############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD check --install=check:Pviz.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings Pviz_1.41.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/Pviz.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 ‘Pviz/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘Pviz’ version ‘1.41.0’ * 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 ‘Pviz’ 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/Pviz.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 .makeParMapping: no visible global function definition for 'assignInNamespace' plot_clade: no visible global function definition for 'tail' drawGD,ProbeTrack: no visible global function definition for 'pushViewport' drawGD,ProbeTrack: no visible global function definition for 'viewport' drawGD,ProbeTrack: no visible global function definition for 'popViewport' drawGD,ProbeTrack: no visible global function definition for 'unit' drawGD,ProbeTrack: no visible global function definition for 'gpar' drawGD,ProbeTrack: no visible global function definition for 'convertWidth' drawGD,ProbeTrack: no visible global function definition for 'stringWidth' drawGD,ProbeTrack: no visible global function definition for 'stringHeight' drawGD,ProbeTrack: no visible global function definition for 'grid.text' drawGD,ProbeTrack: no visible global function definition for 'grid.rect' drawGD,ProbeTrack: no visible global function definition for 'dataViewport' drawGD,ProbeTrack : : no visible global function definition for 'grid.rect' drawGD,ProbeTrack : : no visible global function definition for 'gpar' drawGD,ProbeTrack : : no visible global function definition for 'grid.text' drawGD,ProteinAxisTrack: no visible global function definition for 'pushViewport' drawGD,ProteinAxisTrack: no visible global function definition for 'dataViewport' drawGD,ProteinAxisTrack: no visible global function definition for 'convertHeight' drawGD,ProteinAxisTrack: no visible global function definition for 'stringHeight' drawGD,ProteinAxisTrack: no visible global function definition for 'popViewport' drawGD,ProteinAxisTrack: no visible global function definition for '.getGapPos' drawGD,ProteinAxisTrack: no visible global function definition for 'gaps' drawGD,ProteinAxisTrack: no visible global function definition for 'viewport' drawGD,ProteinAxisTrack: no visible global function definition for 'grid.segments' drawGD,ProteinAxisTrack: no visible global function definition for 'gpar' drawGD,ProteinAxisTrack: no visible global function definition for 'coord2ext' drawGD,ProteinAxisTrack: no visible global function definition for 'grid.text' drawGD,ProteinAxisTrack: no visible global function definition for 'convertWidth' drawGD,ProteinAxisTrack: no visible global function definition for 'stringWidth' drawGD,ProteinSequenceTrack: no visible global function definition for 'pushViewport' drawGD,ProteinSequenceTrack: no visible global function definition for 'dataViewport' drawGD,ProteinSequenceTrack: no visible global function definition for 'gpar' drawGD,ProteinSequenceTrack: no visible global function definition for 'popViewport' drawGD,ProteinSequenceTrack: no visible global function definition for 'convertUnit' drawGD,ProteinSequenceTrack: no visible global function definition for 'stringWidth' drawGD,ProteinSequenceTrack: no visible global function definition for 'grid.lines' drawGD,ProteinSequenceTrack: no visible global function definition for 'unit' drawGD,ProteinSequenceTrack: no visible global function definition for 'grid.text' drawGD,ProteinSequenceTrack: no visible global function definition for 'grid.rect' Undefined global functions or variables: .getGapPos assignInNamespace convertHeight convertUnit convertWidth coord2ext dataViewport gaps gpar grid.lines grid.rect grid.segments grid.text popViewport pushViewport stringHeight stringWidth tail unit viewport Consider adding importFrom("utils", "assignInNamespace", "tail") to your NAMESPACE file. * checking Rd files ... OK * checking Rd metadata ... OK * checking Rd cross-references ... WARNING Missing link(s) in Rd file 'ATrack.Rd': ‘GdObject’ Missing link(s) in Rd file 'DTrack.Rd': ‘GdObject’ Missing link(s) in Rd file 'ProbeTrack.Rd': ‘GdObject’ See section 'Cross-references' in the 'Writing R Extensions' manual. Found the following Rd file(s) with Rd \link{} targets missing package anchors: ATrack.Rd: AnnotationTrack, GdObject DTrack.Rd: DataTrack, GdObject ProbeTrack.Rd: GdObject ProteinAxisTrack.Rd: GenomeAxisTrack ProteinSequenceTrack.Rd: SequenceTrack, DisplayPars plot_clade.Rd: plotTracks plot_inter.Rd: plotTracks 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 installed files from ‘inst/doc’ ... OK * checking files in ‘vignettes’ ... OK * checking examples ... 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: 6 WARNINGs, 5 NOTEs See ‘/home/biocbuild/bbs-3.21-bioc/meat/Pviz.Rcheck/00check.log’ for details.