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### Running command:
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###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:ggseqalign.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings ggseqalign_1.0.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/ggseqalign.Rcheck’
* using R version 4.4.2 (2024-10-31)
* 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 ‘ggseqalign/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘ggseqalign’ version ‘1.0.0’
* 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 ‘ggseqalign’ 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
alignment_table: no visible binding for global variable ‘XStringSet’
alignment_table: no visible binding for global variable ‘.’
alignment_table: no visible binding for global variable ‘PatternName’
alignment_table: no visible binding for global variable ‘PatternId’
alignment_table: no visible binding for global variable ‘start’
alignment_table: no visible binding for global variable ‘end’
alignment_table: no visible binding for global variable
  ‘SubjectSubstring’
alignment_table: no visible binding for global variable ‘PatternLength’
alignment_table: no visible binding for global variable ‘alig_start’
alignment_table: no visible binding for global variable ‘start_ins’
alignment_table: no visible binding for global variable ‘feature’
plot_sequence_alignment: no visible binding for global variable ‘query’
plot_sequence_alignment: no visible binding for global variable
  ‘subject’
plot_sequence_alignment: no visible binding for global variable
  ‘feature’
plot_sequence_alignment: no visible binding for global variable
  ‘PatternName’
plot_sequence_alignment: no visible binding for global variable ‘start’
plot_sequence_alignment: no visible binding for global variable ‘end’
plot_sequence_alignment: no visible binding for global variable
  ‘SubjectStart’
plot_sequence_alignment: no visible binding for global variable
  ‘PatternSubstring’
Undefined global functions or variables:
  . PatternId PatternLength PatternName PatternSubstring SubjectStart
  SubjectSubstring XStringSet alig_start end feature query start
  start_ins subject
Consider adding
  importFrom("stats", "end", "start")
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 ... OK
* 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
plot_sequence_alignment 8.43  0.408   8.876
* 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 NOTE
See
  ‘/Users/biocbuild/bbs-3.20-bioc/meat/ggseqalign.Rcheck/00check.log’
for details.