############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:GateFinder.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings GateFinder_1.14.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.14-bioc/meat/GateFinder.Rcheck’ * using R version 4.1.3 (2022-03-10) * using platform: x86_64-apple-darwin17.0 (64-bit) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘GateFinder/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘GateFinder’ version ‘1.14.0’ * 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 ‘GateFinder’ 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 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 ... NOTE Found the following apparent S3 methods exported but not registered: plot.GateFinder See section ‘Registering S3 methods’ in the ‘Writing R Extensions’ manual. * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE .ah2sp: no visible global function definition for ‘CRS’ .ah2sp: no visible global function definition for ‘anglesArc’ .ah2sp: no visible global function definition for ‘Line’ .ah2sp: no visible global function definition for ‘Lines’ .ah2sp: no visible global function definition for ‘SpatialLines’ .ah2sp: no visible global function definition for ‘slot’ .ah2sp : : no visible global function definition for ‘slot’ .ah2sp: no visible global function definition for ‘SpatialPolygons’ .ah2sp: no visible global function definition for ‘Polygons’ .ah2sp : : no visible global function definition for ‘Polygon’ .ah2sp: no visible binding for global variable ‘SpatialPolygonsDataFrame’ .ah2sp: no visible global function definition for ‘SpatialPolygonsDataFrame’ .binsearch: no visible global function definition for ‘test’ .flowFPOutliers: no visible global function definition for ‘new’ .getBestPoly: no visible global function definition for ‘quantile’ .getBestPoly: no visible global function definition for ‘chull’ .getBestPoly: no visible global function definition for ‘ahull’ .getBestPoly : : no visible global function definition for ‘ahull’ .getBestPoly : : no visible global function definition for ‘chull’ .getGates : : no visible global function definition for ‘chull’ .spline.poly: no visible global function definition for ‘spline’ GateFinder: no visible global function definition for ‘median’ GateFinder: no visible global function definition for ‘new’ plot.GateFinder: no visible global function definition for ‘par’ plot.GateFinder: no visible global function definition for ‘colors’ plot.GateFinder: no visible global function definition for ‘points’ plot.GateFinder: no visible global function definition for ‘axis’ plot.GateFinder: no visible global function definition for ‘box’ plot.GateFinder: no visible global function definition for ‘lines’ plot,GatingProjection-ANY: no visible global function definition for ‘par’ plot,GatingProjection-ANY: no visible global function definition for ‘lines’ plot,GatingProjection-ANY: no visible global function definition for ‘legend’ Undefined global functions or variables: CRS Line Lines Polygon Polygons SpatialLines SpatialPolygons SpatialPolygonsDataFrame ahull anglesArc axis box chull colors legend lines median new par points quantile slot spline test Consider adding importFrom("grDevices", "chull", "colors") importFrom("graphics", "axis", "box", "legend", "lines", "par", "points") importFrom("methods", "new", "slot") importFrom("stats", "median", "quantile", "spline") 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 contents of ‘data’ directory ... OK * checking data for non-ASCII characters ... OK * checking data for ASCII and uncompressed saves ... OK * checking sizes of PDF files under ‘inst/doc’ ... OK * checking files in ‘vignettes’ ... OK * checking examples ... OK * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘runTests.R’ 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 ‘/Users/biocbuild/bbs-3.14-bioc/meat/GateFinder.Rcheck/00check.log’ for details.