############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:safe.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings safe_3.32.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.13-bioc/meat/safe.Rcheck’ * using R version 4.1.1 (2021-08-10) * using platform: x86_64-apple-darwin17.0 (64-bit) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘safe/DESCRIPTION’ ... OK * this is package ‘safe’ version ‘3.32.0’ * 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: .git_fetch_output.txt .git_merge_output.txt 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 ‘safe’ can be installed ... OK * 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 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 'library' or 'require' call to ‘SparseM’ which was already attached by Depends. Please remove these calls from your code. 'library' or 'require' calls in package code: ‘GO.db’ ‘GOstats’ ‘PFAM.db’ ‘Rgraphviz’ ‘doRNG’ ‘foreach’ ‘reactome.db’ ‘survival’ Please use :: or requireNamespace() instead. See section 'Suggested packages' in the 'Writing R Extensions' manual. * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE getCOXresiduals: no visible global function definition for ‘Surv’ getCOXresiduals: no visible global function definition for ‘coxph’ getCOXresiduals: no visible global function definition for ‘residuals’ getCmatrix: no visible binding for global variable ‘GOTERM’ safe: no visible binding for global variable ‘reactomeEXTID2PATHID’ safe: no visible global function definition for ‘safe.express’ safe: no visible global function definition for ‘getDoParWorkers’ safe: no visible global function definition for ‘%dorng%’ safe: no visible global function definition for ‘foreach’ safe.toptable: no visible binding for global variable ‘GOTERM’ safe.toptable: no visible binding for global variable ‘PFAMSCOP’ safe.toptable: no visible binding for global variable ‘reactome.db’ safedag: no visible binding for global variable ‘GOTERM’ safedag: no visible global function definition for ‘GOGraph’ safedag: no visible global function definition for ‘makeNodeAttrs’ safedag: no visible global function definition for ‘subGraph’ safedag: no visible global function definition for ‘agopen’ safeplot: no visible binding for global variable ‘GOTERM’ safeplot: no visible binding for global variable ‘PFAMID’ Undefined global functions or variables: %dorng% GOGraph GOTERM PFAMID PFAMSCOP Surv agopen coxph foreach getDoParWorkers makeNodeAttrs reactome.db reactomeEXTID2PATHID residuals safe.express subGraph Consider adding importFrom("stats", "residuals") 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 sizes of PDF files under ‘inst/doc’ ... NOTE ‘qpdf’ made some significant size reductions: compacted ‘SAFEmanual3.pdf’ from 778Kb to 382Kb consider running tools::compactPDF() on these files * checking files in ‘vignettes’ ... OK * checking examples ... OK * 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-3.13-bioc/meat/safe.Rcheck/00check.log’ for details.