* using log directory ‘/srv/hornik/tmp/CRAN_pretest/ReMIXTURE.Rcheck’ * using R Under development (unstable) (2025-11-05 r88988) * using platform: x86_64-pc-linux-gnu * R was compiled by Debian clang version 19.1.7 (7) Debian flang-new version 19.1.7 (7) * running under: Debian GNU/Linux forky/sid * using session charset: UTF-8 * checking for file ‘ReMIXTURE/DESCRIPTION’ ... OK * this is package ‘ReMIXTURE’ version ‘0.1.0’ * package encoding: UTF-8 * checking CRAN incoming feasibility ... [3s/4s] NOTE Maintainer: ‘M Timothy Rabanus-Wallace ’ New submission Possibly misspelled words in DESCRIPTION: Rabanus (9:61) ReMIXTURE (2:8, 8:27) Tripodi (9:51) al (9:81) et (9:78) The Title field is just the package name: provide a real title. Size of tarball: 11658111 bytes * 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 whether package ‘ReMIXTURE’ can be installed ... [11s/11s] OK * checking package directory ... OK * checking for future file timestamps ... 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 ... [0s/0s] 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 ... [0s/0s] OK * checking loading without being on the library search path ... [0s/0s] OK * checking whether startup messages can be suppressed ... [0s/0s] OK * checking use of S3 registration ... 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 ... [3s/3s] NOTE equirectangular: no visible binding for global variable ‘lon’ equirectangular: no visible binding for global variable ‘lat’ fillPathDtLL: no visible binding for global variable ‘nextLat’ fillPathDtLL: no visible binding for global variable ‘lat’ fillPathDtLL: no visible binding for global variable ‘plotGrp’ fillPathDtLL: no visible binding for global variable ‘nextLon’ fillPathDtLL: no visible binding for global variable ‘lon’ fillPathDtLL: no visible binding for global variable ‘toNextLat’ fillPathDtLL: no visible binding for global variable ‘toNextLon’ fillPathDtLL: no visible binding for global variable ‘fillNext’ fillPathDtXY: no visible binding for global variable ‘nextY’ fillPathDtXY: no visible binding for global variable ‘Y’ fillPathDtXY: no visible binding for global variable ‘plotGrp’ fillPathDtXY: no visible binding for global variable ‘nextX’ fillPathDtXY: no visible binding for global variable ‘X’ fillPathDtXY: no visible binding for global variable ‘toNextY’ fillPathDtXY: no visible binding for global variable ‘toNextX’ fillPathDtXY: no visible binding for global variable ‘fillNext’ makeBorder: no visible binding for global variable ‘plotGrp’ makeBorder: no visible binding for global variable ‘ptIdx’ makeMapDataLatLonLines: no visible binding for global variable ‘lon’ makeMapDataLatLonLines: no visible binding for global variable ‘lat’ plotMapBorder: no visible binding for global variable ‘LR’ plotMapBorder: no visible binding for global variable ‘x’ plotMapBorder: no visible binding for global variable ‘TB’ plotMapBorder: no visible binding for global variable ‘y’ plotMapBorder: no visible binding for global variable ‘plotGrp’ plotMapBorder: no visible binding for global variable ‘ptIdx’ plotMapItem: no visible binding for global variable ‘plotGrp’ rotateLatLonDtLL: no visible binding for global variable ‘nextLon’ rotateLatLonDtLL: no visible binding for global variable ‘lon’ rotateLatLonDtLL: no visible binding for global variable ‘plotGrp’ rotateLatLonDtLL: no visible binding for global variable ‘nextLat’ rotateLatLonDtLL: no visible binding for global variable ‘lat’ rotateLatLonDtLL: no visible binding for global variable ‘crossLon’ rotateLatLonDtLL: no visible binding for global variable ‘lon_flipped’ rotateLatLonDtLL: no visible binding for global variable ‘ptIdx’ truncateLatLonDtLL: no visible binding for global variable ‘inBox’ truncateLatLonDtLL: no visible binding for global variable ‘lon’ truncateLatLonDtLL: no visible binding for global variable ‘lat’ truncateLatLonDtLL: no visible binding for global variable ‘clampGrps’ truncateLatLonDtLL: no visible binding for global variable ‘plotGrp’ truncateLatLonDtLL: no visible global function definition for ‘clampNearestLat’ truncateLatLonDtLL: no visible binding for global variable ‘outRunIdx’ truncateLatLonDtLL: no visible binding for global variable ‘inPlot’ Undefined global functions or variables: LR TB X Y clampGrps clampNearestLat crossLon fillNext inBox inPlot lat lon lon_flipped nextLat nextLon nextX nextY outRunIdx plotGrp ptIdx toNextLat toNextLon toNextX toNextY x y * checking Rd files ... [0s/0s] OK * checking Rd metadata ... OK * checking Rd line widths ... NOTE Rd file 'ReMIXTURE.Rd': \examples lines wider than 100 characters: # ReMIXTURE is written using the [R6](https://r6.r-lib.org/index.html) Object Orientated Programming system. You can read more about OO ... [TRUNCATED] # Create ReMIXTURE analysis object from an included dataset (Tripodi & Rabanus-Wallace et al. 2021. PNAS). # A run involves taking a subsample of all the samples in the distance matrix, such that every region has the same number of samples in ... [TRUNCATED] # Ideally, a collection of parameter settings are chosen and the results assessed to choose a good one. By default, the run function tr ... [TRUNCATED] rm$run(iterations = 25) # Iterations set low as we will be doing several runs and comparing results, so we can sacrifice a little accur ... [TRUNCATED] # For in an intuitive look at how the diversity metric changes with the parameter settings, view them simply as a grid, for each run (p ... [TRUNCATED] # - Circle sizes represent the diversity within a region (diagonals) or overlapped between regions (off-diagonals) # - The white inner circle represents the diversity unique to the focal region. The black outer band therefore represents the amount of ... [TRUNCATED] # Comparing the results between runs should make it clear why a ReMIXTURE analysis on one data set can not be straightforwardly compare ... [TRUNCATED] # A good balance can be found by summing region-unique/-overlapping clusters. At some point they are expected to cross over. # Note also that the number of multi-region clusters reaches a maximum, when the H is big enough to produce many such clusters, but bef ... [TRUNCATED] # H values between the crossover point and the multi-region maximum are usually good for showing a balanced representation. I prefer th ... [TRUNCATED] # BEWARE: What we are doing is great for a demo but before you publish you should be sure to do the rest of this tutorial. # Note the overlapped diversity is now shown by the width/alpha of a line joining the focal region to each other region. # Finally let's do this as a plot with all maps using the standard R layout options. I will also show each region's diversity metrics ... [TRUNCATED] #focalRegion = "Africa", # without this argument, will sequentially plot maps for all focal regions # Diagnostic tools -- the distribution of distances between/within different regions, and how they relate to the distribution of H rm$plot_distance_densities(HdistFromRun=4) # will plot all sequentially including H distribution as used in run 4 # We can plot MDS plots as we perform a run, and draw hulls surrounding the clusters. This is great for giving an impression of how the ... [TRUNCATED] # That's essentially all the package's functionality, though there are some more details in the documentation for the specific methods. These lines will be truncated in the PDF manual. * 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 contents of ‘data’ directory ... OK * checking data for non-ASCII characters ... [1s/1s] OK * checking LazyData ... OK * checking data for ASCII and uncompressed saves ... OK * checking examples ... [33s/33s] NOTE Examples with CPU (user + system) or elapsed time > 5s user system elapsed ReMIXTURE 32.714 0.171 32.905 * checking PDF version of manual ... [3s/3s] OK * checking HTML version of manual ... [0s/0s] OK * checking for non-standard things in the check directory ... OK * checking for detritus in the temp directory ... OK * DONE Status: 4 NOTEs