##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:immunogenViewer.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings immunogenViewer_0.99.4.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/immunogenViewer.Rcheck’
* using R version 4.4.1 (2024-06-14)
* 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 12.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘immunogenViewer/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘immunogenViewer’ 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 ‘immunogenViewer’ 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
addImmunogensToPlot: no visible binding for global variable ‘xmin’
addImmunogensToPlot: no visible binding for global variable ‘xmax’
addImmunogensToPlot: no visible binding for global variable ‘ymin’
addImmunogensToPlot: no visible binding for global variable ‘ymax’
addImmunogensToPlot: no visible binding for global variable ‘x’
addImmunogensToPlot: no visible binding for global variable ‘y’
addImmunogensToPlot: no visible binding for global variable ‘label’
plotAccessibility: no visible binding for global variable
  ‘SolventAccessibility’
plotSecondaryStructure: no visible binding for global variable
  ‘SecondaryStructure’
plotSinglePositions: no visible binding for global variable ‘Location’
plotSinglePositions: no visible binding for global variable ‘y’
Undefined global functions or variables:
  Location SecondaryStructure SolventAccessibility label x xmax xmin y
  ymax ymin
* 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 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/immunogenViewer.Rcheck/00check.log’
for details.

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL immunogenViewer
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library’
* installing *source* package ‘immunogenViewer’ ...
** 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 (immunogenViewer)

R version 4.4.1 (2024-06-14) -- "Race for Your Life"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20

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(immunogenViewer)
> 
> test_check("immunogenViewer")
[1] "Immunogen name: A12"
[1] "Immunogen sequence: GHLFAINYTGASMNPARSFGPAVIMGNWENH (Residues 200 - 230)"
[1] "No immunogen specified, evaluating all immunogens."
[1] "Immunogen name: SecondaryStructure"
[1] "Immunogen sequence:  (Residues Inf - -Inf)"
[1] "Immunogen name: SolventAccessibility"
[1] "Immunogen sequence:  (Residues Inf - -Inf)"
[1] "Immunogen name: ProteinBinding"
[1] "Immunogen sequence: SGGHINNLTAGNYTGASMNPARS (Residues 92 - 217)"
[1] "Immunogen name: DisulfideBridge"
[1] "Immunogen sequence:  (Residues Inf - -Inf)"
[1] "Immunogen name: A12"
[1] "Immunogen sequence: GHLFAINYTGASMNPARSFGPAVIMGNWENH (Residues 200 - 230)"
[ FAIL 0 | WARN 6 | SKIP 0 | PASS 35 ]

[ FAIL 0 | WARN 6 | SKIP 0 | PASS 35 ]
> 
> proc.time()
   user  system elapsed 
 12.204   0.585  25.697