############################################################################## ############################################################################## ### ### 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_1.31.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/Pigengene.Rcheck’ * using R version 4.4.0 Patched (2024-04-24 r86482) * 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 12.7.4 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘Pigengene/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘Pigengene’ version ‘1.31.0’ * 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 136.482 12.243 184.766 one.step.pigengene 105.490 2.991 127.112 Pigengene-package 102.774 3.508 139.745 module.heatmap 78.678 2.431 97.662 make.decision.tree 21.963 0.669 27.021 compact.tree 20.935 0.672 26.642 learn.bn 18.710 0.582 23.806 make.filter 17.421 0.381 20.799 apply.filter 16.451 0.359 22.147 gene.mapping 14.397 1.493 30.638 combine.networks 15.238 0.154 19.660 determine.modules 14.846 0.118 17.655 wgcna.one.step 13.661 0.094 15.806 pigengene 10.529 0.848 13.223 plot.pigengene 10.700 0.460 13.787 compute.pigengene 10.236 0.517 12.640 project.eigen 9.603 0.425 11.647 * 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-3.20-bioc/meat/Pigengene.Rcheck/00check.log’ for details.