############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD check --install=check:SCAN.UPC.install-out.txt --library=/home/biocbuild/bbs-3.14-bioc/R/library --no-vignettes --timings SCAN.UPC_2.36.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.14-bioc/meat/SCAN.UPC.Rcheck’ * using R version 4.1.3 (2022-03-10) * using platform: x86_64-pc-linux-gnu (64-bit) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘SCAN.UPC/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘SCAN.UPC’ version ‘2.36.0’ * checking package namespace information ... OK * checking package dependencies ... NOTE Depends: includes the non-default packages: 'Biobase', 'oligo', 'Biostrings', 'GEOquery', 'affy', 'affyio', 'foreach', 'sva' Adding so many packages to the search path is excessive and importing selectively is preferable. * 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 ‘SCAN.UPC’ can be installed ... OK * checking installed package size ... OK * checking package directory ... OK * checking ‘build’ directory ... OK * checking DESCRIPTION meta-information ... NOTE License components which are templates and need '+ file LICENSE': MIT * 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 BatchAdjust: no visible global function definition for ‘varLabels’ BatchAdjust: no visible global function definition for ‘exprs<-’ BatchAdjust: no visible global function definition for ‘pData’ BatchAdjustFromFile: no visible global function definition for ‘sampleNames’ BatchAdjustFromFile: no visible global function definition for ‘pData’ BatchAdjustFromFile: no visible global function definition for ‘varLabels’ BatchAdjustFromFile: no visible global function definition for ‘pData<-’ InstallBrainArrayPackage: no visible global function definition for ‘download.file’ InstallBrainArrayPackage: no visible global function definition for ‘install.packages’ ProcessGtfSubset: no visible global function definition for ‘IRanges’ RS_BC: no visible global function definition for ‘median’ RS_BC: no visible global function definition for ‘dlnorm’ RS_BC: no visible global function definition for ‘rlnorm’ UPC_Generic_ExpressionSet: no visible global function definition for ‘pData’ UPC_Generic_ExpressionSet: no visible global function definition for ‘featureData’ UPC_Generic_ExpressionSet: no visible global function definition for ‘DNAStringSet’ UPC_Generic_ExpressionSet: no visible global function definition for ‘exprs<-’ UPC_RNASeq: no visible global function definition for ‘runif’ UPC_RNASeq: no visible global function definition for ‘sampleNames<-’ UPC_RNASeq: no visible global function definition for ‘featureNames<-’ UPC_nb: no visible global function definition for ‘dnbinom’ UPC_nn: no visible global function definition for ‘median’ UPC_nn: no visible global function definition for ‘var’ UPC_nn: no visible global function definition for ‘dnorm’ UPC_nn: no visible global function definition for ‘rnorm’ UPC_nn_bayes: no visible global function definition for ‘median’ UPC_nn_bayes: no visible global function definition for ‘var’ assign_bin: no visible global function definition for ‘rnorm’ channelNormalize: no visible global function definition for ‘var’ downloadBeadChipFromGEO: no visible global function definition for ‘untar’ downloadFromGEO: no visible global function definition for ‘untar’ iglNormalize: no visible global function definition for ‘loess’ madNormalize: no visible global function definition for ‘median’ processCelFiles: no visible global function definition for ‘%dopar%’ processCelFiles: no visible global function definition for ‘sampleNames<-’ processCelFiles: no visible global function definition for ‘featureNames<-’ processTwoColor: no visible global function definition for ‘sampleNames<-’ processTwoColor: no visible global function definition for ‘featureNames<-’ readAgilentData: no visible global function definition for ‘read.delim’ Undefined global functions or variables: %dopar% DNAStringSet IRanges dlnorm dnbinom dnorm download.file exprs<- featureData featureNames<- install.packages loess median pData pData<- read.delim rlnorm rnorm runif sampleNames sampleNames<- untar var varLabels Consider adding importFrom("stats", "dlnorm", "dnbinom", "dnorm", "loess", "median", "rlnorm", "rnorm", "runif", "var") importFrom("utils", "download.file", "install.packages", "read.delim", "untar") 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 files in ‘vignettes’ ... OK * checking examples ... 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: 3 NOTEs See ‘/home/biocbuild/bbs-3.14-bioc/meat/SCAN.UPC.Rcheck/00check.log’ for details.