############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:flowBin.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings flowBin_1.42.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/flowBin.Rcheck’ * using R version 4.4.2 (2024-10-31) * using platform: x86_64-pc-linux-gnu * R was compiled by gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0 GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0 * running under: Ubuntu 24.04.1 LTS * using session charset: UTF-8 * checking for file ‘flowBin/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘flowBin’ version ‘1.42.0’ * checking package namespace information ... OK * checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib: cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES' 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 ‘flowBin’ 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 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 dependencies in R code ... NOTE Package in Depends field not imported from: ‘flowCore’ 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 ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE .getBinExpr.def : getBinFrame: no visible global function definition for ‘exprs<-’ .getBinExpr.def : getBinFrame: no visible global function definition for ‘exprs’ .getBinExpr.def : scaleData: no visible global function definition for ‘pData’ .getBinExpr.def : getOnePopExpr : extractOneTube : : no visible global function definition for ‘exprs’ .getBinExpr.def : getOnePopExpr : extractOneTube: no visible global function definition for ‘pData’ .getBinExpr.def : getOneBinMeds : : no visible global function definition for ‘median’ .getBinExpr.def : getOneBinMeds : : no visible global function definition for ‘exprs’ .getBinExpr.def : getOneBinMeds: no visible global function definition for ‘pData’ checkQNorm.func: no visible global function definition for ‘flowSet’ checkQNorm.func: no visible global function definition for ‘par’ checkQNorm.func: no visible binding for global variable ‘sd’ flowFPBin.def: no visible global function definition for ‘flowSet’ kMeansBin.def: no visible global function definition for ‘exprs’ kMeansBin.def: no visible global function definition for ‘pData’ kMeansBin.def: no visible global function definition for ‘kmeans’ mapBinsKNN.def : mapClustersKNN: no visible global function definition for ‘exprs’ mapBinsKNN.def: no visible global function definition for ‘capture.output’ mapBinsKNN.def: no visible global function definition for ‘parLapply’ medianFI: no visible global function definition for ‘median’ medianFIDist: no visible global function definition for ‘median’ proportionPositive: no visible global function definition for ‘quantile’ qnorm.func : normCol : : no visible global function definition for ‘exprs’ qnorm.func : normCol : getCol: no visible global function definition for ‘exprs’ qnorm.func : normCol : getCol: no visible global function definition for ‘runif’ qnorm.func : normCol : setCol: no visible global function definition for ‘exprs’ qnorm.func : normCol : setCol: no visible global function definition for ‘exprs<-’ checkQNorm,FlowSample-FlowSample: no visible global function definition for ‘flowSet’ checkQNorm,FlowSample-FlowSample: no visible global function definition for ‘par’ checkQNorm,FlowSample-FlowSample: no visible binding for global variable ‘sd’ flowFPBin,FlowSample: no visible global function definition for ‘flowSet’ getBinExpr,BinnedFlowSample : getBinFrame: no visible global function definition for ‘exprs<-’ getBinExpr,BinnedFlowSample : getBinFrame: no visible global function definition for ‘exprs’ getBinExpr,BinnedFlowSample : scaleData: no visible global function definition for ‘pData’ getBinExpr,BinnedFlowSample : getOnePopExpr : extractOneTube : : no visible global function definition for ‘exprs’ getBinExpr,BinnedFlowSample : getOnePopExpr : extractOneTube: no visible global function definition for ‘pData’ getBinExpr,BinnedFlowSample : getOneBinMeds : : no visible global function definition for ‘median’ getBinExpr,BinnedFlowSample : getOneBinMeds : : no visible global function definition for ‘exprs’ getBinExpr,BinnedFlowSample : getOneBinMeds: no visible global function definition for ‘pData’ kMeansBin,FlowSample: no visible global function definition for ‘exprs’ kMeansBin,FlowSample: no visible global function definition for ‘pData’ kMeansBin,FlowSample: no visible global function definition for ‘kmeans’ mapBinsKNN,FlowSample : mapClustersKNN: no visible global function definition for ‘exprs’ mapBinsKNN,FlowSample: no visible global function definition for ‘capture.output’ mapBinsKNN,FlowSample: no visible global function definition for ‘parLapply’ quantileNormalise,FlowSample : normCol : : no visible global function definition for ‘exprs’ quantileNormalise,FlowSample : normCol : getCol: no visible global function definition for ‘exprs’ quantileNormalise,FlowSample : normCol : getCol: no visible global function definition for ‘runif’ quantileNormalise,FlowSample : normCol : setCol: no visible global function definition for ‘exprs’ quantileNormalise,FlowSample : normCol : setCol: no visible global function definition for ‘exprs<-’ show,FlowSample: no visible global function definition for ‘str’ Undefined global functions or variables: capture.output exprs exprs<- flowSet kmeans median pData par parLapply quantile runif sd str Consider adding importFrom("graphics", "par") importFrom("stats", "kmeans", "median", "quantile", "runif", "sd") importFrom("utils", "capture.output", "str") to your NAMESPACE file. * checking Rd files ... OK * checking Rd metadata ... NOTE Invalid package aliases in Rd file 'flowBin.Rd': ‘flowbin-package’ * 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 files in ‘vignettes’ ... OK * checking examples ... OK * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking re-building of vignette outputs ... OK * checking PDF version of manual ... OK * DONE Status: 3 NOTEs See ‘/home/biocbuild/bbs-3.20-bioc/meat/flowBin.Rcheck/00check.log’ for details.