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### Running command:
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###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:Ularcirc.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings Ularcirc_1.25.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/Ularcirc.Rcheck’
* using R Under development (unstable) (2024-11-20 r87352)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.7.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘Ularcirc/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘Ularcirc’ version ‘1.25.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
  cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
 INFO
Imports includes 26 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
* 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 code 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 : filtersteps: no visible binding for global
  variable ‘type’
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 type
* 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 Rd file 'Junction_Sequence_from_Genome.Rd'
  ‘SelectUniqueJunct_Value’
Documented arguments not in \usage in Rd file 'Junction_Sequence_from_Genome.Rd':
  ‘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 ... OK
Examples with CPU (user + system) or elapsed time > 5s
                           user system elapsed
Compatible_Annotation_DBs 7.223  0.301   7.534
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 WARNING, 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.21-bioc/meat/Ularcirc.Rcheck/00check.log’
for details.