############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:GOSim.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings GOSim_1.38.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/GOSim.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 ‘GOSim/DESCRIPTION’ ... OK * this is package ‘GOSim’ version ‘1.38.0’ * 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 ‘GOSim’ can be installed ... OK * used C compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’ * 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 ... OK * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE GOGraph: no visible global function definition for ‘new’ GOenrichment: no visible global function definition for ‘new’ calc.diffusion.kernel: no visible global function definition for ‘as’ evaluateClustering: no visible global function definition for ‘median’ evaluateClustering: no visible global function definition for ‘mad’ evaluateClustering: no visible global function definition for ‘as.dist’ norm: no visible global function definition for ‘dist’ pca: no visible global function definition for ‘prcomp’ selectPrototypes : : no visible global function definition for ‘cutree’ selectPrototypes : : no visible global function definition for ‘hclust’ selectPrototypes : : no visible global function definition for ‘dist’ selectPrototypes: no visible binding for global variable ‘BIC’ setEvidenceLevel: no visible global function definition for ‘is’ Undefined global functions or variables: BIC as as.dist cutree dist hclust is mad median new prcomp Consider adding importFrom("methods", "as", "is", "new") importFrom("stats", "BIC", "as.dist", "cutree", "dist", "hclust", "mad", "median", "prcomp") to your NAMESPACE file (and ensure that your DESCRIPTION Imports field contains 'methods'). * checking Rd files ... NOTE checkRd: (-1) setEvidenceLevel.Rd:39: Escaped LaTeX specials: \$ checkRd: (-1) setEvidenceLevel.Rd:41: Escaped LaTeX specials: \$ \$ checkRd: (-1) setEvidenceLevel.Rd:43: Escaped LaTeX specials: \$ \$ \$ checkRd: (-1) setEvidenceLevel.Rd:46: Escaped LaTeX specials: \$ \$ \$ checkRd: (-1) setEvidenceLevel.Rd:49: Escaped LaTeX specials: \$ \$ \$ checkRd: (-1) setEvidenceLevel.Rd:52: Escaped LaTeX specials: \$ \$ checkRd: (-1) setEvidenceLevel.Rd:54: Escaped LaTeX specials: \$ \$ \$ checkRd: (-1) setEvidenceLevel.Rd:58: Escaped LaTeX specials: \$ \$ \$ checkRd: (-1) setEvidenceLevel.Rd:61: Escaped LaTeX specials: \$ \$ \$ checkRd: (-1) setEvidenceLevel.Rd:64: Escaped LaTeX specials: \$ checkRd: (-1) setEvidenceLevel.Rd:66: Escaped LaTeX specials: \$ \$ checkRd: (-1) setEvidenceLevel.Rd:68: Escaped LaTeX specials: \$ \$ \$ checkRd: (-1) setEvidenceLevel.Rd:71: Escaped LaTeX specials: \$ \$ \$ checkRd: (-1) setEvidenceLevel.Rd:74: Escaped LaTeX specials: \$ \$ \$ checkRd: (-1) setEvidenceLevel.Rd:78: Escaped LaTeX specials: \$ \$ checkRd: (-1) setEvidenceLevel.Rd:80: Escaped LaTeX specials: \$ \$ \$ checkRd: (-1) setEvidenceLevel.Rd:84: Escaped LaTeX specials: \$ \$ \$ checkRd: (-1) setEvidenceLevel.Rd:87: Escaped LaTeX specials: \$ \$ \$ * 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 * 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 getGeneSimPrototypes 331.409 19.638 538.993 getTermSim 10.571 0.129 16.498 getMinimumSubsumer 10.395 0.201 16.437 getDisjCommAnc 9.938 0.320 15.769 setEnrichmentFactors 8.101 0.160 12.733 * 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: 4 NOTEs See ‘/Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/GOSim.Rcheck/00check.log’ for details.