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### Running command:
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###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:CNViz.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings CNViz_1.14.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/CNViz.Rcheck’
* using R version 4.4.1 (2024-06-14)
* 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 ‘CNViz/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘CNViz’ version ‘1.14.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
  cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
 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 ‘CNViz’ 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
launchCNViz: no visible global function definition for 'is'
launchCNViz: no visible binding for global variable 'gene'
launchCNViz: no visible binding for global variable 'mutation_id'
launchCNViz: no visible binding for global variable 'ref'
launchCNViz: no visible binding for global variable 'alt'
launchCNViz: no visible binding for global variable 'sampleNames'
launchCNViz : server: no visible binding for global variable 'gene'
launchCNViz : server: no visible binding for global variable 'weight'
launchCNViz : server: no visible binding for global variable
  'mean_log2'
launchCNViz : server: no visible binding for global variable 's'
launchCNViz : server: no visible binding for global variable 'e'
launchCNViz : server: no visible binding for global variable 'cn'
launchCNViz : server: no visible binding for global variable
  'total_weight'
launchCNViz : server: no visible binding for global variable 'loh'
launchCNViz : server: no visible binding for global variable 'chrom'
launchCNViz : server: no visible binding for global variable
  'chr1_subplot'
launchCNViz : server: no visible binding for global variable
  'chr2_subplot'
launchCNViz : server: no visible binding for global variable
  'chr3_subplot'
launchCNViz : server: no visible binding for global variable
  'chr4_subplot'
launchCNViz : server: no visible binding for global variable
  'chr5_subplot'
launchCNViz : server: no visible binding for global variable
  'chr6_subplot'
launchCNViz : server: no visible binding for global variable
  'chr7_subplot'
launchCNViz : server: no visible binding for global variable
  'chr8_subplot'
launchCNViz : server: no visible binding for global variable
  'chr9_subplot'
launchCNViz : server: no visible binding for global variable
  'chr10_subplot'
launchCNViz : server: no visible binding for global variable
  'chr11_subplot'
launchCNViz : server: no visible binding for global variable
  'chr12_subplot'
launchCNViz : server: no visible binding for global variable
  'chr13_subplot'
launchCNViz : server: no visible binding for global variable
  'chr14_subplot'
launchCNViz : server: no visible binding for global variable
  'chr15_subplot'
launchCNViz : server: no visible binding for global variable
  'chr16_subplot'
launchCNViz : server: no visible binding for global variable
  'chr17_subplot'
launchCNViz : server: no visible binding for global variable
  'chr18_subplot'
launchCNViz : server: no visible binding for global variable
  'chr19_subplot'
launchCNViz : server: no visible binding for global variable
  'chr20_subplot'
launchCNViz : server: no visible binding for global variable
  'chr21_subplot'
launchCNViz : server: no visible binding for global variable
  'chr22_subplot'
launchCNViz : server: no visible binding for global variable
  'chrX_subplot'
launchCNViz : server: no visible binding for global variable
  'chrY_subplot'
launchCNViz : server: no visible binding for global variable
  'study_name'
launchCNViz : server: no visible binding for global variable
  'hugoGeneSymbol'
launchCNViz : server: no visible binding for global variable 'Gain'
launchCNViz : server: no visible binding for global variable
  'Amplification'
launchCNViz : server: no visible binding for global variable
  'ShallowDeletion'
launchCNViz : server: no visible binding for global variable
  'DeepDeletion'
launchCNViz : server : <anonymous>: no visible binding for global
  variable 'loh'
Undefined global functions or variables:
  Amplification DeepDeletion Gain ShallowDeletion alt chr10_subplot
  chr11_subplot chr12_subplot chr13_subplot chr14_subplot chr15_subplot
  chr16_subplot chr17_subplot chr18_subplot chr19_subplot chr1_subplot
  chr20_subplot chr21_subplot chr22_subplot chr2_subplot chr3_subplot
  chr4_subplot chr5_subplot chr6_subplot chr7_subplot chr8_subplot
  chr9_subplot chrX_subplot chrY_subplot chrom cn e gene hugoGeneSymbol
  is loh mean_log2 mutation_id ref s sampleNames study_name
  total_weight weight
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 R/sysdata.rda ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... 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-3.20-bioc/meat/CNViz.Rcheck/00check.log’
for details.

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### Running command:
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###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL CNViz
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library’
* installing *source* package ‘CNViz’ ...
** using staged installation
** R
** data
** 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 (CNViz)