##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:barbieQ.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings barbieQ_0.99.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/barbieQ.Rcheck’
* using R version 4.5.0 RC (2025-04-04 r88126)
* 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 ‘barbieQ/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘barbieQ’ version ‘0.99.1’
* 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 ‘barbieQ’ can be installed ... OK
* checking installed package size ... INFO
  installed size is  5.7Mb
  sub-directories of 1Mb or more:
    data      2.6Mb
    extdata   2.9Mb
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... NOTE
File
  LICENSE
is not mentioned in the DESCRIPTION file.
* 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
createBarbieQ: no visible global function definition for ‘is’
extractBarcodePairs: no visible global function definition for ‘is’
extractSampleMetadataAndPrimaryFactor: no visible global function
  definition for ‘is’
plotBarcodeMA: no visible binding for global variable ‘Amean’
plotBarcodeMA: no visible binding for global variable ‘meanDiff’
plotBarcodeMA: no visible binding for global variable ‘tendencyTo’
plotBarcodeMA: no visible binding for global variable ‘totalOcc’
plotBarcodeMA: no visible binding for global variable ‘logOR’
plotBarcodePValue: no visible binding for global variable ‘adj.P.Val’
plotBarcodePValue: no visible binding for global variable ‘tendencyTo’
plotBarcodePairCorrelation: no visible binding for global variable
  ‘coefficient’
plotBarcodePairCorrelation: no visible binding for global variable
  ‘count’
plotBarcodePairCorrelation: no visible binding for global variable
  ‘..y..’
plotBarcodePareto: no visible binding for global variable ‘group’
plotBarcodePareto: no visible binding for global variable ‘value’
plotBarcodePareto: no visible binding for global variable ‘id’
plotBarcodeSankey: no visible binding for global variable ‘category’
plotBarcodeSankey: no visible binding for global variable ‘value’
plotBarcodeSankey: no visible binding for global variable ‘variable’
plotSamplePairCorrelation: no visible binding for global variable
  ‘rowNumber’
plotSignifBarcodeProportion: no visible binding for global variable
  ‘tendencyTo’
plotSignifBarcodeProportion: no visible global function definition for
  ‘everything’
plotSignifBarcodeProportion: no visible binding for global variable
  ‘sampleGroup’
plotSignifBarcodeProportion: no visible binding for global variable
  ‘id’
plotSignifBarcodeProportion: no visible binding for global variable
  ‘mid_point’
Undefined global functions or variables:
  ..y.. Amean adj.P.Val category coefficient count everything group id
  is logOR meanDiff mid_point rowNumber sampleGroup tendencyTo totalOcc
  value variable
Consider adding
  importFrom("methods", "is")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... 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: 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.21-bioc/meat/barbieQ.Rcheck/00check.log’
for details.

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


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library’
* installing *source* package ‘barbieQ’ ...
** this is package ‘barbieQ’ version ‘0.99.1’
** using staged installation
** R
** data
** 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 (barbieQ)

R version 4.5.0 RC (2025-04-04 r88126) -- "How About a Twenty-Six"
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(barbieQ)
> 
> test_check("barbieQ")
sample names set up in line with `object`
continuing with missing `factorColors`.
processing Barcode pairwise pearson correlation.
Barcode names of `preDefinedCluster` set up in line with `barbieQ`.
processing Barcode pairwise pearson correlation.
processing Barcode pairwise pearson correlation.
sample names set up in line with `object`
continuing with missing `factorColors`.
processing Barcode pairwise pearson correlation.
Barcode names of `preDefinedCluster` set up in line with `barbieQ`.
processing Barcode pairwise pearson correlation.
sample names set up in line with `object`
continuing with missing `factorColors`.
processing Barcode pairwise pearson correlation.
identified 0 clusters, including 0 Barcodes.
Barcode names of `preDefinedCluster` set up in line with `barbieQ`.
processing Barcode pairwise pearson correlation.
identified 1 clusters, including 10 Barcodes.
Barcode names of `preDefinedCluster` set up in line with `barbieQ`.
processing Barcode pairwise pearson correlation.
sample names set up in line with `object`
continuing with missing `factorColors`.
sample names set up in line with `object`
continuing with missing `factorColors`.
sample names set up in line with `object`
sample names set up in line with `object`
inheriting `assay`, `colData`, `roweData` and `metadata`. Other slots including `proportion`, `CPM`, `occurrence` and `rank` will be recalculated based on `assay`.
sample names set up in line with `object`
inheriting `assay`, `colData`, `roweData` and `metadata`. Other slots including `proportion`, `CPM`, `occurrence` and `rank` will be recalculated based on `assay`.
sample names set up in line with `object`
inheriting `assay`, `colData`, `roweData` and `metadata`. Other slots including `proportion`, `CPM`, `occurrence` and `rank` will be recalculated based on `assay`.
sample names set up in line with `object`
inheriting `assay`, `colData`, `roweData` and `metadata`. Other slots including `proportion`, `CPM`, `occurrence` and `rank` will be recalculated based on `assay`.
sample names set up in line with `object`
attempting to convert first column as Barcode IDs.
treating first column as barcode IDs; column number -1
sample names set up in line with `object`
continuing with missing `factorColors`.
setting Treat as the primary factor in `sampleMetadata`.
sample names set up in line with `object`
setting Treat as the primary factor in `sampleMetadata`.
setting Treat as the primary factor in `sampleMetadata`.
setting Treat as the primary factor in `sampleMetadata`.
setting Treat as the primary factor in `sampleMetadata`.
setting Treat as the primary factor in `sampleMetadata`.
sample names set up in line with `object`
sample names set up in line with `object`
sample names set up in line with `object`
sample names set up in line with `object`
continuing with missing `factorColors`.
setting Treat as the primary factor in `sampleMetadata`.
setting up contrastFormula: Treatdrug - Treatctrl
no block specified, so there are no duplicate measurements.
sample names set up in line with `object`
continuing with missing `factorColors`.
setting Treat as the primary factor in `sampleMetadata`.
setting up contrastFormula: Treatdrug - Treatctrl
no block specified, so there are no duplicate measurements.
setting Treat as the primary factor in `sampleMetadata`.
setting up contrastFormula: Treatdrug - Treatctrl
sample names set up in line with `object`
continuing with missing `factorColors`.
setting Treat as the primary factor in `sampleMetadata`.
setting up contrastFormula: Treatdrug - Treatctrl
no block specified, so there are no duplicate measurements.
setting testingBarcode as the primary factor in `sampleMetadata`.
sample names set up in line with `object`
setting Treat as the primary factor in `sampleMetadata`.
displaying pearson correlation coefficient between samples on Barcode log2 CPM+1.
setting Treat as the primary factor in `sampleMetadata`.
displaying pearson correlation coefficient between samples on Barcode log2 CPM+1.
sample names set up in line with `object`
continuing with missing `factorColors`.
setting Treat as the primary factor in `sampleMetadata`.
setting up contrastFormula: Treatdrug - Treatctrl
no block specified, so there are no duplicate measurements.
sample names set up in line with `object`
sample names set up in line with `object`
sample names set up in line with `object`
sample names set up in line with `object`
continuing with missing `factorColors`.
Consensus correlation of Barcode proportion within sample duplicates: -0.043317533893066
Consensus correlation of Barcode proportion within sample duplicates: -0.043317533893066
Consensus correlation of Barcode proportion within sample duplicates: -0.00502352679952019
sample names set up in line with `object`
continuing with missing `factorColors`.
sample names set up in line with `object`
continuing with missing `factorColors`.
setting Treat as the primary factor in `sampleMetadata`.
setting up contrastFormula: Treatdrug - Treatctrl
no block specified, so there are no duplicate measurements.
setting Treat as the primary factor in `sampleMetadata`.
setting up contrastFormula: Treatdrug - Treatctrl
no block specified, so there are no duplicate measurements.
setting Treat as the primary factor in `sampleMetadata`.
setting up contrastFormula: Treatdrug - Treatctrl
no block specified, so there are no duplicate measurements.
setting Treat as the primary factor in `sampleMetadata`.
no block specified, so there are no duplicate measurements.
setting Treat as the primary factor in `sampleMetadata`.
no block specified, so there are no duplicate measurements.
setting Treat as the primary factor in `sampleMetadata`.
no block specified, so there are no duplicate measurements.
setting Treat as the primary factor in `sampleMetadata`.
no block specified, so there are no duplicate measurements.
setting Treat as the primary factor in `sampleMetadata`.
no block specified, so there are no duplicate measurements.
setting Treat as the primary factor in `sampleMetadata`.
no block specified, so there are no duplicate measurements.
setting Treat as the primary factor in `sampleMetadata`.
no block specified, so there are no duplicate measurements.
setting Time as the primary factor in `sampleMetadata`.
setting up contrastFormula: Time
no block specified, so there are no duplicate measurements.
setting Time as the primary factor in `sampleMetadata`.
setting up contrastFormula: Time
no block specified, so there are no duplicate measurements.
setting Time as the primary factor in `sampleMetadata`.
setting up contrastFormula: Time
setting Time as the primary factor in `sampleMetadata`.
setting up contrastFormula: Time
binding `sampleGroup` to `sampleMetadata`, set up as primary factor in `sampleMetadata`.
deleting 1 nested factor(s) because `designMatrix` must be full rank.
setting up contrastFormula: sampleGroup
no block specified, so there are no duplicate measurements.
setting Treat as the primary factor in `sampleMetadata`.
setting up contrastFormula: Treat2 - Treat1
no block specified, so there are no duplicate measurements.
[ FAIL 0 | WARN 5 | SKIP 0 | PASS 94 ]

[ FAIL 0 | WARN 5 | SKIP 0 | PASS 94 ]
> 
> proc.time()
   user  system elapsed 
  7.696   0.313   8.171