Running 'testthat.R' [4s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > ## follow http://adv-r.had.co.nz/Testing.html
  > print(sprintf("Test seqminer [version %s]", packageVersion("seqminer")))
  [1] "Test seqminer [version 9.7]"
  > print("Platform")
  [1] "Platform"
  > print(str(.Platform))
  List of 8
   $ OS.type   : chr "windows"
   $ file.sep  : chr "/"
   $ dynlib.ext: chr ".dll"
   $ GUI       : chr "RTerm"
   $ endian    : chr "little"
   $ pkgType   : chr "win.binary"
   $ path.sep  : chr ";"
   $ r_arch    : chr "x64"
  NULL
  > 
  > print("Sys.info()")
  [1] "Sys.info()"
  > print(Sys.info())
         sysname        release        version       nodename        machine 
       "Windows"   "Server x64"  "build 20348"     "CRANWIN2"       "x86-64" 
           login           user effective_user 
          "CRAN"         "CRAN"         "CRAN" 
  > 
  > print(citation("seqminer"))
  To cite package 'seqminer' in publications use:
  
    Zhan X, Liu D (2015). "SEQMINER: An R-Package to Facilitate the
    Functional Interpretation of Sequence-Based Associations." _Genetic
    Epidemiology_, *39*(8), 1242. doi:10.1002/gepi.21918
    <https://doi.org/10.1002/gepi.21918>, seqminer version 9.7,
    <http://dx.doi.org/10.1002/gepi.21918>.
  
  A BibTeX entry for LaTeX users is
  
    @Article{,
      title = {SEQMINER: An R-Package to Facilitate the Functional Interpretation of Sequence-Based Associations},
      author = {Xiaowei Zhan and Dajiang J Liu},
      journal = {Genetic Epidemiology},
      volume = {39},
      number = {8},
      pages = {1242},
      year = {2015},
      note = {seqminer version 9.7},
      web = {http:/zhanxw.github.io/seqminer},
      publisher = {Wiley Online Library},
      url = {http://dx.doi.org/10.1002/gepi.21918},
      doi = {10.1002/gepi.21918},
    }
  > 
  > library(testthat)
  > library(seqminer)
  > ## ## test code are under inst/tests
  > ## ## test_package("seqminer", reporter="tap")
  > ## test_package("seqminer")
  > test_check("seqminer")
  1 gene/region to be extracted.
  Read score tests...
  In study 0
  Done read score file: D:/RCompile/CRANpkg/lib/4.4/seqminer/test-triallelic/bi.MetaScore.assoc.gz
  Read cov files ... 
  In study 0
  Done read cov file: D:/RCompile/CRANpkg/lib/4.4/seqminer/test-triallelic/bi.MetaCov.assoc.gz
  Finished calculation.
  [1] "1:1" "1:2" "1:3"
  [[1]]
  [1] "G" "G" "G"
  
  [[1]]
             [,1]       [,2]       [,3]
  [1,]  0.5126420 -0.0427202  0.0427202
  [2,] -0.0427202  0.1993610 -0.0284801
  [3,]  0.0427202 -0.0284801  0.1139210
  
  Skipped: encounter a duplicated site: [ 1:1 ] in file [ D:/RCompile/CRANpkg/lib/4.4/seqminer/test-triallelic/tri.MetaScore.assoc.gz ]
  1 gene/region to be extracted.
  Read score tests...
  In study 0
  Error: encounter a duplicated location: [ 1:1 ] in file [ D:/RCompile/CRANpkg/lib/4.4/seqminer/test-triallelic/tri.MetaScore.assoc.gz ], will overwrite previous results!
  Done read score file: D:/RCompile/CRANpkg/lib/4.4/seqminer/test-triallelic/tri.MetaScore.assoc.gz
  Read cov files ... 
  In study 0
  Done read cov file: D:/RCompile/CRANpkg/lib/4.4/seqminer/test-triallelic/tri.MetaCov.assoc.gz
  Finished calculation.
  [1] "1:1" "1:3"
  [[1]]
  [1] "T" "G"
  
  [[1]]
             [,1]       [,2]
  [1,]  0.1993610 -0.0284801
  [2,] -0.0284801  0.1139210
  
  1 gene/region to be extracted.
  Read score tests...
  In study 0
  Done read score file: D:/RCompile/CRANpkg/lib/4.4/seqminer/test-triallelic/tri.MetaScore.assoc.gz
  Read cov files ... 
  In study 0
  Done read cov file: D:/RCompile/CRANpkg/lib/4.4/seqminer/test-triallelic/tri.MetaCov.assoc.gz
  Finished calculation.
  [1] "1:1_A/G" "1:1_A/T" "1:3_A/G"
  [[1]]
  [1] "G" "T" "G"
  
  [[1]]
             [,1]       [,2]       [,3]
  [1,]  0.5126420 -0.0427202  0.0427202
  [2,] -0.0427202  0.1993610 -0.0284801
  [3,]  0.0427202 -0.0284801  0.1139210
  
  [1] "============="
  Total 3 line loaded, now put them to matrix [ 3 x 3 ] in R ...
             1:1        1:2        1:3
  1:1  0.5126420 -0.0427202  0.0427202
  1:2 -0.0427202  0.1993610 -0.0284801
  1:3  0.0427202 -0.0284801  0.1139210
             1:1        1:2        1:3
  1:1  0.5126420 -0.0427202  0.0427202
  1:2 -0.0427202  0.1993610 -0.0284801
  1:3  0.0427202 -0.0284801  0.1139210
  Total 3 line loaded, now put them to matrix [ 3 x 3 ] in R ...
               1:1      1:1/1        1:3
  1:1    0.5126420 -0.0427202  0.0427202
  1:1/1 -0.0427202  0.1993610 -0.0284801
  1:3    0.0427202 -0.0284801  0.1139210
  [1] "============="
  $pos
  [1] 1 2 3
  
  $ref
  [1] "A" "A" "A"
  
  $alt
  [1] "G" "G" "G"
  
  $nSample
  [1] 9 9 9
  
  $af
  [1] 0.3333330 0.1111110 0.0555556
  
  $ac
  [1] 6 2 1
  
  $callRate
  [1] 1 1 1
  
  $hwe
  [1] "1" "1" "1"
  
  $nref
  [1] 4 7 8
  
  $nhet
  [1] 4 2 1
  
  $nalt
  [1] 1 0 0
  
  $ustat
  [1] 0.283603 0.000000 0.325521
  
  $vstat
  [1] 2.14797 1.33950 1.01256
  
  $effect
  [1] 0.0614687 0.0000000 0.3174930
  
  $pVal
  [1] 0.894958 1.000000 0.747845
  
  $anno
  [1] "" "" ""
  
  $annoFull
  [1] "" "" ""
  
  $pos
  [1] 1 1 3
  
  $ref
  [1] "A" "A" "A"
  
  $alt
  [1] "G" "T" "G"
  
  $nSample
  [1] 9 9 9
  
  $af
  [1] 0.3333330 0.1111110 0.0555556
  
  $ac
  [1] 6 2 1
  
  $callRate
  [1] 1 1 1
  
  $hwe
  [1] "1" "1" "1"
  
  $nref
  [1] 4 7 8
  
  $nhet
  [1] 4 2 1
  
  $nalt
  [1] 1 0 0
  
  $ustat
  [1] 0.283603 0.000000 0.325521
  
  $vstat
  [1] 2.14797 1.33950 1.01256
  
  $effect
  [1] 0.0614687 0.0000000 0.3174930
  
  $pVal
  [1] 0.894958 1.000000 0.747845
  
  $anno
  [1] "" "" ""
  
  $annoFull
  [1] "" "" ""
  
  Skipped: encounter a duplicated site: [ 1:1 ] in file [ D:/RCompile/CRANpkg/lib/4.4/seqminer/test-triallelic/test2.study1.MetaScore.assoc.gz ]
  1 gene/region to be extracted.
  Read score tests...
  In study 0
  Error: encounter a duplicated location: [ 1:1 ] in file [ D:/RCompile/CRANpkg/lib/4.4/seqminer/test-triallelic/test2.study1.MetaScore.assoc.gz ], will overwrite previous results!
  Done read score file: D:/RCompile/CRANpkg/lib/4.4/seqminer/test-triallelic/test2.study1.MetaScore.assoc.gz
  In study 1
  Done read score file: D:/RCompile/CRANpkg/lib/4.4/seqminer/test-triallelic/test2.study2.MetaScore.assoc.gz
  Read cov files ... 
  In study 0
  Done read cov file: D:/RCompile/CRANpkg/lib/4.4/seqminer/test-triallelic/test2.study1.MetaCov.assoc.gz
  In study 1
  Done read cov file: D:/RCompile/CRANpkg/lib/4.4/seqminer/test-triallelic/test2.study2.MetaCov.assoc.gz
  Finished calculation.
  1 gene/region to be extracted.
  Read score tests...
  In study 0
  Done read score file: D:/RCompile/CRANpkg/lib/4.4/seqminer/test-triallelic/test2.study1.MetaScore.assoc.gz
  In study 1
  Done read score file: D:/RCompile/CRANpkg/lib/4.4/seqminer/test-triallelic/test2.study2.MetaScore.assoc.gz
  Read cov files ... 
  In study 0
  Done read cov file: D:/RCompile/CRANpkg/lib/4.4/seqminer/test-triallelic/test2.study1.MetaCov.assoc.gz
  In study 1
  Done read cov file: D:/RCompile/CRANpkg/lib/4.4/seqminer/test-triallelic/test2.study2.MetaCov.assoc.gz
  Finished calculation.
  Loading objects:
    apoe
    cfh
    cfh.all
    cfh.nonsyn
    cfh.nonsyn.2
    cfh.range
    cfh.syn
    cfh.syn.2
    out.gene.1
    out.gene.2
    out.gene.3
    out.range.1
    ssss
  --------------- test readVCFToMatrixByRange ---------------
  1 region to be extracted.
  1 region to be extracted.
  2 region to be extracted.
  1 region to be extracted.
  1 region to be extracted.
  range of [ CFH ] is [ 1:196621007-196716634 ]
  1 region to be extracted.
  range of [ APOE ] is [ 19:45409038-45412650 ]
  1 region to be extracted.
  range of [ ssss ] is [  ]
  range of [ CFH ] is [ 1:196621007-196716634 ]
  range = 1:196621007-196716634
  range of [ CFH ] is [ 1:196621007-196716634 ]
  range = 1:196621007-196716634
  range of [ CFH ] is [ 1:196621007-196716634 ]
  range = 1:196621007-196716634
  1 region to be extracted.
  1 region to be extracted.
  1 region to be extracted.
  range of [ CFH ] is [ 1:196621007-196716634 ]
  range of [ CFH ] is [ 1:196621007-196716634 ]
  range = 1:196621007-196716634
  start
  file = D:/RCompile/CRANpkg/lib/4.4/seqminer/plink/all.anno.filtered.extract
  Mon Jan 19 23:46:22 2026 - read bim
  Mon Jan 19 23:46:22 2026 - read fam
  extract 2 marker and 3 sample out of 166 marker and 3 sample
  Mon Jan 19 23:46:22 2026 - read bed
  Binary PLINK BED file is ready to read
  build a look-up table
  assigned 6 values 
  allocate dim and dimnames
  Mon Jan 19 23:46:22 2026 - end
  --------------- test openPlink ---------------
  --------------- test readPlinkBySubscript ---------------
  start
  file = D:/RCompile/CRANpkg/lib/4.4/seqminer/plink/all.anno.filtered.extract.bed
  extract 2 marker and 3 sample out of 166 marker and 3 sample
  Binary PLINK BED file is ready to read
  build a look-up table
  assigned 6 values 
  allocate dim
  Mon Jan 19 23:46:22 2026 - end
  --------------- test readSingleChromosomeVCFToMatrixByRange ---------------
  fsize = 2688
  query [0, 0]
  Found 1 results
  found 1 position, e.g. 0 2384
  Inferred 3 samples from header
  1 region to be extracted.
  query [196621007, 196716634]
  Found 166 results
  found 166 position, e.g. 1.96623e+08 2454
  --------------- test createSingleChromosomeVCFIndex ---------------
  header line has 3 samples
  offset = 2384
  Indexing finished with 3 samples and 166 markers
  created index file [ D:\temp\2026_01_19_01_50_00_22770\RtmpqYrPyU\filea26890058b2 ]
  Saving _problems/test-vcf-167.R
  --------------- test readSingleChromosomeBCFToMatrixByRange ---------------
  fsize = 2688
  l_text = 4206
  Total contig parse = 1, total header index used = 47
  Inferred 3 samples from header
  1 region to be extracted.
  query [196621006, 196716633]
  Found 166 results
  1.96623e+08 4215
  found 166 position, e.g. 1.96623e+08 4215
  sampleNames.size() = 3, markerNames.size() = 166
  --------------- test createSingleChromosomeBCFIndex ---------------
  l_text = 4206
  Total contig parse = 1, total header index used = 47
  offset_header = 4135
  sample size = 3
  last character is s[after_chrom_size-1] = 0
  Indexing finished with 3 samples and 166 markers
  created index file [ D:\temp\2026_01_19_01_50_00_22770\RtmpqYrPyU\filea2686b70173a ]
  Saving _problems/test-vcf-181.R
  [ FAIL 2 | WARN 0 | SKIP 0 | PASS 72 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-vcf.R:167:5'): createSingleChromosomeVCFIndex ──────────────────
  Error in `expect(nchar(cfh) > 0)`: `failure_message` must be a character vector, not absent.
  Backtrace:
      ▆
   1. └─testthat::expect(failure_message = <empty>) at test-vcf.R:167:5
   2.   └─testthat:::check_character(failure_message)
   3.     └─testthat:::stop_input_type(...)
   4.       └─rlang::abort(message, ..., call = call, arg = arg)
  ── Error ('test-vcf.R:181:5'): createSingleChromosomeBCFIndex ──────────────────
  Error in `expect(nchar(cfh) > 0)`: `failure_message` must be a character vector, not absent.
  Backtrace:
      ▆
   1. └─testthat::expect(failure_message = <empty>) at test-vcf.R:181:5
   2.   └─testthat:::check_character(failure_message)
   3.     └─testthat:::stop_input_type(...)
   4.       └─rlang::abort(message, ..., call = call, arg = arg)
  
  [ FAIL 2 | WARN 0 | SKIP 0 | PASS 72 ]
  Error:
  ! Test failures.
  Execution halted