############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD check --install=check:biomvRCNS.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings biomvRCNS_1.47.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/biomvRCNS.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 ‘biomvRCNS/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘biomvRCNS’ version ‘1.47.0’ * 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 for sufficient/correct file permissions ... OK * checking whether package ‘biomvRCNS’ 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/biomvRCNS.Rcheck/00install.out’ for details. * used C compiler: ‘aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0’ * 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 'library' or 'require' calls in package code: 'GenomicFeatures' 'cluster' 'dynamicTreeCut' 'parallel' Please use :: or requireNamespace() instead. See section 'Suggested packages' in the 'Writing R Extensions' manual. * 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 biomvRGviz: no visible global function definition for 'rainbow' biomvRGviz: no visible global function definition for 'hasArg' biomvRGviz: no visible global function definition for 'graphics.off' biomvRGviz: no visible global function definition for 'setEPS' biomvRGviz: no visible global function definition for 'postscript' biomvRGviz: no visible global function definition for 'pdf' biomvRGviz: no visible global function definition for 'dev.off' biomvRhsmm: no visible global function definition for 'is' biomvRhsmm: no visible binding for global variable 'mclapply' biomvRhsmm : : : no visible global function definition for 'DataFrame' biomvRhsmm : : : no visible global function definition for 'Rle' biomvRhsmm: no visible global function definition for 'DataFrame' biomvRhsmm: no visible binding for global variable 'DataFrame' biomvRhsmm: no visible global function definition for 'new' biomvRmgmr: no visible global function definition for 'seqlevels<-' biomvRmgmr: no visible global function definition for 'DataFrame' biomvRmgmr: no visible global function definition for 'new' biomvRseg: no visible global function definition for 'seqlevels<-' biomvRseg: no visible global function definition for 'DataFrame' biomvRseg: no visible global function definition for 'new' estEmis: no visible global function definition for 'clara' gammaFit: no visible global function definition for 'cov.wt' hsmmRun: no visible global function definition for 'Rle' hsmmRun : : no visible global function definition for 'Rle' hsmmRun: no visible global function definition for 'seqlevels<-' initEmis : : no visible global function definition for 'dpois' initEmis : : no visible global function definition for 'dnorm' initEmis : : no visible global function definition for 'dnbinom' initEmis : : no visible global function definition for 'cov2cor' initEmis : : no visible global function definition for 'dt' initEmis : : no visible global function definition for 'cov.wt' initEmis : : no visible global function definition for 'weighted.mean' initSojDd : : no visible global function definition for 'dgamma' initSojDd : : no visible global function definition for 'dpois' initSojDd : : no visible global function definition for 'dnbinom' maxGapminRun: no visible global function definition for 'Rle' maxGapminRun: no visible global function definition for 'runValue' nbinomCLLDD: no visible global function definition for 'cov.wt' nbinomCLLDD: no visible global function definition for 'dnbinom' poisFit : : no visible global function definition for 'dpois' preClustGrp: no visible global function definition for 'dist' preClustGrp: no visible global function definition for 'hclust' preClustGrp: no visible global function definition for 'cutreeDynamic' regionSegAlphaNB: no visible global function definition for 'mclapply' regionSegCost: no visible global function definition for 'mclapply' simSegData: no visible global function definition for 'runValue' simSegData: no visible global function definition for 'Rle' simSegData: no visible global function definition for 'pdf' simSegData: no visible global function definition for 'ts.plot' simSegData: no visible global function definition for 'dev.off' simUvSegData: no visible global function definition for 'rnorm' simUvSegData: no visible global function definition for 'rt' simUvSegData: no visible global function definition for 'rgamma' simUvSegData: no visible global function definition for 'rpois' simUvSegData: no visible global function definition for 'rnbinom' sojournAnno: no visible global function definition for 'is' sojournAnno: no visible global function definition for 'transcripts' sojournAnno: no visible global function definition for 'seqlengths' sojournAnno: no visible global function definition for 'exons' sojournAnno: no visible global function definition for 'intronsByTranscript' splitFarNeighbouryhat: no visible global function definition for 'runValue' tmvtfFit: no visible global function definition for 'cov.wt' unifMJ : : no visible global function definition for 'dunif' unifMJ : : : no visible global function definition for 'dunif' plot,biomvRCNS-ANY: no visible binding for global variable 'ssetst' Undefined global functions or variables: DataFrame Rle clara cov.wt cov2cor cutreeDynamic dev.off dgamma dist dnbinom dnorm dpois dt dunif exons graphics.off hasArg hclust intronsByTranscript is mclapply new pdf postscript rainbow rgamma rnbinom rnorm rpois rt runValue seqlengths seqlevels<- setEPS ssetst transcripts ts.plot weighted.mean Consider adding importFrom("grDevices", "dev.off", "graphics.off", "pdf", "postscript", "rainbow", "setEPS") importFrom("methods", "hasArg", "is", "new") importFrom("stats", "cov.wt", "cov2cor", "dgamma", "dist", "dnbinom", "dnorm", "dpois", "dt", "dunif", "hclust", "rgamma", "rnbinom", "rnorm", "rpois", "rt", "ts.plot", "weighted.mean") to your NAMESPACE file (and ensure that your DESCRIPTION Imports field contains 'methods'). * checking Rd files ... NOTE checkRd: (-1) sojournAnno.Rd:32: Lost braces 32 | \item{\\code{...}}{distribution parameters, 'lambda' and 'shift' for 'pois'; 'size', 'mu' and 'shift' for 'nbinom'; 'scale' and 'shape' for 'gamma'} | ^ * 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 ... 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 data for ASCII and uncompressed saves ... OK * checking line endings in C/C++/Fortran sources/headers ... OK * checking compiled code ... NOTE Note: information on .o files is not available * checking files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed biomvRhsmm 9.097 1.413 6.365 biomvRGviz 6.236 0.315 6.566 * 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, 7 NOTEs See ‘/home/biocbuild/bbs-3.21-bioc/meat/biomvRCNS.Rcheck/00check.log’ for details.