############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:PloGO2.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/site-library --timings PloGO2_1.12.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/PloGO2.Rcheck’ * using R version 4.3.1 (2023-06-16) * using platform: x86_64-pc-linux-gnu (64-bit) * R was compiled by gcc (Ubuntu 11.3.0-1ubuntu1~22.04.1) 11.3.0 GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04.1) 11.3.0 * running under: Ubuntu 22.04.3 LTS * using session charset: UTF-8 * checking for file ‘PloGO2/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘PloGO2’ version ‘1.12.0’ * 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 ‘PloGO2’ 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 loading without being on the library search path ... OK * checking dependencies in R code ... OK * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE Children: no visible global function definition for ‘Ontology’ ExcelToPloGO: no visible binding for global variable ‘Term’ ExcelToPloGO: no visible binding for global variable ‘Ontology’ GOGraphWrapper: no visible global function definition for ‘Ontology’ GOParent: no visible global function definition for ‘Ontology’ GOTermList: no visible global function definition for ‘Ontology’ PloGO: no visible global function definition for ‘read.delim’ PloGO: no visible global function definition for ‘unzip’ PloGO: no visible global function definition for ‘read.csv’ PloPathway: no visible global function definition for ‘unzip’ PloPathway : : no visible global function definition for ‘read.table’ PloPathway: no visible global function definition for ‘read.csv’ abundancePlot: no visible binding for global variable ‘eps’ aggregateAbundance : : no visible global function definition for ‘Term’ aggregateAbundance : : no visible global function definition for ‘aggregate’ annotationPlot : : no visible global function definition for ‘Term’ compareAnnot: no visible global function definition for ‘fisher.test’ compareAnnot : : no visible global function definition for ‘Term’ compareAnnot: no visible global function definition for ‘p.adjust’ countAndAbundance: no visible global function definition for ‘par’ countAndAbundance: no visible global function definition for ‘barplot’ countAndAbundance: no visible global function definition for ‘axTicks’ countAndAbundance: no visible global function definition for ‘axis’ countAndAbundance: no visible global function definition for ‘title’ genAnnotationFiles: no visible global function definition for ‘read.csv’ genAnnotationFiles: no visible global function definition for ‘write.table’ genWegoFile: no visible global function definition for ‘useMart’ genWegoFile: no visible global function definition for ‘useDataset’ genWegoFile: no visible global function definition for ‘getBM’ genWegoFile: no visible global function definition for ‘aggregate’ genWegoFile: no visible global function definition for ‘write.table’ getGoID: no visible binding for global variable ‘Term’ getUniprotBatch: no visible binding for global variable ‘IDList’ inGraph: no visible global function definition for ‘nodes’ plotAbundanceBar: no visible global function definition for ‘par’ plotAbundanceBar: no visible global function definition for ‘barplot’ plotAbundanceBar: no visible global function definition for ‘rainbow’ plotAbundanceBar: no visible global function definition for ‘legend’ plotMat: no visible global function definition for ‘colorRampPalette’ plotMat : : no visible global function definition for ‘Term’ processAnnotFile: no visible global function definition for ‘read.csv’ processGoFile : : no visible global function definition for ‘Term’ processGoFile: no visible global function definition for ‘read.csv’ processPathFile: no visible global function definition for ‘read.csv’ read.annot.file: no visible global function definition for ‘read.table’ read.annot.file: no visible global function definition for ‘aggregate’ tabulateAnnot : : no visible global function definition for ‘Term’ writeGOannot: no visible global function definition for ‘read.csv’ writeGOannot: no visible global function definition for ‘write.csv’ writeGOannot: no visible global function definition for ‘write.table’ Undefined global functions or variables: IDList Ontology Term aggregate axTicks axis barplot colorRampPalette eps fisher.test getBM legend nodes p.adjust par rainbow read.csv read.delim read.table title unzip useDataset useMart write.csv write.table Consider adding importFrom("grDevices", "colorRampPalette", "rainbow") importFrom("graphics", "axTicks", "axis", "barplot", "legend", "par", "title") importFrom("stats", "aggregate", "fisher.test", "p.adjust") importFrom("utils", "read.csv", "read.delim", "read.table", "unzip", "write.csv", "write.table") 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 R/sysdata.rda ... OK * checking files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed PloGO 34.613 0.620 35.262 abundancePlot 22.291 0.264 22.522 writeAnnotation 17.689 0.144 17.833 processAnnotation 17.290 0.155 17.446 getGoID 15.832 0.116 15.948 processGoFile 10.089 0.056 10.144 * checking for unstated dependencies in vignettes ... OK * checking package vignettes in ‘inst/doc’ ... OK * checking running R code from vignettes ... ‘PloGO2_vignette.Rnw’... OK ‘PloGO2_with_WGNCA_vignette.Rnw’... failed WARNING Errors in running code in vignettes: when running code in ‘PloGO2_with_WGNCA_vignette.Rnw’ ... \hline \end{tabular} \end{table} > source(file.path(system.file("script", package = "PloGO2"), + "WGCNA_proteomics.R")) When sourcing ‘PloGO2_with_WGNCA_vignette.R’: Error: there is no package called ‘heatmap3’ Execution halted * checking re-building of vignette outputs ... NOTE Error(s) in re-building vignettes: --- re-building ‘PloGO2_vignette.Rnw’ using Sweave Loading required package: GO.db Loading required package: AnnotationDbi Loading required package: stats4 Loading required package: BiocGenerics Attaching package: ‘BiocGenerics’ The following objects are masked from ‘package:stats’: IQR, mad, sd, var, xtabs The following objects are masked from ‘package:base’: Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append, as.data.frame, basename, cbind, colnames, dirname, do.call, duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted, lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table, tapply, union, unique, unsplit, which.max, which.min Loading required package: Biobase Welcome to Bioconductor Vignettes contain introductory material; view with 'browseVignettes()'. To cite Bioconductor, see 'citation("Biobase")', and for packages 'citation("pkgname")'. Loading required package: IRanges Loading required package: S4Vectors Attaching package: ‘S4Vectors’ The following object is masked from ‘package:utils’: findMatches The following objects are masked from ‘package:base’: I, expand.grid, unname Loading required package: GOstats Loading required package: Category Loading required package: Matrix Attaching package: ‘Matrix’ The following object is masked from ‘package:S4Vectors’: expand Loading required package: graph Attaching package: ‘GOstats’ The following object is masked from ‘package:AnnotationDbi’: makeGOGraph No encoding supplied: defaulting to UTF-8. --- finished re-building ‘PloGO2_vignette.Rnw’ --- re-building ‘PloGO2_with_WGNCA_vignette.Rnw’ using Sweave Loading required package: GO.db Loading required package: AnnotationDbi Loading required package: stats4 Loading required package: BiocGenerics Attaching package: ‘BiocGenerics’ The following objects are masked from ‘package:stats’: IQR, mad, sd, var, xtabs The following objects are masked from ‘package:base’: Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append, as.data.frame, basename, cbind, colnames, dirname, do.call, duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted, lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table, tapply, union, unique, unsplit, which.max, which.min Loading required package: Biobase Welcome to Bioconductor Vignettes contain introductory material; view with 'browseVignettes()'. To cite Bioconductor, see 'citation("Biobase")', and for packages 'citation("pkgname")'. Loading required package: IRanges Loading required package: S4Vectors Attaching package: ‘S4Vectors’ The following object is masked from ‘package:utils’: findMatches The following objects are masked from ‘package:base’: I, expand.grid, unname Loading required package: GOstats Loading required package: Category Loading required package: Matrix Attaching package: ‘Matrix’ The following object is masked from ‘package:S4Vectors’: expand Loading required package: graph Attaching package: ‘GOstats’ The following object is masked from ‘package:AnnotationDbi’: makeGOGraph Error: processing vignette 'PloGO2_with_WGNCA_vignette.Rnw' failed with diagnostics: chunk 2 (label = wgcnaplots) Error in library(heatmap3) : there is no package called ‘heatmap3’ --- failed re-building ‘PloGO2_with_WGNCA_vignette.Rnw’ SUMMARY: processing the following file failed: ‘PloGO2_with_WGNCA_vignette.Rnw’ Error: Vignette re-building failed. Execution halted * checking PDF version of manual ... OK * DONE Status: 1 WARNING, 2 NOTEs See ‘/home/biocbuild/bbs-3.17-bioc/meat/PloGO2.Rcheck/00check.log’ for details.