############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:maigesPack.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings --no-examples maigesPack_1.68.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/maigesPack.Rcheck’ * using R version 4.4.0 beta (2024-04-14 r86421) * using platform: x86_64-apple-darwin20 * 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 12.7.1 * using session charset: UTF-8 * using options ‘--no-examples --no-vignettes’ * checking for file ‘maigesPack/DESCRIPTION’ ... OK * this is package ‘maigesPack’ version ‘1.68.0’ * 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 ... NOTE Found the following hidden files and directories: .BBSoptions These were most likely included in error. See section ‘Package structure’ in the ‘Writing R Extensions’ manual. * checking for portable file names ... OK * checking for sufficient/correct file permissions ... OK * checking whether package ‘maigesPack’ can be installed ... OK * used C compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’ * used SDK: ‘MacOSX11.3.sdk’ * checking installed package size ... OK * checking package directory ... OK * checking ‘build’ directory ... OK * checking DESCRIPTION meta-information ... NOTE Malformed Description field: should contain one or more complete sentences. * checking top-level files ... OK * checking for left-over files ... OK * checking index information ... OK * checking package subdirectories ... OK * checking code 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 whether startup messages can be suppressed ... OK * checking dependencies in R code ... NOTE 'library' or 'require' calls in package code: ‘OLIN’ ‘annotate’ ‘rgl’ Please use :: or requireNamespace() instead. See section 'Suggested packages' in the 'Writing R Extensions' manual. * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE activeMod: no visible global function definition for ‘sessionInfo’ activeModScoreHTML: no visible binding for global variable ‘data’ activeNet: no visible global function definition for ‘sessionInfo’ activeNetScoreHTML: no visible binding for global variable ‘data’ blackBlue: no visible global function definition for ‘col2rgb’ blackBlue: no visible global function definition for ‘rgb’ classifyKNN: no visible global function definition for ‘sessionInfo’ classifyKNNsc: no visible global function definition for ‘sessionInfo’ classifyLDA: no visible global function definition for ‘sessionInfo’ classifyLDAsc: no visible global function definition for ‘sessionInfo’ classifySVM: no visible global function definition for ‘sessionInfo’ classifySVMsc: no visible global function definition for ‘sessionInfo’ createMaigesRaw: no visible global function definition for ‘sessionInfo’ createTDMS: no visible global function definition for ‘write.table’ deGenes2by2BootT: no visible global function definition for ‘sessionInfo’ deGenes2by2Ttest: no visible global function definition for ‘sessionInfo’ deGenes2by2Wilcox: no visible global function definition for ‘sessionInfo’ deGenesANOVA: no visible global function definition for ‘sessionInfo’ designANOVA: no visible global function definition for ‘sessionInfo’ greenRed: no visible global function definition for ‘col2rgb’ greenRed: no visible global function definition for ‘rgb’ loadData: no visible global function definition for ‘read.table’ loadData: no visible global function definition for ‘sessionInfo’ normLoc: no visible global function definition for ‘sessionInfo’ normOLIN: no visible global function definition for ‘sessionInfo’ normRepLoess: no visible global function definition for ‘sessionInfo’ normScaleLimma: no visible global function definition for ‘sessionInfo’ normScaleMarray: no visible global function definition for ‘sessionInfo’ print.maiges: no visible global function definition for ‘str’ print.maigesANOVA: no visible global function definition for ‘str’ print.maigesPreRaw: no visible global function definition for ‘str’ print.maigesRaw: no visible global function definition for ‘str’ relNet2TGF.maigesRelNetB: no visible global function definition for ‘write.table’ relNet2TGF.maigesRelNetM: no visible global function definition for ‘write.table’ relNetworkB: no visible global function definition for ‘sessionInfo’ relNetworkM: no visible global function definition for ‘sessionInfo’ selSpots: no visible global function definition for ‘sessionInfo’ summarizeReplicates: no visible global function definition for ‘sessionInfo’ tableClass: no visible global function definition for ‘write.table’ tablesDE: no visible global function definition for ‘setRepository’ tablesDE: no visible global function definition for ‘write.table’ Undefined global functions or variables: col2rgb data read.table rgb sessionInfo setRepository str write.table Consider adding importFrom("grDevices", "col2rgb", "rgb") importFrom("utils", "data", "read.table", "sessionInfo", "str", "write.table") to your NAMESPACE file. * checking Rd files ... NOTE checkRd: (-1) addPaths.Rd:11: Escaped LaTeX specials: \# checkRd: (-1) loadData.Rd:51: Escaped LaTeX specials: \_ * 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 contents of ‘data’ directory ... OK * checking data for non-ASCII characters ... OK * checking data for ASCII and uncompressed saves ... OK * checking line endings in C/C++/Fortran sources/headers ... OK * checking compiled code ... NOTE Note: information on .o files is not available * checking sizes of PDF files under ‘inst/doc’ ... OK * checking files in ‘vignettes’ ... OK * checking examples ... SKIPPED * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking running R code from vignettes ... SKIPPED * checking re-building of vignette outputs ... SKIPPED * checking PDF version of manual ... OK * DONE Status: 6 NOTEs See ‘/Users/biocbuild/bbs-3.19-bioc/meat/maigesPack.Rcheck/00check.log’ for details.