############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD check --install=check:BufferedMatrixMethods.install-out.txt --library=/home/biocbuild/bbs-3.14-bioc/R/library --no-vignettes --timings BufferedMatrixMethods_1.58.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.14-bioc/meat/BufferedMatrixMethods.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 ‘BufferedMatrixMethods/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘BufferedMatrixMethods’ version ‘1.58.0’ * 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 for sufficient/correct file permissions ... OK * checking whether package ‘BufferedMatrixMethods’ can be installed ... OK * checking installed package size ... OK * checking package 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 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 ... NOTE 'library' or 'require' calls in package code: ‘affy’ ‘affyio’ Please use :: or requireNamespace() instead. See section 'Suggested packages' in the 'Writing R Extensions' manual. Packages in Depends field not imported from: ‘BufferedMatrix’ ‘methods’ These packages need to be imported from (in the NAMESPACE file) for when this namespace is loaded but not attached. * checking S3 generic/method consistency ... NOTE Found the following apparent S3 methods exported but not registered: median.polish.summarize See section ‘Registering S3 methods’ in the ‘Writing R Extensions’ manual. * checking replacement functions ... OK * checking foreign function calls ... NOTE Foreign function calls to a different package: .Call("ReadHeader", ..., PACKAGE = "affyio") .Call("read_probeintensities", ..., PACKAGE = "affyio") See chapter ‘System and foreign language interfaces’ in the ‘Writing R Extensions’ manual. * checking R code for possible problems ... NOTE NB: .First.lib is obsolete and will not be used in R >= 3.0.0 BufferedMatrix.bg.correct.normalize.quantiles: no visible global function definition for ‘is’ BufferedMatrix.bg.correct.normalize.quantiles: no visible global function definition for ‘duplicate’ BufferedMatrix.bg.correct.normalize.quantiles : bg.dens: no visible global function definition for ‘density’ BufferedMatrix.justRMA: no visible global function definition for ‘new’ BufferedMatrix.justRMA: no visible global function definition for ‘pData’ BufferedMatrix.justRMA: no visible global function definition for ‘read.celfile.header’ BufferedMatrix.justRMA: no visible global function definition for ‘cleancdfname’ BufferedMatrix.justRMA: no visible global function definition for ‘pmindex’ BufferedMatrix.justRMA: no visible global function definition for ‘geneNames’ BufferedMatrix.justRMA: no visible global function definition for ‘set.buffer.dim’ BufferedMatrix.justRMA: no visible global function definition for ‘RowMode’ BufferedMatrix.justRMA: no visible global function definition for ‘notes<-’ BufferedMatrix.read.celfiles: no visible global function definition for ‘createBufferedMatrix’ BufferedMatrix.read.celfiles: no visible global function definition for ‘read.celfile’ BufferedMatrix.read.celfiles: no visible global function definition for ‘AddColumn’ BufferedMatrix.read.probematrix: no visible global function definition for ‘new’ BufferedMatrix.read.probematrix: no visible global function definition for ‘cleancdfname’ BufferedMatrix.read.probematrix: no visible global function definition for ‘getCdfInfo’ BufferedMatrix.read.probematrix: no visible global function definition for ‘createBufferedMatrix’ BufferedMatrix.read.probematrix: no visible global function definition for ‘AddColumn’ bg.correct.BufferedMatrix: no visible global function definition for ‘is’ bg.correct.BufferedMatrix: no visible global function definition for ‘duplicate’ bg.correct.BufferedMatrix : bg.dens: no visible global function definition for ‘density’ normalize.BufferedMatrix.quantiles: no visible global function definition for ‘is’ normalize.BufferedMatrix.quantiles: no visible global function definition for ‘duplicate’ Undefined global functions or variables: AddColumn RowMode cleancdfname createBufferedMatrix density duplicate geneNames getCdfInfo is new notes<- pData pmindex read.celfile read.celfile.header set.buffer.dim Consider adding importFrom("methods", "is", "new") importFrom("stats", "density") to your NAMESPACE file (and ensure that your DESCRIPTION Imports field contains 'methods'). * 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 line endings in C/C++/Fortran sources/headers ... OK * checking compiled code ... NOTE Note: information on .o files is not available * checking examples ... NONE * checking PDF version of manual ... OK * DONE Status: 6 NOTEs See ‘/home/biocbuild/bbs-3.14-bioc/meat/BufferedMatrixMethods.Rcheck/00check.log’ for details.