############################################################################## ############################################################################## ### ### Running command: ### ### D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:ConsensusClusterPlus.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings ConsensusClusterPlus_1.59.0.tar.gz ### ############################################################################## ############################################################################## * using log directory 'D:/biocbuild/bbs-3.15-bioc/meat/ConsensusClusterPlus.Rcheck' * using R Under development (unstable) (2021-11-21 r81221) * using platform: x86_64-w64-mingw32 (64-bit) * using session charset: ISO8859-1 * using option '--no-vignettes' * checking for file 'ConsensusClusterPlus/DESCRIPTION' ... OK * checking extension type ... Package * this is package 'ConsensusClusterPlus' version '1.59.0' * 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 whether package 'ConsensusClusterPlus' 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. Non-standard license specification: GPL version 2 Standardizable: TRUE Standardized license specification: GPL-2 * 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 dependencies in R code ... NOTE Namespace in Imports field not imported from: 'ALL' All declared Imports should be used. * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE ConsensusClusterPlus: warning in heatmap(pc, Colv = NA, Rowv = NA, symm = FALSE, scale = "none", col = tmyPal, na.rm = TRUE, labRow = F, labCol = F, mar = c(5, 5), main = paste("consensus matrix k=", tk, sep = ""), ColSideCol = oc): partial argument match of 'mar' to 'margins' ConsensusClusterPlus: warning in heatmap(pc, Colv = NA, Rowv = NA, symm = FALSE, scale = "none", col = tmyPal, na.rm = TRUE, labRow = F, labCol = F, mar = c(5, 5), main = paste("consensus matrix k=", tk, sep = ""), ColSideCol = oc): partial argument match of 'ColSideCol' to 'ColSideColors' ConsensusClusterPlus: warning in heatmap(pc, Colv = as.dendrogram(hc), Rowv = NA, symm = FALSE, scale = "none", col = tmyPal, na.rm = TRUE, labRow = F, labCol = F, mar = c(5, 5), main = paste("consensus matrix k=", tk, sep = ""), ColSideCol = colorList[[1]]): partial argument match of 'mar' to 'margins' ConsensusClusterPlus: warning in heatmap(pc, Colv = as.dendrogram(hc), Rowv = NA, symm = FALSE, scale = "none", col = tmyPal, na.rm = TRUE, labRow = F, labCol = F, mar = c(5, 5), main = paste("consensus matrix k=", tk, sep = ""), ColSideCol = colorList[[1]]): partial argument match of 'ColSideCol' to 'ColSideColors' ConsensusClusterPlus: no visible global function definition for 'bitmap' ConsensusClusterPlus: no visible global function definition for 'postscript' calcICL: no visible global function definition for 'postscript' calcICL: no visible global function definition for 'bitmap' Undefined global functions or variables: bitmap postscript Consider adding importFrom("grDevices", "bitmap", "postscript") 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 files in 'vignettes' ... OK * checking examples ... OK * 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 NOTEs See 'D:/biocbuild/bbs-3.15-bioc/meat/ConsensusClusterPlus.Rcheck/00check.log' for details.