############################################################################## ############################################################################## ### ### 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.