R Under development (unstable) (2025-11-05 r88988 ucrt) -- "Unsuffered Consequences"
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> # This file is part of the standard setup for testthat.
> # It is recommended that you do not modify it.
> #
> # Where should you do additional test configuration?
> # Learn more about the roles of various files in:
> # * https://r-pkgs.org/tests.html
> # * https://testthat.r-lib.org/reference/test_package.html#special-files
> 
> library(testthat)
> library(vcfppR)
> 
> test_check("vcfppR")
please call the `output()` function first to creat an output VCF
the length of s must be divisable by nsamples()[1] 2
[1] "AF=0.000616523;AN=3244;DP=2498;FS=0;MLEAC=1;MLEAF=0.0003083;MQ=17.07;MQ0=0;QD=17.52;SOR=3.258;VQSLOD=-32.6;culprit=MQ;AN_EUR=658;AN_EAS=548;AN_AMR=520;AN_SAS=624;AN_AFR=894;AF_EUR=0;AF_EAS=0;AF_AMR=0.00384615;AF_SAS=0;AF_AFR=0;AC_EUR=0;AC_EAS=0;AC_AMR=2;AC_SAS=0;AC_AFR=0;AC_Het_EUR=0;AC_Het_EAS=0;AC_Het_AMR=0;AC_Het_SAS=0;AC_Het_AFR=0;AC_Het=0;AC_Hom_EUR=0;AC_Hom_EAS=0;AC_Hom_AMR=2;AC_Hom_SAS=0;AC_Hom_AFR=0;AC_Hom=2;HWE_EUR=1;ExcHet_EUR=1;HWE_EAS=1;ExcHet_EAS=1;HWE_AMR=0.00192678;ExcHet_AMR=1;HWE_SAS=1;ExcHet_SAS=1;HWE_AFR=1;ExcHet_AFR=1;HWE=0.000308356;ExcHet=1;ME=0;AN_EUR_unrel=508;AN_EAS_unrel=448;AN_AMR_unrel=330;AN_SAS_unrel=484;AN_AFR_unrel=666;AF_EUR_unrel=0;AF_EAS_unrel=0;AF_AMR_unrel=0;AF_SAS_unrel=0;AF_AFR_unrel=0;AC_EUR_unrel=0;AC_EAS_unrel=0;AC_AMR_unrel=0;AC_SAS_unrel=0;AC_AFR_unrel=0;AC_Het_EUR_unrel=0;AC_Het_EAS_unrel=0;AC_Het_AMR_unrel=0;AC_Het_SAS_unrel=0;AC_Het_AFR_unrel=0;AC_Hom_EUR_unrel=0;AC_Hom_EAS_unrel=0;AC_Hom_AMR_unrel=0;AC_Hom_SAS_unrel=0;AC_Hom_AFR_unrel=0"
there is no AA in the FORMAT
[ FAIL 0 | WARN 0 | SKIP 85 | PASS 147 ]

══ Skipped tests (85) ══════════════════════════════════════════════════════════
• On Windows (79): 'test-vcf-comp.R:11:3', 'test-vcf-comp.R:23:3',
  'test-vcf-comp.R:34:3', 'test-vcf-comp.R:47:3', 'test-vcf-comp.R:56:3',
  'test-vcf-comp.R:65:3', 'test-vcf-comp.R:78:3', 'test-vcf-comp.R:89:3',
  'test-vcf-comp.R:122:3', 'test-vcf-comp.R:148:3', 'test-vcf-comp.R:175:3',
  'test-vcf-comp.R:197:3', 'test-vcf-comp.R:230:3', 'test-vcf-comp.R:246:3',
  'test-vcf-comp.R:260:3', 'test-vcf-errors.R:7:3', 'test-vcf-errors.R:13:3',
  'test-vcf-errors.R:19:3', 'test-vcf-errors.R:25:3', 'test-vcf-errors.R:32:3',
  'test-vcf-errors.R:43:3', 'test-vcf-errors.R:51:3', 'test-vcf-errors.R:63:3',
  'test-vcf-errors.R:74:3', 'test-vcf-errors.R:92:3', 'test-vcf-errors.R:99:3',
  'test-vcf-errors.R:111:3', 'test-vcf-errors.R:122:3',
  'test-vcf-errors.R:135:3', 'test-vcf-errors.R:145:3',
  'test-vcf-errors.R:157:3', 'test-vcf-errors.R:174:3',
  'test-vcf-errors.R:207:3', 'test-vcf-errors.R:217:3',
  'test-vcf-errors.R:234:3', 'test-vcf-errors.R:247:3',
  'test-vcf-errors.R:262:3', 'test-vcf-plot.R:7:3', 'test-vcf-plot.R:17:3',
  'test-vcf-plot.R:29:3', 'test-vcf-plot.R:39:3', 'test-vcf-plot.R:49:3',
  'test-vcf-plot.R:63:3', 'test-vcf-plot.R:73:3', 'test-vcf-plot.R:86:3',
  'test-vcf-plot.R:99:3', 'test-vcf-plot.R:111:3', 'test-vcf-plot.R:122:3',
  'test-vcf-plot.R:132:3', 'test-vcf-plot.R:145:3', 'test-vcf-subset.R:6:3',
  'test-vcf-subset.R:19:3', 'test-vcf-subset.R:32:3', 'test-vcf-subset.R:47:3',
  'test-vcf-subset.R:60:3', 'test-vcf-subset.R:72:3', 'test-vcf-subset.R:83:3',
  'test-vcf-subset.R:95:3', 'test-vcf-subset.R:108:3',
  'test-vcf-subset.R:121:3', 'test-vcf-subset.R:133:3',
  'test-vcf-subset.R:145:3', 'test-vcf-subset.R:158:3',
  'test-vcf-subset.R:169:3', 'test-vcf-subset.R:181:3',
  'test-vcf-subset.R:192:3', 'test-vcf-subset.R:204:3',
  'test-vcf-subset.R:219:3', 'test-vcf-table.R:88:3', 'test-vcf-table.R:127:3',
  'test-vcf-table.R:147:3', 'test-vcf-table.R:200:3', 'test-vcf-table.R:215:3',
  'test-vcf-table.R:234:3', 'test-vcf-table.R:259:3', 'test-vcf-table.R:275:3',
  'test-vcf-table.R:289:3', 'test-vcf-table.R:300:3', 'test-vcf-writer.R:14:3'
• to be fixed (6): 'test-vcf-comp.R:107:3', 'test-vcf-comp.R:217:3',
  'test-vcf-errors.R:184:3', 'test-vcf-table.R:107:3',
  'test-vcf-table.R:167:3', 'test-vcf-table.R:184:3'

[ FAIL 0 | WARN 0 | SKIP 85 | PASS 147 ]
> 
> proc.time()
   user  system elapsed 
   4.14    0.60    4.75