##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:RTCGA.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings RTCGA_1.32.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.18-bioc/meat/RTCGA.Rcheck’
* using R version 4.3.2 Patched (2023-11-01 r85457)
* using platform: x86_64-apple-darwin20 (64-bit)
* R was compiled by
    Apple clang version 14.0.3 (clang-1403.0.22.14.1)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘RTCGA/DESCRIPTION’ ... OK
* this is package ‘RTCGA’ version ‘1.32.0’
* 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 ‘RTCGA’ 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 R 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 startup messages can be suppressed ... 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
availableDates: no visible binding for global variable ‘.’
downloadTCGA: no visible binding for global variable ‘.’
ggbiplot: no visible binding for global variable ‘xvar’
ggbiplot: no visible binding for global variable ‘yvar’
ggbiplot: no visible global function definition for ‘muted’
ggbiplot: no visible binding for global variable ‘varname’
ggbiplot: no visible binding for global variable ‘angle’
ggbiplot: no visible binding for global variable ‘hjust’
read.mutations: no visible binding for global variable ‘.’
read.rnaseq: no visible binding for global variable ‘.’
survivalTCGA: no visible binding for global variable ‘times’
whichDateToUse: no visible binding for global variable ‘.’
Undefined global functions or variables:
  . angle hjust muted times varname xvar yvar
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... NOTE
Unknown packages ‘RTCGA.rnaseq.20160128’, ‘RTCGA.clinical.20160128’, ‘RTCGA.mutations.20160128’, ‘RTCGA.CNV.20160128’, ‘RTCGA.RPPA.20160128’, ‘RTCGA.mRNA.20160128’, ‘RTCGA.miRNASeq.20160128’, ‘RTCGA.methylation.20160128’ in Rd xrefs
* 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                  user system elapsed
boxplotTCGA     17.343  1.593  19.126
expressionsTCGA  9.766  0.743  10.643
heatmapTCGA      7.325  0.515   7.926
kmTCGA           6.871  0.171   7.146
survivalTCGA     6.341  0.137   6.555
checkTCGA        0.256  0.023   6.609
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... 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-3.18-bioc/meat/RTCGA.Rcheck/00check.log’
for details.