############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:triplex.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings triplex_1.42.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.18-bioc/meat/triplex.Rcheck’ * using R version 4.3.2 Patched (2023-11-01 r85457) * using platform: x86_64-apple-darwin20 (64-bit) * R was compiled by Apple clang version 14.0.3 (clang-1403.0.22.14.1) GNU Fortran (GCC) 12.2.0 * running under: macOS Monterey 12.7.1 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘triplex/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘triplex’ version ‘1.42.0’ * 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 ‘triplex’ can be installed ... WARNING Found the following significant warnings: Warning: replacing previous import ‘grid::pattern’ by ‘Biostrings::pattern’ when loading ‘triplex’ See ‘/Users/biocbuild/bbs-3.18-bioc/meat/triplex.Rcheck/00install.out’ for details. * used C compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’ * used SDK: ‘MacOSX11.3.sdk’ * 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 ... NOTE 'library' or 'require' call to ‘rgl’ in package code. Please use :: or requireNamespace() instead. See section 'Suggested packages' in the 'Writing R Extensions' manual. Unexported object imported by a ':::' call: ‘IRanges:::new_Views’ See the note in ?`:::` about the use of this operator. * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE countBend: no visible global function definition for ‘optimize’ drawBase: no visible global function definition for ‘rgl.triangles’ join: no visible global function definition for ‘rgl.quads’ joinRect: no visible global function definition for ‘rgl.quads’ triplex.3D: no visible global function definition for ‘installed.packages’ triplex.3D: no visible global function definition for ‘nlm’ triplex.3D: no visible global function definition for ‘rgl.bg’ triplex.3D: no visible global function definition for ‘rgl.spheres’ Undefined global functions or variables: installed.packages nlm optimize rgl.bg rgl.quads rgl.spheres rgl.triangles Consider adding importFrom("stats", "nlm", "optimize") importFrom("utils", "installed.packages") to your NAMESPACE file. * checking Rd files ... WARNING checkRd: (5) TriplexViews-class.Rd:68-71: \item in \describe must have non-empty label checkRd: (5) TriplexViews-class.Rd:72-75: \item in \describe must have non-empty label checkRd: (5) TriplexViews-class.Rd:76-80: \item in \describe must have non-empty label checkRd: (5) TriplexViews-class.Rd:81-84: \item in \describe must have non-empty label checkRd: (5) TriplexViews-class.Rd:85-88: \item in \describe must have non-empty label checkRd: (5) TriplexViews-class.Rd:89-92: \item in \describe must have non-empty label checkRd: (5) TriplexViews-class.Rd:93-96: \item in \describe must have non-empty label checkRd: (5) TriplexViews-class.Rd:97-100: \item in \describe must have non-empty label checkRd: (5) TriplexViews-class.Rd:101-104: \item in \describe must have non-empty label * checking Rd metadata ... OK * checking Rd cross-references ... OK * 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 line endings in C/C++/Fortran sources/headers ... OK * checking compiled code ... NOTE Note: information on .o files is not available * checking sizes of PDF files under ‘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, 3 NOTEs See ‘/Users/biocbuild/bbs-3.18-bioc/meat/triplex.Rcheck/00check.log’ for details.