############################################################################## ############################################################################## ### ### Running command: ### ### D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:Pviz.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings Pviz_1.29.0.tar.gz ### ############################################################################## ############################################################################## * using log directory 'D:/biocbuild/bbs-3.15-bioc/meat/Pviz.Rcheck' * using R Under development (unstable) (2021-11-21 r81221) * using platform: x86_64-w64-mingw32 (64-bit) * using session charset: ISO8859-1 * using option '--no-vignettes' * checking for file 'Pviz/DESCRIPTION' ... OK * checking extension type ... Package * this is package 'Pviz' version '1.29.0' * 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 whether package 'Pviz' can be installed ... WARNING Found the following significant warnings: Rd warning: D:/biocbuild/bbs-3.15-bioc/meat/Pviz/man/ATrack.Rd:34: missing link 'GdObject' Rd warning: D:/biocbuild/bbs-3.15-bioc/meat/Pviz/man/DTrack.Rd:30: missing link 'GdObject' Rd warning: D:/biocbuild/bbs-3.15-bioc/meat/Pviz/man/ProbeTrack.Rd:68: missing link 'GdObject' See 'D:/biocbuild/bbs-3.15-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 R 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 ... OK * checking whether the namespace can be unloaded cleanly ... OK * checking dependencies in R code ... OK * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE .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 or links in documentation object 'ATrack.Rd': 'GdObject' Missing link or links in documentation object 'DTrack.Rd': 'GdObject' Missing link or links in documentation object 'ProbeTrack.Rd': 'GdObject' See section 'Cross-references' in the 'Writing R Extensions' manual. * checking for missing documentation entries ... OK * checking for code/documentation mismatches ... OK * checking Rd \usage sections ... OK * 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 in 'inst/doc' ... OK * checking running R code from vignettes ... SKIPPED * checking re-building of vignette outputs ... SKIPPED * checking PDF version of manual ... OK * DONE Status: 2 WARNINGs, 1 NOTE See 'D:/biocbuild/bbs-3.15-bioc/meat/Pviz.Rcheck/00check.log' for details.