##############################################################################
##############################################################################
###
### Running command:
###
### F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:Ularcirc.install-out.txt --library=F:\biocbuild\bbs-3.17-bioc\R\library --no-vignettes --timings Ularcirc_1.17.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory 'F:/biocbuild/bbs-3.17-bioc-rtools43/meat/Ularcirc.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 '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 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 ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: 1 ERROR, 1 WARNING, 2 NOTEs
See
'F:/biocbuild/bbs-3.17-bioc-rtools43/meat/Ularcirc.Rcheck/00check.log'
for details.