##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:abseqR.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings abseqR_1.26.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/abseqR.Rcheck’
* using R version 4.5.1 RC (2025-06-05 r88288)
* using platform: x86_64-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 Monterey 12.7.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘abseqR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘abseqR’ version ‘1.26.0’
* 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 ‘abseqR’ 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
.aminoAcidBar: no visible binding for global variable ‘position’
.aminoAcidBar: no visible binding for global variable ‘proportion’
.aminoAcidBar: no visible binding for global variable ‘aa’
.boxPlot: no visible binding for global variable ‘x’
.boxPlot: no visible binding for global variable ‘y’
.cloneDistHist: no visible binding for global variable ‘prop’
.cloneDistHist: no visible binding for global variable ‘..count..’
.cloneDistMarginal: no visible binding for global variable ‘prop’
.cloneDistMarginal: no visible binding for global variable ‘..scaled..’
.hmFromMatrix: no visible binding for global variable ‘Var2’
.hmFromMatrix: no visible binding for global variable ‘Var1’
.hmFromMatrix: no visible binding for global variable ‘value’
.plotDist: no visible binding for global variable ‘x’
.plotDist: no visible binding for global variable ‘y’
.plotDuplication: no visible binding for global variable ‘x’
.plotDuplication: no visible binding for global variable ‘y’
.plotDuplication: no visible binding for global variable ‘region’
.plotRarefaction: no visible binding for global variable ‘x’
.plotRarefaction: no visible binding for global variable ‘y’
.plotRarefaction: no visible binding for global variable ‘region’
.plotRarefaction: no visible binding for global variable ‘ci’
.plotRarefaction: no visible binding for global variable ‘compound’
.plotRecapture: no visible binding for global variable ‘x’
.plotRecapture: no visible binding for global variable ‘y’
.plotRecapture: no visible binding for global variable ‘region’
.plotRecapture: no visible binding for global variable ‘ci’
.plotRecapture: no visible binding for global variable ‘compound’
.plotSpectratype: no visible binding for global variable ‘percent’
.productivityPlot: no visible binding for global variable ‘Percentage’
.productivityPlot: no visible binding for global variable ‘Reason’
.regionAnalysis: no visible binding for global variable ‘cdr3’
.regionAnalysis: no visible binding for global variable ‘value’
.regionAnalysis: no visible binding for global variable ‘variable’
.scatterPlot: no visible binding for global variable ‘Count.x’
.scatterPlot: no visible binding for global variable ‘Count.y’
.scatterPlotComplex: no visible binding for global variable ‘prop.x’
.scatterPlotComplex: no visible binding for global variable ‘prop.y’
.topNDist: no visible binding for global variable ‘normPerc’
.topNDist: no visible binding for global variable ‘Clonotype’
Undefined global functions or variables:
  ..count.. ..scaled.. Clonotype Count.x Count.y Percentage Reason Var1
  Var2 aa cdr3 ci compound normPerc percent position prop prop.x prop.y
  proportion region value variable x y
* 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 sizes of PDF files under ‘inst/doc’ ... 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-3.21-bioc/meat/abseqR.Rcheck/00check.log’
for details.

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


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library’
* installing *source* package ‘abseqR’ ...
** this is package ‘abseqR’ version ‘1.26.0’
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
*** copying figures
** 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 (abseqR)

R version 4.5.1 RC (2025-06-05 r88288) -- "Great Square Root"
Copyright (C) 2025 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.

> library(testthat)
> library(abseqR)
> 
> test_check("abseqR")
2025-10-13 23:52:33.183 R[90967:3851192] XType: com.apple.fonts is not accessible.
2025-10-13 23:52:33.184 R[90967:3851192] XType: XTFontStaticRegistry is enabled.
[ FAIL 0 | WARN 2 | SKIP 0 | PASS 30 ]

[ FAIL 0 | WARN 2 | SKIP 0 | PASS 30 ]
> 
> proc.time()
   user  system elapsed 
 98.344   2.270 101.927