Running ‘testthat.R’ [30s/31s]
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/RtmpvbIN16/file2247306f628a /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/RtmpvbIN16/file22473cad6dc2 -remove  -protocol ensGene -operation g -nastring NA  -vcfinput
  ── 1. Error: BioConductor (@test_auto.R#20)  ───────────────────────────────────
  could not find function ".makeSortEnum"
  1: annotation(dat = gene, anno.name = "bioc_gene2alias") at testthat/test_auto.R:20
  2: do.call(func, params)
  3: (function (anno.name = NULL, database.cfg = NULL, bioc_dbname = NULL, keytype = NULL, 
         columns = NULL, ...) 
     {
         dependence_db <- NULL
         params <- list(...)
         auto.parameters <- c("dependence_db", "keytype", "columns")
         for (item in auto.parameters) {
             item.value <- eval(parse(text = item))
             if (is.null(item.value)) {
                 params[[item]] <- get.cfg.value.by.name(anno.name, database.cfg, key = item, 
                     coincident = TRUE, extra.list = list(anno.name = anno.name), rcmd.parse = TRUE)
             }
             else {
                 params[[item]] <- item.value
             }
         }
         if (is.null(bioc_dbname)) {
             bioc_dbname_raw <- params[["dependence_db"]]
             bioc_dbname <- str_replace(bioc_dbname_raw, "^db_bioc_", "")
         }
         else if (!str_detect(bioc_dbname, "^db_bioc_")) {
             bioc_dbname_raw <- paste0("db_bioc_", bioc_dbname)
         }
         else {
             bioc_dbname_raw <- bioc_dbname
         }
         pkg.raw <- (.packages())
         download.database(bioc_dbname_raw)
         tryCatch(suppressMessages(do.call("require", list(package = bioc_dbname))))
         pkg.new <- (.packages())
         params$x <- eval.parse.null(bioc_dbname)
         params$keys <- params$dat
         params$dat <- NULL
         x <- as.data.table(do.call("select", params))
         for (i in pkg.new[!pkg.new %in% pkg.raw]) {
             detach(paste0("package:", i), character.only = TRUE)
         }
         return(x)
     })(dat = c("TP53", "NSD2"), anno.name = "bioc_gene2alias", buildver = "hg19", annovar.anno.names = "", 
         database.dir = "", db.type = NULL, mysql.connect.params = list(host = "", dbname = "", 
             table.name = "", user = "", password = ""), sqlite.connect.params = list(
             dbname = ""), database.cfg = "/data/gannet/ripley/R/packages/tests-devel/annovarR.Rcheck/annovarR/extdata/config/databases.toml")
  4: as.data.table(do.call("select", params))
  5: do.call("select", params)
  6: select(buildver = "hg19", annovar.anno.names = "", database.dir = "", db.type = NULL, 
         mysql.connect.params = list(host = "", dbname = "", table.name = "", user = "", 
             password = ""), sqlite.connect.params = list(dbname = ""), dependence_db = "db_bioc_org.Hs.eg.db", 
         keytype = "SYMBOL", columns = "ALIAS", x = new("OrgDb", .xData = <environment>), 
         keys = c("TP53", "NSD2"))
  7: select(buildver = "hg19", annovar.anno.names = "", database.dir = "", db.type = NULL, 
         mysql.connect.params = list(host = "", dbname = "", table.name = "", user = "", 
             password = ""), sqlite.connect.params = list(dbname = ""), dependence_db = "db_bioc_org.Hs.eg.db", 
         keytype = "SYMBOL", columns = "ALIAS", x = new("OrgDb", .xData = <environment>), 
         keys = c("TP53", "NSD2"))
  8: .select(x, keys, columns, keytype, jointype = jointype, ...)
  9: .legacySelect(x, keys, cols, keytype, jointype)
  10: resort_base(res, keys, jointype, oriTabCols)
  11: .dropUnwantedRows(tab, keys, jointype)
  12: order(match(tab[[jointype]], keys))
  13: standardGeneric("order")
  14: eval(mc, env)
  15: eval(mc, env)
  16: eval(mc, env)
  17: order(...)
  
  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-devel/annovarR.Rcheck/annovarR/extdata/demo/vcfanno_demo/conf.toml input.vcf > output.vcf
  ── 2. 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 [2018-03-30 06:26:44] info.msg
  [1] "print.vb"
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 86 SKIPPED: 0 FAILED: 2
  1. Error: BioConductor (@test_auto.R#20) 
  2. Error: select.dat.full.match (@test_utils.R#22) 
  
  Error: testthat unit tests failed
  Execution halted