############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:BioTIP.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings BioTIP_1.18.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/BioTIP.Rcheck’ * using R version 4.4.0 beta (2024-04-14 r86421) * 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 ‘BioTIP/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘BioTIP’ version ‘1.18.0’ * package encoding: UTF-8 * 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 ‘BioTIP’ 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 ... OK * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE BioTIP.wrap: warning in getMaxMCImember(membersL[["members"]], membersL[["MCI"]], min = getTopMCI.gene.minsize, n = n.getMaxMCImember): partial argument match of 'min' to 'minsize' getCluster: warning in cluster_walktrap(igraphL[[i]], weight = abs(E(igraphL[[i]])$weight), steps = steps[i]): partial argument match of 'weight' to 'weights' BioTIP.wrap: no visible global function definition for ‘assayNames’ BioTIP.wrap : myplotIc: no visible global function definition for ‘pdf’ BioTIP.wrap : myplotIc: no visible global function definition for ‘par’ BioTIP.wrap : myplotIc: no visible global function definition for ‘text’ BioTIP.wrap : myplotIc: no visible global function definition for ‘dev.off’ BioTIP.wrap: no visible global function definition for ‘getTopHVGs’ BioTIP.wrap: no visible global function definition for ‘normalized_counts’ BioTIP.wrap: no visible global function definition for ‘logcounts’ BioTIP.wrap: no visible global function definition for ‘pdf’ BioTIP.wrap: no visible global function definition for ‘abline’ BioTIP.wrap: no visible global function definition for ‘dev.off’ BioTIP.wrap: no visible global function definition for ‘par’ BioTIP.wrap: no visible binding for global variable ‘getTopMCI.gene.maxsiz’ cor.shrink: no visible binding for global variable ‘sd’ getBiotypes: no visible global function definition for ‘is’ getBiotypes: no visible global function definition for ‘queryHits’ getBiotypes: no visible global function definition for ‘subjectHits’ getBiotypes: no visible global function definition for ‘aggregate’ getCluster_methods : : no visible global function definition for ‘hclust’ getCluster_methods : : no visible global function definition for ‘dist’ getCluster_methods: no visible global function definition for ‘par’ getCluster_methods : : no visible global function definition for ‘cutree’ getIc : : no visible global function definition for ‘cor’ getMCI : : no visible global function definition for ‘cor’ getMCI : : no visible binding for global variable ‘sd’ getMCI_inner : : no visible global function definition for ‘cor’ getMCI_inner : : no visible binding for global variable ‘sd’ getNextMaxStats: no visible binding for global variable ‘maxMCIms’ getReadthrough: no visible global function definition for ‘subjectHits’ getReadthrough: no visible binding for global variable ‘readthrough’ getReadthrough : : no visible global function definition for ‘queryHits’ getReadthrough : : no visible global function definition for ‘subjectHits’ optimize.sd_selection: no visible binding for global variable ‘pb’ optimize.sd_selection : : no visible binding for global variable ‘sd’ optimize.sd_selection : : : no visible global function definition for ‘sd’ plot_Ic_Simulation: no visible global function definition for ‘matplot’ plot_Ic_Simulation: no visible global function definition for ‘boxplot’ plot_Ic_Simulation: no visible global function definition for ‘points’ plot_Ic_Simulation: no visible global function definition for ‘mtext’ plot_Ic_Simulation: no visible global function definition for ‘axis’ plot_Ic_Simulation: no visible global function definition for ‘abline’ plot_MCI_Simulation: no visible global function definition for ‘boxplot’ plot_MCI_Simulation: no visible global function definition for ‘axis’ plot_MCI_Simulation: no visible global function definition for ‘points’ plot_MCI_Simulation: no visible global function definition for ‘abline’ plot_SS_Simulation: no visible global function definition for ‘density’ plot_SS_Simulation: no visible global function definition for ‘abline’ plot_SS_Simulation: no visible global function definition for ‘legend’ plotBar_MCI: no visible global function definition for ‘par’ plotBar_MCI: no visible global function definition for ‘barplot’ plotBar_MCI: no visible global function definition for ‘rainbow’ plotBar_MCI: no visible global function definition for ‘title’ plotBar_MCI: no visible global function definition for ‘text’ plotIc: no visible global function definition for ‘matplot’ plotIc: no visible global function definition for ‘axis’ plotMaxMCI: no visible global function definition for ‘is’ plotMaxMCI: no visible global function definition for ‘matplot’ plotMaxMCI: no visible global function definition for ‘text’ plotMaxMCI: no visible global function definition for ‘axis’ sd_selection : : no visible binding for global variable ‘sd’ sd_selection: no visible binding for global variable ‘sd’ sd_selection: no visible binding for global variable ‘i’ simulation_Ic_sample: no visible global function definition for ‘density’ simulation_Ic_sample: no visible global function definition for ‘abline’ simulation_Ic_sample: no visible global function definition for ‘text’ Undefined global functions or variables: abline aggregate assayNames axis barplot boxplot cor cutree density dev.off dist getTopHVGs getTopMCI.gene.maxsiz hclust i is legend logcounts matplot maxMCIms mtext normalized_counts par pb pdf points queryHits rainbow readthrough sd subjectHits text title Consider adding importFrom("graphics", "abline", "axis", "barplot", "boxplot", "legend", "matplot", "mtext", "par", "points", "text", "title") importFrom("grDevices", "dev.off", "pdf", "rainbow") importFrom("methods", "is") importFrom("stats", "aggregate", "cor", "cutree", "density", "dist", "hclust", "sd") to your NAMESPACE file (and ensure that your DESCRIPTION Imports field contains 'methods'). * checking Rd files ... NOTE checkRd: (-1) cod.Rd:11: Lost braces 11 | \item{ranges}{ranges}{chromosome ranges on the genome (10906201-11029719)} | ^ checkRd: (-1) plot_Ic_Simulation.Rd:26: Lost braces; missing escapes or markup? 26 | \item{las}{Numeric in {0, 1, 2, 3}; the style of axis labels. | ^ checkRd: (-1) plot_MCI_Simulation.Rd:23: Lost braces; missing escapes or markup? 23 | \item{las}{Numeric in {0, 1, 2, 3}; the style of axis labels. Default is 0, meaning labels are parallel. | ^ checkRd: (-1) plot_SS_Simulation.Rd:25: Lost braces; missing escapes or markup? 25 | \item{las}{Numeric in {0, 1, 2, 3}; the style of axis labels. | ^ checkRd: (-1) plotIc.Rd:24: Lost braces; missing escapes or markup? 24 | \item{las}{Numeric in {0, 1, 2, 3}; the style of axis labels. | ^ checkRd: (-1) plotMaxMCI.Rd:18: Lost braces; missing escapes or markup? 18 | \item{las}{Numeric in {0, 1, 2, 3}; the style of axis labels. Default is 0, meaning labels are parallel. | ^ * checking Rd metadata ... OK * checking Rd cross-references ... NOTE Package unavailable to check Rd xrefs: ‘TSdist’ * checking for missing documentation entries ... WARNING Undocumented code objects: ‘getNextMaxStats’ ‘getTopMCI’ ‘membersL’ ‘subcounts’ Undocumented data sets: ‘membersL’ ‘subcounts’ All user-level objects in a package 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 Rd file 'avg.cor.shrink.Rd': avg.cor.shrink Code: function(X, Y = NULL, MARGIN = c(1, 2), shrink = TRUE, abs = FALSE, target = 0) Docs: function(X, Y = NULL, MARGIN = c(1, 2), shrink = TRUE, abs = FALSE, target = c("zero", "average", "half")) Mismatches in argument default values: Name: 'target' Code: 0 Docs: c("zero", "average", "half") Codoc mismatches from Rd file 'cor.shrink.Rd': cor.shrink Code: function(X, Y = NULL, MARGIN = c(1, 2), shrink = TRUE, target = 0) Docs: function(X, Y = NULL, MARGIN = c(1, 2), shrink = TRUE, target = c("zero", "average", "half")) Mismatches in argument default values: Name: 'target' Code: 0 Docs: c("zero", "average", "half") Codoc mismatches from Rd file 'getIc.Rd': getIc Code: function(counts, sampleL, genes, output = c("Ic", "PCCg", "PCCs"), fun = c("cor", "BioTIP"), shrink = TRUE, use = c("everything", "all.obs", "complete.obs", "na.or.complete", "pairwise.complete.obs"), PCC_sample.target = 1) Docs: function(counts, sampleL, genes, output = c("Ic", "PCCg", "PCCs"), fun = c("cor", "BioTIP"), shrink = TRUE, use = c("everything", "all.obs", "complete.obs", "na.or.complete", "pairwise.complete.obs")) Argument names in code not in docs: PCC_sample.target Codoc mismatches from Rd file 'getIc.new.Rd': getIc.new Code: function(X, method = c("BioTIP", "Ic"), PCC_sample.target = 1, output = c("Ic", "PCCg", "PCCs")) Docs: function(X, method = c("BioTIP", "Ic"), PCC_sample.target = c("average", "zero", "half"), output = c("IndexScore", "PCCg", "PCCs")) Mismatches in argument default values: Name: 'PCC_sample.target' Code: 1 Docs: c("average", "zero", "half") Name: 'output' Code: c("Ic", "PCCg", "PCCs") Docs: c("IndexScore", "PCCg", "PCCs") Codoc mismatches from Rd file 'getMaxMCImember.Rd': getMaxMCImember Code: function(membersL, MCIl, minsize = 1, n = 1) Docs: function(membersL, MCIl, minsize = 1) Argument names in code not in docs: n Codoc mismatches from Rd file 'plotBar_MCI.Rd': plotBar_MCI Code: function(MCIl, ylim = NULL, nr = 1, nc = NULL, order = NULL, minsize = 3, states = NULL, title.size = 30) Docs: function(MCIl, ylim = NULL, nr = 1, nc = NULL, order = NULL, minsize = 3, states = NULL) Argument names in code not in docs: title.size Codoc mismatches from Rd file 'plotIc.Rd': plotIc Code: function(Ic, las = 0, order = NULL, ylab = "Ic.shrink", col = "black", main = NULL, add = FALSE, ylim = NULL, lty = 1:5, lwd = 1) Docs: function(Ic, las = 0, order = NULL, ylab = "Ic", col = "black", main = NULL, add = FALSE, ylim = NULL, lty = 1:5, lwd = 1) Mismatches in argument default values: Name: 'ylab' Code: "Ic.shrink" Docs: "Ic" Codoc mismatches from Rd file 'plot_Ic_Simulation.Rd': plot_Ic_Simulation Code: function(Ic, simulation, las = 0, ylim = NULL, order = NULL, main = NULL, ylab = "Ic.shrink", fun = c("matplot", "boxplot"), which2point = NULL) Docs: function(Ic, simulation, las = 0, ylim = NULL, order = NULL, main = NULL, ylab = "Ic", fun = c("matplot", "boxplot"), which2point = NULL) Mismatches in argument default values: Name: 'ylab' Code: "Ic.shrink" Docs: "Ic" Codoc mismatches from Rd file 'plot_SS_Simulation.Rd': plot_SS_Simulation Code: function(Ic, simulation, las = 0, xlim = NULL, ylim = NULL, order = NULL, main = "1st max - 2nd max", ylab = "Density") Docs: function(Ic, simulation, las = 0, xlim = NULL, ylim = NULL, order = NULL, main = "1st max - 2nd max", ylab = "1st max - 2nd max") Mismatches in argument default values: Name: 'ylab' Code: "Density" Docs: "1st max - 2nd max" Codoc mismatches from Rd file 'simulationMCI.Rd': simulationMCI Code: function(len, samplesL, df, adjust.size = FALSE, B = 1000, fun = c("cor", "BioTIP"), M = NULL) Docs: function(len, samplesL, df, adjust.size = FALSE, B = 1000, fun = c("cor", "BioTIP")) Argument names in code not in docs: M Codoc mismatches from Rd file 'simulation_Ic.Rd': simulation_Ic Code: function(obs.x, sampleL, counts, B = 1000, fun = c("cor", "BioTIP"), shrink = TRUE, use = c("everything", "all.obs", "complete.obs", "na.or.complete", "pairwise.complete.obs"), output = c("Ic", "PCCg", "PCCs"), PCC_sample.target = 1) Docs: function(obs.x, sampleL, counts, B = 1000, fun = c("cor", "BioTIP"), shrink = TRUE, use = c("everything", "all.obs", "complete.obs", "na.or.complete", "pairwise.complete.obs"), output = c("Ic", "PCCg", "PCCs")) Argument names in code not in docs: PCC_sample.target Codoc mismatches from Rd file 'simulation_Ic_sample.Rd': simulation_Ic_sample Code: function(counts, sampleNo, Ic = NULL, genes, B = 1000, ylim = NULL, main = "simulation of samples", fun = c("cor", "BioTIP"), shrink = TRUE, use = c("everything", "all.obs", "complete.obs", "na.or.complete", "pairwise.complete.obs"), output = c("Ic", "PCCg", "PCCs"), plot = FALSE, PCC_sample.target = 1) Docs: function(counts, sampleNo, Ic = NULL, genes, B = 1000, ylim = NULL, main = "simulation of samples", fun = c("cor", "BioTIP"), shrink = TRUE, use = c("everything", "all.obs", "complete.obs", "na.or.complete", "pairwise.complete.obs"), output = c("Ic", "PCCg", "PCCs"), plot = FALSE) Argument names in code not in docs: PCC_sample.target * 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 ... NOTE Note: found 15 marked UTF-8 strings * checking LazyData ... OK * checking data for ASCII and uncompressed saves ... OK * checking files in ‘vignettes’ ... OK * checking examples ... OK * 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: 2 WARNINGs, 4 NOTEs See ‘/Users/biocbuild/bbs-3.19-bioc/meat/BioTIP.Rcheck/00check.log’ for details.