* using log directory ‘/srv/hornik/tmp/CRAN/ultrapolaRplot.Rcheck’ * using R Under development (unstable) (2024-03-29 r86229) * using platform: x86_64-pc-linux-gnu * R was compiled by Debian clang version 17.0.6 (5) Debian flang-new version 17.0.6 (5) * running under: Debian GNU/Linux trixie/sid * using session charset: UTF-8 * checking for file ‘ultrapolaRplot/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘ultrapolaRplot’ version ‘0.1.0’ * package encoding: UTF-8 * checking CRAN incoming feasibility ... [1s/1s] WARNING Maintainer: ‘’ The maintainer field lacks a name New submission Non-FOSS package license (Available under GPLv3.) Possibly misspelled words in DESCRIPTION: SSANOVA (11:5) TextGrids (16:45) UltraTrace (14:42) textgrid (16:10) ultrapolaRplot (8:18, 13:15) The Description field contains [UltraTrace](https:// github.com/SwatPhonLab/UltraTrace). UltraTrace Please enclose URLs in angle brackets (<...>). * 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 executable files ... OK * checking for hidden files and directories ... OK * checking for portable file names ... OK * checking for sufficient/correct file permissions ... OK * checking serialization versions ... OK * checking whether package ‘ultrapolaRplot’ can be installed ... [2s/2s] OK * checking package directory ... OK * checking for future file timestamps ... OK * checking DESCRIPTION meta-information ... WARNING Non-standard license specification: Available under GPLv3. Standardizable: FALSE * checking top-level files ... NOTE File LICENSE is not mentioned in the DESCRIPTION file. Non-standard file/directory found at top level: ‘ultrapolaRplot.Rproj’ * 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 ... [1s/1s] OK * checking whether the package can be loaded with stated dependencies ... [0s/0s] OK * checking whether the package can be unloaded cleanly ... [0s/0s] OK * checking whether the namespace can be loaded with stated dependencies ... [0s/0s] OK * checking whether the namespace can be unloaded cleanly ... [1s/1s] OK * checking loading without being on the library search path ... [1s/1s] OK * checking use of S3 registration ... OK * checking dependencies in R code ... WARNING '::' or ':::' imports not declared from: ‘plyr’ ‘purrr’ ‘readr’ ‘stringr’ * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... [4s/4s] NOTE plotTraces: warning in plotStyleTraces(matrixIntersection = matrixIntersection, compiledList = compiledList, dataOfEachCurve = dataOfEachCurveNNj, uniqueSegments = uniqueSegments, rayIncrement = rayIncrement, mean.lines = mean.lines, points.display = points.display, palette = palette, bands.lines = bands.lines, legend.position = legend.position, bands.fill = bands.fill, means.styles = means.styles, standard.deviation.styles = standard.deviation.styles, plot.ticks = plot.ticks, legend.size = legend.size, transparency = transparency, : partial argument match of 'dataOfEachCurve' to 'dataOfEachCurveNNj' plotTraces: warning in pdf.filename = pdf.filename, bands.linewidth = bands.linewidth, plot.labels = plot.labels, png.filename = png.filename, legend.linewidth = legend.linewidth, means.linewidth = means.linewidth, tick.size = tick.size): partial argument match of 'dataOfEachCurve' to 'dataOfEachCurveNNj' loadTraces: no visible binding for global variable ‘xmin’ loadTraces: no visible binding for global variable ‘xmax’ plotStyleTraces: no visible global function definition for ‘sd’ plotStyleTraces: no visible global function definition for ‘cairo_pdf’ plotStyleTraces: no visible global function definition for ‘png’ plotStyleTraces: no visible global function definition for ‘par’ plotStyleTraces: no visible global function definition for ‘axis’ plotStyleTraces : : no visible global function definition for ‘na.omit’ plotStyleTraces: no visible global function definition for ‘lines’ plotStyleTraces: no visible global function definition for ‘polygon’ plotStyleTraces: no visible global function definition for ‘adjustcolor’ plotStyleTraces: no visible global function definition for ‘points’ plotStyleTraces: no visible global function definition for ‘legend’ plotStyleTraces: no visible global function definition for ‘dev.off’ Undefined global functions or variables: adjustcolor axis cairo_pdf dev.off legend lines na.omit par png points polygon sd xmax xmin Consider adding importFrom("grDevices", "adjustcolor", "cairo_pdf", "dev.off", "png") importFrom("graphics", "axis", "legend", "lines", "par", "points", "polygon") importFrom("stats", "na.omit", "sd") to your NAMESPACE file. * checking Rd files ... [0s/0s] OK * checking Rd metadata ... OK * checking Rd line widths ... NOTE Rd file 'Summary_ultrapolaRplot.Rd': \usage lines wider than 90 characters: rawTraces <- loadTraces('/path/to/project/', 'vowels') # project directory containing UltraTrace metadata file; tier to identify non-e ... [TRUNCATED] \examples lines wider than 100 characters: legend.position = "bottomright", points.display = FALSE, bands.lines = TRUE, bands.fill = TRUE, transparency = 0.2, mean.lines = TRUE, ... [TRUNCATED] These lines will be truncated in the PDF manual. * checking Rd cross-references ... OK * checking for missing documentation entries ... WARNING Undocumented code objects: ‘add_annotation_num’ ‘calculateIntersection2’ ‘example_textgrid’ ‘find_intersection_with_ray’ ‘formating_data’ ‘get_field’ ‘get_field_dbl’ ‘get_field_list’ ‘get_unique_segments’ ‘identifyPlotBounds’ ‘identifyXAverage’ ‘loadTraces’ ‘makeTracesPolar’ ‘parse_interval_tier’ ‘parse_item_lines’ ‘parse_point_tier’ ‘parse_textgrid_lines’ ‘plotStyleTraces’ ‘plotTraces’ ‘read_in_data’ ‘read_textgrid’ ‘read_textgrid_lines’ ‘remove_na’ ‘slice_sections’ ‘sortedOrder’ ‘str_detect_any’ ‘str_unquote’ 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 Codoc mismatches from Rd file 'Summary_ultrapolaRplot.Rd': plotTraces Code: function(myXY_data, compiledList, interval = 1, mean.lines = TRUE, points.display = FALSE, palette = c(), bands.lines = FALSE, bands.fill = TRUE, legend.position = "topleft", means.styles = c(), standard.deviation.styles = "l", plot.ticks = FALSE, plot.labels = FALSE, legend.size = 3, transparency = 0.37, pdf.filename = c(), bands.linewidth = 0.3, png.filename = c(), legend.linewidth = 5, means.linewidth = 3, tick.size = 2) Docs: function(rawTraces, polarTraces) Argument names in code not in docs: myXY_data compiledList interval mean.lines points.display palette bands.lines bands.fill legend.position means.styles standard.deviation.styles plot.ticks plot.labels legend.size transparency pdf.filename bands.linewidth png.filename legend.linewidth means.linewidth tick.size Argument names in docs not in code: rawTraces polarTraces Mismatches in argument names: Position: 1 Code: myXY_data Docs: rawTraces Position: 2 Code: compiledList Docs: polarTraces * checking Rd \usage sections ... WARNING Undocumented arguments in Rd file 'Summary_ultrapolaRplot.Rd' ‘rawTraces’ ‘polarTraces’ Objects in \usage without \alias in Rd file 'Summary_ultrapolaRplot.Rd': ‘plotTraces’ Assignments in \usage in Rd file 'Summary_ultrapolaRplot.Rd': rawTraces <- loadTraces("/path/to/project/", "vowels") polarTraces <- makeTracesPolar(rawTraces) Functions with \usage entries need to have the appropriate \alias entries, and all their arguments documented. The \usage entries must correspond to syntactically valid R code. See chapter ‘Writing R documentation files’ in the ‘Writing R Extensions’ manual. * checking Rd contents ... OK * checking for unstated dependencies in examples ... OK * checking examples ... [1s/1s] ERROR Running examples in ‘ultrapolaRplot-Ex.R’ failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: ultrapolaRplot > ### Title: ultrapolaRplot > ### Aliases: ultrapolaRplot > > ### ** Examples > > library(ultrapolaRplot) > rawTraces <- loadTraces('../palatals/', 'cons') Error in loadTraces("../palatals/", "cons") : metadata file does not exist in given directory Execution halted * checking PDF version of manual ... [3s/3s] WARNING LaTeX errors when creating PDF version. This typically indicates Rd problems. LaTeX errors found: ! LaTeX Error: Unicode character ʲ (U+02B2) not set up for use with LaTeX. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ! LaTeX Error: Unicode character ɯ (U+026F) not set up for use with LaTeX. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ! LaTeX Error: Unicode character ɑ (U+0251) not set up for use with LaTeX. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. * checking PDF version of manual without index ... ERROR * checking HTML version of manual ... [0s/0s] OK * checking for non-standard things in the check directory ... NOTE Found the following files/directories: ‘ultrapolaRplot-manual.tex’ * checking for detritus in the temp directory ... OK * DONE Status: 2 ERRORs, 7 WARNINGs, 4 NOTEs