############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:Pigengene.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings Pigengene_1.33.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/Pigengene.Rcheck’ * using R Under development (unstable) (2025-01-20 r87609) * using platform: x86_64-pc-linux-gnu * R was compiled by gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0 GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0 * running under: Ubuntu 24.04.1 LTS * using session charset: UTF-8 * checking for file ‘Pigengene/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘Pigengene’ version ‘1.33.0’ * 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 loading without being on the library search path ... 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 ... 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 files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed one.step.pigengene 77.197 0.784 77.985 Pigengene-package 73.368 1.206 74.545 get.enriched.pw 62.595 3.674 66.292 module.heatmap 36.881 0.513 37.389 learn.bn 15.781 0.255 16.027 make.filter 14.472 0.249 14.725 apply.filter 13.986 0.278 14.265 combine.networks 13.885 0.010 13.890 determine.modules 13.614 0.004 13.620 wgcna.one.step 12.665 0.013 12.678 compute.pigengene 11.777 0.207 11.985 make.decision.tree 10.741 0.102 10.843 compact.tree 10.614 0.087 10.702 gene.mapping 6.959 1.344 22.862 pigengene 6.589 0.108 6.697 plot.pigengene 6.175 0.055 6.230 project.eigen 5.821 0.043 5.865 * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking re-building of vignette outputs ... OK * checking PDF version of manual ... OK * DONE Status: 3 NOTEs See ‘/home/biocbuild/bbs-3.21-bioc/meat/Pigengene.Rcheck/00check.log’ for details.