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###
### 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_1.1.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/immunogenViewer.Rcheck’
* using R Under development (unstable) (2025-01-20 r87609)
* using platform: aarch64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Ventura 13.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘immunogenViewer/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘immunogenViewer’ version ‘1.1.0’
* 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 ‘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 ... ERROR
Running examples in ‘immunogenViewer-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: addImmunogen
> ### Title: Add an immunogen to the Protein DataFrame
> ### Aliases: addImmunogen
> 
> ### ** Examples
> 
> proteinDF <- getProteinFeatures("P55087")
Error in accessPredictProtein(uniprot) : 
  Error fetching data from PredictProtein for P55087
Calls: getProteinFeatures -> accessPredictProtein
Execution halted
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 ERROR
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
   1. ├─testthat::expect_s3_class(getProteinFeatures("P55087"), "data.frame") at test-getProteinFeatures.R:8:3
   2. │ └─testthat::quasi_label(enquo(object), arg = "object")
   3. │   └─rlang::eval_bare(expr, quo_get_env(quo))
   4. └─immunogenViewer::getProteinFeatures("P55087")
   5.   └─immunogenViewer:::accessPredictProtein(uniprot)
  ── Error ('test-plotImmunogen.R:2:1'): (code run outside of `test_that()`) ─────
  Error in `accessPredictProtein(uniprot)`: Error fetching data from PredictProtein for P55087
  Backtrace:
      ▆
   1. └─immunogenViewer::getProteinFeatures("P55087") at test-plotImmunogen.R:2:1
   2.   └─immunogenViewer:::accessPredictProtein(uniprot)
  
  [ FAIL 4 | WARN 0 | SKIP 0 | PASS 16 ]
  Error: Test failures
  Execution halted
* 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: 2 ERRORs, 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.21-bioc/meat/immunogenViewer.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL immunogenViewer
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library’
* installing *source* package ‘immunogenViewer’ ...
** this is package ‘immunogenViewer’ version ‘1.1.0’
** 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 Under development (unstable) (2025-01-20 r87609) -- "Unsuffered Consequences"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: aarch64-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")
[ FAIL 4 | WARN 0 | SKIP 0 | PASS 16 ]

══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-addImmunogen.R:2:1'): (code run outside of `test_that()`) ──────
Error in `accessPredictProtein(uniprot)`: Error fetching data from PredictProtein for P55087
Backtrace:
    ▆
 1. └─immunogenViewer::getProteinFeatures("P55087") at test-addImmunogen.R:2:1
 2.   └─immunogenViewer:::accessPredictProtein(uniprot)
── Error ('test-evaluateImmunogen.R:2:1'): (code run outside of `test_that()`) ──
Error in `accessPredictProtein(uniprot)`: Error fetching data from PredictProtein for P55087
Backtrace:
    ▆
 1. └─immunogenViewer::getProteinFeatures("P55087") at test-evaluateImmunogen.R:2:1
 2.   └─immunogenViewer:::accessPredictProtein(uniprot)
── Error ('test-getProteinFeatures.R:8:3'): Dataframe is returned if successul ──
Error in `accessPredictProtein(uniprot)`: Error fetching data from PredictProtein for P55087
Backtrace:
    ▆
 1. ├─testthat::expect_s3_class(getProteinFeatures("P55087"), "data.frame") at test-getProteinFeatures.R:8:3
 2. │ └─testthat::quasi_label(enquo(object), arg = "object")
 3. │   └─rlang::eval_bare(expr, quo_get_env(quo))
 4. └─immunogenViewer::getProteinFeatures("P55087")
 5.   └─immunogenViewer:::accessPredictProtein(uniprot)
── Error ('test-plotImmunogen.R:2:1'): (code run outside of `test_that()`) ─────
Error in `accessPredictProtein(uniprot)`: Error fetching data from PredictProtein for P55087
Backtrace:
    ▆
 1. └─immunogenViewer::getProteinFeatures("P55087") at test-plotImmunogen.R:2:1
 2.   └─immunogenViewer:::accessPredictProtein(uniprot)

[ FAIL 4 | WARN 0 | SKIP 0 | PASS 16 ]
Error: Test failures
Execution halted