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### Running command:
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###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:Ularcirc.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings Ularcirc_1.17.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/Ularcirc.Rcheck’
* using R Under development (unstable) (2023-01-14 r83615)
* using platform: aarch64-unknown-linux-gnu (64-bit)
* R was compiled by
    gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
    GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
* running under: Ubuntu 22.04.1 LTS
* using session charset: UTF-8
* checking for file ‘Ularcirc/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘Ularcirc’ version ‘1.17.0’
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘Ularcirc’ 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 ... NOTE
Namespaces in Imports field not imported from:
  ‘DT’ ‘GenomeInfoDb’ ‘GenomeInfoDbData’ ‘Organism.dplyr’ ‘ggplot2’
  ‘ggrepel’ ‘mirbase.db’ ‘moments’ ‘shinyFiles’ ‘shinydashboard’
  ‘shinyjs’ ‘yaml’
  All declared Imports should be used.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
FilterChimericJuncs: no visible global function definition for
  ‘Filter_by_Data_Set’
FilterChimericJuncs: no visible binding for global variable
  ‘strandDonor’
FilterChimericJuncs: no visible binding for global variable
  ‘startDonor’
FilterChimericJuncs: no visible binding for global variable
  ‘startAcceptor’
Junction_Sequence_from_Genome: no visible global function definition
  for ‘extractGenomeSequence’
SelectUniqueJunctions : filtersteps: no visible global function
  definition for ‘.’
SelectUniqueJunctions: no visible binding for global variable
  ‘BSjuncName’
SelectUniqueJunctions: no visible binding for global variable
  ‘JuncType’
SelectUniqueJunctions: no visible binding for global variable
  ‘strandDonor’
loadSTAR_chimeric: no visible binding for global variable
  ‘..returnColIdx’
Undefined global functions or variables:
  . ..returnColIdx BSjuncName Filter_by_Data_Set JuncType
  extractGenomeSequence startAcceptor startDonor strandDonor
* 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 'Junction_Sequence_from_Genome'
  ‘SelectUniqueJunct_Value’
Documented arguments not in \usage in documentation object 'Junction_Sequence_from_Genome':
  ‘SelectUniqueJunct_value’

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 files in ‘vignettes’ ... OK
* checking examples ... ERROR
Running examples in ‘Ularcirc-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plot_AllJunctions
> ### Title: plot_AllJunctions
> ### Aliases: plot_AllJunctions
> 
> ### ** Examples
> 
> 
> library('Ularcirc')
>  # BSJ data.table
>  BSJ_data <- data.table::data.table(chrom1="chr2", 
+                 start1=c(40139400, 40160764, 40428472, 40428472), 
+                 end1=c(40139400, 40160764,40428472, 40428472), 
+                 chrom2="chr2", start2=c(40178494,40178494,40430302,40430305),
+                  end2=c(40178494,40178494,40430302,40430305),
+                score=c(13,20,360,1751))
> 
>  # FSJ
>  FSJstarts1 <- c(40115630,40139677,40160865,40164985,40170350,40174721,
+                               40174843,40175282,40278771,40430302,40430305)
>  FSJstarts2 <- c(40139400,40160764,40164853,40170280,40174705,40174824,
+                                40175260,40178386,40428472,40453160,40512348)
>  FSJ_data <- data.table::data.table(chrom1="chr2", start1=FSJstarts1, end1=FSJstarts1,
+                      chrom2="chr2", start2=FSJstarts2, end2=FSJstarts2, 
+                      score=c(225,825,685,666,633,596,517,542,685,101,171))
>                      
>  plot_AllJunctions(assembly="hg38", chrom="chr2", 
+                      chromstart=40096769, chromend=40611554,
+                      BSJData=BSJ_data, FSJData=FSJ_data, geneSymbol="SLC8A1") 
Error in mtfrm.default(list(path = "GRID.VP.1", name = "page", n = 2L)) : 
  cannot mtfrm
Calls: plot_AllJunctions ... check_placement -> check_page -> %in% -> mtfrm -> mtfrm.default
Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
  ‘Ularcirc.Rmd’ using ‘UTF-8’... OK
 NONE
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 1 ERROR, 1 WARNING, 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.17-bioc/meat/Ularcirc.Rcheck/00check.log’
for details.

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### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL Ularcirc
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* installing to library ‘/home/biocbuild/bbs-3.17-bioc/R/library’
* installing *source* package ‘Ularcirc’ ...
** 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 (Ularcirc)