* using log directory 'd:/RCompile/CRANincoming/R-devel/vcfppR.Rcheck'
* using R Under development (unstable) (2024-03-22 r86169 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 13.2.0
    GNU Fortran (GCC) 13.2.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* checking for file 'vcfppR/DESCRIPTION' ... OK
* this is package 'vcfppR' version '0.4.1'
* package encoding: UTF-8
* checking CRAN incoming feasibility ... NOTE
Maintainer: 'Zilong Li <zilong.dk@gmail.com>'

New submission

Package was archived on CRAN

Possibly misspelled words in DESCRIPTION:
  BCF (10:332)
  VCF (2:55, 10:182, 10:328, 10:394)

CRAN repository db overrides:
  X-CRAN-Comment: Archived on 2024-03-15 as issues were not corrected
    in time.

Size of tarball: 7086496 bytes
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking whether package 'vcfppR' can be installed ... OK
* used C++ compiler: 'g++.exe (GCC) 13.2.0'
* checking installed package size ... OK
* checking package directory ... OK
* checking for future file timestamps ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking use of S3 registration ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd line widths ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking line endings in shell scripts ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking use of PKG_*FLAGS in Makefiles ... OK
* checking use of SHLIB_OPENMP_*FLAGS in Makefiles ... OK
* checking include directives in Makefiles ... OK
* checking pragmas in C/C++ headers and code ... OK
* checking compilation flags used ... OK
* checking compiled code ... OK
* checking examples ... OK
* checking for unstated dependencies in 'tests' ... OK
* checking tests ... [59s] ERROR
  Running 'testthat.R' [59s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > # 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(filename)` function first
  please call the `output(filename)` function first
  [1] "##fileformat=VCF4.3\n##FILTER=<ID=PASS,Description=\"All filters passed\">\n##contig=<ID=chr20>\n##INFO=<ID=AF,Number=A,Type=Float,Description=\"Estimated allele frequency in the range (0,1)\">\n##FORMAT=<ID=GP,Number=3,Type=Float,Description=\"Posterior genotype probability of 0/0, 0/1, and 1/1\">\n##INFO=<ID=INFO,Number=1,Type=Float,Description=\"INFO score of imputation\">\n##FORMAT=<ID=DS,Number=1,Type=Float,Description=\"Diploid dosage\">\n##FORMAT=<ID=AC,Number=1,Type=Integer,Description=\"Allele counts\">\n##FORMAT=<ID=STR,Number=1,Type=String,Description=\"Test String type\">\n#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT\tNA12878\tNA12879\n"
  the length of s must be divisable by nsamples()[1] "chr20\t2006060\trs146931526\tG\tC\t100\tPASS\tAF=0.000998403\tGP:DS:AC:STR\t0.966,0.034,0:0.034:3:HHH\t0.003,0.872,0.125:1.122:4:JJJ\n"
  [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"
  [1] 2
  there is no AA in the FORMAT
  [1] "##fileformat=VCF4.3\n##FILTER=<ID=PASS,Description=\"All filters passed\">\n##ALT=<ID=NON_REF,Description=\"Represents any possible alternative allele at this location\">\n##contig=<ID=chr20>\n##INFO=<ID=AF,Number=A,Type=Float,Description=\"Estimated allele frequency in the range (0,1)\">\n#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\n"
  [ FAIL 0 | WARN 0 | SKIP 0 | PASS 123 ]
  > 
  > proc.time()
     user  system elapsed 
     2.90    0.28    3.15 
* checking PDF version of manual ... [13s] OK
* checking HTML version of manual ... OK
* DONE
Status: 1 ERROR, 1 NOTE