############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:BUS.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings BUS_1.60.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/BUS.Rcheck’ * using R version 4.4.0 (2024-04-24) * 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 13.6.5 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘BUS/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘BUS’ version ‘1.60.0’ * 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 ‘BUS’ 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 ... OK * 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 dependencies in R code ... NOTE Package in Depends field not imported from: ‘minet’ 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 ... OK * checking replacement functions ... OK * checking foreign function calls ... NOTE Call with DUP: .Call("MINempirical", mat, nat, N, n1, n2, DUP = FALSE) DUP is no longer supported and will be ignored. * checking R code for possible problems ... NOTE gene.pvalue : fi: warning in matrix(1:nrow(EXP), nc = 1): partial argument match of 'nc' to 'ncol' gene.pvalue: warning in matrix(1:nrow(EXP), nc = 1): partial argument match of 'nc' to 'ncol' gene.pvalue : fi: warning in matrix(1:ncol(real), nc = 1): partial argument match of 'nc' to 'ncol' gene.pvalue: warning in matrix(1:nrow(real), nc = 1): partial argument match of 'nc' to 'ncol' gene.pvalue : fi1: warning in matrix(1:ncol(real), nc = 1): partial argument match of 'nc' to 'ncol' gene.trait.pvalue: warning in matrix(0, nr = nrow(EXP), nc = nrow(trait)): partial argument match of 'nr' to 'nrow' gene.trait.pvalue: warning in matrix(0, nr = nrow(EXP), nc = nrow(trait)): partial argument match of 'nc' to 'ncol' gene.trait.pvalue : fi: warning in matrix(1:nrow(trait), nc = 1): partial argument match of 'nc' to 'ncol' gene.trait.pvalue: warning in matrix(1:nrow(EXP), nc = 1): partial argument match of 'nc' to 'ncol' gene.trait.pvalue : fi: warning in matrix(1:ncol(real), nc = 1): partial argument match of 'nc' to 'ncol' gene.trait.pvalue: warning in matrix(1:nrow(real), nc = 1): partial argument match of 'nc' to 'ncol' gene.trait.pvalue : fj: warning in matrix(1:nrow(real), nc = 1): partial argument match of 'nc' to 'ncol' gene.trait.pvalue: warning in matrix(1:ncol(real), nc = 1): partial argument match of 'nc' to 'ncol' gene.pvalue: multiple local function definitions for ‘fi’ with different formal arguments gene.similarity : s.similarity: no visible global function definition for ‘build.mim’ gene.similarity : s.similarity: no visible global function definition for ‘mrnet’ gene.similarity : s.similarity: no visible global function definition for ‘aracne’ gene.similarity : s.similarity: no visible global function definition for ‘clr’ gene.trait.pvalue: multiple local function definitions for ‘fi’ with different formal arguments Undefined global functions or variables: aracne build.mim clr mrnet * checking Rd files ... NOTE checkRd: (-1) pred.network.Rd:15: Lost braces 15 | A MxM matrix of the predicted network, where cell emph{ij} infers a link between gene i and j and set 0 when the p-value is not significant (no link). | ^ * 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’ ... OK * 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-3.19-bioc/meat/BUS.Rcheck/00check.log’ for details.