############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD check --install=check:DaMiRseq.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings DaMiRseq_2.19.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/DaMiRseq.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 ‘DaMiRseq/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘DaMiRseq’ version ‘2.19.0’ * package encoding: UTF-8 * checking package namespace information ... OK * checking package dependencies ... INFO Imports includes 24 non-default packages. Importing from so many packages makes the package vulnerable to any of them becoming unavailable. Move as many as possible to Suggests and use conditionally. * 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 ‘DaMiRseq’ 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/DaMiRseq.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 DaMiR.Clustplot: warning in pheatmap(count_data, clustering_distance_rows = d_r, clustering_distance_cols = d_c, scale = "row", col = colors, annotation_col = df): partial argument match of 'col' to 'color' DaMiR.Allplot: no visible binding for global variable ‘X1’ DaMiR.Allplot: no visible binding for global variable ‘X2’ DaMiR.Allplot: no visible binding for global variable ‘PC1’ DaMiR.Allplot: no visible binding for global variable ‘PC2’ DaMiR.Allplot: no visible binding for global variable ‘value’ DaMiR.Allplot: no visible binding for global variable ‘variable’ DaMiR.EnsembleLearning2cl: no visible binding for global variable ‘Classifiers’ DaMiR.EnsembleLearning2cl: no visible binding for global variable ‘Accuracy’ DaMiR.EnsembleLearning2cl: no visible binding for global variable ‘MCC’ DaMiR.EnsembleLearning2cl: no visible binding for global variable ‘Specificity’ DaMiR.EnsembleLearning2cl: no visible binding for global variable ‘Sensitivity’ DaMiR.EnsembleLearning2cl: no visible binding for global variable ‘PPV’ DaMiR.EnsembleLearning2cl: no visible binding for global variable ‘NPV’ DaMiR.EnsembleLearning2cl: no visible global function definition for ‘colSds’ DaMiR.EnsembleLearningNcl: no visible binding for global variable ‘Classifiers’ DaMiR.EnsembleLearningNcl: no visible binding for global variable ‘Accuracy’ DaMiR.EnsembleLearningNcl: no visible global function definition for ‘colSds’ DaMiR.MDSplot: no visible binding for global variable ‘X1’ DaMiR.MDSplot: no visible binding for global variable ‘X2’ DaMiR.ModelSelect: no visible binding for global variable ‘Metrics’ DaMiR.ModelSelect: no visible binding for global variable ‘N.predictors’ DaMiR.ModelSelect: no visible binding for global variable ‘Counts’ DaMiR.iTSadjust: no visible binding for global variable ‘value’ DaMiR.iTSadjust: no visible binding for global variable ‘variable’ DaMiR.iTSnorm: no visible binding for global variable ‘value’ DaMiR.iTSnorm: no visible binding for global variable ‘variable’ Undefined global functions or variables: Accuracy Classifiers Counts MCC Metrics N.predictors NPV PC1 PC2 PPV Sensitivity Specificity X1 X2 colSds value variable * checking Rd files ... OK * checking Rd metadata ... OK * checking Rd cross-references ... NOTE Found the following Rd file(s) with Rd \link{} targets missing package anchors: DaMiR.FReduct.Rd: rcorr, findCorrelation DaMiR.FSelect.Rd: bve_pls DaMiR.FSort.Rd: relief DaMiR.SV.Rd: sva DaMiR.SVadjust.Rd: removeBatchEffect DaMiR.corrplot.Rd: rcorr, corrplot DaMiR.iTSadjust.Rd: ComBat DaMiR.iTSnorm.Rd: dispersionFunction, varianceStabilizingTransformation, rlog, cpm DaMiR.makeSE.Rd: SummarizedExperiment DaMiR.normalization.Rd: varianceStabilizingTransformation, rlog Please provide package anchors for all Rd \link{} targets not in the package itself and the base packages. * 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 ... NOTE Warning: program compiled against libxml 212 using older 211 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 ... OK * checking for unstated dependencies in examples ... OK * checking contents of ‘data’ directory ... OK * checking data for non-ASCII characters ... OK * checking LazyData ... OK * checking data for ASCII and uncompressed saves ... OK * checking files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed DaMiR.Allplot 7.213 0.199 7.424 * 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: 5 WARNINGs, 6 NOTEs See ‘/home/biocbuild/bbs-3.21-bioc/meat/DaMiRseq.Rcheck/00check.log’ for details.