############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:flowCHIC.install-out.txt --library=F:\biocbuild\bbs-3.19-bioc\R\library --no-vignettes --timings flowCHIC_1.38.0.tar.gz ### ############################################################################## ############################################################################## * using log directory 'F:/biocbuild/bbs-3.19-bioc/meat/flowCHIC.Rcheck' * using R version 4.4.0 (2024-04-24 ucrt) * using platform: x86_64-w64-mingw32 * R was compiled by gcc.exe (GCC) 13.2.0 GNU Fortran (GCC) 13.2.0 * running under: Windows Server 2022 x64 (build 20348) * using session charset: UTF-8 * using option '--no-vignettes' * checking for file 'flowCHIC/DESCRIPTION' ... OK * checking extension type ... Package * this is package 'flowCHIC' version '1.38.0' * package encoding: UTF-8 * 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 whether package 'flowCHIC' can be installed ... OK * checking installed package size ... NOTE installed size is 5.9Mb sub-directories of 1Mb or more: extdata 5.7Mb * 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 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 fcs_to_img,character: warning in hexbin(x, y, xbin = 128): partial argument match of 'xbin' to 'xbins' img_sub,character: warning in hexbin(x, y, xbin = xbin): partial argument match of 'xbin' to 'xbins' fcs_to_img,character: no visible global function definition for 'png' fcs_to_img,character: no visible binding for global variable 'count' fcs_to_img,character: no visible global function definition for 'dev.off' img_sub,character: no visible global function definition for 'png' img_sub,character: no visible binding for global variable 'count' img_sub,character: no visible global function definition for 'dev.off' plot_nmds,data.frame-data.frame: no visible global function definition for 'as.dist' plot_nmds,data.frame-data.frame: no visible global function definition for 'par' plot_nmds,data.frame-data.frame: no visible global function definition for 'hclust' plot_nmds,data.frame-data.frame: no visible global function definition for 'points' plot_nmds,data.frame-data.frame: no visible global function definition for 'text' plot_nmds,data.frame-data.frame: no visible global function definition for 'legend' Undefined global functions or variables: as.dist count dev.off hclust legend par png points text Consider adding importFrom("grDevices", "dev.off", "png") importFrom("graphics", "legend", "par", "points", "text") importFrom("stats", "as.dist", "hclust") 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 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 Examples with CPU (user + system) or elapsed time > 5s user system elapsed calculate_overlaps_xor 8.20 3.35 17.05 plot_nmds 4.75 1.83 7.19 * 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: 3 NOTEs See 'F:/biocbuild/bbs-3.19-bioc/meat/flowCHIC.Rcheck/00check.log' for details.