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###
### Running command:
###
###   /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD check --install=check:staRgate.install-out.txt --library=/home/biocbuild/bbs-3.23-bioc/R/site-library --timings staRgate_0.99.4.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.23-bioc/meat/staRgate.Rcheck’
* using R Under development (unstable) (2025-12-22 r89219)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
    GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.3 LTS
* using session charset: UTF-8
* checking for file ‘staRgate/DESCRIPTION’ ... OK
* this is package ‘staRgate’ version ‘0.99.4’
* 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 ‘staRgate’ 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
getDensityDerivs: no visible binding for global variable ‘y’
getDensityDerivs: no visible binding for global variable ‘x_avg’
getDensityDerivs: no visible binding for global variable
  ‘original_row_num’
getDensityDerivs: no visible binding for global variable ‘y_avg’
getDensityDerivs: no visible binding for global variable ‘first_deriv’
getDensityDerivs: no visible binding for global variable ‘second_deriv’
getDensityDerivs: no visible binding for global variable ‘third_deriv’
getDensityDerivs: no visible binding for global variable
  ‘first_deriv_sign’
getDensityDerivs: no visible binding for global variable
  ‘second_deriv_sign’
getDensityGates : <anonymous>: no visible binding for global variable
  ‘MARKER’
getDensityGates : <anonymous> : <anonymous>: no visible binding for
  global variable ‘cutoff’
getDensityGates : <anonymous> : <anonymous>: no visible binding for
  global variable ‘x_avg’
getDensityMats: no visible binding for global variable ‘data’
getDensityMats: no visible binding for global variable ‘dens_obj’
getDensityMats: no visible binding for global variable ‘dens_peaks’
getDensityMats : <anonymous>: no visible binding for global variable
  ‘peak’
getDensityMats : <anonymous>: no visible binding for global variable
  ‘x_avg’
getDensityMats: no visible binding for global variable ‘peak_loc’
getDensityMats: no visible binding for global variable ‘flag_pos_peak’
getDensityMats: no visible binding for global variable
  ‘dens_peaks_flip’
getDensityMats : <anonymous>: no visible binding for global variable
  ‘cutoff’
getDensityMats : <anonymous>: no visible binding for global variable
  ‘original_row_num’
getDensityPeakCutoff: no visible binding for global variable
  ‘local_peak’
getDensityPeakCutoff: no visible binding for global variable ‘y_avg’
getDensityPeakCutoff : <anonymous>: no visible binding for global
  variable ‘y_avg’
getDensityPeakCutoff: no visible binding for global variable ‘ratio’
getDensityPeakCutoff: no visible binding for global variable
  ‘original_row_num’
getDensityPeakCutoff: no visible binding for global variable ‘peak’
getDensityPeakCutoff : <anonymous>: no visible binding for global
  variable ‘original_row_num’
getDensityPeakCutoff : <anonymous>: no visible binding for global
  variable ‘new_anchor’
getDensityPeakCutoff: no visible binding for global variable
  ‘first_deriv_sign’
getDensityPeakCutoff: no visible binding for global variable
  ‘first_deriv_change’
getDensityPeakCutoff: no visible binding for global variable
  ‘second_deriv’
getGatedDat: no visible binding for global variable ‘data’
getGatedDat: no visible binding for global variable ‘gated_data’
getPerc : <anonymous>: no visible binding for global variable
  ‘denom_filters’
getPerc: no visible binding for global variable ‘denom_filters’
Undefined global functions or variables:
  MARKER cutoff data denom_filters dens_obj dens_peaks dens_peaks_flip
  first_deriv first_deriv_change first_deriv_sign flag_pos_peak
  gated_data local_peak new_anchor original_row_num peak peak_loc ratio
  second_deriv second_deriv_sign third_deriv x_avg y y_avg
Consider adding
  importFrom("utils", "data")
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 ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 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
  ‘/home/biocbuild/bbs-3.23-bioc/meat/staRgate.Rcheck/00check.log’
for details.

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD INSTALL staRgate
###
##############################################################################
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* installing to library ‘/home/biocbuild/bbs-3.23-bioc/R/site-library’
* installing *source* package ‘staRgate’ ...
** this is package ‘staRgate’ version ‘0.99.4’
** 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 (staRgate)

R Under development (unstable) (2025-12-22 r89219) -- "Unsuffered Consequences"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> # This file is part of the standard setup for testthat.
> # It is recommended that you do not modify it.
> #
> # Where should you do additional test configuration?
> # Learn more about the roles of various files in:
> # * https://r-pkgs.org/testing-design.html#sec-tests-files-overview
> # * https://testthat.r-lib.org/articles/special-files.html
> 
> library(testthat)
> library(staRgate)
> 
> test_check("staRgate")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 46 ]
> 
> proc.time()
   user  system elapsed 
  6.220   0.187   6.394