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### Running command:
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###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:cnvGSA.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings cnvGSA_1.48.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.19-bioc-mac-arm64/meat/cnvGSA.Rcheck’
* using R version 4.4.0 (2024-04-24)
* 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 13.6.5
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘cnvGSA/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘cnvGSA’ version ‘1.48.0’
* 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 ‘cnvGSA’ 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 ... NOTE
Packages in Depends field not imported from:
  ‘brglm’ ‘doParallel’ ‘foreach’ ‘splitstackshape’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
cnvGSAgsTables: no visible global function definition for ‘detectCores’
cnvGSAgsTables: no visible binding for global variable ‘SID’
cnvGSAgsTables: no visible binding for global variable ‘geneID_TYPE’
cnvGSAgsTables: no visible binding for global variable ‘SubjCnvKey’
cnvGSAgsTables: no visible global function definition for
  ‘registerDoParallel’
cnvGSAgsTables: no visible global function definition for ‘%dopar%’
cnvGSAgsTables: no visible global function definition for ‘foreach’
cnvGSAgsTables: no visible binding for global variable ‘i’
cnvGSAgsTables: no visible binding for global variable ‘CHR’
cnvGSAgsTables: no visible binding for global variable ‘BP1’
cnvGSAgsTables: no visible binding for global variable ‘BP2’
cnvGSAgsTables: no visible binding for global variable ‘TYPE’
cnvGSAgsTables: no visible binding for global variable ‘geneID’
cnvGSAgsTables: no visible binding for global variable ‘Symbol’
cnvGSAgsTables: no visible binding for global variable ‘Symbol_TYPE’
cnvGSAgsTables: no visible binding for global variable ‘GsKey’
cnvGSAlogRegTest: no visible binding for global variable ‘GsID’
cnvGSAlogRegTest: no visible binding for global variable ‘GsKey’
cnvGSAlogRegTest: no visible binding for global variable ‘OlpKL_SID’
cnvGSAlogRegTest : f.testGLM_wrap: no visible binding for global
  variable ‘Condition’
cnvGSAlogRegTest : f.testGLM_wrap: no visible global function
  definition for ‘detectCores’
cnvGSAlogRegTest : f.testGLM_wrap: no visible global function
  definition for ‘registerDoParallel’
cnvGSAlogRegTest : f.testGLM_wrap: no visible global function
  definition for ‘%dopar%’
cnvGSAlogRegTest : f.testGLM_wrap: no visible global function
  definition for ‘foreach’
cnvGSAlogRegTest : f.testGLM_wrap: no visible binding for global
  variable ‘i’
cnvGSAlogRegTest : f.testGLM_unit: no visible global function
  definition for ‘glm’
cnvGSAlogRegTest : f.testGLM_unit: no visible global function
  definition for ‘as.formula’
cnvGSAlogRegTest : f.testGLM_unit: no visible global function
  definition for ‘binomial’
cnvGSAlogRegTest : f.testGLM_unit: no visible binding for global
  variable ‘logit’
cnvGSAlogRegTest : f.testGLM_unit: no visible global function
  definition for ‘anova’
cnvGSAlogRegTest: no visible global function definition for ‘p.adjust’
cnvGSAlogRegTest: no visible global function definition for
  ‘write.table’
f.enrProcess: no visible global function definition for ‘write.table’
f.makeViz: no visible global function definition for ‘write.table’
f.makeViz: no visible global function definition for ‘pdf’
f.makeViz: no visible global function definition for ‘par’
f.makeViz: no visible global function definition for ‘barplot’
f.makeViz: no visible global function definition for ‘dev.off’
f.readConfig: no visible global function definition for ‘read.table’
f.readData: no visible global function definition for ‘read.table’
f.readData: no visible binding for global variable ‘IID’
f.readData: no visible binding for global variable ‘FID’
f.readData: no visible binding for global variable ‘AFF’
f.readData: no visible binding for global variable ‘SID’
f.readData: no visible binding for global variable ‘gs_all.ls’
f.readData: no visible binding for global variable ‘gsid2name.chv’
f.readData: no visible global function definition for ‘GRanges’
f.readData: no visible global function definition for ‘Rle’
f.readData: no visible global function definition for ‘IRanges’
f.readData: no visible global function definition for ‘strand’
f.readData: no visible global function definition for ‘start’
f.readData: no visible global function definition for ‘ranges’
f.readData: no visible global function definition for ‘end’
f.readData: no visible global function definition for ‘mcols’
f.readData: no visible binding for global variable ‘OlpKL_CNV’
f.readData: no visible global function definition for ‘stack’
f.readData: no visible binding for global variable ‘geneID_type’
f.readData: no visible binding for global variable ‘CnvKey’
f.readData: no visible binding for global variable ‘OlpKL_SID’
f.readData: no visible binding for global variable ‘geneID_TYPE’
f.readData: no visible binding for global variable ‘SubjCnvKey’
f.readData: no visible binding for global variable ‘GsKey’
f.readData: no visible binding for global variable ‘GsID’
f.readData: no visible binding for global variable ‘GsName’
f.readData: no visible global function definition for ‘cSplit’
f.readData: no visible binding for global variable ‘Symbol’
f.readData: no visible global function definition for ‘aggregate’
Undefined global functions or variables:
  %dopar% AFF aggregate anova as.formula barplot binomial BP1 BP2 CHR
  CnvKey Condition cSplit detectCores dev.off end FID foreach geneID
  geneID_type geneID_TYPE glm GRanges gs_all.ls GsID gsid2name.chv
  GsKey GsName i IID IRanges logit mcols OlpKL_CNV OlpKL_SID p.adjust
  par pdf ranges read.table registerDoParallel Rle SID stack start
  strand SubjCnvKey Symbol Symbol_TYPE TYPE write.table
Consider adding
  importFrom("graphics", "barplot", "par")
  importFrom("grDevices", "dev.off", "pdf")
  importFrom("stats", "aggregate", "anova", "as.formula", "binomial",
             "end", "glm", "p.adjust", "start")
  importFrom("utils", "read.table", "stack", "write.table")
to your NAMESPACE file.
* 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 installed files from ‘inst/doc’ ... 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: 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.19-bioc-mac-arm64/meat/cnvGSA.Rcheck/00check.log’
for details.

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### Running command:
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###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL cnvGSA
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library’
* installing *source* package ‘cnvGSA’ ...
** using staged installation
** R
** 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 (cnvGSA)