##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:VDJdive.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings VDJdive_1.8.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/VDJdive.Rcheck’
* using R version 4.4.2 (2024-10-31)
* 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 12.7.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘VDJdive/DESCRIPTION’ ... OK
* this is package ‘VDJdive’ version ‘1.8.0’
* 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 ‘VDJdive’ can be installed ... NOTE
Found the following notes/warnings:
  Non-staged installation was used
See ‘/Users/biocbuild/bbs-3.20-bioc/meat/VDJdive.Rcheck/00install.out’ for details.
* used C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
* used SDK: ‘MacOSX11.3.sdk’
* 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
abundanceVDJ,clonoStats: no visible binding for global variable ‘count’
abundanceVDJ,clonoStats: no visible binding for global variable ‘y’
barVDJ,Matrix: no visible binding for global variable ‘count’
boxVDJ,matrix: no visible binding for global variable ‘group’
boxVDJ,matrix: no visible binding for global variable ‘Diversity’
pieVDJ,Matrix: no visible binding for global variable ‘count’
scatterVDJ,matrix: no visible binding for global variable ‘clono’
scatterVDJ,matrix: no visible binding for global variable ‘normentropy’
scatterVDJ,matrix: no visible binding for global variable ‘sampleType’
Undefined global functions or variables:
  Diversity clono count group normentropy sampleType y
* checking Rd files ... NOTE
checkRd: (-1) clonoStats.Rd:98-102: Lost braces in \itemize; meant \describe ?
checkRd: (-1) clonoStats.Rd:103-105: Lost braces in \itemize; meant \describe ?
checkRd: (-1) clonoStats.Rd:106-107: Lost braces in \itemize; meant \describe ?
checkRd: (-1) clonoStats.Rd:108-111: Lost braces in \itemize; meant \describe ?
checkRd: (-1) clonoStats.Rd:112-114: Lost braces in \itemize; meant \describe ?
* 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 line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
              user system elapsed
runBreakaway 5.601  0.128   6.817
* 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: 4 NOTEs
See
  ‘/Users/biocbuild/bbs-3.20-bioc/meat/VDJdive.Rcheck/00check.log’
for details.