############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:diggit.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings diggit_1.24.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.13-bioc/meat/diggit.Rcheck’ * using R version 4.1.1 (2021-08-10) * using platform: x86_64-apple-darwin17.0 (64-bit) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘diggit/DESCRIPTION’ ... OK * this is package ‘diggit’ version ‘1.24.0’ * 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 ... NOTE Found the following hidden files and directories: .git_fetch_output.txt .git_merge_output.txt These were most likely included in error. See section ‘Package structure’ in the ‘Writing R Extensions’ manual. * checking for portable file names ... OK * checking for sufficient/correct file permissions ... OK * checking whether package ‘diggit’ can be installed ... OK * checking installed package size ... OK * checking package directory ... OK * checking ‘build’ directory ... OK * checking DESCRIPTION meta-information ... NOTE Malformed Description field: should contain one or more complete sentences. * checking top-level files ... OK * checking for left-over files ... OK * checking index information ... OK * checking package subdirectories ... WARNING Invalid citation information in ‘inst/CITATION’: Error in citeEntry(entry = "article", author = c(person(c("Mariano", "J"), "Alvarez"), person(c("James", "C"), "Chen"), person("Andrea", "Califano")), title = "{DIGGIT}: a Bioconductor package to infer genetic variants driving cellular phenotypes", journal = "Bioinformatics", year = 2015, volume = 31, number = 24, pages = "4032--4", textVersion = "Alvarez, M.J., Chen, J.C., and Califano, A. (2015) DIGGIT: a Bioconductor package to infer genetic variants driving cellular phenotypes. Bioinformatics 31(24):4032--4."): could not find function "citeEntry" * 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 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 aecdf: no visible global function definition for ‘quantile’ aecdf: no visible global function definition for ‘ecdf’ aecdf: no visible global function definition for ‘knots’ aecdf: no visible global function definition for ‘lm’ aecdf: no visible global function definition for ‘approxfun’ aecdf : dnull: no visible global function definition for ‘predict’ aecdf : dnull: no visible global function definition for ‘qnorm’ conditionalInternal: no visible global function definition for ‘p.adjust’ conditionalInternal : : no visible global function definition for ‘fisher.test’ conditionalInternal: no visible global function definition for ‘hclust’ conditionalInternal: no visible global function definition for ‘as.dist’ conditionalInternal: no visible global function definition for ‘cutree’ conditionalInternal : : : : no visible global function definition for ‘fisher.test’ conditionalInternal : : : no visible global function definition for ‘fisher.test’ correlation : : no visible global function definition for ‘cor’ correlation: no visible global function definition for ‘cor’ cortest: no visible global function definition for ‘pnorm’ distMode: no visible global function definition for ‘density’ fet: no visible global function definition for ‘fisher.test’ internalMIfb: no visible global function definition for ‘dnorm’ mutualInfo: no visible global function definition for ‘qnorm’ mutualInfo: no visible global function definition for ‘combn’ mutualInfo: no visible global function definition for ‘txtProgressBar’ mutualInfo : : no visible global function definition for ‘setTxtProgressBar’ plothm: no visible global function definition for ‘rgb2hsv’ plothm: no visible global function definition for ‘col2rgb’ plothm: no visible global function definition for ‘hsv’ plothm: no visible global function definition for ‘image’ plothm: no visible global function definition for ‘box’ aqtl,diggit: no visible global function definition for ‘p.adjust’ aqtl,diggit: no visible global function definition for ‘pnorm’ conditional,diggit: no visible global function definition for ‘p.adjust’ conditional,diggit: no visible global function definition for ‘pnorm’ conditional,diggit: no visible global function definition for ‘txtProgressBar’ conditional,diggit : : no visible global function definition for ‘setTxtProgressBar’ marina,matrix: no visible global function definition for ‘qnorm’ mindyFiltering,diggit: no visible global function definition for ‘p.adjust’ plot,diggit-ANY: no visible global function definition for ‘abline’ plot,diggit-ANY: no visible global function definition for ‘text’ plot,diggit-ANY: no visible global function definition for ‘axis’ Undefined global functions or variables: abline approxfun as.dist axis box col2rgb combn cor cutree density dnorm ecdf fisher.test hclust hsv image knots lm p.adjust pnorm predict qnorm quantile rgb2hsv setTxtProgressBar text txtProgressBar Consider adding importFrom("grDevices", "col2rgb", "hsv", "rgb2hsv") importFrom("graphics", "abline", "axis", "box", "image", "text") importFrom("stats", "approxfun", "as.dist", "cor", "cutree", "density", "dnorm", "ecdf", "fisher.test", "hclust", "knots", "lm", "p.adjust", "pnorm", "predict", "qnorm", "quantile") importFrom("utils", "combn", "setTxtProgressBar", "txtProgressBar") to your NAMESPACE file. * checking Rd files ... OK * checking Rd metadata ... OK * checking Rd cross-references ... OK * checking for missing documentation entries ... WARNING Undocumented S4 methods: generic 'plot' and siglist 'diggit,ANY' All user-level objects in a package (including S4 classes and methods) should have documentation entries. See chapter ‘Writing R documentation files’ in the ‘Writing R Extensions’ manual. * checking for code/documentation mismatches ... WARNING Codoc mismatches from documentation object 'aecdf': aecdf Code: function(dnull, symmetric = FALSE, n = 100) Docs: function(dnull, symmetric = FALSE) Argument names in code not in docs: n * checking Rd \usage sections ... OK * checking Rd contents ... OK * checking for unstated dependencies in examples ... 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 marina-methods 115.908 24.008 47.977 conditional-methods 17.077 2.030 19.120 diggit-plot 16.898 1.831 18.744 aqtl-methods 15.186 2.375 17.639 diggit-methods 6.789 0.220 7.013 * checking for unstated dependencies in vignettes ... OK * checking package vignettes in ‘inst/doc’ ... OK * checking running R code from vignettes ... SKIPPED * checking re-building of vignette outputs ... SKIPPED * checking PDF version of manual ... OK * DONE Status: 3 WARNINGs, 3 NOTEs See ‘/Users/biocbuild/bbs-3.13-bioc/meat/diggit.Rcheck/00check.log’ for details.