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###
### Running command:
###
###   D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:igvR.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings igvR_1.15.10.tar.gz
###
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* using log directory 'D:/biocbuild/bbs-3.15-bioc/meat/igvR.Rcheck'
* using R Under development (unstable) (2021-11-21 r81221)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'igvR/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'igvR' version '1.15.10'
* 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 'igvR' can be installed ... OK
* checking installed package size ... NOTE
  installed size is 17.5Mb
  sub-directories of 1Mb or more:
    browserCode  12.1Mb
    extdata       4.5Mb
* 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 ... WARNING
---- unloading
Error in .mergeMethodsTable(generic, mtable, tt, attach) : 
  trying to get slot "defined" from an object of a basic class ("environment") with no slots
Calls: unloadNamespace ... <Anonymous> -> .updateMethodsInTable -> .mergeMethodsTable
Execution halted
* 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
setTrackHeight,igvR: no visible binding for global variable 'igv'
trackSize,GFF3Track: no visible binding for global variable
  'NA_INTEGER_'
Undefined global functions or variables:
  NA_INTEGER_ igv
* 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 ... WARNING
Undocumented arguments in documentation object 'GFF3Track-class'
  'trackColor'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking include directives in Makefiles ... OK
* checking files in 'vignettes' ... OK
* checking examples ... ERROR
Running examples in 'igvR-Ex.R' failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: GFF3Track-class
> ### Title: Constructor for GFF3Track
> ### Aliases: GFF3Track-class .GFF3Track GFF3Track
> 
> ### ** Examples
> 
> tbl.gff3 <- read.table(system.file(package="igvR", "extdata", "GRCh38.94.NDUFS2.gff3"),
+                        sep="\t", as.is=TRUE)
Warning in file(file, "rt") :
  file("") only supports open = "w+" and open = "w+b": using the former
Error in read.table(system.file(package = "igvR", "extdata", "GRCh38.94.NDUFS2.gff3"),  : 
  no lines available in input
Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in 'inst/doc' ... WARNING
  Found 'inst/doc/makefile': should be 'Makefile' and will be ignored
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 ERROR, 3 WARNINGs, 2 NOTEs
See
  'D:/biocbuild/bbs-3.15-bioc/meat/igvR.Rcheck/00check.log'
for details.

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###
### Running command:
###
###   D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL igvR
###
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* installing to library 'D:/biocbuild/bbs-3.15-bioc/R/library'
* installing *source* package 'igvR' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
See system.file("LICENSE", package="MotifDb") for use restrictions.
** help
*** installing help indices
  converting help for package 'igvR'
    finding HTML links ... done
    BedpeInteractionsTrack-class            html  
    DataFrameAnnotationTrack-class          html  
    DataFrameQuantitativeTrack-class        html  
    GFF3Track-class                         html  
    GRangesAnnotationTrack-class            html  
    GRangesQuantitativeTrack-class          html  
    GWASTrack-class                         html  
    GenomicAlignmentTrack-class             html  
    QuantitativeTrack-class                 html  
    RemoteAlignmentTrack-class              html  
    Track-class                             html  
    UCSCBedAnnotationTrack-class            html  
    UCSCBedGraphQuantitativeTrack-class     html  
    VariantTrack-class                      html  
    displayTrack                            html  
    enableMotifLogoPopups                   html  
    getGenomicRegion                        html  
    getSupportedGenomes                     html  
    getTrackNames                           html  
    igvAnnotationTrack-class                html  
    igvR-class                              html  
    ping                                    html  
    removeTracksByName                      html  
    saveToSVG                               html  
    setCustomGenome                         html  
    setGenome                               html  
    setTrackClickFunction                   html  
    setTrackHeight                          html  
    showGenomicRegion                       html  
    showTrackLabels                         html  
    trackInfo                               html  
    trackSize-BedpeInteractionsTrack-method
                                            html  
    trackSize-DataFrameAnnotationTrack-method
                                            html  
    trackSize-DataFrameQuantitativeTrack-method
                                            html  
    trackSize-GFF3Track-method              html  
    trackSize-GRangesAnnotationTrack-method
                                            html  
    trackSize-GRangesQuantitativeTrack-method
                                            html  
    trackSize-GWASTrack-method              html  
    trackSize-GenomicAlignmentTrack-method
                                            html  
    trackSize-UCSCBedAnnotationTrack-method
                                            html  
    trackSize-UCSCBedGraphQuantitativeTrack-method
                                            html  
    trackSize-VariantTrack-method           html  
    trackSize                               html  
    zoomIn                                  html  
    zoomOut                                 html  
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
See system.file("LICENSE", package="MotifDb") for use restrictions.
** testing if installed package can be loaded from final location
See system.file("LICENSE", package="MotifDb") for use restrictions.
** testing if installed package keeps a record of temporary installation path
* DONE (igvR)
Making 'packages.html' ...Warning in packageDescription(i, lib.loc = lib, fields = "Title", encoding = "UTF-8") :
  DESCRIPTION file of package 'GenVisR' is missing or broken
Warning in packageDescription(i, lib.loc = lib, fields = "Title", encoding = "UTF-8") :
  DESCRIPTION file of package 'SplicingGraphs' is missing or broken
Warning in packageDescription(i, lib.loc = lib, fields = "Title", encoding = "UTF-8") :
  DESCRIPTION file of package 'strandCheckR' is missing or broken
 done