############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:ggbio.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings ggbio_1.51.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/ggbio.Rcheck’ * using R version 4.4.0 Patched (2024-04-24 r86482) * using platform: x86_64-apple-darwin20 * R was compiled by Apple clang version 14.0.0 (clang-1400.0.29.202) GNU Fortran (GCC) 12.2.0 * running under: macOS Monterey 12.7.4 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘ggbio/DESCRIPTION’ ... OK * this is package ‘ggbio’ version ‘1.51.0’ * 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 ‘ggbio’ can be installed ... OK * 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 ... OK * checking whether the namespace can be unloaded cleanly ... OK * checking whether startup messages can be suppressed ... OK * checking dependencies in R code ... NOTE ':::' call which should be '::': 'ggplot2:::set_last_plot' See the note in ?`:::` about the use of this operator. Unexported objects imported by ':::' calls: 'S4Vectors:::top_prenv' 'ggplot2:::add_ggplot' 'ggplot2:::cunion' 'ggplot2:::rescale01' 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 .combineNames: no visible binding for global variable '.layout_circle.stats' Ideogram: no visible global function definition for 'data' Ideogram: no visible binding for global variable 'ideoCyto' getNR: no visible global function definition for 'se' getNR: no visible global function definition for 'indexProbesProcessed' getNR: no visible global function definition for 'coefs' scale_x_sequnit: no visible binding for global variable '.x' autoplot,ExpressionSet: no visible binding for global variable 'variable' autoplot,RangedSummarizedExperiment: no visible binding for global variable 'variable' autoplot,VCF: no visible binding for global variable 'stepping' autoplot,VCF: no visible binding for global variable 'value' autoplot,VRanges: no visible binding for global variable 'midpoint' autoplot,Views: no visible binding for global variable 'x' autoplot,Views: no visible binding for global variable 'value' geom_alignment,BamFile: no visible binding for global variable 'fl' geom_alignment,BamFile: no visible binding for global variable 'stepping' height,GGbio: no visible binding for global variable 'mt' height,Tracked: no visible binding for global variable 'mt' height,gg: no visible binding for global variable 'mt' layout_karyogram,GRanges: no visible binding for global variable 'gieStain' layout_karyogram,GRanges: no visible binding for global variable 'x' layout_karyogram,GRanges: no visible binding for global variable 'xend' layout_karyogram,GRanges: no visible binding for global variable 'y2' layout_karyogram,GRanges: no visible binding for global variable 'yend2' layout_karyogram,GRanges: no visible binding for global variable 'name' plotFragLength,character-GRanges: no visible binding for global variable '.fragLength' plotSpliceSum,character-EnsDb: possible error in GRangesFilter(which, condition = "overlapping"): unused argument (condition = "overlapping") stat_mismatch,GRanges: no visible binding for global variable 'sts' stat_mismatch,GRanges: no visible binding for global variable 'eds' stat_mismatch,GRanges: no visible binding for global variable 'read' Undefined global functions or variables: .fragLength .layout_circle.stats .x coefs data eds fl gieStain ideoCyto indexProbesProcessed midpoint mt name read se stepping sts value variable x xend y2 yend2 Consider adding importFrom("utils", "data") to your NAMESPACE file. * checking Rd files ... NOTE checkRd: (-1) autoplot-method.Rd:353-355: Lost braces in \itemize; meant \describe ? checkRd: (-1) autoplot-method.Rd:357-360: Lost braces in \itemize; meant \describe ? checkRd: (-1) autoplot-method.Rd:442-448: Lost braces in \itemize; meant \describe ? checkRd: (-1) autoplot-method.Rd:445: Escaped LaTeX specials: \~ checkRd: (-1) autoplot-method.Rd:449-455: Lost braces in \itemize; meant \describe ? checkRd: (-1) geom_arch-method.Rd:28: Lost braces in \itemize; meant \describe ? checkRd: (-1) geom_arch-method.Rd:29: Lost braces in \itemize; meant \describe ? checkRd: (-1) geom_arch-method.Rd:30: Lost braces in \itemize; meant \describe ? checkRd: (-1) ggplot-method.Rd:91: Lost braces in \itemize; meant \describe ? checkRd: (-1) ggplot-method.Rd:92: Lost braces in \itemize; meant \describe ? checkRd: (-1) ggplot-method.Rd:93: Lost braces in \itemize; meant \describe ? checkRd: (-1) tracks.Rd:295-302: Lost braces in \itemize; meant \describe ? checkRd: (-1) tracks.Rd:303-306: Lost braces in \itemize; meant \describe ? checkRd: (-1) tracks.Rd:307-309: Lost braces in \itemize; meant \describe ? * checking Rd metadata ... OK * checking Rd cross-references ... OK * checking for missing documentation entries ... WARNING Undocumented S4 methods: generic '+' and siglist 'Tracks,ANY' generic '+' and siglist 'Tracks,Tracks' generic '+' and siglist 'Tracks,cartesian' generic '+' and siglist 'Tracks,position_c' generic '+' and siglist 'Tracks,theme' generic '+' and siglist 'Tracks,zoom' All user-level objects in a package (including S4 classes and methods) should have documentation entries. See chapter ‘Writing R documentation files’ in the ‘Writing R Extensions’ manual. * checking for code/documentation mismatches ... WARNING Codoc mismatches from Rd file 'geom_alignment-method.Rd': \S4method{geom_alignment}{GRanges} Code: function(data, ..., xlab, ylab, main, facets = NULL, stat = c("stepping", "identity"), range.geom = c("rect", "arrowrect"), gap.geom = c("chevron", "arrow", "segment"), rect.height = NULL, group.selfish = TRUE) Docs: function(data, ..., xlab, ylab, main, facets = NULL, stat = c("stepping", "identity"), range.geom = c("rect", "arrowrect"), gap.geom = c("chevron", "arrow", "segment"), rect.height = NULL, group.selfish = TRUE, label = TRUE) Argument names in docs not in code: label Codoc mismatches from Rd file 'ggsave.Rd': ggsave Code: function(filename, plot = last_plot(), device = NULL, path = NULL, scale = 1, width = NA, height = NA, units = c("in", "cm", "mm"), dpi = 300, limitsize = TRUE, ...) Docs: function(filename, plot = last_plot(), device = default_device(filename), path = NULL, scale = 1, width = par("din")[1], height = par("din")[2], units = c("in", "cm", "mm"), dpi = 300, limitsize = TRUE, ...) Mismatches in argument default values: Name: 'device' Code: NULL Docs: default_device(filename) Name: 'width' Code: NA Docs: par("din")[1] Name: 'height' Code: NA Docs: par("din")[2] * checking Rd \usage sections ... OK * checking Rd contents ... NOTE Argument items with no description in Rd file 'autoplot-method.Rd': ‘rotate’ * checking for unstated dependencies in examples ... OK * checking line endings in Makefiles ... OK * checking for GNU extensions in Makefiles ... OK * checking include directives in Makefiles ... OK * checking sizes of PDF files under ‘inst/doc’ ... OK * checking files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed autoplot-method 190.640 3.748 235.463 geom_alignment-method 65.904 1.350 75.224 tracks 48.283 0.558 63.797 layout_karyogram-method 43.004 0.447 50.181 plotRangesLinkedToData 21.851 0.347 25.662 stat_reduce-method 16.893 0.323 29.032 stat_aggregate-method 16.855 0.169 20.163 ggplot-method 16.642 0.196 18.297 layout_circle-method 15.903 0.169 18.258 geom_arrow-method 12.778 0.099 14.875 plotGrandLinear 12.234 0.242 14.476 geom_chevron-method 10.944 0.090 12.225 stat_bin-method 10.306 0.098 12.067 geom_arrowrect-method 7.938 0.068 9.271 geom_rect-method 7.312 0.068 8.060 geom_segment-method 6.911 0.061 7.864 arrangeGrobByParsingLegend 6.735 0.229 7.855 scale_fill_giemsa 6.847 0.080 8.046 stat_slice-method 6.232 0.085 11.480 stat_identity-method 5.884 0.130 6.949 stat_stepping-method 5.435 0.079 9.955 stat_coverage-method 4.923 0.060 5.794 theme 3.792 0.070 5.863 stat_table-method 3.596 0.068 5.162 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘test-all.R’ 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: 2 WARNINGs, 4 NOTEs See ‘/Users/biocbuild/bbs-3.20-bioc/meat/ggbio.Rcheck/00check.log’ for details.