############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:Risa.install-out.txt --library=F:\biocbuild\bbs-3.17-bioc\R\library --no-vignettes --timings Risa_1.41.0.tar.gz ### ############################################################################## ############################################################################## * using log directory 'F:/biocbuild/bbs-3.17-bioc-rtools43/meat/Risa.Rcheck' * using R Under development (unstable) (2022-12-25 r83502 ucrt) * using platform: x86_64-w64-mingw32 (64-bit) * R was compiled by gcc.exe (GCC) 10.4.0 GNU Fortran (GCC) 10.4.0 * running under: Windows Server x64 (build 20348) * using session charset: UTF-8 * using option '--no-vignettes' * checking for file 'Risa/DESCRIPTION' ... OK * this is package 'Risa' version '1.41.0' * 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 'Risa' 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 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 getPackagesInBiocView: no visible global function definition for 'data' readISAtabZip: no visible global function definition for 'unzip' suggestBiocPackage: no visible global function definition for 'read.csv' write.assay.file: no visible global function definition for 'write.table' write.investigation.file: no visible global function definition for 'write.table' write.study.file: no visible global function definition for 'write.table' initialize,ISATab: no visible global function definition for 'count.fields' initialize,ISATab: no visible global function definition for 'read.table' initialize,ISATab : : no visible global function definition for 'read.table' initialize,ISATab : : : no visible global function definition for 'read.table' initialize,ISATab: no visible global function definition for 'na.omit' Undefined global functions or variables: count.fields data na.omit read.csv read.table unzip write.table Consider adding importFrom("stats", "na.omit") importFrom("utils", "count.fields", "data", "read.csv", "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 sizes of PDF files under 'inst/doc' ... OK * checking files in 'vignettes' ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed processAssayXcmsSet.1factor 1.84 0.00 23.28 processAssayXcmsSet 0.66 0.08 22.68 * 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: 1 NOTE See 'F:/biocbuild/bbs-3.17-bioc-rtools43/meat/Risa.Rcheck/00check.log' for details.