* using log directory ‘/srv/hornik/tmp/CRAN/OnomasticDiversity.Rcheck’ * using R Under development (unstable) (2024-02-02 r85855) * 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 ‘OnomasticDiversity/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘OnomasticDiversity’ version ‘0.1’ * checking CRAN incoming feasibility ... [3s/4s] NOTE Maintainer: ‘Maria Jose Ginzo Villamayor ’ New submission Possibly misspelled words in DESCRIPTION: Cressie (10:373) Hedrick (10:197) Heip (10:334) Lasker (10:164) Margalef (10:270) Menhinick (10:280) Nei (10:209) Onomastic (3:8) isonymy (10:138, 10:147) Found the following (possibly) invalid URLs: URL: https://www.ige.eu/igebdt/esq.jsp?idioma=gl&ruta=onomast/notamet.jsp (moved to https://www.ige.gal/igebdt/esq.jsp?idioma=gl&ruta=onomast/notamet.jsp) From: man/namesmengal16.Rd man/nameswomengal16.Rd man/surnamesgal14.Rd Status: 301 Message: Moved Permanently For content that is 'Moved Permanently', please change http to https, add trailing slashes, or replace the old by the new URL. The Title field should be in title case. Current version is: ‘Onomastic diversity measures’ In title case that is: ‘Onomastic Diversity Measures’ The Description field should not start with the package name, 'This package' or similar. The Date field is over a month old. * 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 ‘OnomasticDiversity’ can be installed ... [2s/2s] 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 R 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 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] OK * checking Rd files ... [0s/0s] NOTE checkRd: (-1) OnomasticDiversity-package.Rd:25: Escaped LaTeX specials: \& checkRd: (-1) OnomasticDiversity-package.Rd:35: Escaped LaTeX specials: \& checkRd: (-1) fCressieRead.Rd:33: Lost braces; missing escapes or markup? 33 | \item{cressieRead}{ the value of {Cressie and Read statistics}.} | ^ checkRd: (-1) fGeneralisedMean.Rd:21: Lost braces; missing escapes or markup? 21 | For a community \eqn{i}{}, the {generalised mean} of relative abundances is defined by | ^ checkRd: (-1) fGeneralisedMean.Rd:23: Lost braces; missing escapes or markup? 23 | where \eqn{N_{ki}^t}{} denotes the number of individuals of species \eqn{k}{} at times \eqn{t}{}, \eqn{t0}{} is the baseline year and \eqn{S_i}{} are all species at the community, {species richness}, and \eqn{\lambda}{} can be any non-zero real number. | ^ checkRd: (-1) fGeneralisedMean.Rd:25: Lost braces; missing escapes or markup? 25 | In {onomastic} context, \eqn{N_{ki}^t}{} denotes the absolute frequency of surname \eqn{k}{} in region (\eqn{\approx}{} community diversity context) \eqn{i}{} at times \eqn{t}{}. | ^ checkRd: (-1) fGeneralisedMean.Rd:30: Lost braces; missing escapes or markup? 30 | \item{\code{generalisedMean}}{ the value of {generalised mean}} | ^ checkRd: (-1) fGeometricMean.Rd:31: Escaped LaTeX specials: \& checkRd: (-1) fGeometricMean.Rd:35: Escaped LaTeX specials: \& checkRd: (-1) fShannon.Rd:7: Lost braces; missing escapes or markup? 7 | This function obtains the {Shannon-Weaver} diversity index introduced by Claude Elwood Shannon (\cite{Shannon1948}). This diversity measure came from information theory and measures the order (or disorder) observed within a particular system. It is a method for quantifying species biodiversity that can be adapted to the context of {onomastics}. | ^ checkRd: (-1) fShannon.Rd:7: Lost braces; missing escapes or markup? 7 | This function obtains the {Shannon-Weaver} diversity index introduced by Claude Elwood Shannon (\cite{Shannon1948}). This diversity measure came from information theory and measures the order (or disorder) observed within a particular system. It is a method for quantifying species biodiversity that can be adapted to the context of {onomastics}. | ^ checkRd: (-1) fShannon.Rd:19: Lost braces; missing escapes or markup? 19 | For a community \eqn{i}{}, the index of {Shannon-Weaver}r is defined by the expression | ^ checkRd: (-1) fShannon.Rd:20: Lost braces; missing escapes or markup? 20 | \eqn{H^{\prime} = -\sum_{k\in S_i} (p_{ki} \log_2 p_{ki})}{}, where \eqn{p_{ki}}{} represents the relative frequency of species \eqn{k}{}, because \eqn{p_{ki} = \frac{N_{ki}}{N_i}}{}, (where \eqn{N_{ki}}{} denotes the number of individuals of species \eqn{k}{} and \eqn{N_i}{} total number of individuals in all \eqn{S_i}{} species at the community, {species richness}. This index is related to the weighted geometric mean of the proportional abundances of the types. | ^ checkRd: (-1) fShannon.Rd:22: Lost braces; missing escapes or markup? 22 | In {onomastic} context, \eqn{p_{ki}}{} denotes the relative frequency of surname \eqn{k}{} in region (\eqn{\approx}{} community diversity context) \eqn{i}{} and \eqn{S_i}{} are all surnames in region \eqn{i}{}. | ^ checkRd: (-1) fShannon.Rd:27: Lost braces; missing escapes or markup? 27 | \item{\code{shannon}}{ the value of the {Shannon-Weaver} diversity index.} | ^ checkRd: (-1) fSheldon.Rd:7: Lost braces; missing escapes or markup? 7 | This function obtains the {Sheldon}'s diversity index introduced by A. L. Sheldon (\cite{Sheldon1969}). It is a method for quantifying species biodiversity that can be adapted to the context of {onomastics}. | ^ checkRd: (-1) fSheldon.Rd:7: Lost braces; missing escapes or markup? 7 | This function obtains the {Sheldon}'s diversity index introduced by A. L. Sheldon (\cite{Sheldon1969}). It is a method for quantifying species biodiversity that can be adapted to the context of {onomastics}. | ^ checkRd: (-1) fSheldon.Rd:20: Lost braces; missing escapes or markup? 20 | For a community \eqn{i}{}, the {Sheldon}'s diversity index is defined by | ^ checkRd: (-1) fSheldon.Rd:23: Lost braces; missing escapes or markup? 23 | In {onomastic} context, \eqn{S_i}{} are all surnames in region (\eqn{\approx}{} community diversity context) \eqn{i}{}. | ^ checkRd: (-1) fSimpson.Rd:7: Lost braces; missing escapes or markup? 7 | This function obtains the {Simpson}'s diversity index and the inverse introduced by Edward Hugh Simpson (\cite{Simpson1949}). It was the first index used in ecology. It is a method for quantifying species biodiversity that can be adapted to the context of {onomastics}. | ^ checkRd: (-1) fSimpson.Rd:7: Lost braces; missing escapes or markup? 7 | This function obtains the {Simpson}'s diversity index and the inverse introduced by Edward Hugh Simpson (\cite{Simpson1949}). It was the first index used in ecology. It is a method for quantifying species biodiversity that can be adapted to the context of {onomastics}. | ^ checkRd: (-1) fSimpson.Rd:19: Lost braces; missing escapes or markup? 19 | For a community \eqn{i}{}, the {Simpson}'s diversity index is defined by | ^ checkRd: (-1) fSimpson.Rd:20: Lost braces; missing escapes or markup? 20 | \eqn{D_{S_i} = \sum \limits_{k\in S_i} p_{ki}^2}{}, where \eqn{p_{ki}}{} represents the relative frequency of species \eqn{k}{}, because \eqn{p_{ki} = \frac{N_{ki}}{N_i}}{}, (where \eqn{N_{ki}}{} denotes the number of individuals of species \eqn{k}{} and \eqn{N_i}{} total number of individuals in all \eqn{S_i}{} species at the community, {species richness}. The {Simpson index} tends to be smaller when the community is more diverse. | ^ checkRd: (-1) fSimpson.Rd:20: Lost braces; missing escapes or markup? 20 | \eqn{D_{S_i} = \sum \limits_{k\in S_i} p_{ki}^2}{}, where \eqn{p_{ki}}{} represents the relative frequency of species \eqn{k}{}, because \eqn{p_{ki} = \frac{N_{ki}}{N_i}}{}, (where \eqn{N_{ki}}{} denotes the number of individuals of species \eqn{k}{} and \eqn{N_i}{} total number of individuals in all \eqn{S_i}{} species at the community, {species richness}. The {Simpson index} tends to be smaller when the community is more diverse. | ^ checkRd: (-1) fSimpson.Rd:22: Lost braces; missing escapes or markup? 22 | In {onomastic} context, \eqn{p_{ki}}{} denotes the relative frequency of surname \eqn{k}{} in region (\eqn{\approx}{} community diversity context) \eqn{i}{}, i.e., {Simpson}'s diversity index is equivalent to the concept of isonymy.. | ^ checkRd: (-1) fSimpson.Rd:22: Lost braces; missing escapes or markup? 22 | In {onomastic} context, \eqn{p_{ki}}{} denotes the relative frequency of surname \eqn{k}{} in region (\eqn{\approx}{} community diversity context) \eqn{i}{}, i.e., {Simpson}'s diversity index is equivalent to the concept of isonymy.. | ^ checkRd: (-1) fSimpsonInf.Rd:7: Lost braces; missing escapes or markup? 7 | This function obtains the Simpson's diversity index and the inverse introduced by Edward Hugh Simpson (\cite{Simpson1949}). It is a method for quantifying species biodiversity that can be adapted to the context of {onomastics}. | ^ checkRd: (-1) fSimpsonInf.Rd:20: Lost braces; missing escapes or markup? 20 | \eqn{D^{\prime}_{S_i} = \sum \limits_{k\in S_i} \frac{n_{ki}(n_{ki}-1)}{n_i(n_i-1)}}{}, where \eqn{n_{ki}}{} represents the number of individuals of species \eqn{k}{} in a sample (in the total is \eqn{N_{ki}}{}) and \eqn{S_i}{} represents all species at the community, {species richness}. | ^ checkRd: (-1) fSimpsonInf.Rd:22: Lost braces; missing escapes or markup? 22 | In {onomastic} context, \eqn{n_{ki}}{} (\eqn{\approx N_{ki}}{}) denotes the absolute frequency of surname \eqn{k}{} in region \eqn{i}{} | ^ checkRd: (-1) surnamesgal14.Rd:7: Lost braces; missing escapes or markup? 7 | This dataset corresponds to 25 most frequent {surnames} by municipality in Galicia in 2014. | ^ * checking Rd metadata ... OK * checking Rd line widths ... 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 contents of ‘data’ directory ... OK * checking data for non-ASCII characters ... [0s/0s] OK * checking data for ASCII and uncompressed saves ... OK * checking examples ... [68s/68s] NOTE Examples with CPU (user + system) or elapsed time > 5s user system elapsed fIsonymyAll 63.739 2.303 66.046 * checking PDF version of manual ... [4s/4s] WARNING LaTeX errors when creating PDF version. This typically indicates Rd problems. LaTeX errors found: ! LaTeX Error: Unicode character € (U+0080) 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 “ (U+0093) 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 ... [1s/1s] OK * checking for non-standard things in the check directory ... NOTE Found the following files/directories: ‘OnomasticDiversity-manual.tex’ * checking for detritus in the temp directory ... OK * DONE Status: 1 ERROR, 1 WARNING, 4 NOTEs