############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R-beta-2024-04-15_r86425/bin/R CMD check --install=check:maigesPack.install-out.txt --library=/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library --no-vignettes --timings maigesPack_1.68.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/maigesPack.Rcheck’ * using R version 4.4.0 beta (2024-04-15 r86425) * using platform: aarch64-unknown-linux-gnu * R was compiled by gcc (GCC) 10.3.1 GNU Fortran (GCC) 10.3.1 * running under: openEuler 22.03 (LTS-SP1) * using session charset: UTF-8 * using option ‘--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: ‘gcc (GCC) 10.3.1’ * 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 loading without being on the library search path ... 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 files in ‘vignettes’ ... OK * checking examples ... ERROR Running examples in ‘maigesPack-Ex.R’ failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: normScaleLimma > ### Title: Scale adjust a cDNA Microarray Object > ### Aliases: normScaleLimma > ### Keywords: classes > > ### ** Examples > > ## Loading the dataset > data(gastro) > > ## Doing the scale adjustment from median-absolute-value method (from > ## limma) > gastro.norm = normScaleLimma(gastro.norm, method="scale") > boxplot(gastro.norm) ## To see the efect of adjustment > > ## To do VSN scale adjustment (from vsn package) use the command. Be > ## carefull that this method adjust the variance along A values and not > ## between chips!! > gastro.norm = normScaleLimma(gastro.raw2, method="vsn") Error in normalizeVSN(toNorm) : vsn package required but is not installed (or can't be loaded) Calls: normScaleLimma -> normalizeVSN Execution halted * 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: 1 ERROR, 6 NOTEs See ‘/home/biocbuild/bbs-3.19-bioc/meat/maigesPack.Rcheck/00check.log’ for details.