############################################################################## ############################################################################## ### ### 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_1.30.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/RTCGA.Rcheck’ * using R version 4.3.1 (2023-06-16) * using platform: aarch64-apple-darwin20 (64-bit) * 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 12.6.7 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘RTCGA/DESCRIPTION’ ... OK * this is package ‘RTCGA’ version ‘1.30.0’ * 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 16.701 0.865 26.907 expressionsTCGA 11.467 0.576 18.115 heatmapTCGA 7.030 0.255 10.748 kmTCGA 6.897 0.110 10.698 survivalTCGA 5.640 0.064 8.739 mutationsTCGA 3.538 0.065 5.532 checkTCGA 0.328 0.036 10.786 * 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-3.17-bioc-mac-arm64/meat/RTCGA.Rcheck/00check.log’ for details.