Running ‘testthat.R’ [34s/44s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(DBI)
  > library(annovarR)
  > 
  > 
  > test_check("annovarR")
  /usr/bin/perl /opt/bin/annovar/table_annovar.pl /tmp/Rtmp6fwnSi/fileafd59a32dcd /opt/bin/annovar/humandb -buildver hg19  -remove -protocol refGene -operation g -nastring NA  
  /usr/bin/perl /opt/bin/annovar//table_annovar.pl /tmp/test.vcf /opt/bin/annovar//humandb -buildver hg19 -out /tmp/Rtmp6fwnSi/fileafd53e223df -remove  -protocol ensGene -operation g -nastring NA  -vcfinput
  trying URL 'https://raw.githubusercontent.com/Miachol/ftp/master/files/GRCh37_MT_ensGene.txt'
  ── 1. Failure: download.database (@test_download.R#9)  ─────────────────────────
  `x` not equal to `expected`.
  1 element mismatch
  
  ── 2. Failure: download.database (@test_download.R#12)  ────────────────────────
  `x` not equal to `expected`.
  1 element mismatch
  
  ── 3. Failure: download.database (@test_download.R#14)  ────────────────────────
  `x` not equal to `expected`.
  'is.NA' value mismatch: 0 in current 1 in target
  
  perl /home/hornik/tmp/annovar.dir/annotate_variation.pl -downdb -buildver hg19 -webfrom annovar avsnp147 /home/hornik/tmp/annovar.dir/humandb
  perl /home/hornik/tmp/annovar.dir/annotate_variation.pl -buildver hg19  /home/hornik/tmp/annovar.dir/humandb
  perl /home/hornik/tmp/annovar.dir/annotate_variation.pl  -regionanno -buildver hg19 -dbtype cytoBand  /home/hornik/tmp/annovar.dir/humandb
  perl /home/hornik/tmp/annovar.dir/annotate_variation.pl -filter -buildver hg19 -dbtype avsnp147  /home/hornik/tmp/annovar.dir/humandb
  perl /home/hornik/tmp/annovar.dir/table_annovar.pl example.avinput /home/hornik/tmp/annovar.dir/humandb -buildver hg19  -remove -protocol refGene,cytoBand,avsnp147 -operation g,r,f -nastring NA  
  perl /home/hornik/tmp/annovar.dir/convert2annovar.pl -format vcf4old example.vcf > example.avinput
  vep --cache_version 91 --assembly GRCh37 --dir /home/hornik/.vep --output_file variant_effect_output.txt --cache --offline --everything 
  vcfanno_linux64 -p 2 /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/annovarR/extdata/demo/vcfanno_demo/conf.toml input.vcf > output.vcf
  INFO [2018-07-05 07:00:02] info.msg
  [1] "print.vb"
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 89 SKIPPED: 0 FAILED: 3
  1. Failure: download.database (@test_download.R#9) 
  2. Failure: download.database (@test_download.R#12) 
  3. Failure: download.database (@test_download.R#14) 
  
  Error: testthat unit tests failed
  Execution halted