############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:flowPeaks.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings flowPeaks_1.40.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.14-bioc/meat/flowPeaks.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 ‘flowPeaks/DESCRIPTION’ ... OK * this is package ‘flowPeaks’ version ‘1.40.0’ * 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 ‘flowPeaks’ can be installed ... WARNING Found the following significant warnings: VoronoiDiagramGenerator.cpp:803:5: warning: logical not is only applied to the left hand side of this bitwise operator [-Wlogical-not-parentheses] See ‘/Users/biocbuild/bbs-3.14-bioc/meat/flowPeaks.Rcheck/00install.out’ for details. * 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 ... OK * checking replacement functions ... OK * checking foreign function calls ... NOTE Call with DUP: .C("Rpack_kmeans", as.double(t(data.matrix(x))), as.integer(n), as.integer(p), as.integer(K), cluster = integer(n), m = double(K * p), nc = integer(K), S = double(K * p * p), Nb = integer(K * K), twss = double(1), as.double(stime), DUP = FALSE, PACKAGE = "flowPeaks") DUP is no longer supported and will be ignored. * checking R code for possible problems ... NOTE getS0K : : no visible global function definition for ‘nclass.FD’ getS0K: no visible global function definition for ‘median’ plot.flowPeaks: no visible global function definition for ‘hist’ plot.flowPeaks: no visible global function definition for ‘points’ plot.flowPeaks: no visible global function definition for ‘text’ plot.flowPeaks: no visible global function definition for ‘par’ plot.flowPeaks: no visible global function definition for ‘segments’ traditional.kmeans: no visible global function definition for ‘kmeans’ traditional.kmeans: no visible global function definition for ‘var’ Undefined global functions or variables: hist kmeans median nclass.FD par points segments text var Consider adding importFrom("grDevices", "nclass.FD") importFrom("graphics", "hist", "par", "points", "segments", "text") importFrom("stats", "kmeans", "median", "var") 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 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 File ‘/Library/Frameworks/R.framework/Versions/4.1/Resources/library/flowPeaks/libs/flowPeaks.so’: Found ‘___stderrp’, possibly from ‘stderr’ (C) Found ‘___stdoutp’, possibly from ‘stdout’ (C) Found ‘_abort’, possibly from ‘abort’ (C) Found ‘_printf’, possibly from ‘printf’ (C) Compiled code should not call entry points which might terminate R nor write to stdout/stderr instead of to the console, nor use Fortran I/O nor system RNGs. The detected symbols are linked into the code but might come from libraries and not actually be called. See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual. * 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 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: 1 WARNING, 3 NOTEs See ‘/Users/biocbuild/bbs-3.14-bioc/meat/flowPeaks.Rcheck/00check.log’ for details.