############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD check --install=check:funtooNorm.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings funtooNorm_1.31.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/funtooNorm.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 ‘funtooNorm/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘funtooNorm’ version ‘1.31.0’ * 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 ‘funtooNorm’ 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/funtooNorm.Rcheck/00install.out’ for details. * checking installed package size ... OK * checking package 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 ... NOTE checkRd: (-1) fromRGChannelSet.Rd:5: Lost braces; missing escapes or markup? 5 | \title{Creates an object of class SampleSet from a RGChannelSet {minfi}} | ^ * 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 Documented arguments not in \usage in Rd file 'show-SampleSet-method.Rd': ‘...’ 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 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 R/sysdata.rda ... OK * checking files in ‘vignettes’ ... WARNING Files in the 'vignettes' directory but no files in 'inst/doc': ‘MyEndnoteLibrary.bib’ ‘funtooNorm.Rmd’ ‘funtooNorm.pdf’ ‘validationcurvesPCRlow.jpg’ Files named as vignettes but with no recognized vignette engine: ‘vignettes/funtooNorm.Rmd’ (Is a VignetteBuilder field missing?) * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed funtooNorm 30.656 0.718 31.433 getNormBeta 28.081 0.303 28.434 getNormM 27.980 0.332 28.363 getSnpM 27.284 0.163 27.491 plotValidationGraph 26.826 0.176 27.051 fromRGChannelSet 15.882 0.464 16.468 getRawBeta 7.332 0.040 7.384 getGRanges 7.213 0.048 7.278 show-SampleSet-method 6.200 0.024 6.233 * checking package vignettes ... NOTE Package has ‘vignettes’ subdirectory but apparently no vignettes. Perhaps the ‘VignetteBuilder’ information is missing from the DESCRIPTION file? * checking PDF version of manual ... OK * DONE Status: 7 WARNINGs, 6 NOTEs See ‘/home/biocbuild/bbs-3.21-bioc/meat/funtooNorm.Rcheck/00check.log’ for details.