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### Running command:
###
###   /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:JohnsonKinaseData.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings JohnsonKinaseData_1.0.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.19-data-experiment/meat/JohnsonKinaseData.Rcheck’
* using R version 4.4.1 (2024-06-14)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
    GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
* running under: Ubuntu 22.04.5 LTS
* using session charset: UTF-8
* checking for file ‘JohnsonKinaseData/DESCRIPTION’ ... OK
* this is package ‘JohnsonKinaseData’ 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 ‘JohnsonKinaseData’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
License stub is invalid DCF.
* 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 whether startup messages can be suppressed ... 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
getKinasePWM : <anonymous>: no visible binding for global variable
  ‘Matrix’
getKinasePWM : <anonymous>: no visible binding for global variable
  ‘Score’
getKinasePWM : <anonymous>: no visible binding for global variable ‘AA’
processPhosphopeptides: no visible binding for global variable
  ‘modified’
processPhosphopeptides: no visible binding for global variable ‘hits’
processPhosphopeptides: no visible binding for global variable
  ‘center2’
processPhosphopeptides: no visible binding for global variable
  ‘center1’
processPhosphopeptides: no visible binding for global variable
  ‘is_lower’
processPhosphopeptides: no visible binding for global variable ‘left’
processPhosphopeptides: no visible binding for global variable ‘right’
processPhosphopeptides: no visible binding for global variable
  ‘processed’
processPhosphopeptides: no visible binding for global variable
  ‘acceptor’
Undefined global functions or variables:
  AA Matrix Score acceptor center1 center2 hits is_lower left modified
  processed right
* 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
getBackgroundScores 111.706  5.520 117.771
getKinaseAnnotation   7.400  1.917  10.294
* 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: 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.19-data-experiment/meat/JohnsonKinaseData.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD INSTALL JohnsonKinaseData
###
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* installing to library ‘/home/biocbuild/bbs-3.19-bioc/R/site-library’
* installing *source* package ‘JohnsonKinaseData’ ...
** 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 (JohnsonKinaseData)

R version 4.4.1 (2024-06-14) -- "Race for Your Life"
Copyright (C) 2024 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(JohnsonKinaseData)
> 
> test_check("JohnsonKinaseData")
see ?JohnsonKinaseData and browseVignettes('JohnsonKinaseData') for documentation
loading from cache
see ?JohnsonKinaseData and browseVignettes('JohnsonKinaseData') for documentation
loading from cache
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 3 ]
> 
> proc.time()
   user  system elapsed 
 12.683   0.625  14.828