############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:seqCNA.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings seqCNA_1.46.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/seqCNA.Rcheck’ * using R version 4.3.1 (2023-06-16) * using platform: aarch64-apple-darwin20 (64-bit) * R was compiled by Apple clang version 14.0.0 (clang-1400.0.29.202) GNU Fortran (GCC) 12.2.0 * running under: macOS Monterey 12.6.7 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘seqCNA/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘seqCNA’ version ‘1.46.0’ * 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 ‘seqCNA’ can be installed ... OK * used C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’ * 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 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 ... NOTE The legacy packages maptools, rgdal, and rgeos, underpinning the sp package, which was just loaded, will retire in October 2023. Please refer to R-spatial evolution reports for details, especially https://r-spatial.org/r/2023/05/15/evolution4.html. It may be desirable to make the sf package available; package maintainers should consider adding sf to Suggests:. The sp package is now running under evolution status 2 (status 2 uses the sf package in place of rgdal) Packages in Depends field not imported from: ‘GLAD’ ‘adehabitatLT’ ‘doSNOW’ ‘methods’ ‘seqCNA.annot’ These packages need to be imported from (in the NAMESPACE file) for when this namespace is loaded but not attached. * checking S3 generic/method consistency ... WARNING The legacy packages maptools, rgdal, and rgeos, underpinning the sp package, which was just loaded, will retire in October 2023. Please refer to R-spatial evolution reports for details, especially https://r-spatial.org/r/2023/05/15/evolution4.html. It may be desirable to make the sf package available; package maintainers should consider adding sf to Suggests:. The sp package is now running under evolution status 2 (status 2 uses the sf package in place of rgdal) See section ‘Generic functions and methods’ in the ‘Writing R Extensions’ manual. * checking replacement functions ... OK * checking foreign function calls ... NOTE The legacy packages maptools, rgdal, and rgeos, underpinning the sp package, which was just loaded, will retire in October 2023. Please refer to R-spatial evolution reports for details, especially https://r-spatial.org/r/2023/05/15/evolution4.html. It may be desirable to make the sf package available; package maintainers should consider adding sf to Suggests:. The sp package is now running under evolution status 2 (status 2 uses the sf package in place of rgdal) See chapter ‘System and foreign language interfaces’ in the ‘Writing R Extensions’ manual. * checking R code for possible problems ... NOTE .autoTrim: no visible global function definition for ‘makeCluster’ .autoTrim: no visible global function definition for ‘registerDoSNOW’ .autoTrim: no visible global function definition for ‘%dopar%’ .autoTrim: no visible global function definition for ‘foreach’ .autoTrim: no visible global function definition for ‘wawotest’ .autoTrim: no visible global function definition for ‘quantile’ .autoTrim: no visible global function definition for ‘stopCluster’ .autoTrim: no visible global function definition for ‘loess’ .autoTrim: no visible global function definition for ‘tail’ .buildGenomeInfo: no visible global function definition for ‘makeCluster’ .buildGenomeInfo: no visible global function definition for ‘registerDoSNOW’ .buildGenomeInfo: no visible global function definition for ‘%dopar%’ .buildGenomeInfo: no visible global function definition for ‘foreach’ .buildGenomeInfo: no visible global function definition for ‘stopCluster’ .makeFormula: no visible global function definition for ‘as.formula’ .olBarplot: no visible global function definition for ‘par’ .olBarplot: no visible global function definition for ‘barplot’ .overLapper : : no visible global function definition for ‘combn’ .resample: no visible global function definition for ‘makeCluster’ .resample: no visible global function definition for ‘registerDoSNOW’ .resample: no visible global function definition for ‘%dopar%’ .resample: no visible global function definition for ‘foreach’ .resample: no visible global function definition for ‘stopCluster’ .seqnorm: no visible binding for global variable ‘head’ .seqnorm: no visible global function definition for ‘tail’ .seqnorm: no visible global function definition for ‘flush.console’ .seqnorm: no visible binding for global variable ‘tail’ .seqnorm: no visible global function definition for ‘makeCluster’ .seqnorm: no visible global function definition for ‘registerDoSNOW’ .seqnorm: no visible global function definition for ‘%dopar%’ .seqnorm: no visible global function definition for ‘foreach’ .seqnorm: no visible global function definition for ‘as.profileCGH’ .seqnorm: no visible global function definition for ‘glad’ .seqnorm : : no visible global function definition for ‘quantile’ .seqnorm : .getSegmLm: no visible global function definition for ‘quantile’ .seqnorm: no visible global function definition for ‘predict’ .seqnorm: no visible global function definition for ‘median’ .seqnorm : : no visible global function definition for ‘median’ .seqnorm: no visible global function definition for ‘stopCluster’ .seqnorm: no visible global function definition for ‘jpeg’ .seqnorm: no visible global function definition for ‘quantile’ .seqnorm: no visible global function definition for ‘layout’ .seqnorm: no visible global function definition for ‘par’ .seqnorm: no visible global function definition for ‘density’ .seqnorm: no visible global function definition for ‘points’ .seqnorm: no visible global function definition for ‘plot.new’ .seqnorm: no visible global function definition for ‘legend’ .seqnorm: no visible global function definition for ‘abline’ .seqnorm: no visible global function definition for ‘dev.off’ .seqnorm: no visible global function definition for ‘lines’ .seqnorm: no visible global function definition for ‘smoothScatter’ .seqnorm: no visible global function definition for ‘colorRampPalette’ .summary.SeqCNAInfo: no visible global function definition for ‘head’ .summary.SeqCNAInfo: no visible global function definition for ‘tail’ .vennPlot: no visible global function definition for ‘symbols’ .vennPlot: no visible global function definition for ‘text’ .vennPlot : plotellipse: no visible global function definition for ‘par’ .vennPlot : ellipseVenn: no visible global function definition for ‘plot.new’ .vennPlot : ellipseVenn: no visible global function definition for ‘text’ applyFilters: no visible global function definition for ‘supported.builds’ applyFilters: no visible global function definition for ‘data’ applyFilters: no visible global function definition for ‘quantile’ applyFilters: no visible global function definition for ‘flush.console’ applyFilters: no visible global function definition for ‘jpeg’ applyFilters: no visible global function definition for ‘layout’ applyFilters: no visible global function definition for ‘par’ applyFilters: no visible global function definition for ‘smoothScatter’ applyFilters: no visible global function definition for ‘colorRampPalette’ applyFilters: no visible global function definition for ‘points’ applyFilters: no visible global function definition for ‘dev.off’ applyFilters: no visible global function definition for ‘density’ applyFilters: no visible global function definition for ‘rect’ applyFilters: no visible global function definition for ‘abline’ applyFilters: no visible global function definition for ‘lines’ applyFilters: no visible global function definition for ‘text’ plotCNProfile: no visible global function definition for ‘jpeg’ plotCNProfile: no visible global function definition for ‘par’ plotCNProfile: no visible global function definition for ‘quantile’ plotCNProfile: no visible global function definition for ‘smoothScatter’ plotCNProfile: no visible global function definition for ‘colorRampPalette’ plotCNProfile: no visible global function definition for ‘abline’ plotCNProfile: no visible global function definition for ‘tail’ plotCNProfile : : no visible global function definition for ‘lines’ plotCNProfile: no visible global function definition for ‘median’ plotCNProfile: no visible global function definition for ‘text’ plotCNProfile: no visible global function definition for ‘dev.off’ readSeqsumm: no visible global function definition for ‘supported.builds’ readSeqsumm: no visible global function definition for ‘flush.console’ readSeqsumm: no visible global function definition for ‘read.table’ readSeqsumm: no visible global function definition for ‘data’ readSeqsumm: no visible global function definition for ‘new’ runGLAD: no visible global function definition for ‘flush.console’ runGLAD: no visible global function definition for ‘makeCluster’ runGLAD: no visible global function definition for ‘registerDoSNOW’ runGLAD: no visible global function definition for ‘%dopar%’ runGLAD: no visible global function definition for ‘foreach’ runGLAD: no visible global function definition for ‘as.profileCGH’ runGLAD: no visible global function definition for ‘glad’ runGLAD: no visible global function definition for ‘stopCluster’ writeCNProfile: no visible global function definition for ‘write.table’ summary,SeqCNAInfo: no visible global function definition for ‘head’ summary,SeqCNAInfo: no visible global function definition for ‘tail’ Undefined global functions or variables: %dopar% abline as.formula as.profileCGH barplot colorRampPalette combn data density dev.off flush.console foreach glad head jpeg layout legend lines loess makeCluster median new par plot.new points predict quantile read.table rect registerDoSNOW smoothScatter stopCluster supported.builds symbols tail text wawotest write.table Consider adding importFrom("grDevices", "colorRampPalette", "dev.off", "jpeg") importFrom("graphics", "abline", "barplot", "layout", "legend", "lines", "par", "plot.new", "points", "rect", "smoothScatter", "symbols", "text") importFrom("methods", "new") importFrom("stats", "as.formula", "density", "loess", "median", "predict", "quantile") importFrom("utils", "combn", "data", "flush.console", "head", "read.table", "tail", "write.table") to your NAMESPACE file (and ensure that your DESCRIPTION Imports field contains 'methods'). * 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 ... NOTE The legacy packages maptools, rgdal, and rgeos, underpinning the sp package, which was just loaded, will retire in October 2023. Please refer to R-spatial evolution reports for details, especially https://r-spatial.org/r/2023/05/15/evolution4.html. It may be desirable to make the sf package available; package maintainers should consider adding sf to Suggests:. The sp package is now running under evolution status 2 (status 2 uses the sf package in place of rgdal) The \usage entries for S3 methods should use the \method markup and not their full name. See chapter ‘Writing R documentation files’ in the ‘Writing R Extensions’ manual. * 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 File ‘/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/seqCNA/libs/seqCNA.so’: Found ‘___stdoutp’, possibly from ‘stdout’ (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 nor [v]sprintf. 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 plotCNProfile 0.489 0.070 11.347 writeCNProfile 0.253 0.039 11.402 applyThresholds 0.243 0.037 11.397 runGLAD 0.233 0.040 10.949 runSeqnorm 0.218 0.029 7.764 * 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, 6 NOTEs See ‘/Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/seqCNA.Rcheck/00check.log’ for details.