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### Running command:
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###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:ggseqalign.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings ggseqalign_1.0.0.tar.gz
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* using log directory ‘/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/meat/ggseqalign.Rcheck’
* using R version 4.4.2 (2024-10-31)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0
    GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0
* running under: Ubuntu 24.04.1 LTS
* using session charset: UTF-8
* 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 loading without being on the library search path ... 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
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 1 NOTE
See
  ‘/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/meat/ggseqalign.Rcheck/00check.log’
for details.

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### Running command:
###
###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD INSTALL ggseqalign
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* installing to library ‘/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library’
* installing *source* package ‘ggseqalign’ ...
** 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 (ggseqalign)