* using log directory ‘/srv/hornik/tmp/CRAN_pretest/sidier.Rcheck’ * using R Under development (unstable) (2025-04-02 r88102) * using platform: x86_64-pc-linux-gnu * R was compiled by Debian clang version 19.1.7 (1+b1) Debian flang-new version 19.1.7 (1+b1) * running under: Debian GNU/Linux trixie/sid * using session charset: UTF-8 * checking for file ‘sidier/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘sidier’ version ‘4.1.1’ * package encoding: UTF-8 * checking CRAN incoming feasibility ... [4s/4s] NOTE Maintainer: ‘A.J. Muñoz-Pajares ’ No Authors@R field in DESCRIPTION. Please add one, modifying Authors@R: c(person(given = c("A.", "Jesus", "Muñoz"), family = "Pajares", role = "aut"), person(given = "A.J.", family = "Muñoz-Pajares", role = "cre", email = "ajesusmp@ugr.es")) as necessary. Package CITATION file contains call(s) to old-style personList() or as.personList(). Please use c() on person objects instead. Package CITATION file contains call(s) to old-style citEntry(). Please use bibentry() instead. * 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 ‘sidier’ can be installed ... [5s/5s] 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 ... NOTE Problems with news in ‘NEWS’: Cannot process chunk/lines: Released June 25, 2021 . Functions for metabarcoding taxonomy assignment Cannot process chunk/lines: Released July 09, 2018 . Modified document package metadata Cannot process chunk/lines: Released June 09, 2017 . Bug fixed in barcode.summary Cannot process chunk/lines: Released June 01, 2017 .Functions for barcode analyses .FilterHaplo for filter haplotypes by occurrence .MCIC suitable for sequences showing only substitutions .mutation.network now depicts frequencies per population. Improved representation of mutations. Cannot process chunk/lines: Released February 27, 2015 .Functions giving an error for matrices showing off-diagonal zeros have changed. Now these function gives a warning only if no percolation threshold is found. .double.plot now includes depicting nodes according to haplotype modules Cannot process chunk/lines: Released November 18, 2014 .Includes new functions to represent mutation and pie networks (mutation.network, double.plot, pie.network), methods to deal with zeros and missing data (zero.thr, NINA.thr, mergeNodes) .Includes more example data sets (ex_alignment1, ex_Coords). .Includes a function to simplify complex networks to improve visualization (simplify.network). .Includes a function to represent nodes (populations) according to their geographic coordinates (spatial.plot). .Improves haplotype definition: (Identifies identical haplotypes even in wrong alignments). .Manual and old functions are revised and improved. Cannot process chunk/lines: Released July 2, 2014 .Includes citation reference. Cannot process chunk/lines: Released July 1, 2013 .Includes new functions to represent distance matrices as networks ('BARRIEL', 'FIFTH' and 'SIC'), to combine more than two distance matrices (distance.comb), to obtain a summary of mutation events contained in the studied alignment ('mutationSummary') and to simulate sequences evolution including both substitutions and indels (simuEvolution) Cannot process chunk/lines: Released March 29, 2013 .The function 'plot.network' has a new name ('single.network') to avoid coincidences with other packages. .Examples and manual are improved. Cannot process chunk/lines: Released Feb 19, 2013 Cannot process chunk/lines: First "official" release of the sidier package including functions for reading and writing fasta sequences, finding unique haplotypes, estimating genetic distances based on gap positions and lengths, combining distance matrices and estimating and plotting percolation networks * 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 ... [1s/1s] OK * checking whether the package can be unloaded cleanly ... [1s/1s] OK * checking whether the namespace can be loaded with stated dependencies ... [1s/1s] 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 ... OK * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... [10s/10s] OK * checking Rd files ... [0s/0s] NOTE checkRd: (-1) pop.dist.Rd:41: Lost braces; missing escapes or markup? 41 | where \emph{dist(i,j)} represents the distance between populations \emph{i} and \emph{j}, \emph{m} and \emph{n} are the number of sequences in populations \emph{i} and \emph{j}, respectively, and \emph{dist(H_{ki},H_{lj})} is the distance between the \emph{k-th} sequence found in population \emph{i} and the \emph{l-th} sequence found in population \emph{j}. | ^ checkRd: (-1) pop.dist.Rd:41: Lost braces; missing escapes or markup? 41 | where \emph{dist(i,j)} represents the distance between populations \emph{i} and \emph{j}, \emph{m} and \emph{n} are the number of sequences in populations \emph{i} and \emph{j}, respectively, and \emph{dist(H_{ki},H_{lj})} is the distance between the \emph{k-th} sequence found in population \emph{i} and the \emph{l-th} sequence found in population \emph{j}. | ^ * 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 ... [3s/3s] OK * checking PDF version of manual ... [3s/3s] OK * checking HTML version of manual ... [1s/1s] OK * checking for non-standard things in the check directory ... OK * checking for detritus in the temp directory ... OK * DONE Status: 3 NOTEs