* using log directory ‘/srv/hornik/tmp/CRAN/DisVar.Rcheck’
* using R Under development (unstable) (2023-08-12 r84939)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    Debian clang version 16.0.6 (6)
    GNU Fortran (Debian 13.2.0-1) 13.2.0
* running under: Debian GNU/Linux trixie/sid
* using session charset: UTF-8
* checking for file ‘DisVar/DESCRIPTION’ ... OK
* this is package ‘DisVar’ version ‘1.1.2’
* package encoding: UTF-8
* checking CRAN incoming feasibility ... [3s/3s] NOTE
Maintainer: ‘Khunanon Chanasongkhram <chanasongkhram.k@gmail.com>’

New submission

Possibly misspelled words in DESCRIPTION:
  VCF (2:31, 7:53, 7:95)

The Description field should start with a capital letter.

Size of tarball: 42329445 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 executable files ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking serialization versions ... OK
* checking whether package ‘DisVar’ can be installed ... [74s/74s] OK
* checking package directory ... OK
* checking for future file timestamps ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... NOTE
Non-standard file/directory found at top level:
  ‘file_name.vcf’
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... [1s/1s] OK
* checking whether the package can be loaded with stated dependencies ... [1s/1s] OK
* checking whether the package can be unloaded cleanly ... [1s/1s] OK
* checking whether the namespace can be loaded with stated dependencies ... [1s/1s] OK
* checking whether the namespace can be unloaded cleanly ... [1s/1s] OK
* checking loading without being on the library search path ... [1s/1s] 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 ... [4s/4s] NOTE
DisVar: no visible global function definition for ‘install.packages’
DisVar: no visible global function definition for ‘data’
DisVar: no visible binding for global variable ‘GWASdb_GRCh38’
DisVar: no visible binding for global variable ‘GRASP_GRCh38’
DisVar: no visible binding for global variable ‘GWAS_catalog_GRCh38’
DisVar: no visible binding for global variable ‘JnO_GRCh38’
DisVar: no visible global function definition for ‘.’
DisVar: no visible binding for global variable ‘V2’
DisVar: no visible binding for global variable ‘V1’
DisVar: no visible binding for global variable ‘P_value’
DisVar: no visible binding for global variable ‘Rsid’
DisVar: no visible binding for global variable ‘Chr’
DisVar: no visible binding for global variable ‘V4’
DisVar: no visible binding for global variable ‘V5’
DisVar: no visible binding for global variable ‘Ref’
DisVar: no visible binding for global variable ‘Alt’
DisVar: no visible binding for global variable ‘Gwas_trait’
DisVar: no visible binding for global variable ‘Gene’
DisVar: no visible binding for global variable ‘Variant_type’
DisVar: no visible binding for global variable ‘V6’
DisVar: no visible binding for global variable ‘V7’
DisVar: no visible binding for global variable ‘V8’
DisVar: no visible global function definition for ‘setNames’
DisVar: no visible binding for global variable ‘Disease’
DisVar: no visible binding for global variable ‘Confident’
DisVar: no visible global function definition for ‘write.table’
Undefined global functions or variables:
  . Alt Chr Confident Disease GRASP_GRCh38 GWAS_catalog_GRCh38
  GWASdb_GRCh38 Gene Gwas_trait JnO_GRCh38 P_value Ref Rsid V1 V2 V4 V5
  V6 V7 V8 Variant_type data install.packages setNames write.table
Consider adding
  importFrom("stats", "setNames")
  importFrom("utils", "data", "install.packages", "write.table")
to your NAMESPACE file.

Found the following calls to data() loading into the global environment:
File ‘DisVar/R/DisVar.R’:
  data(GWASdb_GRCh38)
  data(GRASP_GRCh38)
  data(GWAS_catalog_GRCh38)
  data(GAD_GRCh38)
  data(JnO_GRCh38)
  data(GAD_GRCh38)
  data(GRASP_GRCh38)
  data(GWAS_catalog_GRCh38)
  data(GWASdb_GRCh38)
  data(JnO_GRCh38)
See section ‘Good practice’ in ‘?data’.
* checking Rd files ... [0s/0s] 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... [8s/8s] OK
* checking LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking examples ... [1s/1s] ERROR
Running examples in ‘DisVar-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: DisVar
> ### Title: Find diseases from the VCF file
> ### Aliases: DisVar
> 
> ### ** Examples
> 
> DisVar("C:/DisVar/file_name.vcf")
Loading required package: sqldf
Loading required package: gsubfn
Loading required package: proto
Loading required package: RSQLite
Loading required package: data.table
Loading required package: dplyr

Attaching package: ‘dplyr’

The following objects are masked from ‘package:data.table’:

    between, first, last

The following objects are masked from ‘package:stats’:

    filter, lag

The following objects are masked from ‘package:base’:

    intersect, setdiff, setequal, union

Error in DisVar("C:/DisVar/file_name.vcf") : File does not exist
Execution halted
* checking PDF version of manual ... [3s/3s] OK
* checking HTML version of manual ... [0s/0s] OK
* checking for non-standard things in the check directory ... OK
* checking for detritus in the temp directory ... OK
* DONE
Status: 1 ERROR, 3 NOTEs