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###
### Running command:
###
###   F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:uncoverappLib.install-out.txt --library=F:\biocbuild\bbs-3.17-bioc\R\library --no-vignettes --timings uncoverappLib_1.9.0.tar.gz
###
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* using log directory 'F:/biocbuild/bbs-3.17-bioc-rtools43/meat/uncoverappLib.Rcheck'
* using R Under development (unstable) (2022-12-25 r83502 ucrt)
* using platform: x86_64-w64-mingw32 (64-bit)
* R was compiled by
    gcc.exe (GCC) 10.4.0
    GNU Fortran (GCC) 10.4.0
* running under: Windows Server x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'uncoverappLib/DESCRIPTION' ... OK
* this is package 'uncoverappLib' version '1.9.0'
* package encoding: UTF-8
* 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 'uncoverappLib' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... 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 R 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 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 ... NOTE
buildInput : riarrange.df: no visible binding for global variable
  'nucleotide'
buildInput : riarrange.df: no visible binding for global variable
  'count'
buildInput: no visible binding for global variable 'seqnames.1'
buildInput: no visible binding for global variable 'start.1'
buildInput: no visible binding for global variable 'end.1'
buildInput: no visible binding for global variable 'width.1'
buildInput: no visible binding for global variable 'strand.1'
buildInput : statistical_operation: no visible binding for global
  variable 'SYMBOL'
buildInput : statistical_operation: no visible binding for global
  variable 'value'
buildInput : statistical_operation: no visible global function
  definition for 'median'
buildInput : statistical_operation: no visible binding for global
  variable '.'
Undefined global functions or variables:
  . SYMBOL count end.1 median nucleotide seqnames.1 start.1 strand.1
  value width.1
Consider adding
  importFrom("stats", "median")
to your NAMESPACE file.
* checking Rd files ... OK
* checking Rd metadata ... 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 files in 'vignettes' ... OK
* checking examples ... ERROR
Running examples in 'uncoverappLib-Ex.R' failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: buildInput
> ### Title: Build input file
> ### Aliases: buildInput
> 
> ### ** Examples
> 
> gene.list<- system.file("extdata", "mygene.txt", package = "uncoverappLib")
> 
> bam_example <- system.file("extdata", "example_POLG.bam",
+ package = "uncoverappLib")
> cat(bam_example, file = "bam.list", sep = "\n")
> temp_dir=tempdir()
> buildInput(geneList= gene.list, genome= "hg19", type_bam= "chr",
+ bamList= "bam.list",type_input="genes", outDir= temp_dir)
Reading gene name started at:
2022-12-29 04:29:34.996531
Read 1 item
'select()' returned 1:many mapping between keys and columns
Error in buildInput(geneList = gene.list, genome = "hg19", type_bam = "chr",  : 
  ERROR: unrecognized GENE NAME. Please remove genes
       stored in preprocessing_log1.txt
Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in 'inst/doc' ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 ERROR, 1 NOTE
See
  'F:/biocbuild/bbs-3.17-bioc-rtools43/meat/uncoverappLib.Rcheck/00check.log'
for details.

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###
### Running command:
###
###   F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD INSTALL uncoverappLib
###
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* installing to library 'F:/biocbuild/bbs-3.17-bioc/R/library'
* installing *source* package 'uncoverappLib' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (uncoverappLib)