• using R Under development (unstable) (2023-12-02 r85657)
• using platform: x86_64-pc-linux-gnu
• R was compiled by     Debian clang version 17.0.5 (1)     Debian flang-new version 17.0.5 (1)
• running under: Debian GNU/Linux trixie/sid
• using session charset: UTF-8
• checking for file ‘netgwas/DESCRIPTION’ ... OK
• checking extension type ... Package
• this is package ‘netgwas’ version ‘1.14.2’
• package encoding: UTF-8
• 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 ‘netgwas’ can be installed ... OK See the install log for details.
• 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 ... [3s/3s] OK
• checking whether the package can be loaded with stated dependencies ... [3s/3s] OK
• checking whether the package can be unloaded cleanly ... [3s/3s] OK
• checking whether the namespace can be loaded with stated dependencies ... [3s/3s] OK
• checking whether the namespace can be unloaded cleanly ... [3s/3s] OK
• checking loading without being on the library search path ... [3s/3s] 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 ... [26s/31s] OK
• checking Rd files ... [1s/1s] NOTE checkRd: (-1) CviCol.Rd:15: Lost braces; missing escapes or markup?     15 | The \emph{Arabidopsis thaliana} genotype data is derived from a RIL cross between Columbia-0 (Col-0) and the Cape Verde Island (Cvi-0), where 367 individuals were genotyped for 90 genetic markers. This is a diploid population with three possible genotpe states \code{(k = 3)}, where the genotypes coded as {0, 1, 2}, where 0 and 2 represent the homozygous genotypes and 1 defines the heterozygous genotype. \cr        | ^ checkRd: (-1) cal.pos.Rd:25: Lost braces; missing escapes or markup?     25 | If \code{pop.typ = "RILn"} the number of generations of selfing is limited to 20 to ensure sensible input. The constructed object is returned as a R/qtl \code{cross} object with the appropriate class structure. For \code{"RILn"} populations the constructed object is given the class {"bcsft"} by using the \pkg{qtl} package conversion function \code{convert2bcsft} with arguments \code{F.gen = n} and \code{BC.gen = 0}. For \code{"ARIL"} populations the constructed object is given the class \code{"riself"}.        | ^ checkRd: (-1) netgwas2cross.Rd:21: Lost braces; missing escapes or markup?     21 | If \code{pop.typ = "RILn"} the number of generations of selfing is limited to 20 to ensure sensible input. The constructed object is returned as a R/qtl \code{cross} object with the appropriate class structure. For \code{"RILn"} populations the constructed object is given the class {"bcsft"} by using the \pkg{qtl} package conversion function \code{convert2bcsft} with arguments \code{F.gen = n} and \code{BC.gen = 0}. For \code{"ARIL"} populations the constructed object is given the class \code{"riself"}.        | ^ checkRd: (-1) simGeno.Rd:26: Lost braces     26 | code{con.dist = "Mt"}. The default value is 3.}        | ^
• 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/1s] OK
• checking data for ASCII and uncompressed saves ... OK
• checking examples ... [28s/31s] OK Examples with CPU (user + system) or elapsed time > 5s          user system elapsed simRIL 5.782 0.059 6.459 R.gibbs 4.889 0.152 5.297
• checking for unstated dependencies in ‘tests’ ... OK
• checking tests ... [29s/34s] OK   Running ‘testthat.R’ [28s/34s]
• checking PDF version of manual ... [6s/9s] OK
• checking HTML version of manual ... [2s/3s] OK
• checking for non-standard things in the check directory ... OK
• DONE

Status: 1 NOTE