############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD check --install=check:canceR.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings canceR_1.41.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/canceR.Rcheck’ * using R Under development (unstable) (2024-11-24 r87369) * using platform: aarch64-unknown-linux-gnu * R was compiled by aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0 GNU Fortran (GCC) 14.2.0 * running under: openEuler 24.03 (LTS) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘canceR/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘canceR’ version ‘1.41.0’ * 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 ‘canceR’ can be installed ... WARNING Found the following significant warnings: Warning: program compiled against libxml 212 using older 211 See ‘/home/biocbuild/bbs-3.21-bioc/meat/canceR.Rcheck/00install.out’ for details. * 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 ... NOTE Warning: program compiled against libxml 212 using older 211 A namespace must be able to be loaded with just the base namespace loaded: otherwise if the namespace gets loaded by a saved object, the session will be unable to start. Probably some imports need to be declared in the NAMESPACE file. * 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 Warning: program compiled against libxml 212 using older 211 * checking S3 generic/method consistency ... WARNING Warning: program compiled against libxml 212 using older 211 See section ‘Generic functions and methods’ in the ‘Writing R Extensions’ manual. * checking replacement functions ... WARNING Warning: program compiled against libxml 212 using older 211 The argument of a replacement function which corresponds to the right hand side must be named ‘value’. * checking foreign function calls ... NOTE Warning: program compiled against libxml 212 using older 211 See chapter ‘System and foreign language interfaces’ in the ‘Writing R Extensions’ manual. * checking R code for possible problems ... NOTE Warning: program compiled against libxml 212 using older 211 * checking Rd files ... OK * checking Rd metadata ... OK * checking Rd cross-references ... OK * checking for missing documentation entries ... WARNING Warning: program compiled against libxml 212 using older 211 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 Warning: program compiled against libxml 212 using older 211 Warning: program compiled against libxml 212 using older 211 Warning: program compiled against libxml 212 using older 211 * checking Rd \usage sections ... WARNING Objects in \usage without \alias in Rd file 'dialogSpecificMut.Rd': ‘getSpecificMut’ Functions with \usage entries need to have the appropriate \alias entries, and all their arguments documented. The \usage entries must correspond to syntactically valid R code. See chapter ‘Writing R documentation files’ in the ‘Writing R Extensions’ manual. Warning: program compiled against libxml 212 using older 211 S3 methods shown with full name in Rd file 'cbind.na.Rd': ‘cbind.na’ S3 methods shown with full name in Rd file 'rbind.na.Rd': ‘rbind.na’ The \usage entries for S3 methods should use the \method markup and not their full name. See chapter ‘Writing R documentation files’ in the ‘Writing R Extensions’ manual. * checking Rd contents ... NOTE Argument items with no description in Rd file 'GSEA.EnrichmentScore.Rd': ‘gene.list’ ‘gene.set’ ‘weighted.score.type’ ‘correl.vector’ Argument items with no description in Rd file 'GSEA.EnrichmentScore2.Rd': ‘gene.list’ ‘gene.set’ ‘weighted.score.type’ ‘correl.vector’ Argument items with no description in Rd file 'GSEA.Gct2Frame.Rd': ‘filename’ Argument items with no description in Rd file 'GSEA.Gct2Frame2.Rd': ‘filename’ Argument items with no description in Rd file 'GSEA.GeneRanking.Rd': ‘A’ ‘class.labels’ ‘gene.labels’ ‘nperm’ ‘permutation.type’ ‘sigma.correction’ ‘fraction’ ‘replace’ ‘reverse.sign’ Argument items with no description in Rd file 'GSEA.NormalizeCols.Rd': ‘V’ Argument items with no description in Rd file 'GSEA.NormalizeRows.Rd': ‘V’ Argument items with no description in Rd file 'GSEA.ReadClsFile.Rd': ‘file’ Argument items with no description in Rd file 'GSEA.Res2Frame.Rd': ‘filename’ Argument items with no description in Rd file 'GSEA.Threshold.Rd': ‘V’ ‘thres’ ‘ceil’ Argument items with no description in Rd file 'GSEA.VarFilter.Rd': ‘V’ ‘fold’ ‘delta’ ‘gene.names’ Argument items with no description in Rd file 'GSEA.write.gct.Rd': ‘gct’ ‘filename’ Argument items with no description in Rd file 'OLD.GSEA.EnrichmentScore.Rd': ‘gene.list’ ‘gene.set’ * checking for unstated dependencies in examples ... OK * checking files in ‘vignettes’ ... OK * checking examples ... OK * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘testthat.R’ 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: 6 WARNINGs, 5 NOTEs See ‘/home/biocbuild/bbs-3.21-bioc/meat/canceR.Rcheck/00check.log’ for details.