##############################################################################
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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:GDCRNATools.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings GDCRNATools_1.26.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/GDCRNATools.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 ‘GDCRNATools/DESCRIPTION’ ... OK
* this is package ‘GDCRNATools’ version ‘1.26.0’
* 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 ‘GDCRNATools’ 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 ... 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
deAnalysislimma: warning in topTable(fit2, coef = 1, n = Inf): partial
  argument match of 'n' to 'number'
gdcDEAnalysis: warning in topTable(fit2, coef = 1, n = Inf): partial
  argument match of 'n' to 'number'
cleanMirFun: no visible global function definition for ‘read.table’
cleanMirFun: no visible global function definition for ‘aggregate’
downloadClientFun: no visible global function definition for
  ‘download.file’
downloadClientFun: no visible global function definition for ‘unzip’
enrichBarPlotFun: no visible binding for global variable ‘Terms’
enrichBarPlotFun: no visible binding for global variable ‘FDR’
enrichBarPlotFun: no visible binding for global variable ‘Category’
enrichBubblePlotFun: no visible binding for global variable ‘Terms’
enrichBubblePlotFun: no visible binding for global variable
  ‘foldEnrichment’
enrichBubblePlotFun: no visible binding for global variable ‘FDR’
enrichBubblePlotFun: no visible binding for global variable ‘Counts’
gdcBarPlot: no visible binding for global variable ‘Regulation’
gdcClinicalDownload: no visible global function definition for
  ‘read.table’
gdcClinicalDownload: no visible global function definition for
  ‘write.table’
gdcCorPlot: no visible global function definition for ‘cor.test’
gdcDEAnalysis: no visible global function definition for ‘model.matrix’
gdcDEAnalysis: no visible global function definition for ‘p.adjust’
gdcGetURL: no visible global function definition for ‘URLencode’
gdcKMPlot: no visible global function definition for ‘pchisq’
gdcKMPlot: no visible global function definition for ‘qnorm’
gdcRNADownload: no visible global function definition for ‘read.table’
gdcRNADownload: no visible global function definition for ‘write.table’
gdcRNAMerge : <anonymous>: no visible global function definition for
  ‘read.table’
gdcRNAMerge: no visible global function definition for ‘read.table’
gdcRNAMerge : <anonymous>: no visible global function definition for
  ‘read.delim’
gdcRNAMerge: no visible global function definition for ‘read.delim’
hyperTestFun: no visible global function definition for ‘phyper’
kmTestFun: no visible global function definition for ‘pchisq’
kmTestFun: no visible global function definition for ‘qnorm’
manifestDownloadFun: no visible global function definition for
  ‘read.table’
mirCorTestFun: no visible global function definition for ‘cor.test’
multiRegFun: no visible global function definition for ‘cor.test’
Undefined global functions or variables:
  Category Counts FDR Regulation Terms URLencode aggregate cor.test
  download.file foldEnrichment model.matrix p.adjust pchisq phyper
  qnorm read.delim read.table unzip write.table
Consider adding
  importFrom("stats", "aggregate", "cor.test", "model.matrix",
             "p.adjust", "pchisq", "phyper", "qnorm")
  importFrom("utils", "URLencode", "download.file", "read.delim",
             "read.table", "unzip", "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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking R/sysdata.rda ... NOTE
  
  Note: significantly better compression could be obtained
        by using R CMD build --resave-data
              old_size new_size compress
  sysdata.rda    3.2Mb    1.6Mb    bzip2
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                     user system elapsed
gdcParseMetadata    0.158  0.008   6.567
gdcRNAMerge         0.155  0.008   7.067
gdcFilterSampleType 0.155  0.006   5.829
* 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/GDCRNATools.Rcheck/00check.log’
for details.

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

R version 4.4.2 (2024-10-31) -- "Pile of Leaves"
Copyright (C) 2024 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.

> library(testthat)
> library(GDCRNATools)


##############################################################################
Pathview is an open source software package distributed under GNU General
Public License version 3 (GPLv3). Details of GPLv3 is available at
http://www.gnu.org/licenses/gpl-3.0.html. Particullary, users are required to
formally cite the original Pathview paper (not just mention it) in publications
or products. For details, do citation("pathview") within R.

The pathview downloads and uses KEGG data. Non-academic uses may require a KEGG
license agreement (details at http://www.kegg.jp/kegg/legal.html).
##############################################################################
> 
> test_check("GDCRNATools")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 1 ]
> 
> proc.time()
   user  system elapsed 
 15.507   0.757  18.911