############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD check --install=check:intansv.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings intansv_1.47.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/intansv.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 ‘intansv/DESCRIPTION’ ... OK * this is package ‘intansv’ 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 ‘intansv’ 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/intansv.Rcheck/00install.out’ for details. * checking installed package size ... OK * checking package directory ... OK * checking ‘build’ directory ... OK * checking DESCRIPTION meta-information ... NOTE License stub is invalid DCF. * 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 DellyCluster: no visible global function definition for 'subjectHits' LumpyCluster: no visible global function definition for 'subjectHits' PindelCluster: no visible global function definition for 'subjectHits' breakDancerCluster: no visible global function definition for 'subjectHits' mergeOLCNVs: no visible global function definition for 'subjectHits' methodsMerge: no visible global function definition for 'subjectHits' plotChromosome: no visible global function definition for 'queryHits' plotChromosome: no visible global function definition for 'subjectHits' plotChromosome: no visible global function definition for 'seqlengths<-' plotChromosome: no visible global function definition for 'seqlengths' plotChromosome: no visible global function definition for 'aes' plotRegion: no visible global function definition for 'seqlengths<-' plotRegion: no visible global function definition for 'subjectHits' plotRegion: no visible global function definition for 'aes' plotRegion: no visible binding for global variable 'name' readCnvnator: no visible global function definition for 'subjectHits' readDelly: no visible global function definition for 'subjectHits' readLumpy: no visible global function definition for 'subjectHits' readPindel: no visible global function definition for 'subjectHits' readSoftSearch: no visible global function definition for 'subjectHits' readSvseq: no visible global function definition for 'subjectHits' readSvseq : : no visible global function definition for 'subjectHits' softSearchCluster: no visible global function definition for 'subjectHits' tellOLPercantage: no visible global function definition for 'queryHits' tellOLPercantage: no visible global function definition for 'subjectHits' Undefined global functions or variables: aes name queryHits seqlengths seqlengths<- subjectHits * checking Rd files ... NOTE checkRd: (-1) plotChromosome.Rd:34: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) plotChromosome.Rd:35: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) plotChromosome.Rd:36-37: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) plotChromosome.Rd:38-39: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) plotChromosome.Rd:40-41: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) plotRegion.Rd:35: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) plotRegion.Rd:36: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) plotRegion.Rd:37: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) plotRegion.Rd:38: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) svAnnotation.Rd:30: Lost braces in \itemize; meant \describe ? checkRd: (-1) svAnnotation.Rd:31: Lost braces in \itemize; meant \describe ? checkRd: (-1) svAnnotation.Rd:32: Lost braces in \itemize; meant \describe ? * 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 files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed methodsMerge 35.251 0.363 35.707 plotChromosome 6.818 0.036 6.869 plotRegion 5.327 0.012 5.354 readLumpy 4.972 0.060 5.047 * 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/intansv.Rcheck/00check.log’ for details.