############################################################################## ############################################################################## ### ### 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_1.30.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/Pigengene.Rcheck’ * using R version 4.4.0 (2024-04-24) * using platform: x86_64-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 Monterey 12.7.1 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘Pigengene/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘Pigengene’ version ‘1.30.0’ * 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:22-23: Lost braces in \itemize; meant \describe ? checkRd: (-1) pigengene-class.Rd:24-26: Lost braces in \itemize; meant \describe ? checkRd: (-1) pigengene-class.Rd:27-34: Lost braces in \itemize; meant \describe ? checkRd: (-1) pigengene-class.Rd:35-36: Lost braces in \itemize; meant \describe ? checkRd: (-1) pigengene-class.Rd:37-39: Lost braces in \itemize; meant \describe ? checkRd: (-1) pigengene-class.Rd:40-42: Lost braces in \itemize; meant \describe ? checkRd: (-1) pigengene-class.Rd:43-44: Lost braces in \itemize; meant \describe ? checkRd: (-1) pigengene-class.Rd:45-47: Lost braces in \itemize; meant \describe ? checkRd: (-1) pigengene-class.Rd:48-50: Lost braces in \itemize; meant \describe ? checkRd: (-1) pigengene-class.Rd:51-52: Lost braces in \itemize; meant \describe ? checkRd: (-1) pigengene-class.Rd:53-54: Lost braces in \itemize; meant \describe ? checkRd: (-1) pigengene-class.Rd:55-58: Lost braces in \itemize; meant \describe ? checkRd: (-1) pigengene-class.Rd:59-63: Lost braces in \itemize; meant \describe ? checkRd: (-1) pigengene-class.Rd:68-71: Lost braces in \itemize; meant \describe ? checkRd: (-1) pigengene-class.Rd:72-74: Lost braces in \itemize; meant \describe ? * 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’ ... OK * checking files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed get.enriched.pw 81.437 6.812 89.552 one.step.pigengene 80.358 2.848 83.913 Pigengene-package 78.891 3.259 82.927 module.heatmap 36.838 2.012 39.396 learn.bn 16.683 0.492 17.355 make.filter 15.541 0.413 16.143 apply.filter 14.763 0.370 15.260 combine.networks 13.887 0.163 14.167 determine.modules 13.711 0.154 13.997 make.decision.tree 12.845 0.700 13.675 compact.tree 12.308 0.674 13.092 wgcna.one.step 12.609 0.145 12.859 gene.mapping 8.331 0.871 14.544 pigengene 7.025 0.635 7.732 plot.pigengene 6.745 0.404 7.213 compute.pigengene 6.658 0.428 7.156 project.eigen 6.289 0.424 6.775 * 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: 3 NOTEs See ‘/Users/biocbuild/bbs-3.19-bioc/meat/Pigengene.Rcheck/00check.log’ for details.