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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_1.27.1.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/Ularcirc.Rcheck’
* using R version 4.5.1 (2025-06-13)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 14.2.0
* 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 ‘1.27.1’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... INFO
Imports includes 25 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’ ‘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’
load_miRBase_fasta: no visible global function definition for
  ‘download.file’
Undefined global functions or variables:
  . ..returnColIdx BSjuncName Filter_by_Data_Set JuncType download.file
  extractGenomeSequence startAcceptor startDonor strandDonor type
Consider adding
  importFrom("utils", "download.file")
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 ... 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’

Undocumented arguments in Rd file 'miR_binding_site_Analysis.Rd'
  ‘species_code’
Documented arguments not in \usage in Rd file 'miR_binding_site_Analysis.Rd':
  ‘speciesCode’

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: circSequence
> ### Title: circSequence This function returns pre-defined full length
> ###   circRNA sequences.
> ### Aliases: circSequence
> 
> ### ** Examples
> 
>       circSequence(circRNA_ID="slc8a1")
Error in circSequence(circRNA_ID = "slc8a1") : 
  could not find function "circSequence"
Execution halted
Examples with CPU (user + system) or elapsed time > 5s
                            user system elapsed
Compatible_Annotation_DBs 10.486  0.468  11.035
* 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 ERROR, 1 WARNING, 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.22-bioc/meat/Ularcirc.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL Ularcirc
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library’
* installing *source* package ‘Ularcirc’ ...
** this is package ‘Ularcirc’ version ‘1.27.1’
** 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)