############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:Pigengene.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings Pigengene_1.35.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/Pigengene.Rcheck’ * using R version 4.5.0 Patched (2025-04-21 r88169) * using platform: aarch64-apple-darwin20 * R was compiled by Apple clang version 16.0.0 (clang-1600.0.26.6) GNU Fortran (GCC) 14.2.0 * running under: macOS Ventura 13.7.1 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘Pigengene/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘Pigengene’ version ‘1.35.0’ * 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 ‘Pigengene’ 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 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 'library' or 'require' calls in package code: ‘AnnotationDbi’ ‘biomaRt’ ‘energy’ ‘org.Hs.eg.db’ ‘org.Mm.eg.db’ 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 Found the following possibly unsafe calls: File ‘Pigengene/R/bn.calculation.R’: assignInNamespace("supported.clusters", fixArgs, "bnlearn") one.step.pigengene: no visible binding for global variable ‘org.Hs.eg.db’ Undefined global functions or variables: org.Hs.eg.db * checking Rd files ... NOTE checkRd: (-1) draw.bn.Rd:47: Lost braces 47 | rename the nodes name. See code{rename.node}.} | ^ checkRd: (-1) eigengenes33.Rd:21-22: Lost braces 21 | {A 202 by 34 matrix. | ^ checkRd: (-1) eigengenes33.Rd:25: Lost braces; missing escapes or markup? 25 | {A 164 by 34 matrix for MDS cases with columns similar to aml.} | ^ checkRd: (-1) eigengenes33.Rd:28: Lost braces; missing escapes or markup? 28 | {A numeric vector of length 9166 labeling members of each module. Named by Entrez ID.} | ^ checkRd: (-1) pigengene-class.Rd:25-26: Lost braces in \itemize; meant \describe ? checkRd: (-1) pigengene-class.Rd:27-29: Lost braces in \itemize; meant \describe ? checkRd: (-1) pigengene-class.Rd:30-39: Lost braces in \itemize; meant \describe ? checkRd: (-1) pigengene-class.Rd:40-41: Lost braces in \itemize; meant \describe ? checkRd: (-1) pigengene-class.Rd:42-44: Lost braces in \itemize; meant \describe ? checkRd: (-1) pigengene-class.Rd:45-47: Lost braces in \itemize; meant \describe ? checkRd: (-1) pigengene-class.Rd:48-49: Lost braces in \itemize; meant \describe ? checkRd: (-1) pigengene-class.Rd:50-52: Lost braces in \itemize; meant \describe ? checkRd: (-1) pigengene-class.Rd:53-55: Lost braces in \itemize; meant \describe ? checkRd: (-1) pigengene-class.Rd:56-57: Lost braces in \itemize; meant \describe ? checkRd: (-1) pigengene-class.Rd:58-59: Lost braces in \itemize; meant \describe ? checkRd: (-1) pigengene-class.Rd:60-63: Lost braces in \itemize; meant \describe ? checkRd: (-1) pigengene-class.Rd:64-68: Lost braces in \itemize; meant \describe ? checkRd: (-1) pigengene-class.Rd:73-76: Lost braces in \itemize; meant \describe ? checkRd: (-1) pigengene-class.Rd:77-79: Lost braces in \itemize; meant \describe ? * checking Rd metadata ... OK * checking Rd cross-references ... NOTE Non-topic package-anchored link(s) in Rd file 'draw.bn.Rd': ‘[bnlearn:bn.class]{bn-class}’ Non-topic package-anchored link(s) in Rd file 'gene.mapping.Rd': ‘[org.Hs.eg.db:org.Hs.egBASE]{org.Hs.eg.db}’ ‘[org.Mm.eg.db:org.Mm.egBASE]{org.Mm.eg.db}’ Non-topic package-anchored link(s) in Rd file 'learn.bn.Rd': ‘[bnlearn:preprocessing]{discretize}’ ‘[bnlearn:bn.class]{bn-class}’ See section 'Cross-references' in the 'Writing R Extensions' manual. * 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’ ... OK * checking files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed one.step.pigengene 34.261 1.228 35.706 Pigengene-package 32.808 1.106 33.932 get.enriched.pw 26.508 2.380 28.982 module.heatmap 11.653 0.934 12.611 make.filter 6.749 0.142 6.906 learn.bn 6.750 0.109 6.865 apply.filter 5.985 0.130 6.116 combine.networks 5.935 0.027 5.965 determine.modules 5.872 0.022 5.900 compute.pigengene 5.239 0.380 5.627 wgcna.one.step 5.578 0.018 5.610 gene.mapping 2.511 0.284 8.103 * 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: 4 NOTEs See ‘/Users/biocbuild/bbs-3.22-bioc/meat/Pigengene.Rcheck/00check.log’ for details.