############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:flowMatch.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings flowMatch_1.42.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/flowMatch.Rcheck’ * using R version 4.4.1 (2024-06-14) * using platform: aarch64-apple-darwin20 * R was compiled by Apple clang version 14.0.0 (clang-1400.0.29.202) GNU Fortran (GCC) 12.2.0 * running under: macOS Ventura 13.6.7 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘flowMatch/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘flowMatch’ 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 ‘flowMatch’ can be installed ... OK * used C++ compiler: ‘Apple clang version 15.0.0 (clang-1500.1.0.2.5)’ * used SDK: ‘MacOSX11.3.sdk’ * 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 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 ClusteredSample: no visible global function definition for ‘cov’ ellipse: no visible global function definition for ‘qchisq’ ellipse: no visible global function definition for ‘lines’ limitcalc: no visible global function definition for ‘qchisq’ plot.cluster.contours: no visible global function definition for ‘par’ plot.cluster.contours: no visible global function definition for ‘plot.new’ plot.cluster.contours: no visible global function definition for ‘mtext’ template.tree,Template: no visible global function definition for ‘as.dendrogram’ Undefined global functions or variables: as.dendrogram cov lines mtext par plot.new qchisq Consider adding importFrom("graphics", "lines", "mtext", "par", "plot.new") importFrom("stats", "as.dendrogram", "cov", "qchisq") to your NAMESPACE file. * checking Rd files ... NOTE checkRd: (-1) ClusteredSample-class.Rd:32: Lost braces 32 | \item{\code{labels } {A vector of integers (from \code{1:num.clusters}) indicating the cluster to which each point is allocated. This is usually obtained from a clustering algorithm.}} | ^ checkRd: (-1) ClusteredSample-class.Rd:33: Lost braces 33 | \item{\code{centers } {A list of length \code{num.clusters} storing the centers of the clusters. The ith entry of the list \code{centers[[i]]} stores the center of the ith cluster. If not specified, the constructor estimates \code{centers} from \code{sample}.}} | ^ checkRd: (-1) ClusteredSample-class.Rd:34: Lost braces 34 | \item{\code{covs } {A list of length \code{num.clusters} storing the covariance matrices of the clusters. The ith entry of the list \code{cov[[i]]} stores the covariance matrix of the ith cluster. If not specified, the constructor estimates \code{cov} from \code{sample}.}} | ^ checkRd: (-1) ClusteredSample-class.Rd:35: Lost braces 35 | \item \code{sample } {A matrix, data frame of observations, or object of class \code{flowFrame}. Rows correspond to observations and columns correspond to variables. It must be passed to the constructor if either \code{centers} or \code{cov} is unspecified; then \code{centers} or \code{cov} is estimated from \code{sample}.} | ^ checkRd: (-1) ClusteredSample-class.Rd:36: Lost braces in \itemize; meant \describe ? checkRd: (-1) ClusteredSample-class.Rd:95: Lost braces 95 | \item{\code{sample: } {A matrix, data.frame or an object of class \code{flowFrame} representing an FC sample.}} | ^ checkRd: (-1) ClusteredSample-class.Rd:96: Lost braces 96 | \item{\code{ClusteredSample: } { An object of class \code{ClusteredSample} storing the clustering of the sample.}} | ^ checkRd: (-1) ClusteredSample-class.Rd:97: Lost braces; missing escapes or markup? 97 | \item{\code{... } {Other usual plotting related parameters.}} | ^ checkRd: (-1) MetaCluster-class.Rd:87: Lost braces 87 | \item{\code{mc } {An object of class \code{MetaCluster} for which the plot function is invoked.}} | ^ checkRd: (-1) MetaCluster-class.Rd:88: Lost braces; missing escapes or markup? 88 | \item{\code{alpha } { (1-alpha)*100\% quantile of the distribution of the clusters or meta-cluster is plotted.}} | ^ checkRd: (-1) MetaCluster-class.Rd:89: Lost braces; missing escapes or markup? 89 | \item{\code{plot.mc } { TRUE/FALSE, when TRUE the functions draws contour of the combined meta-cluster and when FALSE the function draws the contours of the individual clusters.}} | ^ checkRd: (-1) MetaCluster-class.Rd:90: Lost braces; missing escapes or markup? 90 | \item{\code{... } {Other usual plotting related parameters.}} | ^ checkRd: (-1) Template-class.Rd:35: Lost braces in \itemize; meant \describe ? checkRd: (-1) Template-class.Rd:36: Lost braces in \itemize; meant \describe ? checkRd: (-1) Template-class.Rd:37: Lost braces in \itemize; meant \describe ? checkRd: (-1) Template-class.Rd:38: Lost braces in \itemize; meant \describe ? checkRd: (-1) Template-class.Rd:95: Lost braces in \itemize; meant \describe ? checkRd: (-1) Template-class.Rd:96: Lost braces in \itemize; meant \describe ? checkRd: (-1) Template-class.Rd:97: Lost braces in \itemize; meant \describe ? checkRd: (-1) Template-class.Rd:98: Lost braces in \itemize; meant \describe ? checkRd: (-1) Template-class.Rd:99: Lost braces in \itemize; meant \describe ? checkRd: (-1) Template-class.Rd:101: Lost braces in \itemize; meant \describe ? * 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 line endings in Makefiles ... OK * checking compilation flags in Makevars ... OK * checking for GNU extensions in Makefiles ... OK * checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK * checking use of PKG_*FLAGS in Makefiles ... OK * checking compiled code ... NOTE Note: information on .o files is not available * checking sizes of PDF files under ‘inst/doc’ ... OK * checking files in ‘vignettes’ ... OK * checking examples ... OK * 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 ‘/Users/biocbuild/bbs-3.20-bioc/meat/flowMatch.Rcheck/00check.log’ for details.