Running ‘testthat.R’ [46s/49s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(DBI)
  > library(annovarR)
  > 
  > 
  > test_check("annovarR")
  OMP: Warning #96: Cannot form a team with 7 threads, using 2 instead.
  OMP: Hint Consider unsetting KMP_DEVICE_THREAD_LIMIT (KMP_ALL_THREADS), KMP_TEAMS_THREAD_LIMIT, and OMP_THREAD_LIMIT (if any are set).
  /usr/bin/perl /opt/bin/annovar/table_annovar.pl /tmp/RtmpBdQeHH/file214514e02d5b /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/RtmpBdQeHH/file21454a741c4a -remove  -protocol ensGene -operation g -nastring NA  -vcfinput
  trying URL 'https://raw.githubusercontent.com/Miachol/ftp/master/files/GRCh37_MT_ensGene.txt'
  Content type 'text/plain; charset=utf-8' length 3131 bytes
  ==================================================
  downloaded 3131 bytes
  
  perl /data/gannet/ripley/tmp/annovar.dir/annotate_variation.pl -downdb -buildver hg19 -webfrom annovar avsnp147 /data/gannet/ripley/tmp/annovar.dir/humandb
  perl /data/gannet/ripley/tmp/annovar.dir/annotate_variation.pl -buildver hg19  /data/gannet/ripley/tmp/annovar.dir/humandb
  perl /data/gannet/ripley/tmp/annovar.dir/annotate_variation.pl  -regionanno -buildver hg19 -dbtype cytoBand  /data/gannet/ripley/tmp/annovar.dir/humandb
  perl /data/gannet/ripley/tmp/annovar.dir/annotate_variation.pl -filter -buildver hg19 -dbtype avsnp147  /data/gannet/ripley/tmp/annovar.dir/humandb
  perl /data/gannet/ripley/tmp/annovar.dir/table_annovar.pl example.avinput /data/gannet/ripley/tmp/annovar.dir/humandb -buildver hg19  -remove -protocol refGene,cytoBand,avsnp147 -operation g,r,f -nastring NA  
  perl /data/gannet/ripley/tmp/annovar.dir/convert2annovar.pl -format vcf4old example.vcf > example.avinput
  vep --cache_version 91 --assembly GRCh37 --dir /data/gannet/ripley/.vep --output_file variant_effect_output.txt --cache --offline --everything 
  vcfanno_linux64 -p 2 /data/gannet/ripley/R/packages/tests-clang/annovarR.Rcheck/annovarR/extdata/demo/vcfanno_demo/conf.toml input.vcf > output.vcf
  ── 1. Error: select.dat.full.match (@test_utils.R#22)  ─────────────────────────
  Failed to connect to database: Unknown database 'annovarr'
  1: dbConnect(RMySQL::MySQL(), dbname = "annovarr") at testthat/test_utils.R:22
  2: dbConnect(RMySQL::MySQL(), dbname = "annovarr")
  3: .local(drv, ...)
  
  INFO [2018-08-08 21:24:45] info.msg
  [1] "print.vb"
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 93 SKIPPED: 0 FAILED: 1
  1. Error: select.dat.full.match (@test_utils.R#22) 
  
  Error: testthat unit tests failed
  Execution halted