############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:BGmix.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings BGmix_1.54.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.14-bioc/meat/BGmix.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 ‘BGmix/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘BGmix’ version ‘1.54.0’ * 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 ‘BGmix’ can be installed ... OK * checking installed package size ... OK * 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 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 ... OK * checking R code for possible problems ... NOTE EstimatePi0: no visible global function definition for ‘median’ EstimatePi0: no visible global function definition for ‘abline’ SimulateFromNull: no visible global function definition for ‘rt’ SimulateFromNull: no visible global function definition for ‘rgamma’ SimulateFromNull: no visible global function definition for ‘pnorm’ TailPP: no visible global function definition for ‘par’ TailPPCalculate: no visible global function definition for ‘qnorm’ histTailPP: no visible global function definition for ‘hist’ histTailPP: no visible global function definition for ‘lines’ histTailPP: no visible global function definition for ‘density’ plotBasic: no visible global function definition for ‘par’ plotCompare: no visible global function definition for ‘plot.default’ plotCompare: no visible global function definition for ‘abline’ plotFDR: no visible global function definition for ‘abline’ plotFDR: no visible global function definition for ‘legend’ plotMixDensity: no visible global function definition for ‘par’ plotMixDensity: no visible global function definition for ‘hist’ plotMixDensity: no visible global function definition for ‘lines’ plotMixDensity: no visible global function definition for ‘density’ plotPredChecks: no visible global function definition for ‘hist’ plotPredChecks: no visible global function definition for ‘abline’ plotTrace: no visible global function definition for ‘par’ plotTrace: no visible global function definition for ‘dev.cur’ plotTrace: no visible global function definition for ‘X11’ Undefined global functions or variables: X11 abline density dev.cur hist legend lines median par plot.default pnorm qnorm rgamma rt Consider adding importFrom("grDevices", "X11", "dev.cur") importFrom("graphics", "abline", "hist", "legend", "lines", "par", "plot.default") importFrom("stats", "density", "median", "pnorm", "qnorm", "rgamma", "rt") 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 shell scripts ... OK * checking line endings in C/C++/Fortran sources/headers ... OK * checking line endings in Makefiles ... OK * checking compilation flags in Makevars ... NOTE Package has both ‘src/Makevars.in’ and ‘src/Makevars’. Installation with --no-configure' is unlikely to work. If you intended ‘src/Makevars’ to be used on Windows, rename it to ‘src/Makevars.win’ otherwise remove it. If ‘configure’ created ‘src/Makevars’, you need a ‘cleanup’ script. * 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 ... NOTE PKG_CFLAGS set in ‘src/Makevars.win’ without any corresponding files * checking compiled code ... NOTE Note: information on .o files is not available File ‘/Library/Frameworks/R.framework/Versions/4.1/Resources/library/BGmix/libs/BGmix.so’: Found ‘__ZNSt3__14cerrE’, possibly from ‘std::cerr’ (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 Examples with CPU (user + system) or elapsed time > 5s user system elapsed FDRforTailPP 6.979 0.391 7.379 BGmix 5.207 0.233 5.460 * 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: 6 NOTEs See ‘/Users/biocbuild/bbs-3.14-bioc/meat/BGmix.Rcheck/00check.log’ for details.