############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD check --install=check:GenomicPlot.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings GenomicPlot_1.5.2.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/GenomicPlot.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 ‘GenomicPlot/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘GenomicPlot’ version ‘1.5.2’ * package encoding: UTF-8 * checking package namespace information ... OK * checking package dependencies ... INFO Imports includes 25 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 ‘GenomicPlot’ 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/GenomicPlot.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 ...Warning: program compiled against libxml 212 using older 211 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 get_targeted_genes: no visible binding for global variable ‘5'UTR’ get_targeted_genes: no visible binding for global variable ‘3'UTR’ handle_bam: no visible global function definition for ‘seqlevelsStyle’ handle_bam: no visible global function definition for ‘seqlevelsStyle<-’ handle_bed: no visible global function definition for ‘seqlevelsStyle’ handle_bed: no visible global function definition for ‘seqlevelsStyle<-’ handle_bedGraph: no visible global function definition for ‘seqlevelsStyle’ handle_bedGraph: no visible global function definition for ‘seqlevelsStyle<-’ handle_bw: no visible global function definition for ‘seqlevelsStyle’ handle_bw: no visible global function definition for ‘seqlevelsStyle<-’ plot_bam_correlation: no visible binding for global variable ‘.’ plot_peak_annotation: no visible binding for global variable ‘.’ Undefined global functions or variables: . 3'UTR 5'UTR seqlevelsStyle seqlevelsStyle<- * 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 ... 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 files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed plot_start_end_with_random 23.247 5.441 27.270 plot_region 19.675 6.986 19.367 plot_locus 18.098 3.697 18.013 plot_5parts_metagene 15.079 6.379 17.781 plot_start_end 15.687 3.360 18.304 plot_locus_with_random 14.409 4.335 15.191 plot_peak_annotation 10.446 0.187 10.655 get_txdb_features 8.962 0.187 9.169 get_targeted_genes 8.709 0.172 8.898 prepare_5parts_genomic_features 6.155 0.036 6.200 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘test-plotFunctions.R’