############################################################################## ############################################################################## ### ### Running command: ### ### C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:lumi.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings lumi_2.44.0.tar.gz ### ############################################################################## ############################################################################## * using log directory 'C:/Users/biocbuild/bbs-3.13-bioc/meat/lumi.Rcheck' * using R version 4.1.1 (2021-08-10) * using platform: x86_64-w64-mingw32 (64-bit) * using session charset: ISO8859-1 * using option '--no-vignettes' * checking for file 'lumi/DESCRIPTION' ... OK * checking extension type ... Package * this is package 'lumi' version '2.44.0' * 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 whether package 'lumi' can be installed ... OK * checking installed package size ... NOTE installed size is 5.6Mb sub-directories of 1Mb or more: R 1.0Mb data 3.6Mb * checking package 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 * loading checks for arch 'i386' ** 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 * loading checks for arch 'x64' ** 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 ... WARNING '::' or ':::' imports not declared from: 'IRanges' 'bigmemoryExtras' * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... OK * checking Rd files ... OK * checking Rd metadata ... OK * checking Rd cross-references ... WARNING Unknown package 'bigmemoryExtras' in Rd xrefs Missing link or links in documentation object 'lumiN.Rd': '[vsn]{vsn}' See section 'Cross-references' in the 'Writing R Extensions' manual. * 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 files in 'vignettes' ... WARNING Files in the 'vignettes' directory but no files in 'inst/doc': 'IlluminaAnnotation.R', 'IlluminaAnnotation.pdf', 'lumi.R', 'lumi.pdf', 'lumi_VST_evaluation.R', 'lumi_VST_evaluation.pdf', 'methylationAnalysis.R', 'methylationAnalysis.pdf' Package has no Sweave vignette sources and no VignetteBuilder field. * checking examples ... ** running examples for arch 'i386' ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed lumiMethyStatus 44.75 0.36 45.10 getChipInfo 5.70 0.31 14.64 ** running examples for arch 'x64' ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed lumiMethyStatus 41.18 0.08 41.25 MAplot-methods 5.02 0.06 5.08 * checking PDF version of manual ... OK * DONE Status: 3 WARNINGs, 1 NOTE See 'C:/Users/biocbuild/bbs-3.13-bioc/meat/lumi.Rcheck/00check.log' for details.