############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:BCRANK.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings BCRANK_1.69.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/BCRANK.Rcheck’ * using R Under development (unstable) (2024-11-20 r87352) * 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 13.7.1 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘BCRANK/DESCRIPTION’ ... OK * this is package ‘BCRANK’ version ‘1.69.0’ * 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 ‘BCRANK’ 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 ... 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 whether startup messages can be suppressed ... OK * checking dependencies in R code ... NOTE 'library' or 'require' call to ‘methods’ which was already attached by Depends. Please remove these calls from your code. * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE File ‘BCRANK/R/AllClasses.R’: .onLoad calls: require("methods", quietly = TRUE) Package startup functions should not change the search path. See section ‘Good practice’ in '?.onAttach'. bcrankRun: no visible global function definition for ‘flush.console’ getBCRANKScore: no visible global function definition for ‘t.test’ hitsForNeighboursInC: no visible global function definition for ‘flush.console’ plot,BCRANKsearch-missing: no visible global function definition for ‘rainbow’ plot,BCRANKsearch-missing: no visible binding for global variable ‘points’ plot,BCRANKsearch-missing: no visible global function definition for ‘legend’ Undefined global functions or variables: flush.console legend points rainbow t.test Consider adding importFrom("grDevices", "rainbow") importFrom("graphics", "legend", "points") importFrom("stats", "t.test") importFrom("utils", "flush.console") 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 compiled code ... NOTE Note: information on .o files is not available * checking sizes of PDF files under ‘inst/doc’ ... NOTE ‘qpdf’ made some significant size reductions: compacted ‘BCRANK.pdf’ from 1.2Mb to 1.0Mb consider running tools::compactPDF() on these files, or build the source package with --compact-vignettes * 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: 5 NOTEs See ‘/Users/biocbuild/bbs-3.21-bioc/meat/BCRANK.Rcheck/00check.log’ for details.