13. base:::withOneRestart(expr, restarts[[1L]])
     14. base:::doWithOneRestart(return(expr), restart)
    
    ══ testthat results ═══════════════════════════════════════════════════════════
    [ OK: 0 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 2 ]
    1. Error: (unknown) (@test-ctDNAtest.R#3)
    2. Error: (unknown) (@test-fragment_size.R#13)
    
    Error: testthat unit tests failed
    Execution halted
• checking for unstated dependencies in vignettes ... OK
• checking package vignettes in ‘inst/doc’ ... OK
• checking running R code from vignettes ... [0s/0s] NONE
    ‘ctDNAtools.Rmd’using ‘UTF-8’... [0s/0s] OK
• checking re-building of vignette outputs ... [2s/2s] WARNING
  Error(s) in re-building vignettes:
    ...
  --- re-building ‘ctDNAtools.Rmd’ using rmarkdown
  Warning in engine$weave(file, quiet = quiet, encoding = enc) :
    Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
  Quitting from lines 42-69 (ctDNAtools.Rmd)
  Error: processing vignette 'ctDNAtools.Rmd' failed with diagnostics:
  there is no package called 'BSgenome.Hsapiens.UCSC.hg19'
  --- failed re-building ‘ctDNAtools.Rmd’
  
  SUMMARY: processing the following file failed:
    ‘ctDNAtools.Rmd’
  
  Error: Vignette re-building failed.
  Execution halted
  
• checking PDF version of manual ... OK
• DONE
  Status: 2 ERRORs, 1 WARNING, 1 NOTE