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### Running command:
###
###   /home/biocbuild/R/R-devel_2024-01-16_r85812/bin/R CMD check --install=check:ReQON.install-out.txt --library=/home/biocbuild/R/R-devel_2024-01-16_r85812/site-library --no-vignettes --timings ReQON_1.49.1.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/ReQON.Rcheck’
* using R Under development (unstable) (2024-01-16 r85812)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
    gcc (GCC) 10.3.1
    GNU Fortran (GCC) 10.3.1
* running under: openEuler 22.03 (LTS-SP1)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘ReQON/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘ReQON’ version ‘1.49.1’
* 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 ‘ReQON’ can be installed ... WARNING
Found the following significant warnings:
  Warning: Package 'seqbias' is deprecated and will be removed from Bioconductor
  Warning: Package 'ReQON' is deprecated and will be removed from Bioconductor
See ‘/home/biocbuild/bbs-3.19-bioc/meat/ReQON.Rcheck/00install.out’ for details.
* 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 loading without being on the library search path ... OK
* checking whether startup messages can be suppressed ... OK
* checking dependencies in R code ... NOTE
Packages in Depends field not imported from:
  ‘Rsamtools’ ‘seqbias’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
FWSEplot: no visible global function definition for ‘title’
FWSEplot: no visible global function definition for ‘rgb’
FWSEplot: no visible global function definition for ‘points’
QualFreqPlot: no visible global function definition for ‘title’
ReQON: no visible global function definition for ‘glm.fit’
ReQON: no visible global function definition for ‘binomial’
ReadPosErrorPlot: no visible global function definition for ‘title’
Undefined global functions or variables:
  binomial glm.fit points rgb title
Consider adding
  importFrom("grDevices", "rgb")
  importFrom("graphics", "points", "title")
  importFrom("stats", "binomial", "glm.fit")
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
ReQON 29.558  1.607  20.678
* 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
  ‘/home/biocbuild/bbs-3.19-bioc/meat/ReQON.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /home/biocbuild/R/R-devel_2024-01-16_r85812/bin/R CMD INSTALL ReQON
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* installing to library ‘/home/biocbuild/R/R-devel_2024-01-16_r85812/site-library’
* installing *source* package ‘ReQON’ ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
Warning message:
Package 'seqbias' is deprecated and will be removed from Bioconductor
  version 3.19 
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
Warning: Package 'seqbias' is deprecated and will be removed from Bioconductor
  version 3.19
Warning: Package 'ReQON' is deprecated and will be removed from Bioconductor
  version 3.20
** testing if installed package can be loaded from final location
Warning: Package 'seqbias' is deprecated and will be removed from Bioconductor
  version 3.19
Warning: Package 'ReQON' is deprecated and will be removed from Bioconductor
  version 3.20
** testing if installed package keeps a record of temporary installation path
* DONE (ReQON)