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### Running command:
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###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:CellBarcode.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings CellBarcode_1.12.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/CellBarcode.Rcheck’
* using R version 4.4.2 (2024-10-31)
* using platform: aarch64-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 Ventura 13.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘CellBarcode/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘CellBarcode’ version ‘1.12.0’
* 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 ‘CellBarcode’ can be installed ... OK
* used C++ compiler: ‘Apple clang version 15.0.0 (clang-1500.0.40.1)’
* 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
bc_extract_sc_fastq: no visible binding for global variable
  ‘cell_barcode’
bc_extract_sc_fastq: no visible binding for global variable ‘umi’
bc_extract_sc_fastq: no visible binding for global variable
  ‘barcode_seq’
process_sc_list: no visible binding for global variable ‘cell_barcode’
process_sc_list: no visible binding for global variable ‘umi’
process_sc_list: no visible binding for global variable ‘barcode_seq’
bc_2matrix,BarcodeObj: no visible binding for global variable
  ‘barcode_seq’
bc_cure_depth,BarcodeObj : <anonymous>: no visible binding for global
  variable ‘barcode_seq’
bc_cure_umi,BarcodeObj : <anonymous>: no visible binding for global
  variable ‘barcode_seq’
bc_cure_umi,BarcodeObj : <anonymous>: no visible binding for global
  variable ‘umi_seq’
bc_extract,data.frame: no visible binding for global variable ‘umi_seq’
bc_extract,data.frame: no visible binding for global variable
  ‘barcode_seq’
bc_plot_count,BarcodeObj: no visible binding for global variable
  ‘barcode_read_count’
bc_plot_count,BarcodeObj: no visible binding for global variable
  ‘raw_read_count’
bc_plot_count,BarcodeObj: no visible binding for global variable
  ‘umi_seq’
bc_plot_count,BarcodeObj: no visible binding for global variable
  ‘barcode_seq’
bc_plot_count,BarcodeObj: no visible binding for global variable
  ‘cell_barcode’
bc_plot_count,BarcodeObj: no visible binding for global variable ‘V1’
bc_plot_count,BarcodeObj: no visible binding for global variable ‘x’
bc_plot_seqQc,BarcodeQcSet: no visible binding for global variable
  ‘sample_name’
bc_subset,BarcodeObj : <anonymous>: no visible binding for global
  variable ‘barcode_seq’
Undefined global functions or variables:
  V1 barcode_read_count barcode_seq cell_barcode raw_read_count
  sample_name umi umi_seq x
* 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 line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... NOTE
Found the following Makefile(s) without a final LF:
  src/Makevars
Some ‘make’ programs ignore lines not ending in LF.
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking use of PKG_*FLAGS in Makefiles ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
* 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: 3 NOTEs
See
  ‘/Users/biocbuild/bbs-3.20-bioc/meat/CellBarcode.Rcheck/00check.log’
for details.